Answer ChemDoodle Sketcher Questions

Some OWLv2 questions require you use the ChemDoodle Sketcher tool to draw a model of a molecule.

ChemDoodle Sketcher lets you draw the structural formula of a molecule by adding atoms, bonds, and rings to your model using the buttons at the top.

A question might begin with the ChemDoodle Sketcher displaying a single atom, an undefined dot, or a model that is nearly complete for you to finish.

  • Click Submit Answer .


Draw a complete structure for a molecule with the molecular formula CH 4 S.

  • Explicitly draw all H atoms.
  • In cases where there is more than one answer, just draw one.

the ChemDoodle Sketcher tool displaying one carbon atom.

  • Open the dropdown menu next to the element button, and select S .

A carbon atom and a sulfur atom connected by a single bond.

  • Open the Set Label dropdown menu and select H .

A sulfur atom connected to a carbon atom and a hydrogen atom by single bonds.

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The Future of Scientific Software<br />

<strong>ChemDoodle</strong><br />

®<br />

<strong>v5.0</strong><br />

<strong>User</strong> <strong>Guide</strong><br />

Copyright © 2006-2012 iChemLabs, LLC.<br />

All Rights Reserved. No part of this document may be reproduced or transmitted in any form or by any means,<br />

electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of iChemLabs.<br />

<strong>ChemDoodle</strong> and MolGrabber are trademarks of iChemLabs, LLC.<br />

All other trademarks are the property of their respective holders.

Content<br />

Introduction<br />

About <strong>ChemDoodle</strong> ............................ 10<br />

About this <strong>Guide</strong> ................................. 10<br />

Additional Information ....................... 10<br />

Installation and System Requirements 11<br />

Microsoft Windows Requirements .. 11<br />

Macintosh OS X Requirements ....... 11<br />

Linux Requirements ......................... 11<br />

Installing Java ...................................... 11<br />

Installation ........................................... 11<br />

Installing for Multiple <strong>User</strong>s on a Single<br />

Computer ............................................. 11<br />

Windows .......................................... 12<br />

Mac OS X ........................................ 12<br />

Linux ................................................ 12<br />

Folder Contents ................................... 12<br />

Standard Operating System Documents<br />

Folder .................................................. 13<br />

Free Trials ........................................... 13<br />

Trial Restrictions ................................. 13<br />

Unrestricted Trials ............................... 13<br />

Student Version Restrictions ............... 13<br />

Activation ............................................ 14<br />

Connection Issues ............................... 14<br />

Firewall Issues ................................. 14<br />

Proxy Issues ..................................... 14<br />

Usage Restrictions .............................. 14<br />

Attributions ......................................... 14<br />

Chapter 1: Introducing<br />

Overview ............................................. 15<br />

The <strong>ChemDoodle</strong> Graphical <strong>User</strong><br />

Interface ............................................... 15<br />

Using the Graphical <strong>User</strong> Interface ..... 17<br />

Doodle Board ...................................... 17<br />

Ruler <strong>Guide</strong>s .................................... 18<br />

Scrollbars ......................................... 18<br />

Tab Tray ........................................... 18<br />

1<br />

Documents .......................................... 19<br />

Creating a Document ....................... 19<br />

Opening a Document ....................... 20<br />

File Chooser Previews ..................... 20<br />

Changing Document Size ................. 21<br />

Discard Recent Changes to a<br />

Document ......................................... 21<br />

Saving Documents ........................... 22<br />

Autosaving ........................................ 22<br />

Reversing Actions ............................ 22<br />

Mouse Cursors ................................. 22<br />

Selected Content .............................. 23<br />

The Workspace .................................... 24<br />

Resizing the Workspace ................... 24<br />

Resetting to the Default Workspace . 24<br />

Reverting to the Last Saved<br />

Workspace ........................................ 24<br />

Saving the Current Workspace ......... 24<br />

Menus .................................................. 25<br />

<strong>ChemDoodle</strong> Menu (Mac OS X Only)<br />

.......................................................... 25<br />

File Menu ......................................... 25<br />

Edit Menu ......................................... 27<br />

View Menu ....................................... 28<br />

Content Menu ................................... 29<br />

Structure Menu ................................. 32<br />

Reaction Menu ................................. 37<br />

Spectrum Menu ................................ 37<br />

Window Menu .................................. 37<br />

Purchase Menu ................................. 38<br />

Help Menu ........................................ 38<br />

Toolbars ............................................... 39<br />

Group Buttons .................................. 39<br />

Files + Formatting Toolbar ............... 40<br />

Content Toolbar ................................ 40<br />

Strokes Toolbar ................................ 41<br />

Labels Toolbar .................................. 41<br />

Rings Toolbar ................................... 41<br />

Bonds Toolbar .................................. 42<br />

Arrows Toolbar ................................ 43<br />

Orbitals Toolbar ............................... 43<br />

Shapes Toolbar ................................. 43<br />

Interface Options ................................. 45

Drawing Controls ............................. 45<br />

Drawing Mode ................................. 45<br />

Optimize Zone Size .......................... 45<br />

Hover Distance ................................. 45<br />

Snap to Grid ..................................... 45<br />

Single Bond Behavior ...................... 45<br />

Label Behavior ................................. 45<br />

Auto-connect Rings and Templates . 45<br />

Fix Bond Lengths ............................. 45<br />

Fix Bond Angles .............................. 45<br />

Require Starting Atom ...................... 45<br />

Rotate Atom Text with Structures .... 46<br />

Bonds are Focusable ........................ 46<br />

3D Rotation Mode ............................ 46<br />

Appearance ....................................... 46<br />

Recently Opened Files ..................... 46<br />

Interface Font ................................... 46<br />

Interface Color ................................. 46<br />

Decorations ...................................... 46<br />

Show Unfixed Drawing<br />

Measurements .................................. 46<br />

Show Transform Measurements ...... 46<br />

View Crawling Ants Effect When<br />

Lassoing ............................................ 46<br />

View Shimmer Effect on Button<br />

Hover ................................................ 46<br />

View Mouse Position on Rules ........ 46<br />

View Selection Bounds on Rulers .... 46<br />

Filechooser Settings ......................... 46<br />

Unified Filechooser Memory ........... 46<br />

Include Previews in Filechooser ...... 46<br />

Chapter 2: Widgets<br />

Overview ............................................. 47<br />

Widget Windows ................................. 47<br />

Widget Expansion ............................... 47<br />

Widget List .......................................... 48<br />

Widget Dock ....................................... 48<br />

Widget Icons ....................................... 49<br />

Elemental Analysis Widget ................. 50<br />

Purpose ............................................. 50<br />

Interface ............................................ 50<br />

History Widget .................................... 50<br />

2<br />

Line Notation Pad Widget ................... 51<br />

Purpose ............................................. 51<br />

Interface ............................................ 51<br />

MolGrabber Widget ............................ 52<br />

Purpose ............................................. 52<br />

Interface ............................................ 52<br />

Directing to the Online Database ..... 54<br />

Database Notes ................................. 54<br />

Multiplet Tool Widget ......................... 56<br />

Purpose ............................................. 56<br />

Interface ............................................ 56<br />

Simulating Multiplets ....................... 57<br />

Setting up the Multiplet Figure ........ 57<br />

Editing Multiplets from the Doodle<br />

Board ................................................ 57<br />

Memory and Runtime Issues ........... 58<br />

NMR SignalSeek Widget .................... 58<br />

Purpose ............................................. 58<br />

Interface ............................................ 58<br />

Simulating NMR .............................. 59<br />

Analyzing the Results ...................... 59<br />

How NMR is Simulated ................... 60<br />

Properties Widget ................................ 60<br />

Purpose ............................................. 60<br />

Interface ............................................ 61<br />

Search Widget ..................................... 62<br />

Purpose ............................................. 62<br />

Interface ............................................ 62<br />

Search Settings ................................. 63<br />

Statistics Widget ................................. 64<br />

Purpose ............................................. 64<br />

Interface ............................................ 64<br />

Symbols Widget .................................. 65<br />

Purpose ............................................. 65<br />

Interface ............................................ 65<br />

Templates Widget ................................ 67<br />

Purpose ............................................. 67<br />

Interface ............................................ 67<br />

Using Templates ............................... 67<br />

TLC Canvas Widget ............................ 68<br />

Purpose ............................................. 68

Interface ............................................ 68<br />

Drawing TLC Plates ......................... 69<br />

Editing TLC Plates from the Doodle<br />

Board ................................................ 70<br />

Chapter 3: Basic Structures<br />

Overview ............................................. 71<br />

KeyBoard Shortcuts ............................ 71<br />

Atoms .................................................. 71<br />

Placing Carbon Atoms ..................... 71<br />

Placing Other Elements .................... 71<br />

Placing Atoms with Non-elemental<br />

Labels ............................................... 72<br />

Hovering Atoms ............................... 72<br />

Selecting Atoms ............................... 72<br />

Changing Atom Labels to other<br />

Elements ........................................... 72<br />

Changing Atom Labels to Nonelemental<br />

Text .................................. 73<br />

Repeating the last Typed Atom Label<br />

for other Atoms ................................ 73<br />

Moving an Atom .............................. 73<br />

Deleting an Atom ............................. 73<br />

Chemical Labels .................................. 73<br />

Atom Label Tool .............................. 73<br />

Atom Label Token Stacking ............. 74<br />

Formatting Atom Labels .................. 74<br />

Atom Label Orientation ................... 75<br />

Bonds .................................................. 75<br />

Placing a Single Bond ...................... 75<br />

Placing Bonds other than Single<br />

Bonds ............................................... 76<br />

Optimize Zone .................................. 76<br />

Placing Bonds with Fixed Lengths<br />

and Angles ........................................ 76<br />

Placing Bonds at Non-fixed Lengths<br />

.......................................................... 76<br />

Placing Bonds at Non-fixed Angles . 76<br />

and Non-fixed Angles ...................... 76<br />

Hovering Bonds ............................... 76<br />

Selecting Bonds ............................... 77<br />

Changing a Bond Type ..................... 77<br />

3<br />

Changing Selected Bonds to Single<br />

Bonds ............................................... 77<br />

Incrementing a Bond Order .............. 77<br />

Deleting a Bond ............................... 77<br />

Deleting Bonds Around Atoms ........ 77<br />

Changing the Z-Order of Bonds ...... 77<br />

Chains ................................................. 78<br />

Placing Chains at Fixed Angles ....... 78<br />

Placing Chains at Non-fixed Angles 79<br />

Forcing the Placement of Chains<br />

Vertically and Horizontally .............. 79<br />

Inverting Carbon Chains .................. 79<br />

Rings ................................................... 79<br />

Placing a Ring .................................. 79<br />

Optimize Zone .................................. 79<br />

Placing Rings with Fixed Lengths and<br />

Angles .............................................. 80<br />

Placing Rings at Non-fixed Lengths 80<br />

Placing Rings at Non-fixed Angles .. 80<br />

Placing Rings at Non-fixed Lengths<br />

and Non-fixed Angles ...................... 80<br />

Adding Rings to Bonds .................... 80<br />

Templates ............................................ 80<br />

Selecting a Template for Use ........... 81<br />

Placing a Template ........................... 81<br />

Optimize Zone .................................. 81<br />

Placing Templates with Fixed Lengths<br />

and Angles ........................................ 81<br />

Placing Templates at Non-fixed<br />

Lengths ............................................. 82<br />

Angles .............................................. 82<br />

Lengths and Non-fixed Angles ........ 82<br />

Saving a New Template .................... 82<br />

Managing your Templates ................ 82<br />

Attributes ............................................. 82<br />

Adding Attributes ............................. 83<br />

Hovering Attributes .......................... 83<br />

Selecting Attributes .......................... 83<br />

Editing Attributes ............................. 83<br />

Moving Attributes ............................ 84<br />

Removing Attributes ........................ 84

Charges ................................................ 84<br />

Adding Charges ................................ 84<br />

Incrementing and Decrementing<br />

Charges ............................................. 84<br />

Removing Charges ........................... 84<br />

Radicals ............................................... 85<br />

Adding Radicals ............................... 85<br />

Incrementing and Decrementing the<br />

Number of Radical Electrons ........... 85<br />

Removing Radicals .......................... 85<br />

Symbols ............................................... 85<br />

Adding Symbols ............................... 86<br />

Removing Symbols .......................... 86<br />

Isotopes ............................................... 86<br />

Setting Published Isotope Mass<br />

Numbers ........................................... 86<br />

Setting Arbitrary Isotope Mass<br />

Removing Mass Numbers ................ 86<br />

Orbitals ................................................ 86<br />

Placing Orbitals at Fixed Lengths and<br />

Angles .............................................. 87<br />

Placing Orbitals at Non-fixed lengths<br />

or Angles .......................................... 88<br />

Forcing Orbitals to be Drawn<br />

Vertically and Horizontally .............. 88<br />

Moving Orbitals ............................... 88<br />

Resizing Orbitals .............................. 88<br />

Removing Orbitals ........................... 88<br />

Chapter 4: Shapes<br />

Overview ............................................. 89<br />

Anchors ............................................... 89<br />

Control Anchors ............................... 89<br />

Corner/Edge Anchors ....................... 89<br />

Lines .................................................... 89<br />

Drawing Lines at Fixed Angles ........ 89<br />

Drawing Lines at Non-fixed Angles 90<br />

Forcing the Lines to be Drawn<br />

Vertically and Horizontally .............. 90<br />

Moving Lines ................................... 90<br />

Resizing Lines .................................. 90<br />

Removing Lines ............................... 90<br />

4<br />

Arcs ..................................................... 90<br />

Drawing Arcs at Fixed Angles ......... 91<br />

Drawing Arcs at Non-fixed Angles .. 91<br />

Forcing the Arcs to be Drawn<br />

Vertically and Horizontally .............. 91<br />

Moving Arcs ..................................... 91<br />

Resizing Arcs ................................... 91<br />

Changing Arc Angles ....................... 92<br />

Flipping an Arc’s Orientation ........... 92<br />

Removing Arcs ................................. 92<br />

Arrows ................................................. 92<br />

Drawing Arrows at Fixed Angles ..... 92<br />

Drawing Arrows at Non-fixed Angles<br />

.......................................................... 93<br />

Vertically and Horizontally .............. 93<br />

Moving Arrows ................................ 93<br />

Resizing Arrows ............................... 93<br />

Changing Arrow Arc Angles ............ 93<br />

Removing Arrows ............................ 94<br />

Editing Arrowheads ......................... 94<br />

Rectangles ........................................... 94<br />

Drawing Rectangles ......................... 94<br />

Drawing Squares .............................. 95<br />

Moving Rectangles .......................... 95<br />

Resizing Rectangles ......................... 95<br />

Converting Between Rounded and<br />

Non-rounded Rectangles .................. 95<br />

Removing Rectangles ...................... 95<br />

Ovals ................................................... 95<br />

Drawing Ovals ................................. 96<br />

Drawing Circles ............................... 96<br />

Moving Ovals ................................... 96<br />

Resizing Ovals ................................. 96<br />

Removing Ovals ............................... 96<br />

Brackets ............................................... 96<br />

Drawing Brackets ............................. 97<br />

Drawing Brackets with Equal Width<br />

and Height ........................................ 97<br />

Moving Brackets .............................. 97<br />

Resizing Brackets ............................. 97<br />

Editing Bracket Lip Protrusion ........ 97<br />

Removing Brackets .......................... 98

Custom Shapes .................................... 98<br />

Drawing with the Pen Tool ............... 98<br />

Drawing with the Polyline Tool ....... 99<br />

Moving Pen Paths and Polylines ...... 99<br />

Modifying Pen Paths and Polylines . 99<br />

Drawing with the Bezier Tool .......... 99<br />

Modifying Bezier Curves ............... 100<br />

Deleting Bezier Control Points ...... 100<br />

Adding Arrows to Bezier Curves ... 100<br />

Closing and Opening Custom Shapes<br />

........................................................ 100<br />

Removing Custom Shapes ............. 101<br />

Rulers ................................................ 101<br />

Drawing Rulers at Fixed Angles .... 101<br />

Drawing Rulers at Non-fixed Angles<br />

........................................................ 101<br />

Forcing Rulers to be Drawn Vertically<br />

and Horizontally ............................ 101<br />

Automatically Measuring Object<br />

Width and Height ........................... 101<br />

Diagonal ......................................... 102<br />

Moving Rulers ............................... 102<br />

Resizing Rulers .............................. 102<br />

Showing and Hiding Major and Minor<br />

Ticks ............................................... 102<br />

Changing the Measurement Unit ... 102<br />

Removing Rulers ........................... 103<br />

Text Areas ......................................... 103<br />

Chapter 5: Editing Content<br />

Overview ........................................... 104<br />

Selecting Content .............................. 104<br />

Selecting Individual Objects .......... 104<br />

Selecting Groups of Objects .......... 104<br />

Select All ........................................ 105<br />

Adding/Removing Individual Objects<br />

from a Selection ............................. 105<br />

Adding/Removing Groups of Objects<br />

Selecting Whole Molecules ........... 105<br />

Selecting Chemical Objects by<br />

SMARTS ........................................ 105<br />

5<br />

Navigating Through Single Shapes 105<br />

Selecting Only Shapes ................... 105<br />

Select the Inverse of the Current<br />

Selection ......................................... 106<br />

Deselecting Objects ....................... 106<br />

Reselecting Objects ........................ 106<br />

Duplicating Content .......................... 106<br />

Copy and Paste ............................... 106<br />

Cut and Paste .................................. 106<br />

Organizing Content ........................... 106<br />

Aligning .......................................... 106<br />

Aligning by Bond ........................... 106<br />

Centering ........................................ 107<br />

Distributing ..................................... 107<br />

Flipping .......................................... 107<br />

Flipping a Bond .............................. 107<br />

Stacking .......................................... 108<br />

Framing Content ............................... 108<br />

Editing Content ................................. 108<br />

Translating ...................................... 108<br />

Translating Horizontally or Vertically<br />

........................................................ 108<br />

Duplicating Content ....................... 108<br />

Rotating .......................................... 108<br />

Moving the Rotation Anchor .......... 109<br />

Scaling ............................................ 109<br />

Fonts ............................................... 110<br />

Drawing Aids .................................... 110<br />

Atom Aids ...................................... 110<br />

Bond Aids ....................................... 110<br />

Ring Aids ....................................... 110<br />

Molecule Aids ................................ 110<br />

Background Aids ............................ 110<br />

Colors ................................................ 110<br />

Color Button ................................... 110<br />

Quick Colors Button ...................... 111<br />

Color Detection .............................. 111<br />

Color Chooser ................................ 111<br />

Modifying the Z-order of Shapes ...... 112<br />

Grouping Content ............................. 112<br />

Grouping ......................................... 113<br />

Ungrouping ..................................... 113<br />

Removing Content ............................ 113

Removing individual Objects ........ 113<br />

Removing Groups of Objects ......... 113<br />

Chapter 6: Advanced Chemistry and<br />

Cheminformatics<br />

Aromaticity ....................................... 114<br />

Toggling between Kekulé and Circle<br />

Representations for Aromatics ....... 114<br />

Forcing Aromaticity ....................... 114<br />

Calculating Covalent Bonds ............. 114<br />

Carbon Labels ................................... 115<br />

Terminal Carbon Labels ................. 115<br />

Chemical Suppliers ........................... 115<br />

Chemical Warnings ........................... 116<br />

Warning Types ............................... 116<br />

Disabling Warnings Globally ......... 116<br />

Disabling Warnings for a Single Atom<br />

........................................................ 116<br />

Hiding Warnings from Rendering .. 117<br />

Cleaning Structures ........................... 117<br />

Optimizing Structures in 2D .......... 117<br />

Distance Geometry Embedding ...... 117<br />

Preserving Stereochemistry ........... 117<br />

Descriptors ........................................ 117<br />

Constitutional ................................. 117<br />

Topological ..................................... 118<br />

Physicochemical ............................. 119<br />

ADME ............................................ 120<br />

Flattening Atomic Coordinates ...... 120<br />

Fragmentation ................................... 120<br />

Formal Charges ................................. 121<br />

Glassware Clipart .............................. 121<br />

Flipping Glassware ......................... 122<br />

Tubing ............................................. 122<br />

Graph Reduction ............................... 123<br />

Reduce 0° (Lone) ........................... 123<br />

Reduce 1° (Terminals) ................... 123<br />

Repeatedly Reduce 1° .................... 123<br />

Reduce 1° + 0° ............................... 123<br />

Reduce 2° (Chains) ........................ 123<br />

Reduce 2° + 1° + 0° ....................... 123<br />

Hydrogens ......................................... 123<br />

Implicit Hydrogen Rendering ......... 123<br />

6<br />

Adding Hydrogens as Atoms ......... 124<br />

Adding Hydrogens as Text ............. 124<br />

Defining when Hydrogens are Added<br />

to Carbons ...................................... 124<br />

IUPAC Naming ................................. 124<br />

Name to Structure .......................... 124<br />

Kekulé Structures .............................. 124<br />

Kekulizing a Single Bond Frame ... 124<br />

Kekulizing a Substructure of<br />

Resonance Bonds ........................... 125<br />

Label Expansion ................................ 125<br />

Expanding Labels ........................... 125<br />

Implicit Hydrogens ........................ 125<br />

Condensed Labels .......................... 125<br />

Abbreviations ................................. 126<br />

Adding Custom Abbreviations ....... 126<br />

Mixing Condensed Notations and<br />

Molecular Formulas ....................... 126<br />

Newman Projections ......................... 127<br />

Ring Perception ................................. 127<br />

Supported Ring Sets ....................... 127<br />

Exploding Ring Sets ...................... 128<br />

Performance Considerations .......... 128<br />

Sequence Tool ................................... 128<br />

Stereochemistry ................................ 128<br />

Chiral Centers ................................ 129<br />

Double Bonds ................................. 129<br />

Resolving Stereochemistry ............ 129<br />

Forcing Stereochemical<br />

Configurations ................................ 129<br />

Structure Perspective ......................... 129<br />

Unique IDs ........................................ 130<br />

Zero Order/Ionic Bonds .................... 130<br />

Chapter 7: Reactions<br />

Overview ........................................... 131<br />

Drawing Reaction Arrows ................. 131<br />

Arrow Types ...................................... 131<br />

Arrowhead Styles ........................... 131<br />

Changing Arrowhead Lengths and<br />

Angles ............................................ 131<br />

Quickly Toggle Arrowheads .......... 131

Connector Styles ............................ 132<br />

Special Arrow Presets .................... 132<br />

Bezier Arrow Ideas ........................... 132<br />

The Chute Arrow ............................ 133<br />

The Loop Arrow ............................. 133<br />

The Escalator Arrow ...................... 133<br />

The Hump Arrow ........................... 133<br />

The Zigzag Arrow .......................... 133<br />

Building Reactions ............................ 133<br />

Implicitly ........................................ 133<br />

Explicitly ........................................ 133<br />

Adding Reaction Conditions .......... 134<br />

Adding Plus Symbols ..................... 134<br />

Dissolving Reactions ........................ 134<br />

Cleaning Reactions ........................... 134<br />

Chapter 8: Spectra<br />

Overview ........................................... 137<br />

Inserting Spectra ................................ 137<br />

Spectra Types ................................. 137<br />

Uninterpretable Spectra .................. 138<br />

Saving Spectra ................................... 138<br />

Simulating Spectra ............................ 138<br />

Editing Spectra .................................. 138<br />

Moving Spectra .............................. 138<br />

Resizing Spectra ............................. 139<br />

Removing Spectra .......................... 139<br />

Expanding the Perspective ............. 139<br />

Editing the Perspective ................... 139<br />

Changing the Title .......................... 140<br />

Changing the Axes ......................... 140<br />

Showing Grids ............................... 140<br />

Showing Integration Lines ............. 140<br />

Chapter 9: Visual Specifications<br />

Overview ........................................... 142<br />

Document Settings ............................ 142<br />

Style Sheets .................................... 142<br />

Setting the Default Document Settings<br />

........................................................ 143<br />

Restore the Original Default<br />

Document Settings ......................... 143<br />

Individual Settings ............................ 143<br />

7<br />

Setting Types .................................. 143<br />

Page ................................................ 144<br />

Atoms ............................................. 144<br />

Attributes ........................................ 146<br />

Bonds ............................................. 146<br />

Rings .............................................. 147<br />

Reactions ........................................ 148<br />

Shapes ............................................ 148<br />

Spectra ............................................ 149<br />

Editing Visual Specifications ............ 149<br />

For Single Objects .......................... 149<br />

For a Group of Objects .................. 150<br />

Conforming a Group of Objects to the<br />

Current Style Sheet ........................ 150<br />

Conforming the Entire Document to a<br />

Different Style Sheet ...................... 150<br />

3D Graphics ...................................... 150<br />

Bond Stroke Styles ............................ 151<br />

Advanced Document Rendering ....... 151<br />

Anti-Aliasing .................................. 152<br />

Font Fractional Metrics .................. 152<br />

Dithering ......................................... 153<br />

Rendering Algorithm ...................... 154<br />

Alpha Interpolation Algorithm ....... 154<br />

Color Rendering Algorithm ............ 154<br />

Stroke Control ................................ 154<br />

Image Scaling ................................. 156<br />

Chapter 10: Sharing Information<br />

Overview ........................................... 157<br />

The System Clipboard ....................... 157<br />

MIME Types .................................. 157<br />

Clipboard Settings .......................... 158<br />

Scalable Vector Graphics ............... 158<br />

Copying Data to Other Applications 159<br />

Using the Copy Function ............... 159<br />

Using the Copy As Function .......... 159<br />

Pasting Data from Other Applications<br />

........................................................... 160<br />

Where Content is Pasted ................ 160<br />

Paste Special... ............................... 160<br />

Pasting Text as Chemical Data ....... 160<br />

Chemical Format Compatibility ....... 161

Image Format Compatibility ............. 161<br />

Supported Input Formats ................ 161<br />

Supported Output Formats ............. 161<br />

Importing Chemical Content from<br />

Images ............................................ 162<br />

Exporting the Document to an Image<br />

........................................................ 162<br />

Exporting only Certain Objects to an<br />

Image .............................................. 162<br />

Image Output Options .................... 162<br />

Inserting Images ................................ 163<br />

Round Trip Editing ............................ 163<br />

Support ........................................... 163<br />

Windows ........................................ 164<br />

Mac OS X ...................................... 164<br />

Linux .............................................. 165<br />

Printing .............................................. 167<br />

Page Setup ..................................... 167<br />

Flipping the Page Orientation ........ 168<br />

Print Preview .................................. 168<br />

Printing a Document ...................... 168<br />

Appendix A: Managing<br />

Overview ........................................... 169<br />

Application and File Icons ................ 169<br />

Updating <strong>ChemDoodle</strong> ...................... 169<br />

Windows Administrator Privileges 170<br />

Skipping Updates ........................... 170<br />

Purchasing Upgrades ..................... 170<br />

Moving your Activated Copy to a New<br />

Computer ........................................... 170<br />

Preparing for a System Restore ......... 171<br />

Using iChemLabs Cloud Services .... 171<br />

Appendix B: Chemical File Types<br />

Overview ........................................... 172<br />

Adherence to Third Party Specifications<br />

........................................................... 172<br />

Be Careful Saving 3rd Party Formats<br />

Testing 3rd Party File Type Output ... 172<br />

Supported Chemical File Types ........ 173<br />

8<br />

File Annotations ................................ 173<br />

File Conversion Tool ......................... 174<br />

iChemLabs <strong>ChemDoodle</strong> Documents<br />

........................................................... 175<br />

iChemLabs <strong>ChemDoodle</strong> Javascript<br />

Data ................................................... 175<br />

ACD/ChemSketch Document ........... 176<br />

Beilstein ROSDAL ............................ 177<br />

CambridgeSoft ChemDraw Files ...... 177<br />

CHARMM CARD File ..................... 180<br />

ChemAxon Marvin Documents ........ 180<br />

Chemical Markup Language ............. 182<br />

Daylight SMILES .............................. 183<br />

IUPAC InChI ..................................... 184<br />

IUPAC JCAMP Data ......................... 185<br />

MDL ISIS Sketch Files ..................... 186<br />

MDL Connection Table Files ............ 190<br />

Molinspiration JME String ................ 192<br />

RCSB Protein Data Bank Files ......... 193<br />

Schrödinger Files .............................. 194<br />

Standard Molecular Data ................... 195<br />

About ............................................. 195<br />

Tripos Mol2 ....................................... 196<br />

Tripos Sybyl Line Notation ............... 197<br />

XYZ .................................................. 197<br />

Appendix C: Compatibility with 3rd<br />

Party Applications<br />

Overview ........................................... 199<br />

Microsoft Office ................................ 199<br />

Word ............................................... 199<br />

Powerpoint ..................................... 199<br />

Excel ............................................... 199<br />

Apple iWork ...................................... 199<br />

Pages .............................................. 199<br />

Keynote .......................................... 199<br />

Numbers ......................................... 199<br />

OpenOffice ........................................ 199<br />

Writer ............................................. 199<br />

Calc ................................................ 200<br />

Impress ........................................... 200<br />

Adobe Products ................................. 200<br />

Photoshop ...................................... 200

Illustrator ........................................ 200<br />

Browsers ........................................... 200<br />

Other .................................................. 200<br />

Appendix D: Elemental Data<br />

Overview ........................................... 201<br />

Elemental Database ........................... 201<br />

References ......................................... 201<br />

Interactive Periodic Table .................. 201<br />

Appendix E: How NMR is<br />

Simulated<br />

Algorithms ........................................ 204<br />

Shift Prediction .............................. 204<br />

Splitting .......................................... 204<br />

Roof Effects ................................... 204<br />

Solvent Peaks ................................. 204<br />

1H Rapid Exchange ........................ 204<br />

1H Anisotropic Effects ................... 204<br />

1H Diastereotopic Pairs ................. 204<br />

13C Quaternary Carbon Intensity<br />

Reductions ...................................... 204<br />

Limitations ........................................ 204<br />

Appendix F: <strong>ChemDoodle</strong> Web<br />

Components<br />

Overview ........................................... 206<br />

Generating <strong>ChemDoodle</strong> Web<br />

Components ...................................... 206<br />

Generating Javascript Data Files for Use<br />

with <strong>ChemDoodle</strong> Web Components 207<br />

Optimizing PDB Files ....................... 207<br />

Generating Components for Mobile<br />

Devices .............................................. 208<br />

Rendering Compatibility .................. 208<br />

License .............................................. 208<br />

Am I allowed to use this? .................. 209<br />

Attributions ....................................... 209<br />

Further Information ........................... 209<br />

Appendix G: <strong>ChemDoodle</strong> Mobile<br />

Overview ........................................... 210<br />

9<br />

Supported Platforms .......................... 210<br />

iOS .................................................. 210<br />

Android .......................................... 210<br />

Logging in to <strong>ChemDoodle</strong> Mobile .. 210<br />

<strong>ChemDoodle</strong> Mobile Features .......... 210<br />

Calculations .................................... 210<br />

Spectra ............................................ 210<br />

Transferring Data between <strong>ChemDoodle</strong><br />

Desktop and <strong>ChemDoodle</strong> Mobile .... 211<br />

Appendix ICL-1: Technical Support<br />

When to Contact Customer Service .. 212<br />

How to Contact Customer Service .... 212<br />

Feature Requests ............................... 213<br />

Following <strong>ChemDoodle</strong> Development<br />

........................................................... 214<br />

Troubleshooting ................................. 214<br />

Windows ........................................ 214<br />

Mac OS X ...................................... 214<br />

Performance Improvements ........... 214

This <strong>User</strong> <strong>Guide</strong> provides information on the<br />

iChemLabs product, <strong>ChemDoodle</strong>.<br />

About <strong>ChemDoodle</strong><br />

<strong>ChemDoodle</strong>, in short, can create images of<br />

molecules. But it is much more than that.<br />

<strong>ChemDoodle</strong> can efficiently generate<br />

chemical documents and figures for use in<br />

publications, produces non-molecular objects<br />

such as spectra and TLC plates, is integrated<br />

with databases, can manipulate a large<br />

number of chemical files and formats, and in<br />

general, streamlines a lot of the tasks that one<br />

is confronted with when trying to do or<br />

explain chemistry in a digital medium.<br />

<strong>ChemDoodle</strong> isn't just another program for<br />

drawing molecules, it's a brand new<br />

application for interacting with chemical data<br />

and creating chemical art!<br />

<strong>ChemDoodle</strong> is designed to be intuitive and<br />

easy to learn. <strong>ChemDoodle</strong> is used by a wide<br />

range of individuals, from high school<br />

students to accomplished professors and we<br />

have done our best to provide the most<br />

intuitive controls for such a diverse group<br />

while remaining thorough and providing<br />

superior quality.<br />

<strong>ChemDoodle</strong> is integrated with the following<br />

iChemLabs Products:<br />

• <strong>ChemDoodle</strong> Web Components<br />

• <strong>ChemDoodle</strong> Mobile<br />

About this <strong>Guide</strong><br />

This <strong>User</strong> <strong>Guide</strong> contains information for the<br />

<strong>ChemDoodle</strong> application for the Windows,<br />

Mac OS X and Linux operating systems. It<br />

10<br />

assumes you are familiar with the basics of<br />

your operating system. If you are not, please<br />

refer to your system manual before using<br />

<strong>ChemDoodle</strong>.<br />

Some tasks described in this guide require the<br />

use of third-party applications such as<br />

Microsoft Office Word or iWork Pages. If you<br />

are not familiar with these third-party<br />

applications, please consult the associated<br />

user guide provided with that product.<br />

The chapters in this guide are organized by<br />

task. They are intended to help you<br />

familiarize yourself with the <strong>ChemDoodle</strong><br />

application and to begin using it as quickly<br />

and efficiently as possible.<br />

Most images are taken from the Mac OS X<br />

version of <strong>ChemDoodle</strong> and will be<br />

representative of all operating systems. If an<br />

operating system specific issue is discussed,<br />

any images are taken from the operating<br />

system under investigation.<br />

Additional Information<br />

Additional sources of <strong>ChemDoodle</strong><br />

information include:<br />

• <strong>ChemDoodle</strong> Support Pages.<br /><br />

• <strong>ChemDoodle</strong> Videos.<br /><br />

• <strong>ChemDoodle</strong> Web Components.<br /><br />

• <strong>ChemDoodle</strong> Mobile.<br /><br />

• iChemLabs Customer Support.<br /><br />

• iChemLabs Website.<br />

Installation and System<br />

Requirements<br />

Microsoft Windows Requirements<br />

• Windows XP, Vista or 7+.<br />

• Oracle Java 1.6 or more recent.<br />

• A minimum of 1GB of memory.<br />

Macintosh OS X Requirements<br />

• Mac OS X 10.6 (Snow Leopard) or 10.7<br />

(Lion) or 10.8 (Mountain Lion).<br />

• Oracle Java 1.6 or more recent (installed by<br />

default on 10.6; for 10.7+, will be<br />

automatically installed when <strong>ChemDoodle</strong><br />

is opened and you accept to install Java).<br />

Linux Requirements<br />

• Any version of Linux, although we test with<br />

and Ubuntu (recommended), Mint, Fedora,<br />

Debian and OpenSUSE Linux.<br />

• Any GUI, although we recommend and test<br />

with GNOME.<br />

• Oracle Java 1.6 or more recent (OpenJDK,<br />

GNU Java, IcedTea or any non-official<br />

distributions are not supported).<br />

Installing Java<br />

<strong>ChemDoodle</strong> requires the official Oracle<br />

(formerly Sun Microsystems) Java<br />

distribution to run. Java is free and can be<br />

easily installed from:<br />

Most contemporary Windows systems will<br />

have Java installed by default.<br />

Mac OS X 10.6 will have Java installed by<br />

default. Mac OS X 10.7+ will prompt you to<br />

install Java when you first run a Java<br />

11<br />

application. Accept that prompt to install<br />

Java.<br />

<strong>ChemDoodle</strong> does NOT support OpenJDK,<br />

IcedTea, GNU Java, or any other non-Oracle<br />

version of Java. With unsupported Java<br />

distributions, <strong>ChemDoodle</strong> will run slowly,<br />

have broken functions and may not even run<br />

at all.<br />

Installation<br />

Installation, activation and uninstallation<br />

instructions are can be found on the<br />

<strong>ChemDoodle</strong> website.<br />

Table 1: Websites for Installation Instructions<br />

Operating<br />

System<br />

Webpage<br />

Windows http://<br /><br />

windows-installationinstructions<br />

Mac OS X http://<br /><br />

Linux http://<br />

linux-installationinstructions<br />

Installing for Multiple <strong>User</strong>s<br />

on a Single Computer<br />

<strong>ChemDoodle</strong> will allow several users to use<br />

<strong>ChemDoodle</strong> on the same computer. All<br />

preferences and settings files are saved<br />

relative to the user’s account, so that each<br />

user may save their own preferences. Note<br />

that even though <strong>ChemDoodle</strong> only needs to<br />

be installed once on the computer, each user

will still have to individually activate<br />

<strong>ChemDoodle</strong> for his/her user account, so he/<br />

she will need access to an activation code.<br />

Instructions for installing <strong>ChemDoodle</strong> for<br />

multiple users is operating system dependent<br />

and is described in the following subsections.<br />

Windows<br />

During the installation, keep the install folder<br />

in C:\Program Files\. All users will be able to<br />

execute <strong>ChemDoodle</strong> from within this folder.<br />

There will be periodic updates to<br />

<strong>ChemDoodle</strong>. For Windows Vista and later,<br />

<strong>ChemDoodle</strong> requires administrator<br />

privileges to update, so you will need to<br />

update <strong>ChemDoodle</strong> as administrator on the<br />

computer if none of the users have<br />

administrator privileges. This only needs to<br />

be done once for the computer, and all users<br />

will be using the update.<br />

Mac OS X<br />

During the installation, drag the <strong>ChemDoodle</strong><br />

folder to the /Applications folder as<br />

instructed. All users will be able to execute<br />

<strong>ChemDoodle</strong> from within this folder.<br />

<strong>ChemDoodle</strong>. Only superusers will be able to<br />

update <strong>ChemDoodle</strong>, so you will need to<br />

update <strong>ChemDoodle</strong> as superuser on the<br />

computer if none of the users are superusers.<br />

This only needs to be done once for the<br />

computer, and all users will be using the<br />

update.<br />

Linux<br />

Run the Linux BIN in a folder that all users<br />

have rights to execute binaries from. After the<br />

installation, verify that all users that will be<br />

using <strong>ChemDoodle</strong> have the necessary<br />

permissions to do so.<br />

<strong>ChemDoodle</strong>. You should restrict write<br />

12<br />

privileges to the <strong>ChemDoodle</strong> installation<br />

folder if you do not want users to update<br />

<strong>ChemDoodle</strong> by themselves. This may be<br />

necessary, for instance, if you do not want<br />

one user to update the application while<br />

another user is finishing some work and does<br />

not yet want to learn the changes the update<br />

will bring. If you restrict write permissions,<br />

you will need to update <strong>ChemDoodle</strong> as root<br />

on the computer when all users are ready.<br />

Folder Contents<br />

There are two folders that the <strong>ChemDoodle</strong><br />

application uses, the main <strong>ChemDoodle</strong><br />

installation folder and the<br />

<strong>ChemDoodle</strong>Settings folder located in the<br />

operating system’s standard Documents<br />

folder.<br />

The contents of the main <strong>ChemDoodle</strong><br />

installation folder are:<br />

1. <strong>ChemDoodle</strong> application -<br />

<strong>ChemDoodle</strong>.exe on Windows,<br />

<strong>ChemDoodle</strong>.app on Mac OS X, and the<br />

<strong>ChemDoodle</strong> shell script on Linux<br />

2. config directory - This folder contains<br />

various configuration files, such as<br />

proxy.config, for setting <strong>ChemDoodle</strong> to<br />

use your proxy. It also contains the site<br />

license configuration file for site licenses.<br />

3. docs directory - This folder contains<br />

documentation such as this user guide.<br />

4. external directory - This folder contains<br />

required packages that <strong>ChemDoodle</strong><br />

needs to start up and run properly. Any<br />

licenses associated with these packages<br />

are also provided.

5. resources directory - This folder contains<br />

native application icon images and other<br />

resources such as the auto-updater and the<br />

<strong>ChemDoodle</strong> Web Components library.<br />

6. <strong>ChemDoodle</strong>.jar - The executable java<br />

jar of <strong>ChemDoodle</strong>. Do not remove this<br />

file! This jar is not present in the Mac OS<br />

X distribution of <strong>ChemDoodle</strong>.<br />

7. <strong>ChemDoodle</strong>.vmoptions - This file is<br />

only present in the Windows distribution<br />

of <strong>ChemDoodle</strong>. It contains parameters<br />

for the Java virtual machine.<br />

WARNING: Do not remove or alter any of<br />

the contents of the <strong>ChemDoodle</strong> installation<br />

folder or unexpected behavior may occur.<br />

To move the application, you must move<br />

the entire <strong>ChemDoodle</strong> folder.<br />

Standard Operating System<br />

Documents Folder<br />

The standard operating system Documents<br />

folder varies depending on the operating<br />

system:<br />

• Windows XP - C:\Documents and Settings\<br />

[username]\My Documents<br />

• Windows Vista/7 - C:\<strong>User</strong>s\[username]<br />

\My Documents<br />

• Mac OS X - /<strong>User</strong>s/[username]/Documents<br />

• Linux - /<strong>User</strong>s/[username]/Documents<br />

Free Trials<br />

Trials may be initiated by clicking the Free<br />

Trial button on the activation screen when<br />

<strong>ChemDoodle</strong> is opened. Trials will remain<br />

active for 14 days. After a trial expires, there<br />

is no option to try it again.<br />

13<br />

Trial Restrictions<br />

• Documents show a watermark at the top<br />

and will render a background texture.<br />

• The Save..., Save as Image... and<br />

Convert... functions are disabled.<br />

• Only images and <strong>ChemDoodle</strong> data can be<br />

pasted from <strong>ChemDoodle</strong>.<br />

• All copied and printed content will contain<br />

a watermark.<br />

• Templates cannot be saved.<br />

• Certain <strong>ChemDoodle</strong> Web Components<br />

functions are disabled (such as PDB file<br />

optimization).<br />

Unrestricted Trials<br />

If your trial has expired and you still require<br />

the use of <strong>ChemDoodle</strong>, or if you would like<br />

to try <strong>ChemDoodle</strong> without the trial<br />

restrictions, you may purchase an unrestricted<br />

14 day trial on the <strong>ChemDoodle</strong> website.<br />

Student Version Restrictions<br />

The student version of <strong>ChemDoodle</strong> has<br />

several restrictions:<br />

• No iChemLabs account is provided.<br />

• Round-trip editing is not available.<br />

• Images output from <strong>ChemDoodle</strong> will not<br />

contain chemical metadata.<br />

• Formatted documents and publishing style<br />

sheets are not available.<br />

• Import/Export of style sheets is disabled.<br />

• Only <strong>ChemDoodle</strong> Documents can be<br />

saved.<br />

• No conversion utility.

• The only chemical data format you can<br />

copy is the <strong>ChemDoodle</strong> format.<br />

Activation<br />

Activation is performed when one uses a<br />

purchased activation code to associate a<br />

license with the <strong>ChemDoodle</strong> application for<br />

a given user account.<br />

Activation can be performed in two ways.<br />

The first is by using the activation code in the<br />

activation screen when <strong>ChemDoodle</strong> has not<br />

been activated or a trial started. The second<br />

way is to use the Activate <strong>ChemDoodle</strong><br />

menu item in the Purchase menu while a trial<br />

is active.<br />

The activation code may be manually typed<br />

into the activation form, but it is easier to just<br />

copy and paste the entire code from the<br />

receipt into the form. Once activated with a<br />

purchased license, all restrictions from the<br />

trial are removed.<br />

Activation requires an active internet<br />

connection. Our server is sent the activation<br />

code which is validated and gives permission<br />

to create the license file. This method<br />

prevents piracy and allows us to minimize the<br />

cost of <strong>ChemDoodle</strong>. There are no exceptions<br />

to this activation procedure.<br />

Connection Issues<br />

Activation is an important part of the setup<br />

procedure, and there are a few issues, usually<br />

in corporate environments, that may occur.<br />

Firewall Issues<br />

If your firewall blocks internet connections<br />

from Java applications, then <strong>ChemDoodle</strong><br />

will not be allowed to connect to the internet.<br />

An administrator should set up a special<br />

exception to allow <strong>ChemDoodle</strong> to connect to<br />

the internet, at least for activation.<br />

14<br />

Proxy Issues<br />

If you use a proxy to access the internet,<br />

<strong>ChemDoodle</strong> will use the default system<br />

proxy information to connect to the internet.<br />

If that fails, then you will need to manually<br />

define the proxy settings in the proxy.config<br />

file that is located in the config folder in the<br />

<strong>ChemDoodle</strong> installation folder.<br />

Usage Restrictions<br />

There are no restrictions on how to use<br />

<strong>ChemDoodle</strong> as long as the user abides by the<br />

license he/she accepts when activating<br />

There are no restrictions on your created<br />

chemical drawings generated from activated<br />

copies of <strong>ChemDoodle</strong>. You may use your<br />

created chemical drawings for whatever<br />

purpose you choose.<br />

Using <strong>ChemDoodle</strong> to output the glassware<br />

graphics for the sole purpose of publishing,<br />

selling, or distributing them individually or as<br />

a set is forbidden.<br />

Attributions<br />

Attribution of graphics and output to<br />

<strong>ChemDoodle</strong> are welcome, but are not<br />

necessary in any form.

Toolbars<br />

Chapter 1:<br />

Introducing<br />

Overview<br />

This section introduces the new user to the<br />

<strong>ChemDoodle</strong> graphical user interface. It<br />

covers the following topics:<br />

• Identifying the parts of the <strong>ChemDoodle</strong><br />

interface.<br />

• Creating, opening and saving documents.<br />

• Introducing the menus and toolbars.<br />

Figure 1.1: <strong>ChemDoodle</strong> on Windows (7)<br />

15<br />

The <strong>ChemDoodle</strong> Graphical<br />

<strong>User</strong> Interface<br />

Although the Windows, Mac OS X and Linux<br />

versions of the <strong>ChemDoodle</strong> graphical user<br />

interface (GUI) differ slightly, the main<br />

elements of the GUI are consistent across<br />

platforms. The Windows version of<br />

<strong>ChemDoodle</strong> is shown in Figure 1.1. The<br />

Mac OS X version of <strong>ChemDoodle</strong> is shown<br />

in Figure 1.2. The Linux version of<br />

<strong>ChemDoodle</strong> is shown in Figure 1.3.<br />

Menu Bar<br />

Doodle Board<br />

Widgets<br />

Widget<br />

Figure 1.2: <strong>ChemDoodle</strong> on Mac OS X (10.6)<br />

Figure 1.3: <strong>ChemDoodle</strong> on Linux (Ubuntu 10.04)<br />

16<br />

Menu Bar Doodle Board<br />

Dock<br />

Using the Graphical <strong>User</strong><br />

Interface<br />

<strong>ChemDoodle</strong>’s functions are accessed<br />

through interaction with several types of<br />

components:<br />

Ruler <strong>Guide</strong>s<br />

• Doodle Board - The main drawing window.<br />

• Menus - Core application functions.<br />

• Toolbars - Quickly access functions and<br />

modify how mouse gestures interact with<br />

the Doodle Board.<br />

• Widgets - Mini applications within<br />

<strong>ChemDoodle</strong> that perform powerful and<br />

complementary tasks.<br />

Figure 1.4: The Doodle Board<br />

Tab Tray<br />

17<br />

These components are identified in Figures<br />

1.1-1.3 and are discussed in the following<br />

sections. Widgets are explained in Chapter 2.<br />

The Doodle Board is the main drawing<br />

window and contains all of the documents<br />

you create and edit. You may use mouse<br />

gestures to interact with the Doodle Board<br />

and to draw your figures. Figure 1.4 displays<br />

the main components of the Doodle Board.<br />

Selected Content<br />

Document<br />

Mouse Cursor<br />

There are two rulers aligned with the<br />

currently displayed document on the Doodle<br />

Board. The ruler to the left of the document<br />

allows for vertical measurements and the<br />

ruler to the top of the document allows for<br />

horizontal measurements.<br />

When the document rendering scale is<br />

changed, the ruler scale will also change to<br />

match the new dimensions. When the<br />

scrollbars are used to focus on a different area<br />

of the document, the rulers will also scroll to<br />

match the new location.<br />

The ruler displays full ticks at each inch, halfticks<br />

at each half-inch, and quarter-ticks every<br />

eighth of an inch. Several colored ticks and<br />

areas may also be present on the rules for<br />

visual feedback. These feedback tips can be<br />

disabled in the Preferences window under the<br />

General tab.<br />

• Margin Areas - Margins are highlighted in<br />

a yellow color.<br />

• Mouse Pointer Ticks - Mouse pointer<br />

locations are ticked on the rules with a red<br />

color.<br />

• Selection Dimension Area - Marks the<br />

bounds of the currently selected content.<br />

This is denoted by an amber area. This area<br />

corresponds to the internal coordinates of<br />

the content and not the visual bounds. For<br />

example, it will denote the bounding box<br />

given the atom coordinates, but will ignore<br />

the dimensions of the labels for those<br />

atoms.<br />

Scrollbars<br />

Scrollbars will appear to the right and bottom<br />

of the document if the height and width,<br />

respectively, of the document are too large to<br />

fit on the Doodle Board. You can click and<br />

drag the scroll bars to change which area of<br />

18<br />

the document is displayed on the Doodle<br />

Board. You can also use the mouse scroll<br />

gesture to change the perspective. Horizontal<br />

mouse scrolling is only supported on Mac OS<br />

X.<br />

The Doodle Board stores all drawing content<br />

and organizes them into documents that can<br />

be saved as files or images. Each document<br />

has a corresponding tab, located at the bottom<br />

of the Doodle Board in the tab tray. When a<br />

tab is pressed, the corresponding document<br />

will be selected and viewed. This allows you<br />

to manage a large number of files at once,<br />

without having to manage a large number of<br />

windows.<br />

The number of tabs present in the tab tray will<br />

change depending on how many documents<br />

are open. If only a single document is present,<br />

then only one tab is displayed and will be<br />

selected. Selected tabs are colored a light<br />

blue, as is shown in Figure 1.5.<br />

Figure 1.5: A single tab.<br />

When multiple documents are open, multiple<br />

tabs will be displayed in the tab tray. The tab<br />

corresponding to the currently selected<br />

document will be selected and displayed over<br />

other tabs as is shown in Figure 1.6.<br />

Figure 1.6: Multiple tabs.<br />

If there are more tabs than can fit in the tab<br />

tray, then only the most recently viewed tabs<br />

that fit in the tab tray will be displayed. A<br />

number and two right-oriented chevrons are<br />

displayed to the right of the last tab to notify<br />

you that some tabs are not displayed as is<br />

shown in Figure 1.7.

Figure 1.7: There is 1 non-displayed tab.<br />

Click on the chevrons and number to open a<br />

popup menu that lists the undisplayed tabs as<br />

is shown in Figure 1.8. Click on a choice to<br />

select that document.<br />

Figure 1.8: List non-displayed tabs.<br />

There are also tab specific functions that can<br />

be accessed by right-clicking on any given<br />

tab:<br />

• Close - Close the current tab. This option is<br />

only enabled if multiple tabs are present.<br />

• Close Others - Close the other tabs, but<br />

leave the current one open. This option is<br />

• New Document - Create a new document<br />

and tab.<br />

• Restore - If the corresponding document<br />

was created by opening a file, then this<br />

function will be enabled, allowing you to<br />

undo all of your changes and reload the file.<br />

The name of the file is displayed on the tab. If<br />

the name is too long, it may be cropped and<br />

appended with “...”. You may also see a '*'<br />

and/or '^' displayed before a file name in a<br />

tab. The '*' is a reminder that the file has been<br />

changed since the last save, and the '^' marks<br />

it as an online file.<br />

Documents<br />

The document represents a virtual sheet of<br />

paper. Each document embodies one page of<br />

the structures, objects and figures that you<br />

19<br />

create. The document is fully customizable<br />

and also contains a definition of the styles of<br />

the content within it. You can create new<br />

blank documents, or read one from a file that<br />

<strong>ChemDoodle</strong> recognizes.<br />

Note: A visual specification is a definition<br />

about how some object is rendered. For<br />

example, a bond line width is a visual<br />

specification for a bond. In this document,<br />

such a concept may be referred to as a<br />

visual specification, a style or a document<br />

setting. They all mean the same thing.<br />

Creating a Document<br />

You can create a new, blank document using<br />

the default <strong>ChemDoodle</strong> document settings,<br />

or use a Chemical Document Settings file to<br />

create a new formatted document.<br />

To create a new blank document using the<br />

default style sheet, select the New menu item<br />

in the File menu.<br />

To create a new blank document using a<br />

predefined style sheet, select New Formatted<br />

Document... in the File menu.<br />

<strong>ChemDoodle</strong> provides built-in Chemical<br />

Document Settings files. For example, the<br />

ACS Document 1996 style is configured to<br />

create documents that are set with the bond<br />

lengths, bond width, spacing, and fonts used<br />

in the 2-column format of all American<br />

Chemical Society journals. Currently,<br />

<strong>ChemDoodle</strong> provides the following style<br />

sheets:<br />

• ACS Document 1996<br />

• Adv. Synth. Catal Document<br />

• J. Chin. Chem. Soc. Document<br />

• J. Het. Chem. Document<br />

• J. Mol. Mod. Document (1 Column)<br />

• J. Mol. Mod. Document (2 Column)

• Phytomedicine Document<br />

• RSC Document (1 Column)<br />

• RSC Document (2 Column)<br />

• Science of Synthesis Document<br />

• SYNTHESIS, SYNLETT Document<br />

• Verlag Helv. Chim. Acta Document<br />

• Wiley Document<br />

These style sheets are presented when you<br />

create a new formatted document as is shown<br />

in Figure 1.9.<br />

Figure 1.9: Creating a New Formatted Document.<br />

The style sheets are organized into 3 sections.<br />

The first contains just the default style sheet,<br />

the second contains all the built-in style<br />

sheets and the last contains custom style<br />

sheets. Select the style sheet that you prefer,<br />

and choose to set any custom dimensions, and<br />

then click the Ok button to create your new<br />

formatted document.<br />

If you would like to modify the document<br />

dimensions of the formatted document, then<br />

select the Use Custom Dimensions checkbox<br />

and edit the Page Size and Margins fields.<br />

20<br />

Opening a Document<br />

To open a document, select the Open... menu<br />

item from the File menu, locate the file you<br />

would like to open with the file chooser that<br />

appears and click the Open button.<br />

<strong>ChemDoodle</strong> can read many file formats, and<br />

the default file type the file chooser searches<br />

for is a <strong>ChemDoodle</strong> Document. To allow<br />

other file types, click on the format drop<br />

down selection at the bottom of the file<br />

chooser and select the file type you would<br />

like to open, or select the All Files type.<br />

NOTE: Selecting All Files will allow you to<br />

select any file, including files that<br />

<strong>ChemDoodle</strong> cannot read. If such a file is<br />

chosen, you will see a file read error<br />

displayed. Otherwise, <strong>ChemDoodle</strong> will try<br />

to determine the type of file chosen by<br />

analyzing the file extension and file content<br />

to open it accordingly.<br />

To open a recently opened document, enter<br />

the Open Recent submenu in the File menu<br />

and select the document you would like to<br />

open. Only the 10 most recently opened files<br />

are remembered.<br />

File Chooser Previews<br />

The file choosers that you use to open your<br />

files will closely resemble the standard file<br />

choosers that you use in all of your other<br />

applications. However, we have added some<br />

enhancements when using <strong>ChemDoodle</strong>. One<br />

addition is chemical file type previews.<br />

On all operating systems, you will see a<br />

preview of chemical files that you select in<br />

file choosers. On Windows, Mac OS X and<br />

Linux, the file chooser will show a preview of<br />

the entire document on the right as shown in<br />

Figures 1.10, 1.11, and 1.12. On Windows<br />

and Linux, these previews are interactive, if<br />

you hover your mouse over the preview, that<br />

area will zoom in for a closer inspection. On

Mac OS X, a tray is added to the bottom of<br />

the file chooser to list the individual<br />

molecules present in the file as shown in<br />

Figure 1.12.<br />

Figure 1.10: The file chooser on Windows<br />

showing the file preview.<br />

Figure 1.11: The file chooser on Linux showing<br />

the file preview.<br />

Figure 1.12: The file chooser on Mac OS X<br />

showing the file preview and preview tray.<br />

21<br />

You can disable file chooser previews in the<br />

Preferences window, under the General tab<br />

in the Filechooser Settings section.<br />

Changing Document Size<br />

To change the size of the current document,<br />

perform the following steps:<br />

1. Choose the Resize Document... menu<br />

item in the Edit menu.<br />

2. Use the form to select a preset document<br />

size or manually type in the desired<br />

document dimensions.<br />

3. Click the Ok button to resize the<br />

document.<br />

To retrieve the last saved version of a file<br />

without using Undo functions, select the<br />

Restore menu item in the File menu. All<br />

changes made to the file since it was last<br />

saved are discarded and the saved version of<br />

the file will appear.

Saving Documents<br />

To save your document as a file, select the<br />

Save or Save As... menu items from the File<br />

menu. Save will automatically save the<br />

document to the file it is associated to, while<br />

Save As... will allow you to save that file to a<br />

new location or override other files. If there is<br />

no file associated with a document, the Save<br />

function will work identically to the Save<br />

As... function.<br />

After selecting a save function, a file chooser<br />

will appear. Select the location you would<br />

like to have the document saved in and type<br />

in a name for the file if you do not like the<br />

default name. You do not need to type in an<br />

extension as <strong>ChemDoodle</strong> will do this for<br />

you.<br />

After you are satisfied with a location and<br />

name, select the file type of the document to<br />

be saved. By default, a <strong>ChemDoodle</strong><br />

Document is chosen, but you can choose<br />

from a large selection of file types that<br />

<strong>ChemDoodle</strong> can interpret.<br />

NOTE: Only the <strong>ChemDoodle</strong> Document<br />

can store your document with 100%<br />

accuracy. Other file types are for other<br />

purposes and may not define the same<br />

objects and properties in <strong>ChemDoodle</strong>.<br />

Keep this in mind while saving files. If you<br />

forget, a small warning will popup when<br />

saving to a file type other than a<br />

<strong>ChemDoodle</strong> Document. These warnings<br />

can be disabled in the Preferences window<br />

under the Saving tab.<br />

After selecting the file type to be used, press<br />

the Save button to save your document as a<br />

file.<br />

Autosaving<br />

<strong>ChemDoodle</strong> will automatically save unsaved<br />

content for you at regular intervals. If your<br />

computer shuts off unexpectedly, the next<br />

22<br />

time <strong>ChemDoodle</strong> opens, all autosaved<br />

content will be displayed.<br />

You can turn off autosaving in the<br />

Preferences window under the Saving tab.<br />

You can also specify the autosave interval in<br />

the same section. The default autosave<br />

interval is 5 minutes.<br />

Reversing Actions<br />

<strong>ChemDoodle</strong> keeps track of the actions you<br />

perform. You can reverse actions one at a<br />

time by selecting the Undo menu item in the<br />

Edit menu then restore them with the Redo<br />

menu item in the Edit menu. Once you close<br />

your document, the undo queue is reset.<br />

More advanced undo/redo functionality is<br />

associated with the History widget.<br />

Mouse Cursors<br />

The mouse pointer is context sensitive and<br />

will change when hovered over the document<br />

to display visual feedback about the current<br />

mouse gestures that can be performed. The<br />

different mouse cursors are described in Table<br />

3.<br />

Table 3: Mouse Cursors<br />

Cursor Means that...<br />

Clicking and dragging perform<br />

obvious functions.<br />

This is the lasso cursor. Clicking<br />

and dragging will generate an<br />

outline following the drag path.<br />

All content within the drag path<br />

will be selected.<br />

This pinpoints the exact location<br />

that your click will hit. This<br />

enhances accuracy when using<br />

the rectangular marquee or when<br />

placing shapes.

This signifies that a single object<br />

may be selected.<br />

This means that content can be<br />

grabbed. Individual objects or<br />

selected content can be grabbed.<br />

This means that content has been<br />

grabbed and dragging gestures<br />

will perform appropriate actions.<br />

This cursor only appears when<br />

rotating structures in 3D. It<br />

means that content can be<br />

grabbed.<br />

means that content has been<br />

grabbed and drag gestures will<br />

perform appropriate actions.<br />

This cursor signifies that resize<br />

actions can be performed by<br />

clicking and dragging. This<br />

cursor will also appear when<br />

translating the rotation anchor.<br />

This cursor signifies that rotation<br />

clicking and dragging.<br />

Content that is selected will be bordered by a<br />

dashed amber line. Selected content can be<br />

used in functions and sent to other<br />

components. A crawling ants effect is on by<br />

default to help the user keep track of selected<br />

content. The crawling ants effect can be<br />

23<br />

For instructions on selecting content and<br />

editing selected content, read Chapter 5.

The Workspace<br />

The <strong>ChemDoodle</strong> workspace consists of the<br />

application window and all interface elements<br />

contained within. You may freely place<br />

toolbars, select widgets, change the document<br />

scale, select view options, etc., and the next<br />

time you open <strong>ChemDoodle</strong>, your choices<br />

will have been remembered. <strong>ChemDoodle</strong><br />

also provides several functions for managing<br />

your workspace, so you have control over<br />

how the application behaves.<br />

Resizing the Workspace<br />

A minimum screen resolution of 1280 by 800<br />

pixels is recommended to neatly fit all of the<br />

components in <strong>ChemDoodle</strong> on the screen.<br />

Slightly smaller resolutions are still<br />

acceptable when shrinking the document<br />

scale. For much smaller resolutions, the<br />

workspace will display scrollbars to access<br />

the entire <strong>ChemDoodle</strong> interface.<br />

On devices that just fit the <strong>ChemDoodle</strong><br />

window, <strong>ChemDoodle</strong> will expand to fit the<br />

entire screen. On larger resolution devices,<br />

<strong>ChemDoodle</strong> will open to take only as much<br />

room as necessary. At any time, you may unexpand<br />

the application or resize it to your<br />

preference. Upon resizing, the widgets will be<br />

replaced to the right of the workspace, and the<br />

Doodle Board will be centered.<br />

The workspace will keep track of the size and<br />

location of <strong>ChemDoodle</strong> when it was last<br />

closed.<br />

Resetting to the Default Workspace<br />

To reset to the default workspace that was<br />

presented when <strong>ChemDoodle</strong> was first<br />

opened, select the Default Workspace menu<br />

item in the Window menu.<br />

24<br />

Workspace<br />

To revert to the last saved workspace, select<br />

the Revert Workspace menu item in the<br />

Window menu.<br />

Saving the Current Workspace<br />

To save the current workspace, which will<br />

override the revert workspace, perform the<br />

following steps:<br />

1. Organize the workspace to your<br />

preference.<br />

2. In the Window menu, select the Save<br />

Workspace menu item.<br />

The current workspace is now saved and can<br />

be reverted to.<br />

Note: <strong>ChemDoodle</strong> will automatically save<br />

your current workspace upon close, so<br />

make sure to revert the workspace to your<br />

saved workspace before you close, if<br />

necessary. Otherwise, <strong>ChemDoodle</strong> will<br />

open up to look exactly like it was when it<br />

was closed.

Menus<br />

Menus are located on the top of the<br />

<strong>ChemDoodle</strong> application. On Mac OS X, the<br />

<strong>ChemDoodle</strong> menu bar is displayed in the<br />

screen menu bar, as would be expected of<br />

Mac OS X applications.<br />

For menu item keyboard shortcuts, consult<br />

the KeyboardShortcuts.pdf document in the<br />

docs folder in the <strong>ChemDoodle</strong> installation<br />

There are 9 menus in the menu bar (10 on<br />

Mac OS X), not including the Purchase<br />

menu that is present during the free trial:<br />

• <strong>ChemDoodle</strong> - This is a Mac OS X specific<br />

menu bar and contains access to several<br />

Mac OS X specific tasks as well as the<br />

About, Preferences and Quit menu items.<br />

• File - This menu handles all input and<br />

output of data, as well as file specific<br />

functions such as Annotations.... You also<br />

have access to your iChemLabs account<br />

through this menu and the Quit menu item<br />

is located here on non-Mac OS X platforms.<br />

• Edit - Standard global document functions<br />

are located here including Cut, Copy and<br />

Paste.<br />

• View - Functions for changing how<br />

documents are shown are located here as<br />

well as access to the elemental and<br />

chemical data provided with <strong>ChemDoodle</strong>.<br />

The dynamic periodic table is also<br />

accessible through this menu.<br />

• Content - Contains all non-chemical<br />

functions for editing content in the current<br />

• Structure - Contains all functions related to<br />

editing and analyzing molecules.<br />

25<br />

• Reaction - Contains all functions related to<br />

editing and analyzing reactions.<br />

• Spectrum - Contains all functions related to<br />

editing and analyzing spectra.<br />

• Window - Manage your workspace and the<br />

entire <strong>ChemDoodle</strong> application window.<br />

• Purchase - This menu is only present<br />

during the free trial and provides functions<br />

for purchasing and activating licenses for<br />

• Help - This menu contains several functions<br />

to access this user guide, list references,<br />

contact customer service and other common<br />

help items.<br />

• About <strong>ChemDoodle</strong> - Display information<br />

about <strong>ChemDoodle</strong>, your activation code<br />

and your license expiration, if any.<br />

• Preferences... - Open the Preferences<br />

window to edit <strong>ChemDoodle</strong> preferences.<br />

• Services - Standard Mac OS X submenu<br />

that will likely be empty.<br />

• Hide <strong>ChemDoodle</strong> - Hide the <strong>ChemDoodle</strong><br />

application.<br />

• Hide Others - Hide other applications.<br />

• Show All - Show all hidden applications.<br />

• Quit <strong>ChemDoodle</strong> - Quit the <strong>ChemDoodle</strong><br />

File Menu<br />

• New - Add a new blank document to the<br />

Doodle Board.<br />

• New Formatted Document... - Add a new<br />

blank formatted document to the Doodle<br />

• Open - Open a recognized chemical file<br />

that you locate with a file chooser.<br />

• Open Recent> - The 10 most recently<br />

opened chemical files are listed here. Click<br />

a file to open it.<br />

• Insert Image... - Add a recognized image<br />

file to the current document that you locate<br />

with a file chooser.<br />

• Close - Close the current document. This<br />

function is only enabled if two or more<br />

documents are present.<br />

• Close Others - Close all but the current<br />

document. This function is only enabled if<br />

two or more documents are present.<br />

• Restore - Restores a file from its last save.<br />

This function will only be enabled for files<br />

that have been previously saved or were<br />

opened from a preexisting file.<br />

• Annotations... - Associate annotations with<br />

the current document or view previously set<br />

annotations.<br />

• Save - Saves the current file with the<br />

present save settings determined when<br />

opening the file or by previously saving it.<br />

This action will act exactly like the Save<br />

As... function if the document is not yet<br />

associated with a save location.<br />

• Save As... - Save the current document as a<br />

file type of your choice in a new file (or<br />

override one) that you will locate with a file<br />

chooser.<br />

• Save As Image... - Save the current<br />

document as an image that you will place<br />

with a file chooser. Several bitmap and<br />

vector image types are supported.<br />

26<br />

• Save Selection As Image... - Save the<br />

currently selected objects as an image that<br />

you will place with a file chooser. Several<br />

bitmap and vector image types are<br />

supported. This menu item is disabled if no<br />

objects are selected.<br />

• Convert... - Displays a window to convert<br />

chemical files to different chemical file<br />

types that <strong>ChemDoodle</strong> interprets. Nothing<br />

is loaded to the Doodle Board, as output is<br />

written directly to a new file that is created.<br />

• Generate Web Component... - Generate a<br />

<strong>ChemDoodle</strong> Web Component. An entire<br />

window will appear for you to define and<br />

edit the <strong>ChemDoodle</strong> Web Component, as<br />

well as preview and generate the Javascript<br />

for it. More information on this feature is<br />

covered in Appendix F.<br />

• Sync with Online Account... - Login to<br />

your iChemLabs Account to access special<br />

online features in <strong>ChemDoodle</strong>.<br />

• Open Online File> - Your online files will<br />

be listed in this submenu. Click on a file to<br />

open it on the Doodle Board.<br />

• Save As Online File... - Save your file<br />

online. This is useful for using<br />

<strong>ChemDoodle</strong> efficiently on several<br />

computers or for interacting with<br />

iChemLabs cloud services. This feature also<br />

allows you to transfer structures drawn on<br />

your desktop to <strong>ChemDoodle</strong> Mobile on<br />

your phone.<br />

• Refresh - Revalidate the menus and re-sync<br />

your information with your online account.<br />

This should be done when you transfer a<br />

new file into your account from a source<br />

other than <strong>ChemDoodle</strong> desktop.

• Logout - Logout from your iChemLabs<br />

account.<br />

• Page Setup... - Display the operating<br />

system specific window for selecting initial<br />

print settings.<br />

• Print Preview - View the current document<br />

in its entirety on the screen, ignoring<br />

extraneous graphics such as errors and<br />

visual aids.<br />

• Print... - Print the current document.<br />

• Exit - Exits <strong>ChemDoodle</strong>. This menu item<br />

is in the <strong>ChemDoodle</strong> menu on Mac OS X,<br />

listed as Quit <strong>ChemDoodle</strong>.<br />

Edit Menu<br />

• Undo - Undo the last action.<br />

• Redo - Redo the last undone action.<br />

• Cut - Copy the selected objects to the<br />

system clipboard in addition to removing<br />

them from the document.<br />

• Copy - Copy the selected objects to the<br />

system clipboard.<br />

• Copy As> - Contains convenience functions<br />

for quickly placing specific data on the<br />

system clipboard as text and as a chemical<br />

to be transferred to a range of 3rd party<br />

applications that use that data type. This<br />

submenu is only enabled if content is<br />

selected.<br />

• Daylight SMILES - Place a SMILES<br />

string for the currently selected content<br />

on the system clipboard as text and as a<br />

chemical.<br />

• IUPAC InChI - Place an InChI string<br />

for the currently selected content on the<br />

27<br />

system clipboard as text and as a<br />

• MDL MOLFile - Place a complete<br />

molfile for the currently selected content<br />

• Tripos SLN - Place a SLN string for the<br />

currently selected content on the system<br />

clipboard as text and as a chemical.<br />

• Paste - Paste the system clipboard data of<br />

highest priority into the document.<br />

• Paste Text as Chemical> - Pastes the<br />

current text on the clipboard, interpreted as<br />

chemical data, as any of the options<br />

provided in the submenu.<br />

• IUPAC InChI - Paste text as InChI.<br />

• Beilstein ROSDAL - Paste text as<br />

ROSDAL.<br />

• Daylight SMILES - Paste text as<br />

SMILES.<br />

• Tripos SLN - Paste text as SLN.<br />

• XYZ-Like Data - Paste text as a<br />

chemical, interpreted from a text blob<br />

where XYZ-like data is parseable.<br />

• Guess Chemical Format - Paste text as<br />

chemical, where the format is guessed<br />

from the content.<br />

• Paste Special... - Lists all data that<br />

<strong>ChemDoodle</strong> can interpret from the system<br />

clipboard. You may then choose the data of<br />

choice to be pasted into the document. This<br />

function is useful, for instance, when you<br />

would like to paste SMILES string text<br />

instead of a structure into the document. A<br />

structure has higher priority than text.

• Clear - Remove all content from the current<br />

• Resize Document... - Resize the current<br />

document. You may also change the page<br />

margins in the Preferences window under<br />

the Visuals tab under the Page tab.<br />

• Conform Document... - Conform all<br />

objects in the current document to a<br />

selected style sheet. This function will also<br />

change all fonts and scale all objects if you<br />

choose to do so.<br />

• Purge Clipboard - This function clears the<br />

• Purge History - This function clears the<br />

undo/redo history, which will reset the<br />

History widget. This may be convenient if<br />

the action list gets so long that it becomes<br />

unmanageable and causes memory issues,<br />

or if you would like to prevent yourself<br />

from undoing past a certain action.<br />

This menu item is in the <strong>ChemDoodle</strong><br />

menu on Mac OS X.<br />

View Menu<br />

• Hide Warnings - Hide all the warnings in<br />

the document.<br />

• Drawing Aids> - Display various guides to<br />

help when drawing figures.<br />

• Atoms> - Display guides associated to<br />

• Show Circular <strong>Guide</strong>lines -<br />

Display circular guides around<br />

atoms with radii equal to the current<br />

bond length document setting.<br />

28<br />

• Show Orthogonal <strong>Guide</strong>lines -<br />

Display vertical and horizontal<br />

guidelines that intersect through the<br />

atom for aiding in alignment tasks.<br />

• Bonds> - Display guides associated to<br />

bonds.<br />

• Show Parallel <strong>Guide</strong>lines - Display<br />

a line that goes through the bond to<br />

extrapolate where they point to.<br />

• Rings> - Display guides associated to<br />

rings.<br />

• Color in Rings - Color in Euler<br />

facet rings with a color code that<br />

depends on the size of the ring.<br />

• Molecules> - Display guides associated<br />

to molecules.<br />

• Show Molecule Bounds - Draw<br />

rectangular bounding guides around<br />

molecules to show their visual<br />

bounds.<br />

center of the molecule for aiding in<br />

alignment tasks.<br />

• Background> - Display guides<br />

associated to the page.<br />

• Show Crosshair - Displays a<br />

crosshair.<br />

• Show Grid <strong>Guide</strong>lines> - Displays<br />

grids.<br />

• Every Quarter-Inch - Displays<br />

a grid with quarter-inch spacing.<br />

• Every Half-Inch - Displays a<br />

grid with half-inch spacing.

• Every Inch - Displays a grid<br />

with inch spacing.<br />

• Show Margin <strong>Guide</strong>lines -<br />

Displays a rectangular region that<br />

specifies the printable area of the<br />

page.<br />

• Unique IDs> - Associates ID attributes to<br />

objects.<br />

• On Atoms> - Associate IDs to atoms.<br />

• Incremental - Associate<br />

incremental IDs to atoms. The atoms<br />

are numbered in chronological order<br />

from when they were created.<br />

• Morgan Indices - Associate<br />

Morgan indices to atoms.<br />

• On Bonds - Associate incremental IDs<br />

to bonds. The bonds are numbered in<br />

chronological order from when they<br />

were created.<br />

• Elemental Data - View the entire elemental<br />

database packaged in <strong>ChemDoodle</strong> that is<br />

used for all calculations and<br />

cheminformatics functions. The data is<br />

displayed in a dynamic table.<br />

• Ionization Energies - View ionization<br />

energies of the elements in a dynamic table.<br />

This data is part of <strong>ChemDoodle</strong>’s<br />

elemental database.<br />

• Isotopes - View isotope data for the<br />

elements in a dynamic table. This data is<br />

part of <strong>ChemDoodle</strong>’s elemental database.<br />

• Interactive Periodic Table - View an<br />

interactive periodic table that can be<br />

customized and printed. You may also use<br />

its dynamic features to create nice<br />

demonstrations.<br />

29<br />

• Actual Size - Negate any zoom effects.<br />

• Current Selection - Center the current<br />

selection on the Doodle Board. This<br />

function is useful if the document<br />

perspective is zoomed in and it is difficult<br />

to locate selected content.<br />

• Zoom Out - Zoom out and decrease the<br />

document scale, you may also use the drop<br />

down selection provided in the Files +<br />

Formatting toolbar.<br />

• Zoom In - Zoom in and increase the<br />

Content Menu<br />

• Select> - Contains various tools for<br />

selecting content.<br />

• All - Select all content in the current<br />

• Inverse - Select all content in the<br />

current document that isn’t currently<br />

selected while deselecting all content in<br />

the current document that is currently<br />

• Next Molecule - Select the next<br />

molecule in the document. This function<br />

will traverse chronologically through<br />

the molecules in the current document<br />

based on the time they were drawn. If a<br />

molecule isn’t currently selected, it will<br />

first select the last molecule drawn.<br />

• Next Shape - Select the next shape in<br />

the document. This function will<br />

traverse chronologically through the<br />

shapes in the current document based on<br />

the time they were drawn. If a shape<br />

isn’t currently selected, it will first<br />

select the last shape drawn.

• SMARTS... - A textfield will appear.<br />

Type in the desired SMARTS pattern<br />

here and then click the Accept button.<br />

Any content in the current document<br />

that matches the SMARTS pattern will<br />

be selected.<br />

• Deselect - Deselect all content that is<br />

currently selected. This function is only<br />

enabled if content is currently selected.<br />

• Reselect - Reselect the last content that was<br />

selected. This function is only enabled if no<br />

content is currently selected. This function<br />

may not work as expected when content is<br />

removed. For instance, if you selected<br />

content and then deleted it, then pressing<br />

reselect will have no action because the<br />

content to be reselected no longer exists.<br />

• Center> - Contains various functions for<br />

centering content.<br />

• All on Page - Center all content on the<br />

• Selection on Page - Center only the<br />

currently selected content on the page.<br />

• Selection Horizontally - Horizontally<br />

center only the currently selected<br />

content.<br />

• Selection Vertically - Vertically center<br />

only the currently selected content.<br />

• Flip> - Contains functions for flipping<br />

selected content.<br />

• Horizontally - Flip the currently<br />

selected content horizontally over its<br />

midpoint.<br />

• Vertically - Flip the currently selected<br />

content vertically over its midpoint.<br />

30<br />

• Rotate> - Contains various functions for<br />

rotating selected content.<br />

• 90° CW - Rotate selected content<br />

clockwise by 90 degrees.<br />

• 90° CCW - Rotate selected content<br />

counterclockwise by 90 degrees.<br />

• 180° - Rotate selected content by 180<br />

degrees.<br />

• Arbitrary... - Rotate selected content by<br />

an arbitrary angle that you input.<br />

• Scale... - Scale the currently selected<br />

objects. You will be presented with a<br />

window to set various options to define how<br />

the content will be scaled. You can even<br />

choose to scale all molecules individually,<br />

to set them all to a common bond length for<br />

instance.<br />

• Align Bond> - Contains functions for<br />

aligning a single selected bond, rotating the<br />

molecule it is contained in. This function is<br />

enabled when only a single bond is selected.<br />

• Up - Align bond up.<br />

• Right - Align bond right.<br />

• Down - Align bond down.<br />

• Left - Align bond left.<br />

• Flip Bond Orientation - Flip the<br />

orientation of the bond. Non-symmetrical<br />

bonds will face the other direction.<br />

• Align> - Contains functions for aligning<br />

• Left Edges - Align all selected content<br />

by the left edges of their visual bounds.

• Horizontal Centers - Align all selected<br />

content by the horizontal centers of their<br />

visual bounds.<br />

• Right Edges - Align all selected content<br />

by the right edges of their visual<br />

• Top Edges - Align all selected content<br />

by the top edges of their visual bounds.<br />

• Vertical Centers - Align all selected<br />

content by the vertical centers of their<br />

• Bottom Edges-Align all selected<br />

content by the bottom edges of their<br />

• Distribute> - Contains functions for<br />

distributing selected content.<br />

• Horizontally on Page - Distribute<br />

selected content horizontally on the<br />

page such that they are evenly<br />

distributed based on their visual bounds<br />

and fit within the page margins.<br />

• Vertically on Page - Distribute selected<br />

content vertically on the page such that<br />

they are evenly distributed based on<br />

their visual bounds and fit within the<br />

page margins.<br />

• Horizontally by Buffer Space... -<br />

Distribute selected content horizontally<br />

on the page such that they are evenly<br />

by a value that you input.<br />

• Vertically by Buffer Space... -<br />

Distribute selected content vertically on<br />

the page such that they are evenly<br />

31<br />

• Grid All on Page... - Grid all content on the<br />

page. A window will appear to ask for row<br />

and column information.<br />

• Stack All on Page - Stack all content on the<br />

page. Stacking will place all content within<br />

the page margins based on their visual<br />

bounds. Stacking proceeds by placing<br />

content from left to right, and then top to<br />

bottom, on the page using a small buffer<br />

space.<br />

• Group - Group the currently selected<br />

content into a single shape. Single items in<br />

grouped content can not be edited and<br />

transformations will affect the entire group<br />

as a whole. Groups can also be grouped into<br />

larger groups.<br />

• Ungroup - Ungroup grouped content.<br />

Ungrouping is not recursive, so if the group<br />

being ungrouped contains a group, then that<br />

inner group will remain grouped.<br />

• Join - If two atoms are selected, then they<br />

will be joined into a single atom, and their<br />

bonds will all point to the new joined atom.<br />

If those atoms were part of two discrete<br />

molecules, then one molecule is translated<br />

to the other. If two bonds are selected, then<br />

they will be joined together, and all bonds<br />

connected to the joined bonds will connect<br />

to the new joined bond. Two bonds within<br />

the same molecule cannot be joined. One<br />

molecule will be translated and rotated to<br />

the other to aesthetically display the new<br />

joined molecule. This function is disabled<br />

in all other cases.<br />

• Flatten - This function will change all zcoordinates<br />

of selected atoms to be 0,<br />

thereby flattening 3D structures.

• Add Frame> - Contains various functions<br />

for surrounding selected content with<br />

shapes based on their visual bounds.<br />

• Square Brackets - Surround selected<br />

content with square brackets based on<br />

the content’s visual bounds.<br />

• Parenthesis - Surround selected content<br />

with parenthesis based on the content’s<br />

• Curly Brackets - Surround selected<br />

content with curly brackets based on the<br />

content’s visual bounds.<br />

• Chevrons - Surround selected content<br />

with chevrons based on the content’s<br />

• Rectangle - Surround selected content<br />

with a rectangle based on the content’s<br />

• Measure> - Contains various functions for<br />

measuring selected content.<br />

• Diagonal - Place one ruler object<br />

diagonally over selected content based<br />

on its visual bounds to measure its<br />

diagonal. You can change the units of<br />

the ruler object.<br />

• Width and Height - Place two ruler<br />

objects, one vertically to the left and one<br />

horizontally below selected content<br />

based on its visual bounds to measure<br />

its width and height. You can change the<br />

units of the ruler object.<br />

• Conform to Document Settings - Conform<br />

all currently selected objects to the current<br />

chemical document settings, including<br />

scaling and changing fonts.<br />

32<br />

Structure Menu<br />

• Add/Remove Hydrogens> - Contains<br />

functions for adding Hydrogens to<br />

structures. Settings for defining how<br />

Hydrogens will be added to structures can<br />

be set in the Preferences window under the<br />

Visuals tab under the Atoms tab.<br />

• All - Add Hydrogens to all structures in<br />

the current document.<br />

• From Selection - Add Hydrogens only<br />

to the currently selected structures.<br />

• Add Attribute... - Add an attribute to the<br />

selected object. This will only be enabled if<br />

a single atom or bond is selected.<br />

• Place Formal Charges - Will place formal<br />

charges on atoms based on their valency.<br />

• Calculate Covalent Bonds - This function<br />

will deduce covalent bonds in structures<br />

based on atomic 3D distances and the<br />

covalent radii present in <strong>ChemDoodle</strong>’s<br />

elemental database. This function is<br />

dependent on the Ångström/Bond Length<br />

document setting present in the Preferences<br />

window under the Visuals tab. Only single<br />

bond orders will be placed. This function is<br />

very useful for working with files that may<br />

not contain explicit topology, such as PDB<br />

or XYZ files.<br />

• Remove Selected Bonds - This function<br />

will remove all selected bonds, leaving the<br />

constituent atoms.<br />

• Saturate - This function will change the<br />

bond orders of all selected bonds to the<br />

single bond order.<br />

• Graph Reduction> - Contains several<br />

functions for reducing the underlying graph<br />

data structures that represent the selected<br />

structures. This is ideal for extracting

information about small molecule building<br />

blocks for drug discovery purposes.<br />

• Reduce 0° (Lone) - This function will<br />

remove all 0 degree nodes, so all lone<br />

atoms will be removed.<br />

• Reduce 1° (Terminals) - This function<br />

will remove all 1 degree nodes, so all<br />

terminal atoms will be removed.<br />

• Repeatedly Reduce 1° - This function<br />

will repeatedly remove all 1 degree<br />

nodes until none remain, so all isolated<br />

chains will be removed.<br />

• Reduce 1° + 0° - This function will<br />

remove all 0 and 1 degree nodes, so all<br />

lone and terminal atoms will be<br />

removed.<br />

• Reduce 2° (Chains) - This function will<br />

remove all 2 degree nodes, so all inner<br />

chain atoms will be removed.<br />

• Reduce 2° + 1° + 0° - This function will<br />

remove all 0, 1 and 2 degree nodes, so<br />

all lone, terminal and chain (including<br />

non-isolated chains) atoms will be<br />

• Expand Labels - Will expand all complex<br />

atom labels to their all-atom equivalents.<br />

• Rings> - Contains several functions for<br />

defining ring sets in selected structures. If a<br />

highly overlapping figure results, just stack<br />

the content for a cleaner layout.<br />

• Explode Smallest Set of Smallest<br />

Rings - Explode out the smallest set of<br />

smallest rings (SSSR) for selected<br />

structures. The SSSR is the standard for<br />

defining ring sets in flat 2D structures.<br />

• Explode Euler Facet Rings - Explode<br />

out the Euler facet rings for selected<br />

33<br />

structures. The Euler facet ring set is<br />

better than the SSSR at defining<br />

essential rings in 2D depictions of 3D<br />

structures.<br />

• Explode Hanser (All) Rings - Explode<br />

every last graph cycle in selected<br />

• Stereochemistry> - Contains several<br />

functions for deducing the stereochemistry<br />

of selected structures.<br />

• Assign R/S (CIP) - Finds and assigns<br />

CIP stereochemistry to chiral centers.<br />

• Assign E/Z (CIP) - Finds and assigns<br />

CIP stereochemistry to stereochemical<br />

double bonds.<br />

• Assign cis/trans - Finds and assigns cis/<br />

trans stereochemistry to appropriate<br />

• Chemical Suppliers> - Contains functions<br />

to search for chemical suppliers for drawn<br />

• Substructure Match - Find chemical<br />

suppliers for the selected structure by<br />

substructure search.<br />

• Exact Match - Find chemical suppliers<br />

for the selected structure by exact<br />

match.<br />

• Clean> - Contains various functions for<br />

optimizing and beautifying selected<br />

• 2D Optimization - The CCG depiction<br />

algorithm is performed on your selected<br />

structures to clean them in 2D.<br />

• Distance Geometry Embedding -<br />

Distance geometry is used on the bond<br />

distance matrix of the selected

structures to embed them in 3D. This is<br />

great for highly connected structures<br />

like buckyballs and will produce<br />

suitable 3D coordinates. It will not work<br />

very well on less connected structures<br />

like chains.<br />

• Descriptors> - Contains various functions<br />

that will display the named descriptor for<br />

the first of the selected molecules. Details<br />

about these algorithms are described in<br />

Chapter 6.<br />

• Last Chosen - This menu item is a<br />

placeholder that will remember the last<br />

chosen descriptor for easy repeat access.<br />

• Constitutional> - Contains any<br />

constitutional descriptors; descriptors<br />

that are defined by the chemical makeup<br />

of the molecule.<br />

• Atom Count - Calculates the atom<br />

count.<br />

• Bond Count - Calculates the bond<br />

• Degree of Unsaturation -<br />

Calculates the degree of<br />

unsaturation.<br />

• Element Counts - Calculates the<br />

element counts.<br />

• Euler Facet Ring Count - Counts<br />

the total number of Euler facet rings<br />

present in a molecule.<br />

• Exhaustive Ring Count - Counts<br />

every last graph cycle in a molecule.<br />

• Frèrejacque Number - Calculates<br />

the Frèrejacque number. This is also<br />

the SSSR number.<br />

34<br />

• Hydrogen Bond Acceptor Count -<br />

Calculates the Hydrogen bond<br />

acceptor count.<br />

• Hydrogen Bond Donor Count -<br />

Calculates the Hydrogen bond donor<br />

• Rotatable Bond Count - Counts the<br />

number of rotatable bonds.<br />

• Total Electron Count - Counts the<br />

total number of electrons present in<br />

the molecule.<br />

• Lightest Isotopic Mass - Calculates<br />

the molecular mass based on the<br />

lightest isotope for each element,<br />

regardless of abundance.<br />

• McGowans Characteristic Volume<br />

- Calculates McGowan’s<br />

characteristic volume.<br />

• Molecular Mass - Calculates the<br />

molecular mass based on<br />

<strong>ChemDoodle</strong>’s elemental database.<br />

• Volume as a Sum of Atomic and<br />

Bond Contributions - Calculates<br />

the ABC volume.<br />

• Empirical Formula - Generates the<br />

empirical formula of the first<br />

selected structure.<br />

• Molecular Formula - Generates the<br />

molecular formula of the first<br />

• Topological> - Contains any<br />

topological descriptors; descriptors that

are defined by the bond connectivity of<br />

• Centric Index - Calculates the<br />

Centric index.<br />

• Diameter - Calculates the longest<br />

topological path in a molecule.<br />

• Hosoya Index - Calculates the<br />

Hosoya index.<br />

• Molecular Topological Index -<br />

Calculates the Molecular<br />

Topological index.<br />

• Platt Index - Calculates the Platt<br />

index.<br />

• Ring Complexity - Calculates the<br />

Ring Complexity.<br />

• Szeged Index - Calculates the<br />

Szeged index.<br />

• Wiener Index - Calculates the<br />

Wiener index.<br />

• Zagreb Indexes - Calculates<br />

various Zegreb indexes.<br />

• Balaban Index - Calculates the<br />

Balaban index.<br />

• Bertz Complexity Index -<br />

Calculates the Bertz Complexity<br />

• Branching Index - Calculates the<br />

Branching index.<br />

• Chi Molecular Connectivity<br />

Indexes> - Calculates various Chi<br />

Molecular Connectivity Indices.<br />

• Fraction Molecular Framework -<br />

Calculates the Fraction Molecular<br />

Framework ratio.<br />

35<br />

• Harary Index - Calculates the<br />

Harary index.<br />

• Kappa Shape Indices> - Calculates<br />

various Kappa Shape Indices.<br />

• Superpendentic Index - Calculates<br />

the Superpendentic index.<br />

• Adjacency Matrix - Generates the<br />

bond connectivity matrix.<br />

• Bond Distance Matrix - Generates<br />

the bond distance matrix.<br />

• Bond Electron Matrix - Generates<br />

the bond electron matrix.<br />

• Detour Matrix - Generates the<br />

detour matrix.<br />

• Incidence Matrix - Generates the<br />

incidence matrix.<br />

• Laplacian Matrix - Generates the<br />

Laplacian matrix.<br />

• Physicochemical> - Contains any<br />

physicochemical descriptors; descriptors<br />

that are defined by physics or chemistry<br />

• Average Molecular Polarizability><br />

- Calculates the average molecular<br />

polarizability given several<br />

algorithms.<br />

• Critical Pressure - Calculates the<br />

critical pressure of a molecule.<br />

• Critical Temperature - Calculates<br />

the critical temperature of a<br />

molecule.<br />

• Critical Volume - Calculates the<br />

critical volume of a molecule.<br />

• Enthalpy of Formation (ideal gas<br />

at 298K) - Calculates the enthalpy

of formation of a molecule at the<br />

stated conditions.<br />

• Enthalpy of Fusion - Calculates the<br />

enthalpy of fusion of a molecule.<br />

• Enthalpy of Vaporization (at Tb) -<br />

Calculates the enthalpy of<br />

vaporization of a molecule at the<br />

• Gibbs Energy of Formation (ideal<br />

gas, unit fugacity, at 298K) -<br />

Calculates the Gibbs energy of<br />

formations of a molecule at the<br />

• Heat Capacity (ideal gas, at 298K)<br />

- Calculates the heat capacity of a<br />

molecule at the stated conditions.<br />

• Lipophilicity, logP> - Calculates<br />

logP given several algorithms.<br />

• Liquid Viscocity (at 298K) -<br />

Calculates the liquid viscocity of a<br />

• Molar Refractivity> - Calculates<br />

the molar refractivity of a molecule<br />

given several algorithms.<br />

• Normal Boiling Point - Calculates<br />

the normal boiling point of a<br />

• Normal Freezing Point - Calculates<br />

the normal freezing point of a<br />

• Topological Polar Surface Area -<br />

Calculates topological polar surface<br />

area (TPSA).<br />

• ADME Filters> - Contains descriptors<br />

that assess bioactivity.<br />

36<br />

• Bioavailability Score - Calculates<br />

the Bioavailability score.<br />

• Egan Violations Count - Calculates<br />

the number of violations to Egan’s<br />

rules.<br />

• Lipinski’s Rule of 5 Violations<br />

Count - Calculates the number of<br />

violations to Lipinski’s rule of 5.<br />

• Veber Violations Count -<br />

Calculates the number of violations<br />

to Veber’s rules.<br />

• Generate Line Notation> - Contains<br />

functions for generating line notations of<br />

selected structures.<br />

• SMILES - Generates simplified<br />

molecular input line entry specification<br />

(SMILES).<br />

• SLN - Generates Sybyl Line Notation<br />

(SLN).<br />

• InChI - Generates the international<br />

chemical identifier (InChI).<br />

• ROSDAL - Generates the<br />

representation of organic structure<br />

descriptions arranged linearly<br />

(ROSDAL).<br />

• Parse IUPAC Name... - A text field will<br />

appear. Type or paste in a correct IUPAC<br />

name and the structure will be generated<br />

and inserted into the current document.<br />

• Abbreviations> - Contains functions for<br />

maintaining <strong>ChemDoodle</strong>’s abbreviations<br />

database.<br />

• Add New... - Pops up a window to add<br />

a new abbreviation to <strong>ChemDoodle</strong>’s<br />

abbreviations database.

• Manage Recognized... - Pops up a<br />

window to add, edit and delete<br />

abbreviations from <strong>ChemDoodle</strong>’s<br />

abbreviations database.<br />

• Manage My Templates... - Contains<br />

functions for maintaining <strong>ChemDoodle</strong>’s<br />

templates database.<br />

Reaction Menu<br />

• Clean - Clean the selected reaction. The<br />

reaction must first be defined using the<br />

Build Implied Reaction or Edit<br />

Reaction... functions. This function will<br />

align and distribute the reaction as well as<br />

beautify the reaction arrow. Settings to<br />

control how reactions are cleaned can be set<br />

in the Preferences window, under the<br />

Visuals tab, under the Reaction tab.<br />

• Build Implied Reaction - When an arrow<br />

and structures are selected, this function<br />

will become enabled. All selected structures<br />

with midpoints to the left of the arrow<br />

midpoint become reactants while all<br />

selected structures with midpoints to the<br />

right of the arrow midpoint become<br />

products.<br />

• Edit Reaction... - Will open up a window<br />

showing all the structures in the current<br />

document. Click and drag structures from<br />

the document tray to the reactant and<br />

product trays to explicitly define the<br />

reaction. This function is enabled when an<br />

arrow is selected.<br />

• Dissolve Reactions - Will dissociate any<br />

selected reaction data structures.<br />

Spectrum Menu<br />

• View XY Data - View the XY plot data of<br />

the first selected spectrum. You can copy<br />

and paste this data into other programs, like<br />

Excel.<br />

37<br />

• Edit Perspective... - Will open up a<br />

window showing several tools for editing<br />

the spectrum view and axis. Once closed,<br />

the spectrum in the document will update.<br />

• Expand Perspective - Will expand the<br />

spectrum perspective to view the entire<br />

domain and range of the plot. This function<br />

is enabled when a spectrum is selected.<br />

• Generate> - Contains various functions for<br />

generating and simulating spectra.<br />

• 1 H NMR - Generate a proton nuclear<br />

magnetic resonance spectrum of the first<br />

• 13 C NMR - Generate a carbon-13<br />

nuclear magnetic resonance spectrum of<br />

the first selected structure.<br />

• Mass Parent Peak - Generate a mass<br />

parent peak from the mass spectrum of<br />

the first selected structure. This will<br />

show the magnitude of the parent ion<br />

and the isotopic distribution.<br />

Window Menu<br />

• Minimize - Iconify the main <strong>ChemDoodle</strong><br />

window to the dock or system tray.<br />

<strong>ChemDoodle</strong>’s menu bar will remain<br />

focused on Mac OS X.<br />

• Zoom - Expand the <strong>ChemDoodle</strong> window<br />

to fill the entire screen without overlapping<br />

any docks or system trays.<br />

• Select Tab Right - This function is enabled<br />

if there are one or more tabs present in the<br />

tab tray. This function will select the tab to<br />

the right of the currently selected tab. If the<br />

currently selected tab it the right-most tab,<br />

then the first tab is selected.

• Select Tab Left - This function is enabled if<br />

there are one or more tabs present in the tab<br />

tray. This function will select the tab to the<br />

left of the currently selected tab. If the<br />

currently selected tab it the left-most tab,<br />

then the last tab is selected.<br />

• Save Document Settings... - Set the<br />

currently defined document settings as the<br />

default document settings.<br />

• Default Workspace - Return the<br />

configuration of windows within the main<br />

<strong>ChemDoodle</strong> window to the default layout.<br />

• Revert Workspace - Revert the<br />

<strong>ChemDoodle</strong> workspace to the last saved<br />

workspace.<br />

• Save Workspace - Save the current<br />

configuration of the windows within the<br />

main <strong>ChemDoodle</strong> window. This also saves<br />

file chooser paths and other workspace<br />

settings. This function is automatically<br />

performed when <strong>ChemDoodle</strong> is closed.<br />

Purchase Menu<br />

This menu is only present during the free<br />

trial, and is removed when <strong>ChemDoodle</strong> is<br />

activated with a purchased activation code.<br />

• Activate <strong>ChemDoodle</strong> - Displays the<br />

activation form to input a purchased<br />

activation code and generate the license for<br />

the <strong>ChemDoodle</strong> application.<br />

• Buy an Activation Code - Opens the<br />

default internet browser to the purchase<br />

page of the <strong>ChemDoodle</strong> website.<br />

Help Menu<br />

and your license expiration, if any. This<br />

38<br />

menu item is in the <strong>ChemDoodle</strong> menu on<br />

Mac OS X.<br />

• <strong>ChemDoodle</strong> <strong>User</strong> <strong>Guide</strong> - View this user<br />

guide in the program most appropriate for<br />

opening PDF files.<br />

• <strong>ChemDoodle</strong> Keyboard Shortcuts - View<br />

a cheat sheet for all keyboard shortcuts and<br />

actions available in <strong>ChemDoodle</strong> in the<br />

program most appropriate for opening PDF<br />

files.<br />

• References - View an organized list of<br />

references for the data and algorithms used<br />

in <strong>ChemDoodle</strong>. You can use this list to<br />

assess <strong>ChemDoodle</strong>’s quality.<br />

• View <strong>User</strong> License - View the user license<br />

that you accepted when you activated<br />

• Deactivate <strong>ChemDoodle</strong> - <strong>ChemDoodle</strong><br />

can only be used on the number of<br />

computers determined in your license. To<br />

switch from one computer to another, use<br />

this function first. This function is also<br />

useful if you need to reinstall your<br />

operating system.<br />

• Contact Customer Service - Open the<br />

iChemLabs customer support form and prepopulate<br />

fields. This is the preferred way to<br />

contact iChemLabs customer service.<br />

• iChemLabs Newsfeed - View the<br />

iChemLabs newsfeed RSS.<br />

• Check for Updates - Check for updates to<br />

<strong>ChemDoodle</strong>. If any are found, you will see<br />

the changes listed and you will be requested<br />

to update <strong>ChemDoodle</strong>. If allowed,<br />

<strong>ChemDoodle</strong> will automatically update<br />

itself. There is no need to redownload or<br />

reinstall <strong>ChemDoodle</strong> for updates.

Toolbars are located at the top-left of the<br />

<strong>ChemDoodle</strong> window. They contain buttons<br />

for changing how mouse gestures affect<br />

documents, such as placing bonds or placing<br />

a rectangle. There are also buttons for quickly<br />

accessing menu items.<br />

Toolbars can be moved at any time. They will<br />

automatically lock to the borders of the main<br />

<strong>ChemDoodle</strong> window and to their original<br />

position. To save the current placement of<br />

toolbars so they will remain in that position<br />

when you next open <strong>ChemDoodle</strong>, select the<br />

Save Workspace menu item in the Window<br />

menu. The placement of toolbars will also be<br />

saved when the <strong>ChemDoodle</strong> application is<br />

There are 8 toolbars:<br />

• Files + Formatting - Contains buttons for<br />

saving files, transferring content and<br />

formatting fonts and scale.<br />

• Content - Contains functions for<br />

manipulating content including the selection<br />

tools.<br />

• Strokes - Contains 3 drop down selections<br />

for defining bond stroke brush styles.<br />

• Labels - Contains preset labels that can be<br />

used on atoms as well as the Atom Label<br />

tool which will allow you to type whatever<br />

content you would like in atom labels.<br />

• Rings - Contains buttons for drawing<br />

common ring types.<br />

• Bonds - Contains buttons for accessing all<br />

bond types in <strong>ChemDoodle</strong>.<br />

• Arrows - Contains 3 drop down selections<br />

for defining arrows and buttons for drawing<br />

39<br />

the defined arrow with several preset arc<br />

angles.<br />

• Orbitals - Contains various orbital graphics<br />

for standalone figures or for attaching to<br />

• Shapes - Contains any remaining buttons,<br />

including shapes, carbon chains, brackets,<br />

pens, glassware clipart, text, etc.<br />

Additionally, there are also text formatting<br />

toolbars that will appear when convenient,<br />

such as when editing text areas.<br />

Group Buttons<br />

In some cases, similar buttons are grouped<br />

into a single unified group button. These<br />

group buttons are decorated with a small<br />

highlighted triangle at the bottom-right of the<br />

button. Clicking on the button will select it<br />

and perform the displayed function as one<br />

would expect.<br />

To change to a different function of the group<br />

button, click down and hold the button for<br />

one second or click down and drag slightly to<br />

expand the group button as is shown in Figure<br />

1.13. Once expanded, just drag the mouse<br />

pointer over the function you would like to<br />

use and release the mouse. The function the<br />

mouse was over when it was released will<br />

become selected and will now display as the<br />

main function of the group button.<br />

Figure 1.13: An expanded group button.

Files + Formatting Toolbar<br />

Figure 1.14: Files+Formatting Toolbar<br />

➡Create a new blank document<br />

➡Create a new blank formatted<br />

document<br />

➡Open a file<br />

➡Save a file<br />

➡Print document<br />

➡Print preview<br />

➡Cut<br />

➡Copy<br />

➡Paste<br />

➡Font family (font functions affect<br />

selected content only)<br />

➡Font size<br />

➡Bold font<br />

➡Italicize font<br />

➡Quick Colors button<br />

➡Color button and<br />

color selection button<br />

➡Document scale<br />

➡Zoom In<br />

➡Zoom Out<br />

40<br />

Content Toolbar<br />

Figure 1.15: Content Toolbar<br />

➡Lasso selection tool<br />

➡Rectangular Marquee selection<br />

tool<br />

➡Lasso only Shapes selection tool<br />

➡Rotate in 3D tool<br />

➡Eraser tool<br />

➡Clear tool<br />

➡Add/Remove Hydrogens<br />

➡Clean Structure<br />

➡Clean Reaction<br />

➡Conform to Document Settings<br />

➡Fragmentation Tools<br />

➡Undo<br />

Strokes Toolbar<br />

Figure 1.16: Strokes Toolbar<br />

➡Stroke Style<br />

➡Stroke Width<br />

➡Texture Magnitude<br />

Labels Toolbar<br />

Figure 1.17: Labels Toolbar<br />

The labels toolbar contains the element<br />

labels: H, C, N, O, F, P, S, Cl, Br and I. It also<br />

41<br />

contains the superatom labels: Ac, Bz, Ph,<br />

Me, Et, R and M. Clicking on any of these<br />

labels will change the cursor to that label and<br />

then clicking on an atom will change that<br />

atom’s label to the selected label.<br />

The middle of the toolbar contains the Set<br />

Atom Label tool . The atom label tool,<br />

when selected, will allow you to click on any<br />

atom and open a text field. Type in anything<br />

you want into the text field and then click on<br />

the page or press the return key to close the<br />

text field, setting the selected atom’s label to<br />

the contents of the text field.<br />

Rings Toolbar<br />

Figure 1.18: Rings Toolbar<br />

Clicking on any ring will change the drawing<br />

mode to place rings.<br />

Rings include, from top-left to bottom-right:<br />

• cyclopropane ring<br />

• cyclobutane ring<br />

• cyclopentane ring<br />

• cyclohexane ring<br />

• cycloheptane ring

• cyclooctane ring<br />

• cyclobutadiene ring<br />

• cyclopentadiene ring<br />

• benzene ring<br />

• cycloheptatriene ring<br />

• cyclohexane chair conformer 1<br />

• cyclohexane chair conformer 2<br />

Bonds Toolbar<br />

Figure 1.19: Bonds Toolbar<br />

Just click any bond type and the drawing<br />

mode will change to place bond orders of that<br />

type. Clicking on a bond will change that<br />

bond’s current bond type to the selected bond<br />

type.<br />

The single bond order will add to other bond<br />

orders by default. So clicking on a single<br />

bond will change it to a double bond, clicking<br />

on a double bond will change it to a triple<br />

bond, etc. Clicking on a sextuple bond will<br />

change it to a single bond. Clicking on<br />

decorated bond orders (protruding,<br />

ambiguous double, etc.) will convert it to a<br />

non-decorated (single, double, etc.) bond<br />

before incrementing it. To stop single bond<br />

42<br />

orders from adding to bonds, you can set the<br />

single bond behavior to instead override other<br />

bond orders in the Preferences window under<br />

the General tab.<br />

Bond types include, from top-left to bottomright:<br />

• Zero Order/Ionic bond<br />

• Half bond<br />

• Zigzag bond<br />

• Wavy bond<br />

• Single bond<br />

• Bold Dashed bond<br />

• Bold Single bond<br />

• Bold Hollow bond<br />

• Resonance bond<br />

• Recessed bond<br />

• Protruding bond<br />

• Double bond<br />

• Double Dashed bond<br />

• Bold and Thin Double bond<br />

• Ambiguous Double bond<br />

• Triple bond<br />

• Quadruple bond<br />

• Quintuple bond<br />

• Sextuple bond<br />

• Two Electron bond<br />

• Covalent bond (coordinate covalent by<br />

default, can be changed to a polar covalent<br />

bond)<br />

• Any Order bond

• Unknown Order bond<br />

Arrows Toolbar<br />

Figure 1.20: Arrows Toolbar<br />

The top row of contains three drop down<br />

selections. The first defines the style of the<br />

start arrow, the second defines the style of the<br />

connector between arrows and the third<br />

defines the style of the end arrow. The first<br />

five buttons beneath the drop down selections<br />

allow you to place the arrow in the document<br />

and will preset a given angle. The preset<br />

angles include (from left to right): 270°, 180°,<br />

120°, 90° and 0°. At any time, you can<br />

change the arc angle of a placed arc to any<br />

arbitrary angle of your choice.<br />

The last button is the special arrow presets<br />

button. This group button contains presets for<br />

common non-standard arrow types, such as<br />

retrosynthetic arrows. The arc angles of these<br />

arrows cannot be changed.<br />

Orbitals Toolbar<br />

Figure 1.21: Orbitals Toolbar<br />

The orbitals toolbar contains two rows of<br />

orbital types that can be placed into figures<br />

and attached to structures. From top-left to<br />

bottom-right are Atomic s, Atomic px|y|z,<br />

Atomic dxz|yz|xy|x 2 -y 2 , Atomic dz 2 , Atomic fxz 2 |<br />

43<br />

xy 2 |x(x 2 -3y 2 )|y(3x 2 -y 2 ), Atomic fz 3 , Hybrid sp 3 ,<br />

Hybrid sp lobe, Bonding σ and Bonding π.<br />

Each button is a group button containing<br />

different shading an fill options for that<br />

orbital shape.<br />

Shapes Toolbar<br />

Figure 1.22: Shapes Toolbar<br />

The shapes toolbar contains many group<br />

buttons and other functions for changing the<br />

current drawing mode to place both chemical<br />

and non-chemical objects.<br />

The tools include, from top-left to bottomright:<br />

• Lines - Straight, dotted, wavy and zigzag.<br />

• Arcs - 90°, 120°, 180° and 270°.<br />

• Ovals - Plain, dotted, shadowed and<br />

shaded.<br />

• Rectangles - Plain, dotted, shadowed,<br />

shaded, plain rounded, dotted rounded,<br />

shadowed rounded and shaded rounded.

• Brackets - Square (pair), parenthesis (pair),<br />

curly (pair), chevrons (pair), dynamic<br />

brackets, square, parenthesis, curly,<br />

chevron.<br />

• Chemical Attributes - increment charge,<br />

add radical, positive dipole, single electron,<br />

radical cation, decrement charge, remove<br />

radical, negative dipole, electron pair,<br />

radical anion and electron pair (bar).<br />

• Carbon Chains - 120° Carbon chains,<br />

Fisher Projection chains and Random<br />

Carbon chains.<br />

• Sequence Tool - Draw an amino acid<br />

sequence.<br />

• Polylines - Pen, pen-poly tool and polyline.<br />

• Rulers - Place a measurement ruler.<br />

• Text Areas - Place a text area with a<br />

background and border that can be resized<br />

44<br />

to any dimension and is associated with text<br />

formatting tools.<br />

• Glassware Templates - Opens the<br />

laboratory glassware templates window to<br />

build diagrams with glassware clipart.

Interface Options<br />

In addition to being a very powerful<br />

application for your chemical data,<br />

<strong>ChemDoodle</strong> is also very customizable so<br />

you can fit its behavior to your preference.<br />

<strong>ChemDoodle</strong> provides many options for<br />

changing the way it looks, how it works, and<br />

the visual effects that you will see.<br />

To access the interface options, select the<br />

Preferences... menu item in the Edit menu<br />

(in the <strong>ChemDoodle</strong> menu on Mac OS X).<br />

The first tab, General, will contain the<br />

interface options.<br />

Drawing Controls<br />

Drawing Mode<br />

There are two drawing modes, Quick and<br />

Control. Quick mode will do a complete<br />

multistep-action in a mousedown-dragmouseup<br />

procedure, while Control mode will<br />

complete a multistep-action in a click-moveclick<br />

procedure. The default is Quick mode.<br />

Optimize Zone Size<br />

The Optimize Zone is a special component in<br />

<strong>ChemDoodle</strong> to help you place bonds in the<br />

optimal position around atoms. It is the blue<br />

circle that appears when placing bonds and<br />

other molecule fragments. To use the<br />

Optimize Zone, just place the mouse pointer<br />

in the blue circle. The bond or fragment being<br />

placed will automatically be oriented in the<br />

most optimal position. You can change the<br />

size of the optimize zone to be Small,<br />

Medium or Large. It is Medium by default.<br />

Hover Distance<br />

The hover distance controls how close the<br />

mouse pointer must be to an object for it to be<br />

considered hovered. The default is 10 pixels,<br />

but you can make this shorter or longer<br />

depending on your preference.<br />

45<br />

Snap to Grid<br />

By default, coordinates for all objects can be<br />

placed anywhere. However, you can set a 5<br />

pixel or 10 pixel grid for objects to snap to.<br />

Single Bond Behavior<br />

By default, Single bonds will increment bond<br />

orders. So using the Single bond tool, if you<br />

click on a Single bond it will become a<br />

Double bond and so forth. However, you can<br />

change this behavior to instead override bond<br />

orders so any bonds clicked on with the<br />

Single bond tool become Single bonds.<br />

Label Behavior<br />

Label tools can either edit the atom clicked on<br />

or add a new bond connected to the atom<br />

clicked on with the new atom having that<br />

label. By default, atom label tools will modify<br />

the selected atom.<br />

Auto-connect Rings and Templates<br />

This option is enabled by default and will<br />

have the atoms placed by ring and template<br />

tools automatically merge with any<br />

overlapping atoms present in the document.<br />

Fix Bond Lengths<br />

This options is enabled by default and fixes<br />

the bond lengths of the drawing tools. You<br />

can quickly reverse this setting when drawing<br />

by holding down the shift key.<br />

Fix Bond Angles<br />

the bond angles of the drawing tools. You can<br />

quickly reverse this setting when drawing by<br />

holding down the alt key.<br />

Require Starting Atom<br />

Many chemical sketchers have the bond as<br />

the smallest building block. <strong>ChemDoodle</strong><br />

uses atoms as the smallest building blocks,<br />

and all drawing functions require a starting<br />

atom. You can disable this requirement and

allow new bonds to be placed with a single<br />

mouse click.<br />

Rotate Atom Text with Structures<br />

By default, text will not rotate when you<br />

rotate structures. This way text is always<br />

horizontally readable. You can enable this<br />

setting to have atom text rotate when you<br />

rotate structures.<br />

Bonds are Focusable<br />

If you are working with only atoms or you<br />

don’t want to touch bonds, enabling this<br />

setting will make editing easier. When<br />

enabled, bonds cannot be hovered or selected.<br />

3D Rotation Mode<br />

When using the structure perspective tool,<br />

mouse movements will correspond to X and<br />

Y axis movements during 3D rotation. You<br />

can change this to correspond to a quaternion<br />

rotation if you are more familiar with that<br />

behavior.<br />

Appearance<br />

Recently Opened Files<br />

Recently opened files can be displayed at the<br />

bottom of the File menu, or in a submenu in<br />

the File menu. By default they are displayed<br />

in a submenu, but you may wish to switch<br />

this option for quicker access if you have a<br />

tall screen.<br />

Interface Font<br />

If you prefer a different font from the<br />

standard sans-serif font that <strong>ChemDoodle</strong><br />

uses, you can change it in the Preferences<br />

window under the General tab in the<br />

Appearance section. This is also helpful if<br />

you need to switch to a different font that<br />

supports characters for another language.<br />

Interface Color<br />

If you prefer a color other than the default<br />

light green color, you can choose to change<br />

this in the Preferences window under the<br />

46<br />

General tab in the Appearance section.<br />

Light, pale color choices are easiest on the<br />

eyes and are least distracting.<br />

Decorations<br />

Show Unfixed Drawing Measurements<br />

When enabled, statistics are rendered to show<br />

you lengths and angles if they are not fixed.<br />

Show Transform Measurements<br />

you how your lasso functions are altering<br />

your figures.<br />

Lassoing<br />

When enabled, the lasso outline will exhibit a<br />

crawling ants effect so you can easily see it.<br />

View Shimmer Effect on Button Hover<br />

When enabled, buttons will display a<br />

shimmer effect when you hover the mouse<br />

cursor over them. This makes it easy to detect<br />

which button you are pressing.<br />

View Mouse Position on Rules<br />

When enabled, the mouse position will be<br />

ticked on the document’s rulers in red.<br />

View Selection Bounds on Rulers<br />

When enabled, the lasso selection will be<br />

highlighted on the document’s rulers in<br />

amber.<br />

Filechooser Settings<br />

Unified Filechooser Memory<br />

By selecting this option, all filechoosers,<br />

regardless of function will remember the last<br />

location of any of the file choosers.<br />

Otherwise, they will each retain their own<br />

memory.<br />

Include Previews in Filechooser<br />

You may wish to disable this to hide file<br />

chooser previews.

Widgets could be individual applications on<br />

their own, but with <strong>ChemDoodle</strong>, they<br />

provide added functionality and benefit from<br />

<strong>ChemDoodle</strong>'s useful capabilities.<br />

This section introduces the new user to<br />

widgets within <strong>ChemDoodle</strong>. It covers the<br />

following topics:<br />

• Identifying the widgets.<br />

• Using the widgets.<br />

• Thorough guides for the widgets.<br />

Widget Windows<br />

Each widget has its own unique interface<br />

contained within a widget window. A widget<br />

window is a simple, movable and resizable<br />

window that contains the widget interface and<br />

other buttons for maximizing and minimizing<br />

the widget as is shown in Figure 2.1 and<br />

Figure 2.2. Widget window decorations will<br />

be slightly different between Windows/Linux<br />

and Mac OS X.<br />

The top bar contains two buttons, one for<br />

minimizing the widget to the <strong>ChemDoodle</strong><br />

desktop tray and one for maximizing the<br />

widget to fit the entire <strong>ChemDoodle</strong><br />

application window. You can also use the drag<br />

anchors to resize widgets.<br />

To move widgets, just click and drag the top<br />

bar. Widgets will automatically lock to the<br />

borders of the <strong>ChemDoodle</strong> application and<br />

to their origins.<br />

47<br />

The entire widget interface is presented in the<br />

rest of the widget window below the title,<br />

which is displayed below the top bar.<br />

Figure 2.1: Widget Window on Windows/Linux<br />

Title<br />

Figure 2.2: Widget Window on Mac OS X<br />

Widget Expansion<br />

Some widgets are initially in a collapsed<br />

state. Each collapsed widget will have some<br />

gesture to expand it. For example, the<br />

MolGrabber widget is initially collapsed.<br />

Just type a search term in the text field and<br />

press the return key to expand it as showing<br />

in Figures 2.3-2.4. Every collapsable widget<br />

will also have a collapse button to collapse it.<br />

Figure 2.3: A collapsed widget<br />

Top Bar<br />

Drag<br />

Figure 2.4: An expanded widget<br />

Widget List<br />

There are currently 12 widgets provided in<br />

<strong>ChemDoodle</strong>:<br />

• Elemental Analysis - Calculates molecular<br />

masses, elemental analysis and isotopic<br />

distributions for structures.<br />

• History - Provides full access to the undo/<br />

redo queue.<br />

• Line Notation Pad - Generates and parses<br />

line notations and will also correct your<br />

input.<br />

• MolGrabber - Search databases for<br />

chemical structures.<br />

48<br />

• Multiplet Tool - Simulate multiplets.<br />

• NMR SignalSeek - Simulate nuclear<br />

magnetic resonance and associate peaks to<br />

nuclei as well as provide more thorough<br />

information about the spectrum and<br />

simulation.<br />

• Properties - Calculates molecular<br />

descriptors.<br />

• Search - Search your computer and<br />

attached storage devices for chemical<br />

• Statistics - Displays document and drawing<br />

statistics.<br />

• Symbols - Quick access to chemically<br />

relevant symbols and the full unicode range.<br />

• Templates - Organizes chemical structure<br />

templates for your use.<br />

• TLC Canvas - Draw thin layer<br />

chromatography plates.<br />

Widget Dock<br />

The Statistics and History widgets are shown<br />

at all times. Only one other widget is shown<br />

in addition to these two at any given time.<br />

You can switch the widget that is shown by<br />

clicking on the widget icon of the widget you<br />

would like to be shown in the widget dock.<br />

The widget dock is located at the bottom-right<br />

of the <strong>ChemDoodle</strong> window and appears as<br />

shown in Figure 2.5.<br />

Figure 2.5: The widget dock<br />

If you hover over any of the icons, that icon<br />

will be enlarged, and the title of the widget<br />

will appear to the left of the widget dock as<br />

shown in Figure 2.6.

Figure 2.6: Hovering an icon in the widget dock<br />

Just click on the hovered widget icon to select<br />

and show the corresponding widget.<br />

You can also move the widget dock along the<br />

bottom of the application desktop, by pressing<br />

the mouse down and dragging on the (< >)<br />

symbol displayed at the bottom right of the<br />

dock.<br />

Widget Icons<br />

In addition to selecting widgets, these icons<br />

may also perform additional functions. For<br />

instance, if you drag a structure onto the Line<br />

Notation Pad widget icon, that structure will<br />

be loaded into the widget. Information on<br />

these additional functions are provided in the<br />

next sections.<br />

Table 4: Widget Buttons<br />

Button Widget<br />

Elemental Analysis<br />

Line Notation Pad<br />

MolGrabber<br />

Multiplet Tool<br />

49<br />

NMR SignalSeek<br />

Properties<br />

Search<br />

Symbols<br />

Templates<br />

Elemental Analysis Widget<br />

Purpose<br />

The Elemental Analysis widget calculates<br />

several data that are useful to chemists. It<br />

calculates formulas and masses, performs<br />

elemental analysis, and simulates isotopic<br />

distributions.<br />

The interface consists of 4 sections. From top<br />

to bottom, the first section displays the<br />

molecular formula, molecular mass and<br />

monoisotopic mass. The second section<br />

shows the elemental analysis, with each<br />

element shown with its percent composition.<br />

The third section lists the isotopic<br />

distribution, with mass values and intensities.<br />

The fourth section shows an interactive<br />

spectrum of the isotopic distribution.<br />

Figure 2.7: Elemental Analysis Widget<br />

50<br />

History Widget<br />

The History widget is an advanced undo/redo<br />

tool and provides access to the complete log<br />

of all actions performed since the document<br />

was created or opened. Click on a given<br />

action to jump back and forth to the document<br />

state when that action was performed.<br />

The interface consists of a single list in a<br />

scrolling pane as shown in Figure 2.8. The<br />

current state of the document is signified with<br />

a green highlight over the left side of the<br />

latest action. Any actions performed earlier<br />

are undecorated and listed above the current<br />

state, while any actions that have been<br />

undone are highlighted in an amber color and<br />

are listed below the current state. By clicking<br />

on any actions above the current state, the<br />

document will revert back to that action,<br />

undoing all actions between the current state<br />

and the action clicked. By clicking on any<br />

actions below the current state, the document<br />

will redo all actions between the current state<br />

and the action clicked. Therefore, the History<br />

widget allows you to easily revert and restore<br />

any actions performed during the edit history<br />

of the document.<br />

Figure 2.8: History Widget

Line Notation Pad Widget<br />

The Line Notation Pad widget can interpret<br />

and generate SMILES, SLN, InChI and<br />

ROSDAL chemical line notation formats as<br />

well as convert between them with ease. The<br />

interface for the Line Notation Pad widget is<br />

shown in Figure 2.9.<br />

Figure 2.9: Line Notation Pad Widget<br />

The interface, from top to bottom, consists of<br />

a Format drop down selection for choosing<br />

the format, a String text field for inputting<br />

and outputting the line notation, a vertical<br />

row of buttons for performing various<br />

functions, the main structure panel and the<br />

input analysis list. Initially, the interface is<br />

collapsed. Drag a structure onto the Line<br />

Notation Pad widget button or type in a line<br />

notation in the String text field and press the<br />

return key to expand it.<br />

Using the Format drop down selection, you<br />

can choose any of the line notations available<br />

51<br />

to set the current line notation format. If<br />

content is present in the text field, then that<br />

content will be converted into the new format.<br />

The String text field will display the<br />

generated line notation when a structure is<br />

dropped on the main structure panel or the<br />

Line Notation Pad widget button. You may<br />

also explicitly type your line notation in this<br />

component and then press the return key or<br />

the View in 2D button to interpret it and<br />

display the corresponding structure in the<br />

main structure panel.<br />

The buttons perform functions as described in<br />

Table 5.<br />

Table 5: Line Notation Pad Widget Buttons<br />

Button Function<br />

The View in 2D button will<br />

interpret the current string in the<br />

String text field using the format<br />

in the Format drop down<br />

selection and display the<br />

structure in the main structure<br />

panel as well as provide feedback<br />

in the input analysis list.<br />

The Add to the Doodle Board<br />

button will place the current<br />

panel onto the current document.<br />

Alternatively, you can click on<br />

the main structure panel and drag<br />

onto the document to place it.

The Choose Start Point button<br />

will allow you to click on an<br />

atom in the main structure panel<br />

to denote it as the start point for<br />

the generation of the line<br />

notation. Note that if the line<br />

notation format is canonical or if<br />

such an option is set, then setting<br />

the starting point will have no<br />

effect.<br />

The Copy to System Clipboard<br />

as Text will copy the current text<br />

in the String text field onto the<br />

system clipboard as plain text.<br />

For MIME type specific<br />

clipboard contents, set the<br />

appropriate options in the<br />

Advanced tab of the Preferences<br />

window, then copy from the<br />

The Clear button will clear the<br />

current contents and collapse the<br />

widget.<br />

Beside the buttons in the main structure panel<br />

which will display the structure associated<br />

with the line notation in the String text field.<br />

You can generate a line notation for a<br />

structure on the Doodle Board by selecting<br />

the structure and then by clicking and<br />

dragging that structure onto the main<br />

structure panel of this widget. Structures from<br />

the main drawing panel can also be dragged<br />

onto the Doodle Board.<br />

The last component of the interface is a<br />

scrollable list. Any errors or warnings<br />

perceived when interpreting the line notation<br />

will be listed here. Use these suggestions to<br />

help correct malformed strings.<br />

52<br />

MolGrabber Widget<br />

MolGrabber is a web application for<br />

obtaining pre-drawn molecular structures and<br />

properties from online databases. The<br />

interface is shown in Figure 2.10. Currently,<br />

MolGrabber interfaces with the following<br />

databases:<br />

• ChemExper -<br />

• ChemSpider -<br />

• PubChem - http://<br /><br />

NOTE: Because MolGrabber connects to<br />

online databases, it requires an active<br />

internet connection for use.<br />

Figure 2.10: MolGrabber Widget<br />

a Search text field for inputting a search

term, a Source drop down selection for<br />

choosing the database to search through<br />

followed by a second drop down selection to<br />

restrict the search, a progress spinner to the<br />

right of those three components to notify you<br />

that a search is currently being performed, a<br />

main structure panel with a button column to<br />

the left of it for performing various functions,<br />

a scrollable list to hold all search results and,<br />

at the bottom, statistics about the search result<br />

with traversal buttons for navigating through<br />

large numbers of results.<br />

Initially, the interface is collapsed. Type a<br />

search term in the Search text field and press<br />

the return key to expand it. This can be any<br />

search term that the associated database can<br />

handle. After pressing the return key, the<br />

progress spinner will activate to notify you<br />

that it is performing the search. After the<br />

search completes, the progress spinner will<br />

deactivate, the results will populate the result<br />

list and the first result will appear in the main<br />

structure panel.<br />

The Source drop down selection can be used<br />

to select which database to search. The<br />

second drop down selection will restrict your<br />

search to a specific data field type supported<br />

by the database. Just choose a specific field<br />

and the search will only match results in that<br />

field for the input search term.<br />

Table 6.<br />

Table 6: MolGrabber Widget Buttons<br />

53<br />

The Search button will begin the<br />

search query using the search<br />

term input into the Search text<br />

field and restrict it to matching<br />

the field selected in the Source<br />

drop down selections.<br />

onto the document to place it.<br />

The Show/Hide Hydrogens<br />

button will add and remove<br />

Hydrogens from the structure in<br />

the main structure panel based on<br />

the coordinates for Hydrogens<br />

provided by the database. Some<br />

databases may not provide<br />

Hydrogen coordinates and<br />

therefore this function will have<br />

no effect.<br />

The Show Associated Data<br />

button will display all associated<br />

database data for the structure<br />

displayed in the main structure<br />

panel.<br />

To the right of the buttons is the main<br />

structure panel that will display the structure<br />

for the selected result. After obtaining the<br />

structures you would like to include in your<br />

figures, all you have to do is drag and drop

the structure from the main structure panel<br />

Below the buttons is the search result list.<br />

This list will display a maximum of 20 results<br />

and follows the following format for each<br />

entry:<br />

Name (Molecular Formula) [Molecular Mass amu]<br />

Click on any of the results to display them in<br />

the main structure panel.<br />

Below the search results is a label to inform<br />

you of which search results are presented in<br />

the current result set along with traversal<br />

buttons to navigate through large numbers of<br />

results. Just press the left and right arrows to<br />

view the previous 20 and next 20 results<br />

respectively. If there are no previous or no<br />

next results, then the corresponding arrow<br />

will be disabled.<br />

NOTE: ChemSpider does not currently<br />

support pagination of results, so be careful<br />

with generic queries as they may return<br />

many, many results and may take a long<br />

time to complete.<br />

Directing to the Online Database<br />

After a molecule has been loaded, clicking on<br />

the Show Associated Data button will list<br />

associated data from that database. The top<br />

item will be the specific database id as a<br />

hyperlink. The link will open up your default<br />

browser to the selected database’s page for<br />

the current result.<br />

Database Notes<br />

<strong>ChemDoodle</strong> only provides an interface to the<br />

databases supported in the MolGrabber<br />

widget. You should inform yourself about the<br />

copyrights, disclaimers and warranty<br />

information provided by these databases<br />

before using them.<br />

ChemExper Disclaimer<br />

54<br /><br />

disclaimer.html<br />

***** USE AT YOUR OWN RISK *****<br />

ChemExper sprl compiles chemical<br />

information from many sources.<br />













The accuracy or reliability of the data is not<br />

guaranteed or warranted in any way and the<br />

Providers disclaim liability of any kind<br />

whatsoever, including, without limitation,<br />

liability for quality, performance,<br />

merchantability and fitness for a particular<br />

purpose arising out of the use, or inability to<br />

use the data.<br />

ChemSpider Disclaimer<br /><br />

General<br />

The ChemSpider website is maintained by<br />

The Royal Society of Chemistry on behalf of<br />

its wholly owned subsidiary RSC Worldwide<br />

Ltd. RSC Worldwide Ltd does not warrant or<br />

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The information may be out of date. RSC<br />

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injury, loss, or damage caused in any manner<br />

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Some ChemSpider webpages link to pages on<br />

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RSC Worldwide Ltd is not responsible for the<br />

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Nor does it endorse or warrant the services,<br />

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information from these sources may be used<br />

to help identify an individual for prosecution.<br />

Data<br />

The data on the ChemSpider website are<br />

sourced from a number of contributors and<br />

collaborators. The majority of data were<br />

originally sourced from the NCBI-PubChem<br />

website and are made available under the<br />

explicit statements and disclaimers provided<br />

by National Center for Biotechnology<br />

Information (NCBI). NCBI places no<br />

restrictions on the use or distribution of the<br />

data contained within their database. RSC<br />

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of NCBI. These are as follows: "While some<br />

submitters of the original data (or the country<br />

55<br />

of origin of such data) may claim patent,<br />

copyright, or other intellectual property rights<br />

in all or a portion of the data (that has been<br />

submitted), NCBI is not in a position to<br />

assess the validity of such claims and,<br />

therefore, cannot provide comment or<br />

unrestricted permission concerning the use,<br />

copying, or distribution of the information<br />

contained in the molecular databases." In this<br />

regard should any contributors to the NCBI-<br />

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removed from the ChemSpider website please<br />

send a detailed request to<br />

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Data on ChemSpider, including structures and<br />

spectra, are sourced also from individuals. In<br />

depositing these data to the ChemSpider<br />

website, these individuals undertake that they<br />

have the rights to do so, and that the rights do<br />

not reside with any third party.<br />

PubChem <strong>User</strong> Requirements<br /><br />

static/eutils_help.html<br />

Do not overload NCBI’s systems. <strong>User</strong>s<br />

intending to send numerous queries and/or<br />

retrieve large numbers of records from Entrez<br />

should comply with the following:<br />

• Run retrieval scripts on weekends or<br />

between 9 pm and 5 am Eastern Time<br />

weekdays for any series of more than 100<br />

requests.<br />

• Make no more than one request every 3<br />

seconds.<br />

• NCBI’s Disclaimer and Copyright notice<br />

must be evident to users of your service.<br />

NLM does not claim the copyright on the<br />

abstracts in PubMed; however, journal<br />

publishers or authors may. NLM provides<br />

no legal advice concerning distribution of

copyrighted materials, consult your legal<br />

counsel.<br />

56<br />

Multiplet Tool Widget<br />

The Multiplet Tool widget is a comprehensive<br />

tool for generating multiplet trees, simulating<br />

signals and producing their figures. It is<br />

perfectly suited for simulating nuclear<br />

magnetic resonance (NMR) or electron<br />

paramagnetic resonance (EPR, a.k.a. ESR)<br />

signals. The interface is shown in Figure 2.11.<br />

Figure 2.11: Multiplet Tool Widget<br />

the main multiplet panel and a row of buttons<br />

for performing various functions.<br />

Use the buttons to set up the simulation and<br />

layout of the multiplet. The buttons perform<br />

functions as described in Table 9.<br />

Table 9: Multiplet Tool Widget Buttons<br />

multiplet from the main multiplet<br />

panel into the current document.

The Input Parameters button<br />

pops up a window for you to<br />

define parameters for the<br />

simulation including the number<br />

of neighboring nuclei, their spin<br />

and coupling magnitude.<br />

The Real-Time Sliders button<br />

provides a window with sliders<br />

for each parameter. Changing the<br />

sliders will affect the simulation<br />

in real time.<br />

The Settings button will display<br />

a window to define how the<br />

simulation is performed and how<br />

the multiplet figure is laid out<br />

and displayed.<br />

Once you have completed your simulation,<br />

just drag and drop the multiplet from the main<br />

multiplet panel onto the Doodle Board.<br />

Simulating Multiplets<br />

To simulate multiplets, define the parameters<br />

in the Input Parameters window that<br />

appears after clicking the Input Parameters<br />

button and then click the Calculate button as<br />

shown in Figure 2.12. Press the reset button<br />

in this window to reset all parameters.<br />

Figure 2.12: Multiplet Input Parameters<br />

57<br />

To tweak the input parameters to analyze their<br />

affect on the simulation, just use the Real-<br />

Time Sliders button and change the values<br />

slowly in the window that appears as shown<br />

in Figure 2.13. When you are satisfied with<br />

the simulation, press the Done button. The<br />

Reset button will reset the parameters to their<br />

initial values before the window was opened.<br />

Figure 2.13: Real-Time Sliders<br />

Setting up the Multiplet Figure<br />

To define how the simulation is performed<br />

and how the multiplet figure is displayed,<br />

click on the Settings button to show the<br />

Multiplet Settings window as shown in<br />

Figure 2.14.<br />

Figure 2.14: Multiplet Settings<br />

Board<br />

To edit a multiplet from the Doodle Board,<br />

just select it and then drag and drop it onto

the Multiplet Tool widget button or onto the<br />

main multiplet panel. A copy will be made<br />

and can be edited using the Multiplet Tool<br />

widget. Just add this new edited multiplet to<br />

the Doodle Board and delete the old one.<br />

Memory and Runtime Issues<br />

A nucleus of any spin may be used, including<br />

hypothetical spins, however more complex<br />

simulations require more memory and<br />

processor power leading to longer runtimes.<br />

Some extremely complex simulations may<br />

cause memory issues.<br />

58<br />

NMR SignalSeek Widget<br />

The NMR SignalSeek widget simulates 1 H<br />

and 13 C nuclear magnetic resonance and also<br />

associates peaks with nuclei. Full information<br />

about each simulation is provided for in-depth<br />

analysis. The interface is shown in Figure<br />

2.15.<br />

Figure 2.15: NMR SignalSeek Widget<br />

The interface, from left to right, consists of<br />

the main structure panel and a row of buttons<br />

for performing various functions, followed by<br />

a set of panels for displaying the simulated<br />

NMR spectra with 13 C displayed on top and<br />

1 H displayed on the bottom.<br />

The main structure panel displays the<br />

structure being analyzed and is interactive.<br />

The spectra are also interactive and display<br />

the simulation results. Use the buttons to set<br />

up the simulation and copy content to the<br />

Doodle Board. The buttons perform<br />

functions as described in Table 10.<br />

Table 10: NMR SignalSeek Widget Buttons<br />

button will place both the<br />

simulated 1 H and 13 C spectra<br />

onto the current document.

simulation is performed.<br />

Simulating NMR<br />

To simulate NMR spectra for a structure, drag<br />

and drop that structure from the Doodle<br />

Board onto the NMR SignalSeek widget<br />

button or the main structure panel. The 1 H<br />

and 13 C NMR spectra are instantly generated<br />

All variables for the simulation can be<br />

customized. To define the variables, click on<br />

the Settings button to display a window<br />

containing the parameters, as show in Figure<br />

2.16. When you are finished, click the<br />

Simulate button to recalculate the spectra.<br />

Adjust these parameters to match an<br />

experimental spectrum for correlated figures<br />

on the Doodle Board. Settings include:<br />

• TMS - Display or hide the reference peak.<br />

• Roof Effects - Simulate roof effects.<br />

• Line Shape - Lorentzian or Gaussian.<br />

• Pulse Frequency - The spectrum<br />

resolution. The value is appropriate for 1 H<br />

NMR. 13 C NMR will be simulated to a<br />

resolution of a quarter of this value to<br />

remain consistent with experimental<br />

spectrometers.<br />

• Line Width - Control the line width.<br />

• Dilution - Affect the solvent/solute<br />

intensity ratio.<br />

• Temperature - Change the simulation<br />

temperature.<br />

• Solvent - Choose a solvent. Splitting is<br />

fully calculated with the appropriate spin of<br />

59<br />

the nuclei (Deuterium has a spin of 1 and<br />

you will see this splitting correctly in the<br />

solvent peaks).<br />

Figure 2.16: NMR Simulation Settings<br />

Analyzing the Results<br />

The spectra are completely interactive. You<br />

can easily change the view of the spectrum by<br />

clicking and dragging to zoom in on the xaxis.<br />

Double clicking on the spectrum will<br />

revert it to the full view. Scrolling will change<br />

the scale of the y-axis.<br />

Peaks and nuclei are hoverable. Hovering<br />

over a peak will highlight the corresponding<br />

nuclei and vice versa. The chemical shift of<br />

the nuclei is displayed above the structure in<br />

Clicking on a highlighted peak or nuclei set<br />

will display further data from the simulation,<br />

including the shift prediction, splitting nuclei<br />

and j-constant predictions as shown in Figure<br />

2.17. Use this to gain further information<br />

about multiplets.<br />

Figure 2.17: In-depth Simulation Information

Lastly, the widget is initially small to<br />

conserve space. But with all widgets, you can<br />

resize or maximize them if you would like<br />

more interaction space.<br />

How NMR is Simulated<br />

The simulations in the NMR SignalSeek<br />

widget are based on empirical algorithms,<br />

with a database of incremental constants<br />

compiled from publications and some<br />

unpublished work. These references are listed<br />

by clicking the References menu item in the<br />

Help menu. Further information on the<br />

algorithms used to simulate NMR is provided<br />

in Appendix E.<br />

60<br />

Properties Widget<br />

The Properties widget calculates and<br />

displays descriptors for molecules. There are<br />

two unique interfaces displayed by the<br />

Properties widget depending on the situation.<br />

If and only if a single molecule is being<br />

drawn, a table will be displayed. Otherwise, a<br />

drop-down tree will be presented to show data<br />

for each of the selected molecules. The<br />

Properties widget will automatically update<br />

to reflect any changes if allowed to. The<br />

interface displayed when a single molecule is<br />

being edited is shown in Figure 2.18, and the<br />

interface displayed when molecules are<br />

selected is shown in Figure 2.19.<br />

Figure 2.18: Properties Widget Interface with a<br />

Single Molecule is being Drawn<br />

Figure 2.19: Properties Widget Interface when<br />

Molecules are Selected

The interface consists of a checkbox and<br />

button at the top that control when the widget<br />

updates and the data component at the bottom<br />

which displays a table or drop-down tree<br />

depending on the situation.<br />

The table is non-interactive and only displays<br />

the most important information. For the rest<br />

of the descriptors, select the molecule to<br />

display the organized tree. To use the tree,<br />

just click the arrow to the left of each item, or<br />

double click on the item to expand it.<br />

When the Auto-update checkbox is selected,<br />

the Properties widget will refresh<br />

automatically when any content is changed.<br />

Deselect the checkbox to improve drawing<br />

performance when handling large molecules.<br />

When the Auto-update checkbox is<br />

deselected, the Update button will be enabled<br />

to manually control when the widget<br />

refreshes.<br />

Currently, the Properties widget calculates<br />

the following properties for each molecule:<br />

61<br />

• Molecular Formula<br />

• Counts<br />

• Atoms<br />

• Bonds<br />

• Rings<br />

• Frèrejacque Number<br />

• All Rings<br />

• Hydrogen Bond Acceptors<br />

• Hydrogen Bond Donors<br />

• Degree of Unsaturation<br />

• Wiener Index<br />

• Calculations<br />

• Molar Refractivity<br />

• Topological Polar Surface Area<br />

• XlogP v2.0<br />

• Mass<br />

• Molecular<br />

• Monoisotopic<br />

• Elemental Composition<br />

To copy content from the Properties widget,<br />

just right-click on any item and choose the<br />

Copy menu item.<br />

It may take a lot of clicks to access<br />

information through the Properties widget.<br />

For quicker access to all molecular<br />

descriptors, use the Descriptors submenu of<br />

the Structure menu.

Search Widget<br />

The Search widget allows you to search your<br />

hard drive and any attached storage devices<br />

for chemical structures. The Search widget<br />

recognizes all formats that <strong>ChemDoodle</strong><br />

understands, so you will be able to find the<br />

old files you thought you lost a long time ago<br />

and edit them in <strong>ChemDoodle</strong>. The interface<br />

is shown in Figure 2.20.<br />

Figure 2.20: Search Widget<br />

a Folder button to select the root directory of<br />

the search, Match and Multiple options to<br />

define how the search is performed, a small<br />

drop panel to drop the structures to be<br />

searched for and to notify you that a search is<br />

currently being performed, a column of<br />

buttons for various functions with a main<br />

structure panel to the right of them, a list of<br />

62<br />

search results and then labels to notify you of<br />

search progress.<br />

The top section will allow you to select a root<br />

folder for the search. Just click on the Folder<br />

button and use the file chooser that appears to<br />

select a folder. Try to be as exclusive as<br />

possible when choosing a root folder, as<br />

searching your entire hard drive can take a<br />

very long time and may cause memory issues.<br />

The Match and Multiple options will affect<br />

how the search is performed. Setting Match<br />

to Entire will guarantee that all results are<br />

exact matches of the query structures, while<br />

selecting Substructure will match any<br />

structures where the query structures are<br />

matched exactly or contained within larger<br />

structures. Setting Multiple to AND will<br />

ensure that all query structures are matched in<br />

a file for that file to be considered a result,<br />

while selecting OR will allow any matched<br />

query structure to qualify the file as a result.<br />

Initially, the interface is collapsed. Drag and<br />

drop a structure or group of structures from<br />

the Doodle Board onto the small drop panel<br />

or onto the Search widget button to expand it<br />

and set the query structure content.<br />

Table 7.<br />

Table 7: Search Widget Buttons<br />

search query using the query<br />

structure(s) dropped on Search<br />

widget button and the search<br />

options set.<br />

The Settings button will allow<br />

you to control search parameters<br />

and improve performance.

The Open button will open the<br />

currently selected result on the<br />

While the search is being performed, a<br />

pulsing stop sign will become visible on top<br />

of the small drop panel to notify you of search<br />

progress. Clicking on the stop sign will<br />

terminate the search. At the bottom of the<br />

interface are two labels. The first label names<br />

the file currently being searched, and will<br />

display Finished! when completed. The<br />

second label displays statistics about the files<br />

searched since the search was initialized in<br />

the following format:<br />

Files Matched/Chemical Files Searched/Total Files Searched<br />

Be careful with the search! Searching large<br />

numbers of files may cause <strong>ChemDoodle</strong> to<br />

run out of memory, causing slow response in<br />

<strong>ChemDoodle</strong>. Choose the root search folder<br />

and the search settings described in the next<br />

section with care.<br />

Once the search is completed, all matched<br />

files will be listed in the results list. Click on<br />

any result to view all the structures in that<br />

file, one at a time, in the main structure panel.<br />

All hits are highlighted in red. If a file<br />

contains multiple structures, clicking the grey<br />

63<br />

arrows that appear to the left and right of the<br />

structure will allow you to browse through<br />

them. The total number of structures in the<br />

file is noted at the bottom left of the main<br />

structure panel. Once you have found the<br />

structure you were looking for, just drag and<br />

drop the structure from the main structure<br />

panel onto the Doodle Board. You can also<br />

use the Open button to open the entire file on<br />

Search Settings<br />

Search parameters can be defined by clicking<br />

on the Settings button. A window with the<br />

options will appear as shown in Figure 2.21.<br />

Figure 2.21: Search Settings for the Search<br />

There are currently 3 options:<br />

1. Search File Size Restriction - This value<br />

determins the maximum file size that the<br />

Search widget will include in its search,<br />

avoiding memory issues.<br />

2. Maximum Number of Search Results -<br />

This value will control the maximum<br />

number of search results. The search will<br />

continue until all the files in the selected<br />

root search folder are visited or when this<br />

maximum result value is reached. Keeping

it low and providing smaller root search<br />

folders will avoid runtime and memory<br />

issues.<br />

3. Exclude PDB Files - Many times, PDB<br />

files are very large and contain molecular<br />

dynamics trajectories or Monte Carlo<br />

distributions. To avoid all of these files,<br />

which will cause runtime and memory<br />

issues, keep this option selected. If you<br />

need to search through PDB files, turn this<br />

option off.<br />

64<br />

Statistics Widget<br />

The Statistics widget will display information<br />

about the current document and hovered or<br />

selected items. Use it to help with drawing<br />

and placement tasks.<br />

The interface is separated into three sections<br />

as shown in Figure 2.22. The top section<br />

displays information about the document, the<br />

middle section displays information about the<br />

content, and the final section displays specific<br />

information about hovered or selected<br />

Figure 2.22: Statistics Widget

Symbols Widget<br />

The Symbols widget is a complement to the<br />

Labels toolbar. This widget contains an<br />

abbreviation library, a periodic table of<br />

elements, arrows, greek letters and many<br />

other symbols. A few selected tabs are shown<br />

in Figures 2.24-2.26.<br />

The content in the Symbols widget is small<br />

and may be difficult to read. As can be seen in<br />

Figure 2.23, hovering over any symbol will<br />

show a larger preview at the top left hand<br />

corner of the widget. Hovering for a few<br />

seconds will also display a tooltip description.<br />

Figure 2.23: Symbol Preview<br />

When abbreviations or elements are chosen,<br />

you may modify atoms as described in the<br />

labels section. Other symbols, such as arrows<br />

may not be used directly as atom labels.<br />

However, you can open up an atom label text<br />

field, and then input the symbol. If you are<br />

modifying any text component, clicked<br />

symbols will be inserted into the component's<br />

65<br />

Figure 2.24: Abbreviations Tab<br />

Figure 2.25: Arrows Tab<br />

Figure 2.26: Elements Tab

If you set an atom's label to one that is not<br />

recognized or parsed by <strong>ChemDoodle</strong>, an<br />

unrecognized warning will appear. You may<br />

dismiss this warning or edit the current list of<br />

abbreviations to allow unrecognized tokens<br />

by selecting the Add New... menu item in the<br />

Structure menu in the Abbreviations<br />

submenu.<br />

Figure 2.27: The Unicode Character Selector<br />

All possible symbols available are accessible<br />

in the Symbols widget, even if they are not<br />

displayed immediately in the tab sets. Just<br />

click the Unicode Character Selection<br />

button at the bottom of the widget to view the<br />

unicode character selector shown in Figure<br />

2.27. Using hex, you can traverse the entire<br />

Unicode range and easily insert any desired<br />

symbols into text components. Note that not<br />

all fonts will have character glyphs assigned<br />

to each hex value. In these cases, a blank<br />

space or empty rectangle will appear in your<br />

text component and in the unsupported<br />

symbol button.<br />

NOTE: Some programs use the Symbol<br />

font to display symbols. This is an archaic<br />

66<br />

solution and the standard is to now use<br />

unicode characters, which <strong>ChemDoodle</strong><br />

fully supports. <strong>ChemDoodle</strong> will try to<br />

recognize and correct such cases when<br />

reading in files from other programs.

Templates Widget<br />

The Templates widget organizes your<br />

templates and allows you to easily use them.<br />

The interface is shown in Figure 2.28.<br />

Figure 2.28: Templates Widget<br />

a main structure panel, a drop down selection<br />

for selecting a template group and a scrollable<br />

list for selecting a template.<br />

The main structure panel displays the selected<br />

template. An atom can be set to be the<br />

substitution point by clicking on it. The<br />

substitution point is the atom that will be<br />

overlapped with the atom the template is<br />

connected to.<br />

The template group drop down selection will<br />

allow you to select a group of templates to<br />

browse. After selecting a template group, the<br />

template list will populate with templates<br />

from that group. Just click on a template to<br />

display it in the main structure panel for use.<br />

67<br />

Using Templates<br />

Drawing with templates and creating<br />

templates is discussed in detail in Chapter 3.

TLC Canvas Widget<br />

The TLC Canvas widget provides a tool for<br />

creating graphics of thin layer<br />

chromatography (TLC) plates. The interface<br />

is shown in Figure 2.29.<br />

Figure 2.29: TLC Canvas Widget<br />

The interface, from left to right, consists of a<br />

column of buttons for spot types, the main<br />

TLC panel for drawing the TLC plate and a<br />

column of buttons for performing various<br />

functions.<br />

The top button in the spot type column sets<br />

the color of spots. Beneath the color button<br />

are 6 different shapes of spots:<br />

• Compact Spot - a small dot<br />

• Expanded Spot - a circle<br />

• Trailing Spot - a small dot with a trail<br />

• Widened Spot - an oval aligned<br />

horizontally<br />

68<br />

• Crescent Spot - a crescent shape with bowl<br />

facing downwards<br />

• Custom Spot - a splatter shape that can be<br />

changed<br />

Click on any of the spot types to set the<br />

drawing mode to place the spot.<br />

Each spot button is a group button. Expand<br />

the group button for more spot styles. For<br />

each spot there are three spot styles:<br />

• Solid Style - Solid throughout<br />

• Empty Style - Just a line border<br />

• Diffuse Style - Gradient from the center to<br />

the edges<br />

The main TLC panel contains the TLC plate<br />

being drawn. You can edit it using the<br />

controls to the right. When finished editing<br />

the TLC plate, use the Add to Doodle Board<br />

button to place it on the Doodle Board.<br />

The right-most button column contains<br />

function buttons to control how to edit the<br />

TLC plate. The buttons perform functions as<br />

described in Table 8.<br />

Table 8: TLC Plate Widget Buttons<br />

button will place the current TLC<br />

plate in the main TLC panel onto<br />

The TLC Settings button will<br />

popup a window to edit the<br />

visual specifications of the TLC<br />

The Move button allows you to<br />

translate spots along their lanes<br />

and allows you to move the<br />

origin and solvent front.<br />

The Resize Spots button will<br />

display the anchor points for all<br />

spots and allow you to click and<br />

drag them to alter spot shapes.<br />

The Delete button will all you to<br />

remove spots by clicking on them<br />

and allow you to delete lanes by<br />

clicking on the lane tick at the<br />

origin.<br />

The Clear button removes all<br />

spots, leaves a single lane, and<br />

resets the origin and solvent<br />

front.<br />

Drawing TLC Plates<br />

There are 13 buttons associated with the TLC<br />

Canvas. The controls on the left are the<br />

simplest. The top button is the color of the<br />

spots, just click it to choose a different color.<br />

The rest of the buttons in that column<br />

correspond to spot shapes. These are the<br />

compact, expanded, trailing, widened,<br />

crescent and custom spots, in that order. Just<br />

click on a spot button, then hover over the<br />

TLC plate for a preview and Rf calculation.<br />

Once you are satisfied with a location, click<br />

to place the spot. You can create new lanes by<br />

placing spots in between the existing lanes.<br />

These spot buttons are group buttons and<br />

more spot styles will appear when hovered.<br />

All of the spots can be initialized with a solid,<br />

hollow or gradient style. The gradient styled<br />

spots most closely represent actual spots.<br />

69<br />

Using the Move button, you hover over spots<br />

to highlight them, and then click and drag to<br />

move them along their lanes. Rf values are<br />

displayed while you move spots. You may<br />

also click and drag the origin and solvent<br />

front to move them, preserving Rf values.<br />

When spots are hovered, you can right click<br />

on them to open a popup menu with the<br />

following functions:<br />

• Duplicate Spot - Will produce a duplicate<br />

spot of the hovered spot, underneath the<br />

hovered spot in the same lane.<br />

• Remove Spot - Will delete the spot.<br />

• Format Spot - Opens the Format Spot<br />

window.<br />

The Format Spot window will provide several<br />

options for precisely defining its color, style,<br />

display settings and position as shown in<br />

Figure 2.30.<br />

Figure 2.30: Format Spot Window<br />

To resize and reshape spots on the TLC plate,<br />

use the Resize Spots button. Just hover over

the control points that appear, and then click<br />

and drag to move them. All spots except the<br />

custom spot are defined by 4 control points.<br />

You may move all four to create different<br />

shapes. The custom spot is unique and is<br />

defined by 8 control points. You may use<br />

custom spots to create much more<br />

complicated shapes.<br />

To remove spots and lanes, use the Delete<br />

button. Hover over spots to highlight them,<br />

then click to remove them. You may delete a<br />

lane by clicking its lane tick at the origin.<br />

Deleting a lane will also delete its contained<br />

spots. To clear and reset the entire TLC plate,<br />

click the Clear button.<br />

To edit a TLC plate from the Doodle Board,<br />

just select it and then drag and drop it onto<br />

the TLC Canvas widget button or onto the<br />

main TLC panel. A copy will be made and<br />

can be edited using the TLC Canvas widget.<br />

Just add this new edited TLC plate to the<br />

Doodle Board and delete the old one.<br />

Chapter 3: Basic<br />

Structures<br />

You can draw any structure imaginable with<br />

<strong>ChemDoodle</strong>. However, with all of the<br />

drawing tools available, drawing basic<br />

structures may seem overwhelming to the<br />

new user.<br />

basic structure drawing tools within<br />

<strong>ChemDoodle</strong>. It covers the following topics:<br />

• Recognizing the structure drawing tools.<br />

• Drawing atoms.<br />

• Setting atom labels.<br />

• Drawing bonds.<br />

• Changing bond orders.<br />

• Drawing chains.<br />

• Drawing rings.<br />

• Drawing templates.<br />

• Adding attributes to structures, such as<br />

charges, radicals and symbols.<br />

• Setting mass number values to isotopes.<br />

• Placing orbitals on structures.<br />

KeyBoard Shortcuts<br />

There are many keyboard shortcuts to help<br />

you draw structures quickly and efficiently.<br />

The full list of keyboard shortcuts is given in<br />

the KeyboardShortcuts.pdf file located in the<br />

docs folder in the main <strong>ChemDoodle</strong><br />

installation folder.<br />

71<br />

Atoms<br />

Atoms are the basic building blocks in<br />

chemistry and are the basic building blocks in<br />

<strong>ChemDoodle</strong>. Before any other chemical<br />

objects can be drawn, an atom must be<br />

present as the starting point.<br />

Placing Carbon Atoms<br />

When you first use <strong>ChemDoodle</strong>, you will<br />

notice a gray dot following your mouse<br />

pointer on the Doodle Board as shown in<br />

Figure 3.1.<br />

Figure 3.1: Trailing Carbon Atom<br />

To set a carbon atom at the current location of<br />

the mouse pointer, just click the mouse. This<br />

will set the carbon atom and structures can be<br />

grown from it.<br />

At any time while drawing chemical<br />

structures, if there is no hovered atom to grow<br />

from, a carbon atom will trail your mouse to<br />

be placed and grow a new structure.<br />

NOTE: More advanced users may find it<br />

inconvenient to always require a starting<br />

atom to draw structures. You can turn off<br />

this restriction in the Preferences window<br />

under the General tab, by check the<br />

Require Starting Atom checkbox. Clicks<br />

with the bond tools will then immediately<br />

place those bonds and ring, templates and<br />

chains will not require a starting atom.<br />

Placing Other Elements<br />

To place atoms with element symbols other<br />

than carbon, use the Labels toolbar or the<br />

Elements panel in the Symbols widget. Just<br />

click on the desired element symbol, and the<br />

mouse cursor will change to be that symbol<br />

with a small arrow at the bottom-left. Once

you have located where to place the atom<br />

using the bottom-left arrow of the new mouse<br />

cursor, just click to place it.<br />

If you click while an atom is hovered, then<br />

that atom’s label will change to the currently<br />

selected element symbol.<br />

Labels<br />

To place atoms with any text you desire, click<br />

on the Set Atom Label tool located in<br />

the Labels toolbar. Then click on the Doodle<br />

Board in the desired location to place the<br />

new atom and to open up an atom label text<br />

field. Type in the desired atom label text into<br />

the text field and then click elsewhere on the<br />

Doodle Board or press the return key to close<br />

the text field and set the atom.<br />

If you click while an atom is hovered, then a<br />

text field will appear for that atom’s label for<br />

you to edit.<br />

Hovering Atoms<br />

With most tools in <strong>ChemDoodle</strong>, atoms can<br />

be hovered. Exceptions include the shape<br />

tools, such as when drawing rectangles.<br />

Hovering an atom is very simple, just get<br />

your mouse close enough to an atom so that it<br />

is surrounded by an amber circle as shown in<br />

Figure 3.2.<br />

Figure 3.2: A Hovered Atom<br />

The atom is then defined as being hovered<br />

and further actions pertaining to it can be<br />

performed.<br />

72<br />

By default, most carbon atoms have their<br />

labels hidden to create skeleton figures. To<br />

modify when carbon labels are displayed,<br />

please refer to the Carbon Labels section in<br />

Selecting Atoms<br />

To select atoms, first hover them and then<br />

press the mouse down. The amber circle will<br />

turn into a blue circle as shown in Figure 3.3.<br />

Figure 3.3: A Selected Atom<br />

The blue circle is actually a special<br />

component called the Optimize Zone, which<br />

will be discussed in the Bonds section.<br />

To deselect atoms, just release the mouse.<br />

Elements<br />

To change an atom’s label to another element<br />

symbol, use the Labels toolbar or the<br />

with a small arrow at the bottom-left. Once<br />

you have hovered the atom with the label to<br />

be changed, just click to set the new label.<br />

Additionally, when an atom is hovered, you<br />

can press any of the letter keys on the<br />

keyboard to cycle through the element<br />

symbols that begin with that letter.

Text<br />

To change an atom’s label to any text you<br />

desire, click on the Set Atom Label tool<br />

located in the Labels toolbar. Then hover the<br />

atom with the label to be changed and click to<br />

open up its atom label text field. Type in the<br />

desired atom label text into the text field and<br />

then click elsewhere on the Doodle Board or<br />

press the return key to close the text field and<br />

set the new label.<br />

Additionally, you can hover the atom in any<br />

mode and then press the space key to open<br />

the atom’s label text field.<br />

for other Atoms<br />

When writing a complex atom label, you may<br />

want to repeatedly use that label for other<br />

atoms. After typing the label, just hover the<br />

other atoms with labels to be changed and<br />

press the enter key. The hovered atom’s label<br />

will be set to the last typed label.<br />

You can also define the label text to be used<br />

by the enter key by opening up a previously<br />

typed atom label text box and then closing it.<br />

Moving an Atom<br />

To move an atom, first select one of the<br />

selection tools discussed in Chapter 5. Make<br />

sure that no content is currently selected by<br />

emptying the lasso. Perform the following<br />

steps:<br />

1. Hover the atom to be moved.<br />

2. Press the mouse down to select the atom.<br />

3. Drag the mouse to move the atom.<br />

4. Release the mouse to finish the move<br />

action.<br />

If the atom is a terminal atom in a molecule,<br />

then the above instructions will move the<br />

73<br />

atom and bond with fixed angles and lengths<br />

as described in the Bonds section.<br />

If the atom is part of a molecule and not a<br />

terminal atom, the the above instructions will<br />

move that entire molecule. Just hold down the<br />

shift key while performing the above<br />

instructions to move the atom by itself.<br />

Deleting an Atom<br />

To delete an atom, hover it and then press the<br />

delete or backspace key. All attached bonds<br />

will also be removed, leaving the adjacent<br />

Chemical Labels<br />

The last section described how to use the<br />

atom label tool to assign any arbitrary text to<br />

an atom. This text is chemically interpreted; a<br />

label of CH3 will be interpreted as one carbon<br />

atom with three hydrogen atoms attached to<br />

it. Much more advanced labels can be written<br />

and parsed. More information on chemical<br />

interpretation, and expanding these labels, is<br />

described in Chapter 6.<br />

In addition to chemical interpretation, the<br />

label will automatically be formatted for<br />

display; the CH3 label will display as CH3.<br />

Stacking will also be applied, so as bond<br />

overlap with labels is kept to a minimum.<br />

<strong>ChemDoodle</strong>’s intuition may not always be<br />

what you intended though, and you may want<br />

to format more advanced labels, such as for<br />

rendering isopropyl groups (iPr and i Pr) or<br />

adding indexes to carbon chain groups (R 10 ).<br />

In these cases, you can override<br />

<strong>ChemDoodle</strong>’s chemical interpretation and<br />

apply your own formatting.<br />

Atom Label Tool<br />

When opening an atom label field, a format<br />

toolbar will appear above it containing<br />

several controls. The only enabled button will

e the Interpret Chemically button, which is<br />

selected by default as shown in Figure 3.4.<br />

Figure 3.4: Only one button is enabled by default.<br />

Without further editing, closing this label will<br />

assign an ethyl group to the atom and the text<br />

will be automatically formatted as CH2CH3.<br />

Atom Label Token Stacking<br />

When labels are chemically interpreted, they<br />

will be split up into tokens that describe each<br />

discrete unit. For instance, NH will be split<br />

into (N)(H) and CCH2COOH will be split<br />

into (C)(CH2)(COOH). More about this is<br />

covered in Chapter 6. <strong>ChemDoodle</strong> will<br />

automatically stack tokens in atom labels<br />

such that they overlap with surrounding<br />

bonds as little as possible as shown in Figure<br />

3.5.<br />

Figure 3.5: Atom label tokens are stacked to<br />

overlap with bonds as little as possible.<br />

By default, if not on a terminal atom, and<br />

stacking will help reduce clutter, the second<br />

token and all subsequent tokens will be<br />

stacked to the next line. There are two visual<br />

specifications for more precise control over<br />

this behavior:<br />

• Stack Lone/Terminal - In the Preferences<br />

window, in the Visuals tab in the Atoms<br />

section under the Labels subsection, you<br />

can set this checkbox to determine if lone<br />

and terminal labels will also stack labels.<br />

74<br />

• Token Stacking - In the Preferences<br />

can set multi-choice option to declare<br />

whether token stacking occurs for all<br />

individual tokens, for only the second token<br />

or never for any token.<br />

In addition to the token behavior settings, you<br />

also have full control of the spacing between<br />

tokens. All of these settings are present in the<br />

Preferences window, in the Visuals tab in the<br />

Atoms section under the Labels subsection.<br />

Formatting Atom Labels<br />

If a different format is desired, just deselect<br />

the Interpret Chemically button and the<br />

formatting options will be enabled as shown<br />

in Figure 3.6.<br />

Figure 3.6: Applying a custom format to an atom<br />

label.<br />

Use the controls in the toolbar that appears<br />

above the atom label field to explicitly format<br />

the atom label. Table 11 lists how to change<br />

the following attributes.<br />

Table 11: How to change these formatting<br />

attributes<br />

Attribute Control<br />

Bold Select the text to be bold<br />

and press the Bold button.<br />

Italics Select the text to be<br />

italicized and press the<br />

Italic button.<br />

Underline Select the text to be<br />

underlined and press the<br />

Underline button.

Strikethrough Select the text to display<br />

the strikethrough and<br />

press the Strikethrough<br />

button.<br />

Superscript Select the text to be<br />

superscript and press the<br />

Superscript button.<br />

Subscript Select the text to be<br />

subscript and press the<br />

Subscript button.<br />

Alignment The entire label will be<br />

aligned to the selection of<br />

the Align Left, Align<br />

Center or Align Right<br />

buttons.<br />

Color Select the text to be<br />

colored and press the<br />

Choose Color button.<br />

Then select the color.<br />

Font Family Select the text to change<br />

the font family of and then<br />

use the font chooser in the<br />

Format toolbar to select<br />

the font family.<br />

Font Size Select the text to change<br />

the font size of and then<br />

use the size chooser in the<br />

the font size.<br />

Note: When disabling chemical<br />

interpretation, the label will lose all<br />

chemical significance, and will not be<br />

expandable or suitable for any chemical<br />

75<br />

Atom Label Orientation<br />

By default, atom label tokens will orient<br />

themselves in the direction of least overlap<br />

with the rest of the structure. Some times, it<br />

may be necessary to force the label to flush in<br />

a specific direction. To do so, perform the<br />

1. Hover the atom with label to orient.<br />

2. Right-click on the atom and expand the<br />

Label Flush submenu.<br />

3. Choose the direction to orient the label.<br />

Choose Auto if you want <strong>ChemDoodle</strong> to<br />

automatically determine the best<br />

orientation.<br />

Bonds<br />

Bonds are the second most important building<br />

blocks in chemistry. Bonds in <strong>ChemDoodle</strong><br />

are graphical connectors between atoms.<br />

There are many options for bond types and<br />

for defining how they look.<br />

Placing a Single Bond<br />

To place a single bond, click the Single Bond<br />

tool in the Bonds toolbar which should<br />

be selected by default when <strong>ChemDoodle</strong> is<br />

opened.<br />

Then hover over an atom and press the mouse<br />

down. A preview of the new bond and atom<br />

will be drawn as shown in Figure 3.7.<br />

Figure 3.7: New Bond Placement Preview<br />

Drag the mouse and use the techniques<br />

discussed in the following subsections to

place the bond in the preferred orientation.<br />

Then release the mouse to set the bond.<br />

To place bond types other than Single bonds,<br />

just click on the desired bond type in the<br />

Bonds toolbar. Then follow the instructions<br />

for placing a Single bond.<br />

Optimize Zone<br />

most optimal position.<br />

The Optimize Zone size can be changed in<br />

the Preferences window under the General<br />

tab.<br />

Placing Bonds with Fixed Lengths and<br />

Angles<br />

By default, fixed widths and fixed angles are<br />

enforced when drawing structures. To place a<br />

bond within these restraints, hover over an<br />

atom and press the mouse down with a bond<br />

tool. You will see the Optimize Zone appear.<br />

Drag the mouse pointer out of the Optimize<br />

Zone. The new bond placement will now<br />

orient towards the mouse pointer.<br />

The default fixed length is defined by the<br />

Bond Length visual specification in the<br />

Preferences window under the Visuals tab<br />

under the Bonds tab. Angles are fixed every<br />

30° starting at 0°.<br />

You can set whether fixed lengths and/or<br />

fixed angles are on by default in the<br />

Preferences window under the General tab.<br />

76<br />

When placing bonds outside of the Optimize<br />

Zone, fixed lengths will be enforced. To<br />

break from fixed lengths, hold down the shift<br />

key while placing the bond.<br />

You may turn off fixed lengths in the<br />

In this case, the shift key will then enforce<br />

fixed lengths.<br />

Placing Bonds at Non-fixed Angles<br />

Zone, fixed angles will be enforced. To break<br />

from fixed angles, hold down the alt key<br />

while placing the bond.<br />

You may turn off fixed angles in the<br />

In this case, the alt key will then enforce<br />

fixed angles.<br />

and Non-fixed Angles<br />

Zone, fixed angles and fixed lengths will be<br />

enforced. To break from fixed lengths and<br />

fixed angles at the same time, hold down both<br />

the shift and alt key while placing the bond.<br />

You may turn off fixed lengths and fixed<br />

angles in the Preferences window under the<br />

General tab. In this case, holding the shift<br />

and alt keys will then enforce fixed lengths<br />

and angles.<br />

Hovering Bonds<br />

With some tools in <strong>ChemDoodle</strong>, bonds can<br />

be hovered. Hovering a bond is very simple,<br />

just get your mouse close enough to the<br />

center of the bond so that it is encapsulated by<br />

a pair of amber semicircles as shown in<br />

Figure 3.8.<br />

Figure 3.8: A Hovered Bond

The bond is then defined as being hovered<br />

Selecting Bonds<br />

Bonds can only be selected when using the<br />

selection tools discussed in Chapter 5. To<br />

select bonds, first hover them and then press<br />

the mouse down. The amber semicircles will<br />

turn a blue color as shown in Figure 3.9.<br />

Figure 3.9: A Selected Bond<br />

Changing a Bond Type<br />

To change a bond type, first select the bond<br />

type you would like to change the bond to in<br />

the Bonds toolbar. Then hover the bond with<br />

the type that you would like to change and<br />

click the mouse. The new bond type will<br />

override the old type.<br />

To change the bond types of a large number<br />

of bonds to all be Single bonds, perform the<br />

1. Select the bonds to be changed to Single<br />

bonds using a selection tool as discussed<br />

in Chapter 5.<br />

77<br />

2. Press the Saturate menu item in the<br />

Structure menu.<br />

Incrementing a Bond Order<br />

When using the Single Bond tool, clicking on<br />

hovered bonds will not override other bond<br />

types. Instead the Single Bond tool will<br />

increment the bond order. For example,<br />

clicking on a Double bond will change it to a<br />

Triple bond and clicking on the Triple bond<br />

will change it to a Quadruple bond. Clicking<br />

on a Sextuple bond will change the order<br />

back to a Single bond.<br />

This functionality can be disabled so that the<br />

Single Bond tool overrides bond types in the<br />

Deleting a Bond<br />

To delete an bond, hover it and then press the<br />

delete or backspace key. The constituent<br />

atoms will remain.<br />

Deleting Bonds Around Atoms<br />

To delete bonds, but retain the atoms<br />

contained in the bonds, perform the following<br />

1. Select the bonds to be removed using a<br />

selection tool as discussed in Chapter 5.<br />

2. Press the Remove Selected Bonds menu<br />

item in the Structure menu.<br />

All selected bonds will be removed, but<br />

atoms will remain present.<br />

Changing the Z-Order of Bonds<br />

When bonds overlap, one bond will be<br />

rendered in front of the other. For structures<br />

with 3D coordinates, the bond with the most<br />

positive z-coordinates will be rendered on<br />

top. Without z-coordinates, the last bond<br />

drawn will be rendered on top.

To change the z-order of bonds when zcoordinates<br />

are present, perform the<br />

1. Select the structure with the z-orders to be<br />

changed.<br />

2. Select the Rotate in 3D tool in the<br />

Content toolbar.<br />

3. Click and drag the mouse to rotate the<br />

structure in 3D so the desired bond is<br />

placed on top.<br />

4. Release the mouse to stop the rotation and<br />

set the new coordinates.<br />

are not present, perform the<br />

1. Delete the bond that is to be rendered on<br />

top.<br />

2. Redraw the bond.<br />

Chains<br />

Chains are a group of carbon atoms, linked<br />

linearly by bonds. Three types of chains are<br />

provided in <strong>ChemDoodle</strong>:<br />

• Carbon Chain - A consistent linear<br />

carbon chain, with all chain angles<br />

alternating at ±120° as shown in Figure<br />

3.10.<br />

Figure 3.10: A Carbon Chain<br />

• Fisher Projection Chain - A straight<br />

carbon chain, with all chain angles at 180°.<br />

All non-terminal chain atoms also have two<br />

additional carbon atoms depicted<br />

78<br />

perpendicular to the chain orientation as<br />

shown in Figure 3.11.<br />

Figure 3.11: A Fisher Projection Chain<br />

• Random Chain - A carbon chain<br />

where all chain angles are at 120°, but the<br />

chain itself can deviate in any direction as<br />

shown in Figure 3.12.<br />

Figure 3.12: A Random Chain<br />

Placing Chains at Fixed Angles<br />

To place chains at fixed angles, perform the<br />

1. Select a chain tool in the Shapes toolbar<br />

using the Chain Tool group button.<br />

2. Choose a starting atom to sprout the chain<br />

from by hovering it. If you do not want to<br />

start the chain from any existing atoms,<br />

create an atom in a new place by clicking<br />

on the Doodle Board where no atoms are<br />

hovered.<br />

3. Press the mouse down on the hovered<br />

atom.<br />

4. Drag the mouse to the desired length of<br />

the chain. When using the Random chain,<br />

drag the mouse in the outline of the chain<br />

you would like to draw and the chain will<br />

grow following that path.<br />

5. Release the mouse to set the chain.

By default, the chains will be oriented at fixed<br />

angles every 15° starting at 0°. All bond<br />

lengths are defined by the Bond Length<br />

visual specification in the Preferences<br />

window under the Visuals tab under the<br />

Bonds tab.<br />

When dragging the mouse to define the chain,<br />

a number will be displayed below the mouse<br />

cursor to keep track of the number of bonds<br />

being added.<br />

Placing Chains at Non-fixed Angles<br />

To place chains at non-fixed angles, hold<br />

down the alt key while dragging the mouse<br />

when defining the chain to break from the<br />

fixed chain orientation angles.<br />

Vertically and Horizontally<br />

To place chains oriented vertically or<br />

horizontally, hold down the shift key while<br />

dragging the mouse when defining the chain.<br />

The chain preview will then automatically<br />

orient vertically or horizontally depending on<br />

angle from the starting atom to the current<br />

mouse cursor position.<br />

Inverting Carbon Chains<br />

Carbon chains can be inverted by holding<br />

down the slash key (/) while placing. The<br />

preview will update to reflect this.<br />

Rings<br />

Rings are a chain of carbon atoms where the<br />

last atom in the chain connects to the first.<br />

There may be bond types other than Single<br />

bonds in rings. Currently the following rings<br />

can be drawn quickly from the Rings toolbar,<br />

with more ring choices in the Templates<br />

widget:<br />

• Cyclopropane ring<br />

• Cyclobutane ring<br />

79<br />

• Cyclopentane ring<br />

• Cyclohexane ring<br />

• Cycloheptane ring<br />

• Cyclooctane ring<br />

• Cyclobutadiene ring<br />

• Cyclopentadiene ring<br />

• Benzene ring<br />

• Cycloheptatriene ring<br />

• Cyclohexane chair conformer 1<br />

• Cyclohexane chair conformer 2<br />

Placing a Ring<br />

To place a ring, click the preferred ring tool in<br />

in the Rings toolbar.<br />

down. A preview of the new ring will be<br />

drawn as shown in Figure 3.13.<br />

Figure 3.13: New Ring Placement Preview<br />

discussed in the following subsections to<br />

place the ring in the preferred orientation.<br />

Then release the mouse to set the ring.<br />

The Optimize Zone can be used to optimize<br />

ring placement as described in the Bonds<br />

ring within these restraints, hover over an<br />

Zone. The new ring placement will now<br />

When placing rings outside of the Optimize<br />

Placing Rings at Non-fixed Angles<br />

80<br />

Adding Rings to Bonds<br />

When adding rings to atoms, you may not<br />

always find it easy to achieve an aesthetic<br />

fuse angle. To solve this, add the ring to a<br />

bond instead of an atom. The ring will<br />

automatically align to the bond it is being<br />

added to.<br />

To add rings to bonds, perform the following<br />

1. Select a ring tool from the Rings toolbar.<br />

2. Hover the bond a ring will be added to.<br />

3. Click and drag the mouse pointer to the<br />

side of the bond the ring should be added<br />

to.<br />

4. Release the mouse to set the ring.<br />

When the mouse pointer is close to the bond<br />

the ring is sprouting from, <strong>ChemDoodle</strong> will<br />

automatically select the optimal side of the<br />

bond to add to.<br />

<strong>ChemDoodle</strong> contains a very advanced<br />

structure templates system. Several sets of<br />

predefined templates are already packaged<br />

with <strong>ChemDoodle</strong> and can be accessed

through the Templates widget. Currently, the<br />

following template sets are provided:<br />

• Amino Acids<br />

• Cycloalkanes<br />

• Functional Groups<br />

• Hexoses<br />

• Nucleotides<br />

• Polycyclic Aromatic Hydrocarbons<br />

• Polycycles<br />

• Ring Conformers<br />

• Stereocenters and Geometries<br />

Selecting a Template for Use<br />

Just follow these three steps to select a<br />

template for use:<br />

Activate the Templates widget by clicking on<br />

the Templates widget button.<br />

1. Choose a template group from the drop<br />

down selection.<br />

2. Click on a template choice to choose a<br />

template from the list.<br />

3. Define a substitution atom by clicking on<br />

the preferred atom in the main structure<br />

panel. The substitution point will overlap<br />

with the atom used as the growth position.<br />

Placing templates is discussed in the<br />

following subsections.<br />

Placing a Template<br />

To place a template, set up a template and<br />

choose a substitution atom in the Templates<br />

Then hover over the atom in the document<br />

that you are attaching the template to and<br />

81<br />

press the mouse down. A preview of the<br />

template will be depicted as in Figure 3.14.<br />

Figure 3.14: New Template Placement Preview<br />

place the template in the preferred orientation.<br />

Then release the mouse to set the template.<br />

template placement as described in the Bonds<br />

section.<br />

and Angles<br />

template within these restraints, hover over an<br />

orient towards the mouse pointed.<br />

Preferences window under the General tab.

Lengths<br />

When placing templates outside of the<br />

Optimize Zone, fixed lengths will be<br />

enforced. To break from fixed lengths, hold<br />

down the shift key while placing the template.<br />

Placing Templates at Non-fixed Angles<br />

Optimize Zone, fixed angles will be<br />

enforced. To break from fixed angles, hold<br />

down the alt key while placing the template.<br />

Lengths and Non-fixed Angles<br />

Optimize Zone, fixed angles and fixed<br />

lengths will be enforced. To break from fixed<br />

lengths and fixed angles at the same time,<br />

hold down both the shift and alt key while<br />

placing the template.<br />

Saving a New Template<br />

To save a template into the Templates widget<br />

library, perform the following steps:<br />

1. Draw the desired template on the Doodle<br />

Board.<br />

2. Select the template with the selection<br />

tools discussed in Chapter 5. Only a<br />

82<br />

single structure can be used in any<br />

template.<br />

3. Right-click after selecting the structure.<br />

4. Press the Add Fragment as Template...<br />

menu item to pop up the Add Template<br />

5. Type in a name for the template in the<br />

Template Name text field.<br />

6. Choose a template group to add the<br />

template to using the drop down selection.<br />

You can create a new template group<br />

using the Add Group button.<br />

7. Click the Done button to add the<br />

All of your templates are stored in the<br />

templates folder in the <strong>ChemDoodle</strong>Settings<br />

folder located in your operating system’s<br />

standard Document folder. You may distribute<br />

your template groups to other <strong>ChemDoodle</strong><br />

users or place third party template groups in<br />

this folder to use them in <strong>ChemDoodle</strong>. If<br />

<strong>ChemDoodle</strong> is open when manually placing<br />

template groups in the templates folder, make<br />

sure to first close and then restart<br />

<strong>ChemDoodle</strong> for changes to take effect.<br />

Managing your Templates<br />

To manage your templates, click on the<br />

Manage My Templates... menu item in the<br />

Attributes<br />

Attributes are special objects in <strong>ChemDoodle</strong><br />

that are associated with other chemical<br />

objects. These include charges, radicals,<br />

symbols and ids on atoms and ids on bonds.<br />

They are both spatially and semantically<br />

linked to the chemical object that they<br />

describe. Any number of attributes can be<br />

added to a single chemical object.

In addition to the standard attributes provided<br />

in <strong>ChemDoodle</strong>, you can add your own text<br />

based attributes as shown for the attribute<br />

with display text of “attribute” for the<br />

nitrogen atom as shown in Figure 3.15.<br />

Figure 3.15: An Attribute on an Atom<br />

Adding Attributes<br />

To add a custom attribute, perform the<br />

1. Hover the atom to add the attribute to.<br />

2. Right-click on the hovered atom.<br />

3. Press the Add Attribute... menu item.<br />

4. Type in the text to be displayed in the<br />

Display text field.<br />

5. Type in an identifying name for the<br />

attribute in the Name text field. This<br />

value is used for the internal semantics<br />

and is not rendered.<br />

6. Press the Add button to set the attribute.<br />

Hovering Attributes<br />

You can hover attributes by using any of the<br />

selection tools. First, make sure the current<br />

selection is empty and then move the mouse<br />

cursor close to the center of the attribute so<br />

that it is closer to the attribute than any other<br />

chemical objects. The attribute will then be<br />

defined as hovered and an amber circle will<br />

be rendered on top of it as shown in Figure<br />

3.16.<br />

Figure 3.16: A Hovered Attribute<br />

83<br />

To help identify which object the attribute<br />

describes, a transparent amber circle is drawn<br />

over that object (the nitrogen atom in Figure<br />

3.16).<br />

Selecting Attributes<br />

Attributes can only be selected when using<br />

the selection tools discussed in Chapter 5. To<br />

select attributes, first hover them and then<br />

turn a blue color as shown in Figure 3.17.<br />

Figure 3.17: A Selected Attribute<br />

Editing Attributes<br />

The display text and names of custom<br />

attributes can be edited at any time by<br />

performing the following steps:<br />

1. Hover the attribute to be edited.

2. Right-click on the hovered attribute.<br />

3. Press the Format Attribute... menu item.<br />

4. In the visual specifications window that<br />

appears, change the Name and Display<br />

text to the new values.<br />

5. Click the Done button to set the new text<br />

values.<br />

Moving Attributes<br />

To move attributes, perform the following<br />

1. Hover the attribute to be moved.<br />

2. Press the mouse down to select the<br />

hovered attribute.<br />

3. Drag the attribute to the new preferred<br />

location.<br />

4. Release the mouse to set the new position.<br />

Attributes can only be moved a certain<br />

distance from the object that they describe.<br />

This distance is specified by the Allow<br />

Distance visual specification in the<br />

under the Attributes tab. Change this to suit<br />

your needs.<br />

Removing Attributes<br />

To remove an attribute, use the Eraser tool<br />

and to click on the hovered symbol or hover<br />

the symbol with the selection tools and press<br />

the delete or backspace key.<br />

Charges<br />

Charges are attributes can be associated with<br />

any atoms as shown in Figure 3.18. Both<br />

positive and negative values can be used.<br />

Figure 3.18: A Charge Attribute<br />

84<br />

Adding Charges<br />

To add charge to an atom, perform the<br />

1. Select the Increase Charge or<br />

Decrease Charge tools in the<br />

Attributes group button in the Shapes<br />

toolbar.<br />

2. Hover the atom to add charge to.<br />

3. Press the mouse down to add the charge.<br />

4. If you prefer to have the charge placed<br />

elsewhere, then before releasing the<br />

mouse, drag the pointer to the desired<br />

5. Release the mouse to set the charge.<br />

To change the charge of an atom, perform the<br />

2. Hover the atom to with the charge to be<br />

3. Click the mouse down to increment or<br />

decrement the charge.<br />

The + and - keys on the keyboard can also be<br />

used to increment and decrement charge<br />

Removing Charges<br />

Removing charges can be done is several<br />

• Decrement or increment the charge value to<br />

0 using the Increase Charge and Decrease<br />

Charge tools.<br />

• Select the Eraser tool and click on a<br />

hovered charge to remove it.<br />

• Hover the charge using the selection tools<br />

and press the delete or backspace key.<br />

Radicals<br />

Radical types can be associated with any<br />

atoms as shown in Figure 3.19. Currently<br />

only Monovalent and Divalent Singlet types<br />

are supported.<br />

Figure 3.19: A Radical Attribute<br />

Adding Radicals<br />

To add a radical electron to an atom, perform<br />

the following steps:<br />

1. Select the Increase Number of Radical<br />

Electrons tool in the Attributes<br />

group button in the Shapes toolbar.<br />

2. Hover the atom to add the radical to.<br />

3. Press the mouse down to add the radical.<br />

4. If you prefer to have the radical placed<br />

5. Release the mouse to set the radical.<br />

Number of Radical Electrons<br />

Electrons or Decrease Number of<br />

85<br />

Radical Electrons tools in the<br />

2. Hover the atom with the radical to be<br />

decrement the the number of radical<br />

electrons.<br />

Removing Radicals<br />

Removing radicals can be done is several<br />

ways:<br />

• Decrement the radical value to 0 using the<br />

Decrease Number of Radical Electrons<br />

hovered radical to remove it.<br />

• Hover the radical using the selection tools<br />

Symbols are standard types of atom<br />

decorations that can be associated with any<br />

atoms such as the Radical Cation symbol<br />

shown in Figure 3.20.<br />

Figure 3.20: A Symbol Attribute<br />

Currently, included symbols are:<br />

1. Single Electron<br />

2. Electron Pair aka. Non-bonding Pair,<br />

Lone Pair<br />

3. Radical Cation<br />

4. Radical Anion<br />

5. Electron Pair (Bar)

6. Positive Dipole<br />

7. Negative Dipole<br />

Adding Symbols<br />

To add a symbol to an atom, perform the<br />

1. Select the desired symbol tool in the<br />

2. Hover the atom the symbol will added to.<br />

3. Press the mouse down to add the symbol.<br />

4. If you prefer to have the symbol placed<br />

5. Release the mouse to set the symbol.<br />

Removing Symbols<br />

To remove a symbol, use the Eraser tool and<br />

to click on the hovered symbol or hover the<br />

symbol with the selection tools and press the<br />

delete or backspace key.<br />

Isotopes<br />

Mass numbers can be associated with atoms<br />

with element symbols as their label to<br />

designate isotopes. All mass numbers are<br />

displayed in superscript format to the left of<br />

element symbols as shown in Figure 3.21.<br />

Figure 3.21: A Carbon-13 Isotope<br />

If you later change an atom’s label and there<br />

is a mass number associated with that atom,<br />

then the mass number will be removed.<br />

Numbers<br />

To set a published mass number to an element<br />

atom, perform the following steps:<br />

86<br />

1. Hover the atom with the mass number to<br />

be set.<br />

3. Expand the Mass Number submenu.<br />

4. Press any of the listed values to set the<br />

mass number of the isotope.<br />

To set an arbitrary mass number to an element<br />

4. Press the Other... menu item.<br />

5. Type in an integer value into the text field<br />

that appears.<br />

6. Click the Accept button to set the mass<br />

number.<br />

Removing Mass Numbers<br />

To remove a mass number from an atom:<br />

be removed.<br />

4. Press the Remove Mass Number menu<br />

item to remove the mass number.<br />

Orbitals<br />

2D graphics for various orbital shapes can be<br />

placed directly into the document or attached<br />

onto structures. Use them to show more<br />

detailed chemical figures. Each orbital shape<br />

has several different shading and fill styles.

The following orbital types are provided:<br />

• Atomic s Orbitals<br />

• Atomic px|y|z Orbitals<br />

• Atomic dxz|yz|xy|x 2 -y 2 Orbitals<br />

• Atomic dz 2 Orbitals<br />

• Atomic fxz 2 |xy 2 |x(x 2 -3y 2 )|y(3x 2 -y 2 ) Orbitals<br />

• Atomic fz 3 Orbitals<br />

• Hybrid sp 3 Orbitals<br />

• Hybrid sp Lobes<br />

• Bonding σ Orbitals<br />

• Bonding π Orbitals<br />

Orbitals are defined by two anchor points as<br />

shown in Figure 3.22. The first anchor point<br />

defines the center of the orbital while the<br />

second anchor point defines the extent of the<br />

orbital.<br />

Figure 3.22: Orbital and Anchors<br />

87<br />

To place an orbital, perform the following<br />

1. Select an orbital tool by expanding any of<br />

the Orbital group button in the Orbitals<br />

2. Press the mouse down on the Doodle<br />

Board to set the center of the orbital.<br />

3. Drag the mouse to preview the placement<br />

of the extent of the orbital. A dotted green<br />

outline of the orbital will be shown.<br />

4. Release the mouse to set the orbital.<br />

You can also click the mouse to set the start<br />

center then move the mouse and click again<br />

to set the extent.<br />

In step 2, you may want to attach the orbital<br />

to an atom or bond center. <strong>ChemDoodle</strong> will<br />

automatically lock onto atoms and bonds<br />

when placing orbitals if the mouse pointer<br />

gets close enough to them. Once the atom or<br />

bond has been highlighted, continue through<br />

step two to place the orbital and set the center<br />

to be the atom or bond center.

or Angles<br />

To place lines at non-fixed lengths or angles,<br />

hold down the alt key while dragging the<br />

mouse when defining the orbital to break<br />

from the fixed lengths and angle orientations.<br />

Forcing Orbitals to be Drawn Vertically<br />

and Horizontally<br />

To place orbitals oriented vertically or<br />

dragging the mouse when defining the orbital.<br />

The orbital preview will then automatically<br />

the angle from the start point to the current<br />

Moving Orbitals<br />

To move orbitals, use a selection tool, either<br />

the lasso or the rectangular marquee. Make<br />

emptying the current selection. Perform the<br />

1. Hover the mouse pointer over the orbital<br />

so an open hand mouse cursor appears<br />

and the rectangle anchor points are drawn<br />

as shown in Figure 3.19.<br />

2. Press the mouse down and drag to move<br />

the orbital.<br />

3. Release the mouse to finish the move<br />

Resizing Orbitals<br />

To resize orbitals, use a selection tool, either<br />

and the orbital anchor points are drawn as<br />

shown in Figure 3.19.<br />

88<br />

2. Move the mouse pointer over one of the<br />

two end anchor points so that anchor point<br />

is filled in with an amber color.<br />

3. Press the mouse down so the anchor point<br />

is filled with a blue color.<br />

4. Drag the anchor point to resize the orbital.<br />

5. Release the mouse to finish the resize<br />

Removing Orbitals<br />

Orbitals can be removed in a number of ways.<br />

You can do the following:<br />

• Use a selection tool to hover the mouse<br />

pointer over the orbital so an open hand<br />

mouse cursor appears and the rectangle<br />

anchor points are drawn as shown in Figure<br />

3.19. Then press the backspace or delete<br />

key.<br />

• Use the eraser tool to hover the mouse<br />

pointer over the orbital so the orbital anchor<br />

points are drawn. Then click with the<br />

In addition to chemical structures,<br />

<strong>ChemDoodle</strong> provides tools for drawing<br />

shapes for advanced figures.<br />

This section introduces the new user to shapes<br />

within <strong>ChemDoodle</strong>. It covers the following<br />

topics:<br />

• The different types of shapes.<br />

• How to draw shapes.<br />

• Adding arrows to figures.<br />

• Adding text to figures.<br />

• How to move shapes.<br />

• How to resize shapes.<br />

• How to remove shapes.<br />

• What the anchor decorations mean.<br />

Anchors<br />

Anchors are points that define a given shape.<br />

By moving them, you modify how the shape<br />

appears. There are two types of anchors,<br />

control anchors and corner/edge anchors.<br />

Control Anchors<br />

Control anchors represent points that can be<br />

moved anywhere and have no relationship to<br />

other anchors, such as in lines, custom shapes<br />

or orbitals. They appear as compass shapes as<br />

shown in Figure 4.1.<br />

Figure 4.1: Control anchors<br />

89<br />

Corner/Edge Anchors<br />

Corner edge anchors define corners and edges<br />

of shapes. Moving these anchors will change<br />

the shape in relationship to the other anchors.<br />

For instance, if you move a left-right pointing<br />

anchor, you will not affect the vertical<br />

positioning of the other anchors. These<br />

anchors are present for box shaped objects,<br />

like rectangles and ovals. They appear as<br />

double sided arrows as shown in Figure 4.2.<br />

Figure 4.2: Corner/Edge Anchors<br />

Lines<br />

Lines are the most basic shape and are<br />

defined by two anchors placed at their<br />

endpoints as shown in Figure 4.3. There is<br />

also a third anchor at the midpoint for<br />

controlling the arc angle. This anchor point is<br />

discussed in the next section (Arcs).<br />

Figure 4.3: Line Shape and Anchors<br />

Drawing Lines at Fixed Angles<br />

To draw a line at fixed angles, perform the<br />

following steps:

1. Select a line tool by expanding the Lines<br />

Board to set the start point of the line.<br />

of the end of the line.<br />

4. Release the mouse to set the line.<br />

point then move the mouse and click again to<br />

set the end point.<br />

By default, lines will be oriented at fixed<br />

angles every 15° starting at 0°.<br />

Drawing Lines at Non-fixed Angles<br />

To place lines at non-fixed angles, hold down<br />

the alt key while dragging the mouse when<br />

defining the line to break from the fixed<br />

orientation angles.<br />

To place lines oriented vertically or<br />

dragging the mouse when defining the line.<br />

The line preview will then automatically<br />

Moving Lines<br />

To move lines, use a selection tool, either the<br />

lasso or the rectangular marquee. Make sure<br />

that no content is currently selected by<br />

1. Hover the mouse pointer over the line so<br />

an open hand mouse cursor appears and<br />

the anchor points are drawn as shown in<br />

Figure 4.3.<br />

the line.<br />

90<br />

Resizing Lines<br />

To resize lines, use a selection tool, either the<br />

the line anchor points are drawn as shown<br />

in Figure 4.3.<br />

4. Drag the anchor point to resize the line.<br />

Removing Lines<br />

Lines can be removed in a number of ways.<br />

pointer over the line so an open hand mouse<br />

cursor appears and the line anchor points<br />

are drawn as shown in Figure 4.3. Then<br />

press the backspace or delete key.<br />

pointer over the line so the line anchor<br />

mouse.<br />

Arcs<br />

Arcs are segments of a circle and are defined<br />

by two anchors placed at their endpoints as<br />

shown in Figure 4.4. There is also a third<br />

anchor at the middle for controlling the arc

angle. Only 90°, 120°, 180° and 270° arcs are<br />

directly provided in the Arcs group button,<br />

but an arc of any angle can be drawn. The<br />

only difference between the line shape and<br />

the arc shape is the angle, and either shape<br />

can be converted into the other by changing<br />

this value.<br />

Figure 4.4: Arc Shape and Anchors<br />

Drawing Arcs at Fixed Angles<br />

To draw an arc at fixed angles, perform the<br />

1. Select an arc tool by expanding the Arcs<br />

Board to set the start point of the arc.<br />

of the end of the arc.<br />

4. Release the mouse to set the arc.<br />

By default, arcs will be oriented at fixed<br />

Drawing Arcs at Non-fixed Angles<br />

To place arcs at non-fixed angles, hold down<br />

defining the arc to break from the fixed<br />

To place arcs oriented vertically or<br />

91<br />

dragging the mouse when defining the arc.<br />

The arc preview will then automatically<br />

Moving Arcs<br />

To move arcs, use a selection tool, either the<br />

1. Hover the mouse pointer over the arc so<br />

the arc anchor points are drawn as shown<br />

in Figure 4.4.<br />

the arc.<br />

Resizing Arcs<br />

To resize arcs, use a selection tool, either the<br />

4. Drag the anchor point to resize the arc.<br />

Changing Arc Angles<br />

Arc angles can be changed using the midpoint<br />

anchor. Choose a selection tool, either the<br />

2. Move the mouse pointer over the middle<br />

anchor point so that it is filled in with an<br />

amber color.<br />

4. Drag the anchor point to change the arc<br />

angle.<br />

5. Release the mouse to set the new arc<br />

While changing the angle of arcs, the arc<br />

angle will be displayed below the mouse<br />

cursor.<br />

Flipping an Arcʼs Orientation<br />

To flip an arc’s orientation, so that the curve<br />

faces the opposite direction. use a selection<br />

tool, either the lasso or the rectangular<br />

marquee. Make sure that no content is<br />

currently selected by emptying the current<br />

selection. Perform the following steps:<br />

2. Right-click on the hovered arc.<br />

3. Select the Flip Arc menu item to flip the<br />

arc’s orientation.<br />

92<br />

You can also click and drag the midpoint to<br />

the other side of the arc to perform this task.<br />

Removing Arcs<br />

Arcs can be removed in a number of ways.<br />

pointer over the arc so an open hand mouse<br />

cursor appears and the arc anchor points are<br />

drawn as shown in Figure 4.4. Then press<br />

the backspace or delete key.<br />

pointer over the arc so the arc anchor points<br />

are drawn. Then click with the mouse.<br />

Arrows<br />

Arrows are essential in chemical graphics for<br />

many reasons, the most important being for<br />

reaction and mechanism diagrams. Arrows<br />

are so important that they have their own<br />

unique toolbar. Essentially, arrow shapes are<br />

just lines and arcs with arrowheads as shown<br />

in Figure 4.5.<br />

Figure 4.5: Arrow Shape and Anchors<br />

<strong>ChemDoodle</strong> also provides advanced features<br />

for building and defining reactions. Reactions<br />

are covered in Chapter 7.<br />

Drawing Arrows at Fixed Angles<br />

To draw an arrow at fixed angles, perform the<br />

1. Select the desired arrowheads and<br />

connector styles in the Arrows toolbar.<br />

2. Click on one of the arc angle buttons in<br />

the Arrows toolbar to enter the arrow<br />

placement mode.

3. Press the mouse down on the Doodle<br />

Board to set the start point of the arrow.<br />

4. Drag the mouse to preview the placement<br />

of the end of the arrow.<br />

5. Release the mouse to set the arrow.<br />

By default, arrows will be oriented at fixed<br />

To place arrows at non-fixed angles, hold<br />

when defining the arrow to break from the<br />

fixed orientation angles.<br />

To place arrows oriented vertically or<br />

dragging the mouse when defining the arrow.<br />

The arrow preview will then automatically<br />

Moving Arrows<br />

To move arrows, use a selection tool, either<br />

1. Hover the mouse pointer over the arrow<br />

and the arrow anchor points are drawn as<br />

shown in Figure 4.5.<br />

the arrow.<br />

93<br />

Resizing Arrows<br />

To resize arrows, use a selection tool, either<br />

4. Drag the anchor point to resize the arrow.<br />

Changing Arrow Arc Angles<br />

Arrow arc angles can be changed using the<br />

midpoint anchor. Choose a selection tool,<br />

either the lasso or the rectangular marquee.<br />

Make sure that no content is currently<br />

selected by emptying the current selection.<br />

Perform the following steps:<br />

anchor point so that anchor point is filled<br />

in with an amber color.<br />

4. Drag the anchor point to change the arrow<br />

5. Release the mouse to set the new arrow<br />

arc angle.<br />

While changing the angle of arrow arcs, the<br />

arrow arc angle will be displayed below the<br />

mouse cursor.<br />

NOTE: A few special arrow types, such as<br />

the retrosynthetic type, are straight, and<br />

you will not be able to change the arc<br />

angles for these types.<br />

Removing Arrows<br />

Arrows can be removed in a number of ways.<br />

pointer over the arrow so an open hand<br />

mouse cursor appears and the arrow anchor<br />

points are drawn as shown in Figure 4.5.<br />

Then press the backspace or delete key.<br />

pointer over the arrow so the arrow anchor<br />

Editing Arrowheads<br />

Arrowheads can be added/removed from the<br />

ends of the line shape. This can be done<br />

before they are drawn, with the Arrow<br />

toolbar, or afterwards by using the Format<br />

Arrow window.<br />

There are several settings that control how<br />

arrowheads are drawn:<br />

• Indented - When selected, the back end of<br />

the arrow will be indented in.<br />

• Filled - When selected, the arrow will be<br />

filled in, otherwise it will just be an outline.<br />

• Chevroned - When selected, the arrow will<br />

be drawn as a simple chevron.<br />

• Length - This setting controls the length of<br />

the arrow head along the line.<br />

94<br />

• Angle - This setting controls the angle of<br />

the arrow, from one side to the other.<br />

Use these settings to control how arrowheads<br />

are drawn.<br />

NOTE: If the arrowhead length is greater<br />

than 50% of the length of the line it is on,<br />

then the length will be decreased to 50% of<br />

the length of the line it is on.<br />

Rectangles<br />

Rectangles can be drawn in several styles and<br />

are defined by two anchor points that<br />

correspond to a pair of rectangle corners<br />

along one of the diagonals as shown in Figure<br />

4.6.<br />

Figure 4.6: Rectangle Shape and Anchors<br />

Drawing Rectangles<br />

To draw a rectangle, perform the following<br />

1. Select a rectangle tool by expanding the<br />

Rectangle group button in the Shapes<br />

Board to set one corner of the rectangle.<br />

of the opposite corner along the diagonal<br />

of the rectangle.<br />

4. Release the mouse to set the rectangle.<br />

set the end point.

Drawing Squares<br />

To draw squares, hold down the shift key<br />

while dragging the mouse when defining the<br />

rectangle to force the width and height to be<br />

equivalent.<br />

Moving Rectangles<br />

To move rectangles, use a selection tool,<br />

1. Hover the mouse pointer over the<br />

rectangle so an open hand mouse cursor<br />

appears and the rectangle anchor points<br />

are drawn as shown in Figure 4.6.<br />

the rectangle.<br />

Resizing Rectangles<br />

To resize rectangles, use a selection tool,<br />

anchor points so that anchor point is filled<br />

4. Drag the anchor point to resize the<br />

rectangle.<br />

95<br />

Non-rounded Rectangles<br />

To change a rectangle into a roundedrectangle<br />

or vice versa, use a selection tool,<br />

appears and the arrow anchor points are<br />

drawn as shown in Figure 4.6.<br />

2. Right-click on the hovered rectangle and<br />

select the Format Rectangle... menu<br />

item.<br />

3. Scroll to the Rectangle section and use<br />

the Rounded on/off choice to set the<br />

rectangle to be rounded or not.<br />

Removing Rectangles<br />

Rectangles can be removed in a number of<br />

ways. You can do the following:<br />

pointer over the rectangle so an open hand<br />

4.4. Then press the backspace or delete key.<br />

pointer over the rectangle so the rectangle<br />

anchor points are drawn. Then click with<br />

the mouse.<br />

Ovals<br />

Ovals can be drawn in several styles and are<br />

defined by two anchor points that correspond<br />

to a pair of rectangle corners along one of the<br />

diagonals that circumscribes the oval as<br />

shown in Figure 4.7.<br />

Figure 4.7: Oval Shape and Anchors

Drawing Ovals<br />

To draw an oval, perform the following steps:<br />

1. Select an oval tool by expanding the Oval<br />

Board to set one corner of the<br />

circumscribing rectangle.<br />

of the circumscribing rectangle.<br />

4. Release the mouse to set the oval.<br />

Drawing Circles<br />

To draw circles, hold down the shift key while<br />

dragging the mouse when defining the oval to<br />

force the major and minor axes lengths to be<br />

Moving Ovals<br />

To move ovals, use a selection tool, either the<br />

1. Hover the mouse pointer over the oval so<br />

the oval anchor points are drawn as shown<br />

in Figure 4.7.<br />

the oval.<br />

96<br />

Resizing Ovals<br />

To resize ovals, use a selection tool, either the<br />

4. Drag the anchor point to resize the oval.<br />

Removing Ovals<br />

Ovals can be removed in a number of ways.<br />

pointer over the oval so an open hand<br />

mouse cursor appears and the oval anchor<br />

points are drawn as shown in Figure 4.7.<br />

pointer over the oval so the oval anchor<br />

Brackets<br />

Brackets can be drawn in several styles and<br />

correspond to a pair of rectangle corners

along one of the diagonals that defines the<br />

bracket space as shown in Figure 4.8.<br />

Figure 4.8: Bracket Shape and Anchors<br />

There are currently 4 bracket styles:<br />

• Square Brackets - [ ]<br />

• Parenthesis - ( )<br />

• Curly Brackets - { }<br />

• Chevrons - < ><br />

Drawing Brackets<br />

To draw a set of brackets, perform the<br />

1. Select a bracket tool by expanding the<br />

Bracket group button in the Shapes<br />

Board to set one corner of the bracket.<br />

of the bracket.<br />

4. Release the mouse to set the bracket.<br />

and Height<br />

To draw square brackets, hold down the shift<br />

key while dragging the mouse when defining<br />

the bracket to force the width and height of<br />

the bracket content to be equivalent.<br />

97<br />

Moving Brackets<br />

To move brackets, use a selection tool, either<br />

1. Hover the mouse pointer over the brackets<br />

and the bracket anchor points are drawn<br />

as shown in Figure 4.8.<br />

the brackets.<br />

Resizing Brackets<br />

To resize brackets, use a selection tool, either<br />

4. Drag the anchor point to resize the bracket<br />

set.<br />

Editing Bracket Lip Protrusion<br />

To change the widths of the current bracket<br />

rendering style, use a selection tool, either the<br />

that no content is currently selected by

shown in Figure 4.8.<br />

select the Format Bracket... menu item.<br />

3. Scroll to the Bracket section and use the<br />

Wideness number slider to define how<br />

protruded bracket lips are rendered.<br />

Removing Brackets<br />

Brackets can be removed in a number of<br />

pointer over the brackets so an open hand<br />

mouse cursor appears and the bracket<br />

4.8. Then press the backspace or delete key.<br />

pointer over the brackets so the bracket<br />

Custom Shapes<br />

In addition to the standard defined shapes<br />

previously discussed, <strong>ChemDoodle</strong> allows<br />

you to create custom shapes. Currently there<br />

are three types of custom shapes:<br />

• Pen - The Pen tool allows you to draw<br />

any shape by clicking and dragging an<br />

outline.<br />

• Bezier Curve - The Bezier Curve tool<br />

allows you to draw a bezier curve by<br />

defining its control points.<br />

98<br />

• Polyline - The Polyline tool allows you<br />

do draw any polygon shape that can be<br />

convex or concave.<br />

Both pen paths and polylines can be open or<br />

closed and are defined by their control points,<br />

which the shape will pass through as shown<br />

in Figure 4.9.<br />

Figure 4.9: Pen and Polyline Control Points<br />

Bezier curves can be open or closed and are<br />

defined by a more complex set of control<br />

points as shown in Figure 4.10.<br />

Figure 4.10: Bezier Control Points<br />

Drawing with the Pen Tool<br />

To draw a custom shape with the Pen tool,<br />

1. Select a Pen tool by expanding the<br />

Custom Shapes group button in the<br />

Shapes toolbar.<br />

Board to begin drawing.

3. Drag the mouse in an outline of the shape<br />

you would like.<br />

4. Release the mouse to set shape.<br />

<strong>ChemDoodle</strong> will automatically simplify your<br />

path for you and generate a cubic<br />

interpolation.<br />

Drawing with the Polyline Tool<br />

To draw a custom shape with the Polyline<br />

tool, perform the following steps:<br />

1. Select the Polyline tool by expanding the<br />

Board to set the first point.<br />

3. Move the mouse to location you prefer the<br />

next point to be placed.<br />

4. Click to place the next point. Points will<br />

automatically connect to previous points.<br />

5. Repeat steps 3 and 4 until finished.<br />

6. Click on the first point drawn or doubleclick<br />

the last point to complete the shape<br />

and set it.<br />

Moving Pen Paths and Polylines<br />

To move custom shapes, use a selection tool,<br />

1. Hover the mouse pointer over the custom<br />

shape so an open hand mouse cursor<br />

appears and the control points are<br />

rendered as shown in Figure 4.9.<br />

the custom shape.<br />

99<br />

Modifying Pen Paths and Polylines<br />

You can move the control points that define<br />

pen paths and polylines. To do so, use a<br />

selection tool, either the lasso or the<br />

rectangular marquee. Make sure that no<br />

content is currently selected by emptying the<br />

current selection. Perform the following<br />

appears and the control points are drawn<br />

as shown in Figure 4.9.<br />

control points that you desire to be moved<br />

so that control point is filled in with an<br />

3. Press the mouse down so the control point<br />

4. Drag the control point to move it.<br />

5. Release the mouse to finish.<br />

Drawing with the Bezier Tool<br />

Bezier curves are defined by pairs of control<br />

points. There is a main point which the curve<br />

passes through, and a second control point<br />

that describes the tangent of the line at the<br />

point that the curve passes through. To draw a<br />

bezier curve, perform the following steps:<br />

1. Select the Bezier Curve tool by<br />

expanding the Custom Shapes group<br />

button in the Shapes toolbar.<br />

3. Drag your mouse to set the paired control<br />

point that defines the tangent of the curve<br />

at the first point. The further from the first<br />

point you make this paired control point,<br />

the tighter the curve will hug the first<br />

4. Release the mouse to set the paired<br />

control point.<br />

5. Move the mouse to location you prefer the<br />

next point to be placed that the curve will<br />

pass through.<br />

6. Press the mouse down to place the next<br />

point. Points will automatically connect to<br />

previous points.<br />

7. Drag your mouse to set the paired control<br />

at the second point. The further from the<br />

second point you make this paired control<br />

point, the tighter the curve will hug the<br />

second point.<br />

8. Repeat steps 5 through 7 until finished.<br />

9. Press the escape key to complete the<br />

shape and set it.<br />

Modifying Bezier Curves<br />

bezier curves in one of two ways. The first<br />

way is by following the same instructions as<br />

in the Modifying Pen Paths and Polylines<br />

section. The second is by using the Bezier<br />

Curve tool. Perform the following steps:<br />

2. Move the mouse pointer over the bezier<br />

curve that you desire to be modified so<br />

that its control points are rendered.<br />

3. Click on the bezier curve so that all of its<br />

control points are rendered as shown in<br />

Figure 4.10.<br />

4. Hover over any of the control points so<br />

that an amber color fills the one you wish<br />

to move.<br />

100<br />

5. Press the mouse down and drag the<br />

control point to the new desired location.<br />

6. Release the mouse to finish moving the<br />

Deleting Bezier Control Points<br />

Only the control points that have the curve<br />

pass through them may be deleted. Deleting<br />

one of these control points will also remove<br />

the corresponding paired control point. To<br />

delete a bezier control point, perform the<br />

4. Hover over the control point that you wish<br />

to remove so that it is filled in with an<br />

5. Press the delete key to delete the control<br />

point.<br />

Adding Arrows to Bezier Curves<br />

To add arrows to bezier curves follow the<br />

same procedures as discussed for the Arrow<br />

shapes earlier in the Chapter. Just right click<br />

on the bezier curve after it is hovered, select<br />

the Format Bezier Curve... menu item, and<br />

define the arrow sections to your preference.<br />

To close or open a custom shape, use a<br />

content is currently selected by emptying the

drawn as shown in Figure 4.9.<br />

2. Right-click on the hovered custom shape<br />

and select the Format Custom Shape...<br />

menu item.<br />

3. Scroll to the Path or Bezier Curve<br />

section and use the Close on/off choice to<br />

set if the custom shape path is closed or<br />

not.<br />

If closed, the custom shape can be filled in<br />

with a desired color.<br />

Removing Custom Shapes<br />

Custom Shapes can be removed in a number<br />

of ways. You can do the following:<br />

pointer over the custom shape so an open<br />

hand mouse cursor appears and the custom<br />

shape anchor points are drawn as shown in<br />

Figure 4.9. Then press the backspace or<br />

delete key.<br />

pointer over the custom shape so the custom<br />

shape anchor points are drawn. Then click<br />

with the mouse.<br />

Rulers<br />

Rulers measure distances in 2 dimensions and<br />

are defined by two anchors placed at their<br />

endpoints as shown in Figure 4.11. There is<br />

also a third midpoint in the middle for<br />

discussed in the next section.<br />

Figure 4.11: Ruler Shape and Anchors<br />

101<br />

Drawing Rulers at Fixed Angles<br />

To draw a ruler at fixed angles, perform the<br />

1. Select a Ruler tool in the Shapes toolbar.<br />

Board to set the start point of the ruler.<br />

of the end of the ruler.<br />

4. Release the mouse to set the ruler.<br />

By default, rulers will be oriented at fixed<br />

To place rulers at non-fixed angles, hold<br />

when defining the ruler to break from the<br />

To place rulers oriented vertically or<br />

dragging the mouse when defining the ruler.<br />

The ruler preview will then automatically<br />

angle from the start point to the current<br />

Automatically Measuring Object Width<br />

To measure the width and height of selected<br />

objects, perform the following procedure:

1. Select the content to be measured using<br />

the selection tools.<br />

2. Select the Width and Height menu item<br />

in the Measure> submenu in the Content<br />

menu.<br />

Two rulers will be placed to measure the<br />

width and height of the selected content.<br />

Diagonal<br />

To measure the diagonal of selected objects,<br />

perform the following procedure:<br />

2. Select the Diagonal menu item in the<br />

Measure> submenu in the Content<br />

A single ruler will be placed across the<br />

diagonal of the selected content.<br />

Moving Rulers<br />

To move rulers, use a selection tool, either the<br />

1. Hover the mouse pointer over the ruler so<br />

Figure 4.11.<br />

the ruler.<br />

Resizing Rulers<br />

To resize rulers, use a selection tool, either<br />

102<br />

the ruler anchor points are drawn as<br />

shown in Figure 4.11.<br />

4. Drag the anchor point to resize the ruler.<br />

Ticks<br />

To show and hide ruler major and minor ticks,<br />

use a selection tool, either the lasso or the<br />

2. Right-click on the hovered ruler and<br />

select the Format Ruler... menu item.<br />

3. Scroll to the Ruler section and use the<br />

Show Major Ticks and Show Minor<br />

Ticks on/off choices to set whether major<br />

and minor ticks are visible or not.<br />

Changing the Measurement Unit<br />

To change the ruler’s measurement unit, use a<br />

Unit drop down selection to select the<br />

unit to be displayed.<br />

Removing Rulers<br />

Rulers can be removed in a number of ways.<br />

pointer over the ruler so an open hand<br />

mouse cursor appears and the ruler anchor<br />

points are drawn as shown in Figure 4.11.<br />

pointer over the ruler so the ruler anchor<br />

Text Areas<br />

In addition to atom labels, you can also add<br />

blocks of text in text area objects. Text areas<br />

can have a border and can have a background,<br />

and can be resized to any dimension.<br />

To place text areas, click on the Text Area<br />

tool in the Shapes toolbar. You can place<br />

text areas and edit them just as you would<br />

Rectangle shapes. The text area is resizable<br />

and can have a border and background. It will<br />

not automatically fit its contained text.<br />

103<br />

When editing the text area, text format<br />

functions will be provided in a toolbar that<br />

appears above it as shown in Figure 4.12.<br />

Figure 4.12: Editing a Text Area<br />

To edit text areas, use the Text Area tool to<br />

click on an existing text area, or hover the<br />

text area using a selection tool and doubleclick.

Chapter 5: Editing<br />

The most important feature of graphical<br />

editors is access to a robust set of content<br />

management tools.<br />

content management tools within<br />

• Selecting content.<br />

• Duplicating content.<br />

• Editing content.<br />

• Organizing content.<br />

• Grouping content.<br />

• Removing content.<br />

Selecting Content<br />

Content can be selected by using any of the<br />

selection tools. There are 3 types of selection<br />

tools provided in <strong>ChemDoodle</strong>:<br />

• Lasso - Define an arbitrary boundary<br />

that follows the mouse and selects any<br />

objects contained within.<br />

• Rectangular Marquee - Define a<br />

rectangle that selects any objects contained<br />

within.<br />

• Lasso Only Shapes - Define an<br />

arbitrary boundary that follows the mouse<br />

and selects only shape objects contained<br />

104<br />

These tools can be quite complex to learn, so<br />

we suggest you practice with them for a<br />

while.<br />

Selected content will show an amber<br />

highlight and will be surrounded by an an<br />

animated amber outline as shown in Figure<br />

5.1.<br />

Figure 5.1: Selected Content<br />

The crawling ants animation can be turned off<br />

in the Preferences window under the<br />

Selecting Individual Objects<br />

To select an individual object, first select a<br />

lasso tool and make sure no content is<br />

currently selected. Then hover the object to<br />

be selected and click. The single object will<br />

then be selected.<br />

Selecting Groups of Objects<br />

To select groups of object, perform the<br />

1. Select a lasso tool.<br />

2. Click and drag to draw an outline with a<br />

lasso or to draw a rectangle with the<br />

rectangular marquee to surround all of the<br />

objects you would like to select.<br />

3. Release the mouse to select the contained<br />

NOTE: It may be difficult to see the full<br />

bounds for some shapes, such as large text

areas with little text in them. If you have<br />

trouble selecting a shape, make sure to<br />

discover where its bounds are and draw the<br />

selection bounds around both anchors.<br />

Select All<br />

To select all content on a page, expand the<br />

Select submenu in the Content menu and<br />

press the All menu item. The keyboard<br />

shortcut to use this function is ctrl-A<br />

(command-A on Mac OS X).<br />

from a Selection<br />

If a selection has already been made, you can<br />

add or remove an individual object from the<br />

selection. Hold down the alt key and hover<br />

the object to be added or removed and click<br />

the mouse. If that object was previously<br />

selected, it will be removed from the<br />

selection, otherwise it will be added to the<br />

selection.<br />

add or remove groups of objects from the<br />

selection. Hold down the shift key and hover<br />

and drag to draw an outline with a lasso or to<br />

draw a rectangle with the rectangular<br />

marquee to surround all of the objects you<br />

would like to select or deselect. Then release<br />

the mouse. Any objects contained within the<br />

new boundary will be removed from the<br />

selection if they were previously selected,<br />

otherwise they will be added to the selection.<br />

Selecting Whole Molecules<br />

Instead of surrounding an entire molecule<br />

with the selection tools to select it, the<br />

following techniques will allow you to select<br />

individual molecules:<br />

105<br />

• Using a selection tool, hold down both the<br />

alt and shift keys and then click on an atom<br />

or bond in the molecule.<br />

• Press the tab key to navigate through<br />

molecules, selecting one at a time, starting<br />

at the last drawn molecule and then<br />

navigating through them chronologically.<br />

SMARTS<br />

SMARTS is single line, text-based query<br />

system for matching chemical objects, similar<br />

to how systems like regular expressions<br />

match text. You may find it very convenient<br />

to select content in files by SMARTS queries.<br />

To do so, perform the following steps:<br />

1. Select the SMARTS... menu item in the<br />

Select> submenu in the Content menu.<br />

2. A window will appear prompting you for<br />

the SMARTS query. Input your query<br />

here and press the Accept button.<br />

Any content that matches the SMARTS string<br />

will then be selected.<br />

Navigating Through Single Shapes<br />

Instead of surrounding an entire shape with<br />

the selection tools to select it or clicking on<br />

the shape, you can also press the tab key<br />

while holding down the shift key to navigate<br />

through shapes, selecting one at a time,<br />

starting at the last drawn shape and then<br />

Selecting Only Shapes<br />

When figures are highly congested, it may be<br />

difficult to select shapes from surrounding<br />

structures. In this case, use the Lasso Only<br />

Shapes tool which will only recognize<br />

shapes. The Lasso Only Shapes tool works<br />

identically to the Lasso tool in every other<br />

Selection<br />

To select the inverse of the current selection<br />

on a page, expand the Select submenu in the<br />

Content menu and press the Inverse menu<br />

Deselecting Objects<br />

To deselect the current selection, perform one<br />

of the following actions:<br />

• Move the mouse cursor away from the<br />

selection so that the lasso cursor icon<br />

appears. Then click the mouse.<br />

• When the mouse cursor is within the current<br />

selection boundary, double-click the mouse.<br />

• Press the Deselect menu item in the<br />

Content menu.<br />

• Press the space key to deselect the current<br />

selection and return to the structure drawing<br />

mode.<br />

Reselecting Objects<br />

If you lost the current selection by mistake,<br />

you can reselect it by selecting the Reselect<br />

menu item in the Content menu.<br />

Duplicating Content<br />

Content in <strong>ChemDoodle</strong> can be duplicated on<br />

the Doodle Board in the current document or<br />

between separate documents through copy<br />

and paste actions. To have <strong>ChemDoodle</strong><br />

objects copied and pasted correctly on the<br />

Doodle Board, make sure to keep<br />

<strong>ChemDoodle</strong> Collage enabled in the<br />

Preferences window under the Advanced<br />

Copy and Paste<br />

To duplicate content, perform the following<br />

1. Select the content to be duplicated.<br />

106<br />

2. Press the Copy menu item in the Edit<br />

menu. The keyboard shortcut to use this<br />

function is ctrl-C (command-C on Mac<br />

OS X).<br />

3. Press the Paste menu item in the Edit<br />

function is ctrl-V (command-V on Mac<br />

Cut and Paste<br />

To duplicate content and remove the original,<br />

2. Press the Cut menu item in the Edit<br />

function is ctrl-X (command-X on Mac<br />

Organizing Content<br />

<strong>ChemDoodle</strong> provides several tools for laying<br />

out content in the document.<br />

Aligning<br />

To align content relative to each other,<br />

1. Select the content to be aligned.<br />

2. Expand the Align submenu in the<br />

Content menu and press the Left Edges,<br />

Horizontal Centers, Right Edges, Top<br />

Edges, Vertical Centers or Bottom<br />

Edges menu items.<br />

Aligning by Bond<br />

To align an entire molecule by a given bond,<br />

1. Hover the bond to align the molecule by.

2. Press the up, down, left or right arrow<br />

keys to align the bond from its first to<br />

second constituent atom in the selected<br />

direction. This will rotate the entire<br />

molecule with the bond.<br />

Centering<br />

To center all content on the page, expand the<br />

Center submenu in the Content menu and<br />

press the All on Page menu item.<br />

To center selected content on the page,<br />

1. Select the content to be centered.<br />

2. Expand the Center submenu in the<br />

Content menu and press the Selection on<br />

Page, Selection Horizontally or<br />

Selection Vertically menu items.<br />

Distributing<br />

To distribute content across the document,<br />

1. Select the content to be distributed.<br />

2. Expand the Distribute submenu in the<br />

Content menu and press the Horizontally<br />

on Page or Vertically on Page menu<br />

items.<br />

To distribute content across the document<br />

using a buffer spacing that you provide,<br />

by Buffer Space... or Vertically by<br />

Buffer Space... menu items.<br />

3. Input a buffer space value into the number<br />

field that appears.<br />

4. Click the Accept button to perform the<br />

distribution.<br />

107<br />

Flipping<br />

To flip content horizontally or vertically,<br />

1. Select the content to be flipped.<br />

2. Expand the Flip submenu in the Content<br />

menu and press the Horizontally or<br />

Vertically menu items.<br />

Flipping a Bond<br />

You may wish to flip non-symmetrical bonds<br />

when you need it to face the other direction,<br />

such as when working with wedge bonds.<br />

There are a few quick ways to do so:<br />

• Hover over the bond and press the f key to<br />

flip it.<br />

• Hover the bond, right-click and select Flip<br />

Bond Orientation.<br />

• Use the bond tool of that bond type and<br />

click on the bond after hovering it.<br />

<strong>ChemDoodle</strong> will detect the bond is being<br />

set to its current bond type and will instead<br />

flip the bond.<br />

Placing in Grid<br />

To place all content in a grid that covers the<br />

document, perform the following steps:<br />

1. Select the Grid All on Page... submenu in<br />

the Content menu.<br />

2. In the prompt that appears, select whether<br />

you want to specify the grid dimensions<br />

by Columns or by Rows by choosing the<br />

corresponding selection from the drop<br />

down menu.<br />

3. Input the dimension of the grid in the<br />

number field. The other dimension will be<br />

automatically calculated based on the<br />

number of objects being placed in the<br />

grid.<br />

4. Select the Grid button.

Stacking<br />

Stacking will place all content on the page<br />

starting from the top-left of the document to<br />

the bottom-right, such that their visual bounds<br />

are separated by a small buffer and that all<br />

objects are within the page margins. To stack<br />

all content on the page, press the Stack All on<br />

Page menu item in the Content menu.<br />

If content is ever placed outside of the page<br />

bounds, red strips will appear at the sides of<br />

the page that the content extends from. Click<br />

on the red strip to stack all of the content that<br />

extends from that side of the page back onto<br />

the page.<br />

Framing Content<br />

Content can be automatically framed with<br />

various different shapes. To frame objects,<br />

1. Select the objects to be framed using the<br />

selection tools.<br />

2. Expand the Add Frame> submenu in the<br />

3. Select the type of frame to use.<br />

The selected content will then be framed.<br />

Editing Content<br />

The selection area is context sensitive and<br />

you can click and drag on the various features<br />

of the selection to perform different actions.<br />

Translating<br />

To translate content, or move it on the page,<br />

1. Select the content to be translated.<br />

2. Hover the mouse cursor over the selection<br />

so that an open hand cursor appears.<br />

108<br />

3. Press the mouse down so the mouse<br />

cursor turns into a closed hand cursor.<br />

4. Drag the mouse to translate the content.<br />

5. Release the mouse to finish the<br />

translation.<br />

During the translation, the change in x<br />

position and change and y position will be<br />

displayed below the mouse cursor. You can<br />

disable this feedback in the Preferences<br />

window under the General tab.<br />

If you hold the shift key down while<br />

translating will lock the content horizontally<br />

or vertically depending on where the mouse<br />

pointer is.<br />

If you hold the shift and alt keys down while<br />

translating content, you will duplicate that<br />

content and it will be locked horizontally or<br />

vertically depending on where the mouse<br />

pointer is. To remove the lock, release the<br />

shift and alt keys.<br />

Rotating<br />

To rotate content, perform the following<br />

1. Select the content to be rotated.<br />

2. Hover the mouse just outside the edge of<br />

the selection border so that the rotation<br />

cursor appears.<br />

3. Press the mouse down and drag it to rotate<br />

the content.<br />

4. Release the mouse to finish the rotation.<br />

During the rotation, the rotation angle will be<br />

window under the General tab.

To more precisely rotate content, perform the<br />

2. Expand the Rotate submenu in the<br />

Content menu and press the 90° CW, 90°<br />

CCW or 180° menu items.<br />

To more precisely rotate content by an<br />

arbitrary angle, perform the following steps:<br />

Content menu and press the Arbitrary...<br />

3. Enter a degree value in the number field<br />

that appears and select whether the<br />

rotation should be done clockwise or<br />

counterclockwise.<br />

4. Press the Rotate button to perform the<br />

rotation to the settings you provided.<br />

Moving the Rotation Anchor<br />

Sometimes you may not want to rotate<br />

content around its center, as is done by<br />

default. For instance, you may desire to rotate<br />

structures around an atom. This can be<br />

achieved by moving the rotation anchor that<br />

is initially found in the center of the selection.<br />

To move the rotation anchor, perform the<br />

1. Move the mouse over the rotation anchor<br />

so that the anchor fills in with an amber<br />

color and the mouse cursor changes to a<br />

resize cursor.<br />

2. Press the mouse down and drag the<br />

rotation anchor to the desired position.<br />

3. Release the mouse to set the new rotation<br />

anchor position.<br />

109<br />

Now all rotations will proceed around the<br />

new rotation anchor position.<br />

When moving the rotation anchor, it will<br />

automatically lock on to atoms within the<br />

selection as you get close to them, aiding you<br />

in setting the rotation anchor over atom<br />

positions.<br />

Scaling<br />

To scale content, perform the following steps:<br />

1. Select the content to be scaled.<br />

2. Hover the mouse over one of the anchor<br />

points in the selection so that the mouse<br />

resize cursor appears.<br />

3. Press the mouse down and drag the<br />

anchor to scale the content.<br />

4. Release the mouse to finish the scale<br />

While scaling, the x scale factor and y scale<br />

factor will be displayed below the mouse<br />

cursor. You can disable this feedback in the<br />

To preserve the width-to-height ratio while<br />

scaling content along the diagonals, just hold<br />

down the shift key while performing the<br />

above steps.<br />

To precisely scale content, perform the<br />

2. Press the Scale... menu item in the<br />

3. Select whether to scale the content by<br />

dimension or bond length and then<br />

specify the rest of the settings.<br />

4. Press the Scale button to scale the content<br />

to the settings you provided.

Fonts<br />

To change the fonts of atom labels and text<br />

based shapes, perform the following steps:<br />

1. Select the atoms and shapes that you<br />

would like to change the fonts of.<br />

2. Choose the font family, font size and font<br />

style in the Files + Formatting toolbar to<br />

change the fonts.<br />

Drawing Aids<br />

Drawing guides will help when precision is<br />

important. There are several categories of<br />

drawing guides, and each have their own<br />

benefit. <strong>Guide</strong>s can be enabled and disabled<br />

in the Drawing Aids> submenu of the View<br />

Atom Aids<br />

Two types of aids can be drawn for atoms:<br />

• Orthogonal - Will show a horizontal and<br />

vertical line through the center of each atom<br />

to help with alignment.<br />

• Circular - Will show a circle around each<br />

atom with radius equal to the current<br />

standard bond length to help with distances.<br />

Bond Aids<br />

A single type of aid can be drawn for bonds:<br />

• Parallel - Will draw a line through each<br />

bond, parallel to its direction to help with<br />

extrapolation.<br />

Ring Aids<br />

Rings can be colored in with a different color<br />

corresponding to the size of the ring to help<br />

with perception.<br />

Molecule Aids<br />

Two types of aids can be drawn for<br />

molecules:<br />

110<br />

• Bounds - Will show a rectangle<br />

representing the bounds of each molecule to<br />

help with placement.<br />

vertical line through the center of each<br />

molecule to help with alignment.<br />

Background Aids<br />

Three types of aids can be drawn on the<br />

background:<br />

• Crosshair - Will render a crosshair and grid<br />

to help with partitioning and aligning<br />

• Grid - Will render a grid at an interval that<br />

you specify to help with aligning objects.<br />

• Margins - Will render the bounds for the<br />

margins.<br />

Colors<br />

There are two features in the Files +<br />

Formatting toolbar for changing the colors<br />

of content, the Color button and the Quick<br />

Colors button.<br />

Color Button<br />

The Color Button was specifically created in<br />

<strong>ChemDoodle</strong> to make it easy to quickly<br />

change the colors of groups of objects. There<br />

are eight colors defined the color button:<br />

• Background<br />

• Borders and Lines<br />

• Fill<br />

• Atom Labels<br />

• Identifier Text<br />

• Other Text<br />

You may change these colors by clicking the<br />

thin rainbow button placed directly to the<br />

right of the Color Button. All objects drawn<br />

after choosing colors will conform to those<br />

choices. To change the colors of a group of<br />

objects to the current selection of colors, just<br />

select them and click the Color Button.<br />

The Color Button will change its display<br />

colors to reflect the current settings. A<br />

breakdown of the sections of the Color<br />

Button is shown in Figure 5.2.<br />

Figure 5.2: Color Button Layout<br />

If you wish for a certain fill to be empty and<br />

to not be colored, then in the color chooser,<br />

click the Empty Color button for the desired<br />

fills to not be painted.<br />

Quick Colors Button<br />

The Color Button is powerful but is certainly<br />

not a quick way to change colors. To quickly<br />

change colors, just use the Quick Colors<br />

Button.<br />

Just selected the content that you would like<br />

colors changed for, and press the quick colors<br />

button. All of the content will be changed to<br />

that color regardless of the content type.<br />

If you click and hover (or drag) over the<br />

Quick Colors button, a palette will appear to<br />

select a new color. Drag the mouse pointer<br />

over one of the preset colors to select it and<br />

111<br />

immediately change the selected content to<br />

that color.<br />

You can also add custom colors to the last<br />

three rows of the Quick Colors palette. Just<br />

release your mouse over the circled plus icon<br />

and release to show a color chooser.<br />

Choose the desired color and press the OK<br />

button to add it to the palette and change the<br />

currently selected content to that color.<br />

The Quick Colors palette is shown in Figure<br />

5.3.<br />

Figure 5.3: The Quick Colors palette.<br />

Color Detection<br />

When working with content that uses non<br />

standard colors, you may wish to detect what<br />

those colors are. To do this, expand the Quick<br />

Colors Button and release the mouse over<br />

the Detect Color button . Then hover<br />

over the color in the document you wish to<br />

detect and press the mouse down when that<br />

color is centered in the cursor. That color will<br />

be added to the Quick Colors Button for<br />

further use.<br />

Color Chooser<br />

The color chooser will be different on all<br />

platforms, with different templates to use to<br />

pick colors from. However, the <strong>ChemDoodle</strong><br />

pinwheel color chooser will be present on all

platforms. The pinwheel color chooser is<br />

shown in Figure 5.3.<br />

Figure 5.3: <strong>ChemDoodle</strong>ʼs Pinwheel Color<br />

Chooser<br />

The color selected can be seen in the preview<br />

bar at the bottom, with the hex value shown<br />

by default. You can also view the RGB value<br />

by enabling the Decimal RGB checkbox.<br />

To select a color, just move the mouse pointer<br />

over the pinwheel until the color you would<br />

like to select is hovered, then click the mouse.<br />

You can also use the mouse wheel to scroll<br />

through colors.<br />

If the pinwheel appears all black, you will<br />

need to increase the Brightness setting by<br />

moving the Brightness slider up. If the<br />

pinwheel appears all white, you will need to<br />

decrease the Saturation setting by moving the<br />

Saturation slider down.<br />

112<br />

Modifying the Z-order of<br />

Shapes<br />

Occasionally, you may want to change how<br />

shapes are z-ordered with respect to each<br />

other and with respect to atoms and bonds.<br />

Shapes, by default, will always render behind<br />

atoms and bonds and will be z-ordered<br />

chronologically.<br />

To modify the z-order of a shape, perform the<br />

1. Hover the shape to change the z-order of.<br />

2. Right-click on the shape.<br />

3. Expand the Arrange submenu.<br />

4. Select the Send Forward, Send<br />

Backward, Send to Front or Send to<br />

Back menu item depending on your<br />

To change if a shape is rendered in front of or<br />

behind atoms and bonds, perform the<br />

4. Select the Place in Front of Structures<br />

or Place in Back of Structures menu<br />

item depending on your preference.<br />

Grouping Content<br />

Content in <strong>ChemDoodle</strong> can be grouped.<br />

Once grouped, you will no longer be able to<br />

edit the member objects individually. Any<br />

transformations performed on the group will<br />

affect all member objects.<br />

Grouping can be nested, so groups can be<br />

grouped into further groups. Ungrouping is

not recursive, so ungrouping a group<br />

containing groups will leave those contained<br />

groups intact.<br />

Grouping<br />

To group content, perform the following<br />

1. Select the content to be grouped.<br />

2. Press the Group menu item in the<br />

Ungrouping<br />

To ungroup content, perform the following<br />

1. Select the groups to be ungrouped.<br />

2. Press the Ungroup menu item in the<br />

Removing Content<br />

Removing individual Objects<br />

Individual objects can be removed by using<br />

the eraser tool to hover the object and then by<br />

clicking to remove it. Additionally, at any<br />

time, when an object is hovered, press the<br />

backspace or delete key.<br />

Removing Groups of Objects<br />

Groups of objects can be removed in a<br />

number of ways. You can do the following:<br />

• Use a selection tool to select the content to<br />

be removed. Then press the backspace or<br />

• First select the content to be removed. Then<br />

use the eraser tool to click on the Doodle<br />

• Select the eraser tool, then press the mouse<br />

down and drag over all of the content to be<br />

removed. Selected content will be<br />

highlighted. Then release the mouse to<br />

remove all highlighted objects. Dragging<br />

113<br />

over content that has already been<br />

highlighted will de-highlight it.

Chapter 6:<br />

Advanced<br />

Chemistry and<br />

<strong>ChemDoodle</strong> is powered by an advanced<br />

cheminformatics engine to perform several<br />

functions for creating graphics, such as ring<br />

perception and structure depiction. This<br />

engine allows for some very powerful<br />

functions to help you create your chemical<br />

graphics and to analyze the structures you<br />

draw.<br />

advanced structure functionality within<br />

<strong>ChemDoodle</strong>. It introduces the following<br />

• The cheminformatics algorithms<br />

implemented in <strong>ChemDoodle</strong>.<br />

• How to use these functions to perform<br />

various advanced tasks.<br />

• How to edit your structures in a more<br />

advanced way than described in Chapter 3.<br />

• How to take full advantage of the functions<br />

provided in <strong>ChemDoodle</strong>.<br />

Aromaticity<br />

Aromaticity is detected based on the Hückel<br />

model. All rings are assumed to be planar.<br />

Any appropriately hybridized heteroatoms<br />

can be constituents in an aromatic ring.<br />

114<br />

Representations for Aromatics<br />

To toggle between viewing aromatics in<br />

Kekulé form (with double bond lines) or with<br />

circles, perform the following steps.<br />

1. Open the Preferences window.<br />

2. Select the Rings tab under the Visuals<br />

3. Check or uncheck the Use Circles visual<br />

specification under the Aromatics section<br />

based on your preference.<br />

Forcing Aromaticity<br />

In rare cases, <strong>ChemDoodle</strong> may determine a<br />

ring to have no aromatic character when it<br />

should be aromatic for some purpose. To<br />

force a ring to be recognized as aromatic,<br />

change all of the ring bonds to Resonance<br />

Calculating Covalent Bonds<br />

Some chemical input read into <strong>ChemDoodle</strong><br />

may not include bond topology such as PDB<br />

and XYZ files as well as some output from<br />

modeling programs. Instead of having to<br />

define the bonds by hand, <strong>ChemDoodle</strong><br />

contains tools for deducing covalent bonds<br />

based on published covalent radii.<br />

To deduce covalent bonds, perform the<br />

1. Select the atoms that you would like<br />

covalent bonds deduced between.<br />

2. Select the Calculate Covalent Bonds<br />

menu item from the Structure menu.<br />

Covalent radii are a best fit from a large<br />

number of experimental covalent radii. In<br />

some cases, a bond distance from a file may<br />

be larger than the distance calculated by<br />

adding the corresponding element covalent

adii together and the bond will not be found.<br />

To address this, <strong>ChemDoodle</strong> multiplies all<br />

covalent radii by a scalar when deducing<br />

bonds. By increasing this multiplier,<br />

<strong>ChemDoodle</strong> will discover bonds at longer<br />

distances. You can change the radius<br />

multiplier in the Preferences window under<br />

the Functions tab.<br />

Carbon Labels<br />

By default, <strong>ChemDoodle</strong> draws skeleton<br />

figures where carbon labels are suppressed.<br />

Regardless, it may be necessary to show the<br />

carbon label for various reasons and this can<br />

be done easily for each atom or globally for<br />

all atoms. To affect this globally, change the<br />

following visual specification for the<br />

document style sheet in the Preferences<br />

window. For each atom, change the following<br />

visual specification in the atom’s Format<br />

The atom Display Carbon Label visual<br />

specification has 4 options for displaying<br />

carbon labels:<br />

• Always - always display the “C” for the<br />

carbon label.<br />

• On Lone and Hidden - only display carbon<br />

labels on lone and hidden carbons.<br />

• On Hidden - only display carbon labels on<br />

hidden carbons. (default)<br />

• Never - never display “C” labels.<br />

The default is On Hidden and only carbon<br />

atoms that are “hidden” between two bonds of<br />

the same bond order will have their label<br />

displayed as shown in Figure 6.1.<br />

Figure 6.1: Hidden carbon labels are shown.<br />

115<br />

Lone carbons are disconnected atoms and<br />

have no bonds attached.<br />

In addition to manually changing this visual<br />

specification, there is a quick method<br />

provided to show/hide carbon labels. To<br />

quickly show individual carbon labels,<br />

1. Hover the carbon atom with label to be<br />

shown.<br />

2. Right-click on the atom and select the<br />

Show Carbon Label menu item.<br />

To hide the carbon label. Perform the same<br />

steps, but instead select the Hide Carbon<br />

Label menu item.<br />

Terminal Carbon Labels<br />

By default, all terminal carbon atoms will<br />

display labels. In some cases, these labels<br />

may clutter a diagram. To hide terminal<br />

carbon labels, uncheck the Show Terminal<br />

Labels visual specification in the Carbons<br />

section in the Atoms section in the Visuals<br />

section of the Preferences window.<br />

Chemical Suppliers<br />

Chemical suppliers for the structures you<br />

draw can be listed by performing the<br />

1. Draw the structure you would like to<br />

search for.<br />

2. Select the structure with a selection tool.<br />

3. In the Structure menu, expand the<br />

Chemical Suppliers menu item.<br />

4. Select the Substructure Match or Exact<br />

Match menu item depending on whether

you want to search for a substructure or<br />

exact match for the selected structure.<br />

5. The ChemExper database will appear in<br />

your default browser with a listing of<br />

matches. Select the match to view the<br />

chemical suppliers.<br />

The ChemExper database provides the<br />

supplier information and you must abide by<br />

their terms of use and any copyrights or<br />

disclaimers presented when using their<br />

service.<br />

Chemical Warnings<br />

<strong>ChemDoodle</strong> will check your structures for<br />

you and flag any questionable objects.<br />

Warning Types<br />

The following warnings are currently<br />

implemented:<br />

• Improper Valency - It is unlikely that this<br />

element can have the current coordination<br />

number. Or the atom label is an<br />

abbreviation and the valency is<br />

overextended.<br />

• Uninterpretable Label - <strong>ChemDoodle</strong><br />

does not understand or interpret the text<br />

present in the atom label as chemically<br />

relevant.<br />

• Unpublished Mass Number - This mass<br />

number is not found in <strong>ChemDoodle</strong>’s<br />

database of published isotopes for the<br />

element.<br />

• Unpublished Oxidation State - The<br />

oxidation state of this atom is not found in<br />

<strong>ChemDoodle</strong>’s database of published<br />

oxidation states for the element.<br />

• Sum of Bonds is not an Integer - The<br />

coordination number of this atom is not a<br />

whole number.<br />

116<br />

• Questionable Stereochemistry - The<br />

stereochemistry of this atom is<br />

questionable.<br />

• Atom Overlaps Another - This pair of<br />

atoms has the same coordinates and will be<br />

perceived as a single atom in graphical<br />

output.<br />

Disabling Warnings Globally<br />

These warnings can be disabled individually<br />

Warnings tab as shown in Figure 6.2. This<br />

tab also contains an option to disable the<br />

display of chemical warning explanations at<br />

the top-left of the document the warnings are<br />

present in.<br />

Figure 6.2: Chemical Warnings<br />

To disable warnings on a single atom,<br />

1. Hover the atom with the warning shown<br />

to be disabled.<br />

Ignore Warnings menu item.

To reenable warnings for an atom that is<br />

ignoring warnings, just right-click on it after<br />

hovering it and select the Check for<br />

Warnings menu item.<br />

Hiding Warnings from Rendering<br />

Chemical warnings will never appear in any<br />

image output or printouts.<br />

If the warnings clutter the document while<br />

drawing, they can be easily suppressed by<br />

selecting the Hide Warnings menu item in<br />

the View menu.<br />

Cleaning Structures<br />

<strong>ChemDoodle</strong> can generate 2D and 3D<br />

coordinates for structures.<br />

Optimizing Structures in 2D<br />

If your structures do not have acceptable or<br />

aesthetic coordinates, <strong>ChemDoodle</strong> can clean<br />

them. To clean your structures, perform the<br />

1. Select the structures to be cleaned.<br />

2. Expand the Clean submenu in the<br />

Structure menu and select the 2D<br />

Optimization menu item.<br />

<strong>ChemDoodle</strong> employs the published CCG<br />

algorithm for cleaning structures. This<br />

method is a statistical approach. Therefore,<br />

repeated applications of the function may<br />

produce different results. If you are not happy<br />

with the first result of the function, try it<br />

again, something better may be generated.<br />

Distance Geometry Embedding<br />

Distance geometry embedding sets 3D<br />

coordinates for a structure based on a<br />

regression of its bond distance matrix. This<br />

function works best on highly embedded<br />

structures such as fullerenes and carbon<br />

nanotubes. To use this method, perform the<br />

117<br />

1. Select the structures to generate 3D<br />

coordinates for by distance geometry<br />

embedding.<br />

Structure menu and select the Distance<br />

Geometry Embedding menu item.<br />

Preserving Stereochemistry<br />

By default, structure cleaning will preserve<br />

stereochemical configurations. To disable<br />

this, deselect Clean Retains<br />

Stereochemistry in the Functions panel in<br />

Preferences.<br />

Descriptors<br />

<strong>ChemDoodle</strong> calculates a large number of<br />

molecular descriptors. The descriptors are<br />

currently categorized into 4 types:<br />

constitutional, topological, physicochemical<br />

and ADME.<br />

Constitutional<br />

Constitutional descriptors are based on the<br />

makeup of the molecule, such as atom counts<br />

and molecular formula. The following<br />

constitutional descriptors are provided:<br />

• Atom Count - The number of atoms in a<br />

• Bond Count - The number of bonds in a<br />

• Degree of Unsaturation - The sum of all<br />

bond orders substracting 1 for each, plus the<br />

number of rings.<br />

• Element Counts - The number of each<br />

element that is present in a molecule.<br />

• Euler Facet Ring Count - The count of all<br />

Euler facets in a molecule. This is defined<br />

as all of the sides of the 3D shape that is<br />

created by expanding the 2D structure on a<br />

• Exhaustive Ring Count - The total number<br />

of graph cycles present in the molecule.<br />

• Frèrejacque Number - The fundamental<br />

ring count. Also known as the cyclomatic<br />

number or the SSSR count.<br />

• Hydrogen Bond Acceptor Count - Counts<br />

the number of atoms with lone pairs capable<br />

of hydrogen bonding.<br />

• Hydrogen Bond Donor Count - Counts all<br />

Nitrogens, Oxygens and Fluorines that have<br />

Hydrogens attached.<br />

• Rotatable Bond Count - Counts all<br />

saturated bonds. Exceptions are Single<br />

bonds connected to Hydrogens or terminal<br />

atoms, Single bonds of amides, thioamides,<br />

sulphonamides and those connecting two<br />

hindered aromatic rings (having at least<br />

three ortho substituents).<br />

• Total Electron Count - Counts all<br />

electrons in a molecule. Takes into account<br />

charges.<br />

• Lightest Isotopic Mass - Calculates the<br />

lightest isotopic mass by summing the<br />

lightest isotope for each atom given its<br />

• McGowan Characteristic Volume -<br />

Calculates the vdW volume with<br />

McGowan’s method.<br />

• Molecular Mass - Calculates the molecular<br />

mass from atomic masses based on the<br />

IUPAC technical reports.<br />

• Monoisotopic Mass - Calculates the<br />

monoisotopic mass from isotopic masses<br />

based on the IUPAC technical reports.<br />

118<br />

• Volume as a Sum of Atomic and Bond<br />

Contributions - Calculates the VABC<br />

vdW volume.<br />

empirical formula for the molecule. The<br />

empirical formula is just the molecular<br />

formula, where all element multiplicities<br />

have been divided by the greatest common<br />

denominator.<br />

molecular formula for the molecule in the<br />

form of CxHy... where ... denotes all other<br />

elements and their counts in alphabetical<br />

order. This is based on the Hill system, so if<br />

no carbon atoms are present, the hydrogen<br />

count will be in alphabetical order with the<br />

rest of the elements.<br />

Topological<br />

Constitutional descriptors are solely based on<br />

the connectivity between atoms in a molecule,<br />

such as a bond distance matrix. The following<br />

topological descriptors are provided:<br />

• Centric Index - Calculates the Centric<br />

index for the molecule (Bonchev et al.).<br />

topological distance in a molecule.<br />

• Hosoya Index - Calculates the Hosoya<br />

index for the molecule.<br />

• Molecular Topological Index - Calculates<br />

the Molecular Topological index for the<br />

molecule (Schultz et al.).<br />

• Platt Index - Calculates the Platt index for<br />

• Ring Complexity - Calculates the Ring<br />

Complexity for the molecule.<br />

• Szeged Index - Calculates the Szeged index<br />

for the molecule.

• Wiener Index - Calculates the Wiener<br />

• Zagreb Indices - First and second order<br />

calculations are supported. (Z1, Z2)<br />

• Balaban Index - Calculates the Balaban<br />

• Bertz Complexity Index - Calculates the<br />

Bertz Complexity index for the molecule.<br />

Branching index for the molecule. The<br />

Branching index is equivalent to 1 χ.<br />

• Chi Molecular Connectivity Indices -<br />

Indices from zeroth to third order are<br />

supported. Both simple and valence models<br />

are calculated. ( 0 χ, 1 χ, 2 χ, 3 χ, 0 χv, 1 χv, 2 χv, 3 χv)<br />

Framework (fMF) ratio for the molecule.<br />

• Harary Index - Calculates the Harary<br />

• Kappa Shape Indices - Indices from the<br />

first to third order are supported. Both<br />

simple and alpha models are calculated. ( 1 κ,<br />

2 κ, 3 κ, 1 κα, 2 κα, 3 κα)<br />

• Superpendentic Index - Calculates the<br />

Superpendentic index for the molecule.<br />

• Adjacency Matrix - Generates a matrix M<br />

of size AxA, where A is the number of<br />

atoms in the molecule. M(Ai, Aj) equals 1 if<br />

there is a bond connecting atoms i and j,<br />

and equals 0 otherwise.<br />

• Bond Distance Matrix - Generates a<br />

matrix M of size AxA, where A is the<br />

number of atoms in the molecule. M(Ai, Aj)<br />

equals the the number of electrons shared<br />

between atoms i and j.<br />

119<br />

• Bond Electron Matrix - Generates a<br />

equals the shortest bond distance between<br />

atoms i and j.<br />

• Detour Matrix - Generates a matrix M of<br />

size BxA, where B is the number of bonds<br />

in the molecule and A is the number of<br />

atoms in the molecule. M(Bi, Aj) equals 1 if<br />

bond i contains atom j, and 0 otherwise.<br />

• Incidence Matrix - Generates a matrix M<br />

atoms in the molecule. M(Ai, Aj) equals the<br />

longest bond distance between atoms i and<br />

j.<br />

• Laplacian Matrix - Generates a matrix M<br />

and equals 0 otherwise. M(i,i) equals the<br />

number of bonds connected to atom Ai.<br />

Physicochemical<br />

Constitutional descriptors describe the<br />

physical or chemical properties of a molecule.<br />

These are estimations of their real physical<br />

values. The following physicochemical<br />

descriptors are provided:<br />

• Average Molecular Polarizability -<br />

Estimates the average molecular<br />

polarizability. Both the average hybrid<br />

components (Miller) and average hybrid<br />

polarizabilities (Kang) methods are<br />

implemented.<br />

• Critical Pressure - Estimates the critical<br />

pressure (Pc) of a substance based on<br />

Joback’s method.<br />

• Critical Temperature - Estimates the<br />

critical temperature (Tc) of a substance<br />

based on Joback’s method.

• Critical Volume - Estimates the critical<br />

volume (Vc) of a substance based on<br />

• Enthalpy of Formation - Estimates the<br />

enthalpy of formation (ΔH 0 f,298) of a<br />

substance (ideal gas at 298K) based on<br />

• Enthalpy of Fusion - Estimates the<br />

enthalpy of fusion (ΔHf) of a substance<br />

based on Joback’s method.<br />

• Enthalpy of Vaporization - Estimates the<br />

enthalpy of vaporization (ΔHvb) of a<br />

substance (at Tb) based on Joback’s method.<br />

• Gibbs Energy of Formation - Estimates<br />

Gibbs energy of formation (ΔG 0 f,298) of a<br />

substance (ideal gas, unit fugacity, at 298K)<br />

• Heat Capacity - Estimates the heat<br />

capacity(C 0 p) of a substance (ideal gas)<br />

• Lipophilicity, logP - Estimates the octanol/<br />

water partition coefficient (logP) of a<br />

substance. The NC+NHET, AlogP98, and<br />

XlogP v2.0 (Wang) algorithms are<br />

• Liquid Viscosity - Estimates the liquid<br />

viscosity (ηL) of a substance (at 298K)<br />

• Molar Refractivity - Estimates the molar<br />

refractivity of a substance. Both the CMR3<br />

and AMR algorithm are implemented.<br />

• Normal Boiling Point - Estimates the<br />

normal boiling point (Tb) of a substance<br />

• Normal Freezing Point - Estimates the<br />

normal freezing point (Tf) of a substance<br />

120<br />

Estimates the topological polar surface area<br />

(TPSA) of a molecule with the algorithm<br />

developed by Ertl et al.<br />

ADME<br />

Descriptors that rank bioactivity of drugs<br />

(ADME stands for absorption, distribution,<br />

metabolism, and excretion):<br />

• Bioavailability Score - Calculates the<br />

bioavailability score (Martin).<br />

• Egan Violations Count - Calculates the<br />

number of violations to Egan’s rules.<br />

• Lipinski’s Rule of 5 Violations Count -<br />

Counts the number of violations to<br />

Lipinski’s rule of 5.<br />

• Veber Violations Count - Calculates the<br />

number of violations to Veber’s rules.<br />

Flattening Atomic Coordinates<br />

In cases where imported chemical data<br />

contains 3D coordinates, you can set all the zcoordinates<br />

to 0 by selecting that content and<br />

choosing the Flatten menu item in the<br />

Fragmentation<br />

<strong>ChemDoodle</strong> contains several functions for<br />

fragmenting molecules with various results.<br />

The fragmentation functions can be found in<br />

the Content toolbar .<br />

There are three fragmentation functions:<br />

• Molecular Weight - The molecules<br />

will be fragmented and each fragment will<br />

have a molecular weight assigned.<br />

• Synthesis - The molecules will be<br />

fragmented and each fragment will be set as

a reactant in a synthetic reaction leading to<br />

the original molecules.<br />

• Retrosynthesis - The molecules will<br />

be fragmented and each fragment will be set<br />

as a product in the retrosynthetic reaction<br />

resulting in the original molecules.<br />

To fragment a molecule or group of<br />

molecules, perform the following steps:<br />

1. Select the desired fragmentation function<br />

in the Content toolbar.<br />

2. Press the mouse down and drag over all<br />

the bonds to be removed, defining how<br />

the molecule is fragmented.<br />

3. Release the mouse to complete the<br />

function.<br />

Formal Charges<br />

While you can place charges on atoms<br />

manually, <strong>ChemDoodle</strong> can also guess the<br />

formal charges for a structure. To have<br />

<strong>ChemDoodle</strong> guess formal charges for a<br />

structure, perform the following steps:<br />

1. Select the atoms for which formal charges<br />

are to be guessed.<br />

2. Choose the Place Formal Charges menu<br />

Glassware Clipart<br />

Figures for glassware setups can be created<br />

by using the glassware clipart library within<br />

To build glassware setups, perform the<br />

1. Click on the Laboratory Glassware<br />

121<br />

2. In the window that appears, select a<br />

glassware piece that you would like to<br />

place into your figure.<br />

3. Press the mouse down on the current<br />

document and drag to place it where you<br />

prefer the piece to be placed. Hold down<br />

the shift key to flip the template<br />

horizontally while placing.<br />

4. Release the mouse to set the glassware<br />

piece.<br />

5. Repeat steps 2-4 until your figure is<br />

complete.<br />

It may prove necessary to be conscious of the<br />

order in which you place the glassware pieces<br />

in the figure, in order to show some piece<br />

over another.<br />

Keep in mind that each template is a complete<br />

image, and it is not possible to show one<br />

piece in between the front and back of<br />

another piece. However, you may export your<br />

figure to be post-edited in vector editing<br />

software (such as Adobe Illustrator) to<br />

achieve this effect.<br />

All glassware clipart is governed by the same<br />

visual specifications that other shapes are. So<br />

you can change the stroke thickness and the<br />

colors of the various components in the<br />

clipart as shown in Figure 6.3.<br />

Figure 6.3: A glassware setup with altered colors.

Flipping Glassware<br />

To flip the clipart graphics, just hold down the<br />

shift key while placing them. The preview<br />

will then show you the flipped graphic.<br />

You can also manually edit whether a clipart<br />

is flipped or not by right-clicking on it with<br />

nothing selected, selecting the Format<br />

Clipart... menu item and then changing the<br />

Flip on/off choice in the Clipart section.<br />

Tubing<br />

You may wish to connect pieces of glassware<br />

via tubing. A good technique for doing this is<br />

by using the Bezier Curve tool to draw the<br />

path of the tubing, and then increasing the<br />

stroke width of the path to the desired<br />

thickness.<br />

One method for doing so is as follows:<br />

122<br />

1. Select the Bezier Curve tool in the<br />

2. Press the mouse down in the middle of the<br />

outlet in the glassware figure where the<br />

first tubing connection will be made.<br />

3. Drag the mouse out in the direction that<br />

the first outlet faces. The longer you drag<br />

out the control point, the longer the curve<br />

will be straight at that point.<br />

4. Press the mouse down in the middle of the<br />

second tubing connection will be made.<br />

5. Drag the mouse out in the direction that<br />

the second outlet faces. The longer you<br />

drag out the control point, the longer the<br />

curve will be straight at that point.<br />

6. Edit the bezier curve if necessary, or press<br />

the escape key to finish drawing the<br />

curve.<br />

7. Hover the curve using a selection tool and<br />

right-click, selecting the Format Bezier<br />

Curve... menu item.<br />

8. In the Strokes section of the settings<br />

window that appears, change the<br />

Thickness setting to 10 pixels.<br />

9. Select the Done button to close the<br />

settings window.<br />

Your completed figure will then contain a<br />

nice smooth curve connecting the outlets that<br />

represents tubing as shown in Figure 6.4.<br />

Figure 6.4: Glassware figure containing tubing

Graph Reduction<br />

To reduce molecule graphs, perform the<br />

1. Select the structure with the graphs you<br />

would like to be reduced.<br />

2. Expand the Graph Reduction submenu<br />

in the Structure menu and select the<br />

preferred reduction method.<br />

Reduce 0° (Lone)<br />

Will remove all selected atoms that have no<br />

bonds attached.<br />

Reduce 1° (Terminals)<br />

Will remove all selected atoms that have only<br />

1 bond attached to them. This process will<br />

stop after the first iteration.<br />

Repeatedly Reduce 1°<br />

continue until it has pruned all terminal<br />

chains from the selection.<br />

123<br />

Reduce 1° + 0°<br />

Will remove all selected lone and terminal<br />

Reduce 2° (Chains)<br />

Will remove all chains from a molecule,<br />

leaving single bonds connecting any<br />

remaining 3° atoms.<br />

Reduce 2° + 1° + 0°<br />

Will remove all lone, terminal and chain<br />

atoms, leaving a simplified core that<br />

represents the embedded ring structure of a<br />

graph.<br />

Hydrogens<br />

Hydrogens do not need to be drawn on<br />

structures as they are implicitly declared. At<br />

any time, Hydrogens can be added to a<br />

structure as text in atom labels or as atoms<br />

with bonds attached.<br />

Implicit Hydrogen Rendering<br />

By default, implicit hydrogens are<br />

automatically rendered on any element labels<br />

that are visible.<br />

To disable the auto-rendering of implicit<br />

hydrogens, uncheck the Show Implicit<br />

Hydrogens visual specification in the<br />

Hydrogens section of the Atom section of<br />

the Visuals tab in the Preferences window.<br />

You can also disable the auto-rendering of<br />

implicit hydrogens for a specific atom by<br />

1. Hover the atom with implicit hydrogens<br />

to remove.<br />

2. Right-click on the atom.<br />

3. Select the Hide Implicit Hydrogens<br />

This will stop the auto-rendering of implicit<br />

hydrogens on that atom. To restore the

implicit hydrogen auto-rendering, just follow<br />

the same steps as above, but choose the Show<br />

Implicit Hydrogens menu item.<br />

Adding Hydrogens as Atoms<br />

To add hydrogens to a structure as atoms as<br />

shown in Figure 6.5, perform the following<br />

1. Select the structure to add hydrogens to.<br />

2. Expand the Add/Remove Hydrogens<br />

submenu in the Structure menu and<br />

select the From Selection menu item.<br />

Figure 6.5: Hydrogens added as atoms<br />

Adding Hydrogens as Text<br />

To add Hydrogens as text into atom labels as<br />

shown in Figure 6.6, change the Add as<br />

setting in the Hydrogens section in the<br />

Preferences window, under the Visuals tab,<br />

under the Atoms tab to Text. Now when using<br />

the Add/Remove Hydrogens functions,<br />

hydrogens will be explicitly added as text.<br />

Figure 6.6: Hydrogens added as text<br />

to Carbons<br />

You can modify how hydrogens are added to<br />

carbon atoms: whether they are always added,<br />

only added to unsaturated carbons or never<br />

added to carbons. These options are presented<br />

in the Preferences window, under the Visuals<br />

tab, under the Atoms tab in the Carbons<br />

124<br />

IUPAC Naming<br />

Currently only generating a structure from an<br />

IUPAC name is supported.<br />

Name to Structure<br />

To parse an IUPAC name and generate a<br />

chemical structure, perform the following<br />

1. Select the Parse IUPAC Name... menu<br />

item from the Structure menu.<br />

2. In the prompt that appears, input the<br />

IUPAC name and select the Accept<br />

The generated structure will then be placed in<br />

Kekulé Structures<br />

<strong>ChemDoodle</strong> contains a function for<br />

assigning Double bonds to a structure such<br />

that pi electron delocalization is maximized.<br />

Both frames of Single bonds and<br />

substructures consisting of only Resonance<br />

bonds can be affected.<br />

Kekulizing a Single Bond Frame<br />

To easily draw Kekulé structures, you may<br />

begin by just drawing a Single bond frame.<br />

This way, <strong>ChemDoodle</strong> can optimally assign<br />

Double bonds to the structure. If there are<br />

other bond types present, <strong>ChemDoodle</strong> will<br />

not Kekulize the structure. However, the<br />

Saturate function in the Structure menu will<br />

change all bond types to Single bonds.<br />

To Kekulize a structure of only Single bonds,<br />

1. Select the structure containing only Single<br />

bonds to be Kekulized.<br />

2. In the Structure menu, select the<br />

Kekulize menu item.

For example, corannulene is generated from a<br />

Kekulization of a Single bond frame in Figure<br />

6.7.<br />

Figure 6.7: Kekulizing a Single bond frame to<br />

generate corannulene.<br />

Resonance Bonds<br />

In some cases, structures may be read in with<br />

Resonance bonds. It may be necessary to<br />

present a Kekulé structure instead of the<br />

resonance model. When Kekulizing a<br />

structure with Resonance bonds, only those<br />

Resonance bonds will be affected.<br />

To Kekulize a substructure of Resonance<br />

bonds, perform the following steps:<br />

1. Select the structure containing the<br />

substructure of Resonance bonds to be<br />

Kekulized.<br />

Kekulize menu item.<br />

For example, the aromatic rings in Viagra are<br />

Kekulized in Figure 6.8.<br />

Figure 6.8: Kekulizing the aromatic rings in the<br />

resonance model for Viagra.<br />

Label Expansion<br />

Atom labels can be much more than just an<br />

element symbol. They may contain implicit<br />

125<br />

hydrogens or chemical shorthand notations or<br />

abbreviations. <strong>ChemDoodle</strong> can expand these<br />

condensed labels to their all atom models.<br />

Expanding Labels<br />

To expand labels, perform the following<br />

1. Select the atoms with labels to be expanded<br />

using any of the selection tools.<br />

2. Select the Expand Labels menu item in<br />

the Structure menu.<br />

Implicit Hydrogens<br />

Implicit hydrogens can be presented as text in<br />

an atom label. They may be added<br />

automatically, can be added manually using<br />

the Atom Label tool or globally using the<br />

Add/Remove Hydrogens function with the<br />

appropriate visual specifications set.<br />

When expanded, implicit hydrogens are<br />

ignored. So the label NH2 will become a N<br />

label when expanded.<br />

Condensed Labels<br />

Chains and functional groups may be denoted<br />

with a condensed label. For instance, a<br />

carboxy group may be denoted by a COOH<br />

atom label or an ethyl group may be denoted<br />

by CH2CH3.<br />

When expanded, condensed labels will be<br />

replaced by the all atom model of the<br />

fragment as shown in Figure 6.9.<br />

Figure 6.9: Left a molecule with condensed atom<br />

labels; right the corresponding expanded<br />

Several constructs are supported by the<br />

condensed interpreter in <strong>ChemDoodle</strong>:<br />

1. Linear Chains - Stringing elements<br />

together will place them in a chain, so<br />

CCCC or CH2CH2CH2CH3 denotes a nbutyl<br />

group.<br />

2. Multiple Attachments - Using parenthesis<br />

will denote multiple attachments, so the<br />

label C(CH3)3 will denote a t-butyl group.<br />

3. Single and Double Bonds - If no bonds<br />

are placed between elements, then Single<br />

bonds are used to connect them. The -<br />

(minus) character will also specify a Single<br />

bond connection and the = (equals)<br />

character will specify a Double bond<br />

connection. Therefore, CC and C-C both<br />

specify an ethyl group while C=C will<br />

specify an vinyl group.<br />

Abbreviations<br />

In addition to condensed formulas,<br />

abbreviations can be used to define fragments<br />

in atom labels. For instance, the Ph<br />

abbreviation defines a phenyl group. All<br />

supported abbreviations are listed in the<br />

Symbols widget in the Abbreviations section.<br />

When expanded, abbreviations will be<br />

replaced by the all atom model they define as<br />

shown in Figure 6.10.<br />

Figure 6.10: Left a molecule with abbreviations;<br />

right the corresponding expanded structure.<br />

<strong>ChemDoodle</strong> can only expand abbreviations<br />

that represent discrete molecules, monovalent<br />

or divalent fragments. <strong>ChemDoodle</strong> will<br />

attempt to interpret abbreviations properly<br />

based on their valency. For instance, the CO2<br />

abbreviation with a valency of 0 is a carbon<br />

126<br />

dioxide molecule while that same label with a<br />

valency of 2 denotes a ester group.<br />

Adding Custom Abbreviations<br />

Custom abbreviations can be added by<br />

1. Select the Add New... menu item in the<br />

Abbreviations submenu of the Structure<br />

2. Type the abbreviation label to be used in<br />

atom labels in the Abbreviation Label text<br />

field.<br />

3. Type the full name of the abbreviation in<br />

the Full Description/Name text field.<br />

4. Provide the SMILES string for the full<br />

atom model of the abbreviation in the<br />

SMILES for Abbreviation text field. If the<br />

valency of the abbreviation is greater than<br />

0, then the attachment atom is the first<br />

atom defined by the SMILES string. If<br />

the abbreviation is divalent, then the last<br />

atom defined in the SMILES string will<br />

be used as the second attachment atom.<br />

5. Select the valency of the abbreviation<br />

using the Valency drop down selection.<br />

6. Press the Add button to add the new<br />

abbreviation.<br />

<strong>ChemDoodle</strong> will update to recognize the<br />

added abbreviation and when used, that<br />

abbreviation will be expanded to the<br />

SMILES string defined.<br />

Abbreviations and condensed notations can<br />

be combined. So the atom label CPh3 will<br />

denote a triphenylmethyl group.<br />

Molecular Formulas<br />

Sometimes you may intend to input a<br />

molecular formula into an atom label, to

calculate a molecular weight, for instance. If a<br />

molecular formula is input, then <strong>ChemDoodle</strong><br />

will associate that atom with an isomer of the<br />

molecular formula, as best as it can as shown<br />

in Figure 6.11. So your calculations of weight<br />

will be correct, but other calculations will<br />

have to be met with scrutiny. For accurate<br />

calculations, make sure to draw a correct<br />

structure or structural formula.<br />

Figure 6.11: <strong>ChemDoodle</strong> expands a molecular<br />

formula to an isomer all atom model as best as it<br />

can.<br />

Newman Projections<br />

To build graphics for Newman Projections,<br />

1. Draw a 2-methylpropane structure.<br />

2. Hover the central atom and right-click.<br />

3. Select the Show Carbon Label menu<br />

4. Again, hover the central atom and rightclick.<br />

5. Select the Format Atom... menu item.<br />

6. In the Elements section, select the Use<br />

Circles checkbox, make sure Coloring is<br />

set to <strong>User</strong> Chosen and Radius<br />

Convention is set to Constant, and then<br />

set the Constant Radius to the preferred<br />

size. You will now see a black circle<br />

appear over the central carbon.<br />

7. Still in the Atom Settings window, under<br />

the Colors section, change the Text Color<br />

to white. You should now see a figure just<br />

like Figure 6.12.<br />

127<br />

Figure 6.12: A half completed Newman Projection.<br />

8. Click on the Done button exit the Atom<br />

Settings window.<br />

9. Draw a second 2-methylpropane structure.<br />

10. Rotate the second structure to the desired<br />

torsion for the Newman Projection.<br />

11. Using a lasso tool, move the second<br />

drawn structure over the first to complete<br />

the Newman Projection.<br />

Figure 6.13: A finished Newman Projection.<br />

You can then edit the terminal labels to<br />

display the structure desired as is shown in<br />

Figure 6.13. It may be convenient to save a<br />

copy of this structure as a file for later use.<br />

Ring Perception<br />

Rings are cycles of atoms and are important,<br />

because <strong>ChemDoodle</strong> uses them to define<br />

graphics such as which direction double<br />

bonds face and calculations such as<br />

aromaticity detection. There are several<br />

published algorithms to define rings in<br />

structures producing different ring sets.<br />

Supported Ring Sets<br />

Currently, <strong>ChemDoodle</strong> can perceive the<br />

following sets:<br />

• Smallest Set of Smallest Rings - The<br />

smallest set of smallest rings (SSSR) is the<br />

standard for defining ring sets in flat 2D<br />


• Euler Facet Rings - The Euler facet ring<br />

set is better than the SSSR at defining<br />

structures. It is defined by all the rings that<br />

make up the faces of a 3D object when the<br />

2D chemical graph is placed on a 3D<br />

sphere.<br />

• Hanser (All) Rings - Every last graph cycle<br />

in selected structures.<br />

Exploding Ring Sets<br />

Ring sets can be exploded from the structure.<br />

In other words, they will be laid out around<br />

the structure to show the rings and where they<br />

are contained. To explode ring sets, perform<br />

1. Select the structures with the rings to be<br />

exploded.<br />

2. Expand the Rings submenu in the<br />

Structure menu and select the Explode<br />

Smallest Set of Smallest Rings, Explode<br />

Euler Facet Rings or Explode Hanser<br />

(All) Rings menu items.<br />

In very complex structures, the exploded ring<br />

diagram will be highly overlapped. Just stack<br />

the rings (in the Content menu) to view them<br />

all clearly.<br />

Performance Considerations<br />

If dealing with heavily embedded structures,<br />

such as zeolites or MOFs, the algorithms may<br />

become very cpu intensive. In these cases,<br />

you can disable deep searching for rings by<br />

selecting Ring Search Cutoff in the<br />

Functions panel in Preferences.<br />

Sequence Tool<br />

<strong>ChemDoodle</strong> provides a tool for generating<br />

sequence structures for common polymer<br />

types. The following polymer types are<br />

supported:<br />

128<br />

1. Three Letter Amino Acid Sequence<br />

To generate sequences, use the Sequence tool<br />

in the Shapes toolbar. To draw a<br />

sequence, perform the following steps:<br />

1. Click on the current document where you<br />

want the sequence to originate from. The<br />

endpoints of the sequence will appear. For<br />

amino acid sequences, a water molecule<br />

will appear.<br />

2. A single atom will be surrounded by a<br />

blue circle; this is the appending atom. All<br />

changes to the sequence append directly<br />

to this atom. You can hover over other<br />

atoms and click to set a new appending<br />

3. Use the keyboard to type the one letter<br />

hotkeys for the residues in the sequence<br />

set. For instance, pressing the A key will<br />

append an Alanine residue, and pressing<br />

the R key will append an Arginine residue.<br />

Sequences will automatically wrap to stay<br />

within the margins of the current document as<br />

shown in Figure 6.14.<br />

Figure 6.14: A wrapped sequence for Crambin.<br />

Use this tool to easily create macromolecular<br />

structures, and to quickly calculate properties<br />

such as weights and isotopic distributions.<br />

Stereochemistry<br />

The stereochemistry of chiral centers and<br />

double bonds can be determined by selecting<br />

the Stereochemistry functions located in the<br />

Structure menu. An Attribute object will be

associated with the stereocenter to denote the<br />

stereochemical configuration. Several<br />

conventions can be used. Centers can be<br />

forced into a particular configuration in<br />

addition to determining the configurations<br />

based on the 2D layout.<br />

Chiral Centers<br />

Cahn-Ingold-Prelog (CIP) priority rules are<br />

used to resolve rectus (R) and sinister (S)<br />

enantiomers.<br />

Forcing a configuration will interchange the<br />

protruding and recessed bonds, if necessary.<br />

If only single bonds are present, then the<br />

appropriate wedge bonds will be placed when<br />

a configuration is forced.<br />

Double Bonds<br />

CIP priority rules are used to resolve<br />

entgegen (E) or zusammen (Z) configurations<br />

around double bonds. The less systematic cis/<br />

trans conventions can also be used to define<br />

olefin enantiomers. The E/Z system will work<br />

for any double bond presented, while the cis/<br />

trans conventions will not return results in<br />

ambiguous cases.<br />

Forcing Double bond stereochemistry will<br />

flip both substituents on one atom's side of<br />

the double bond through the double bond<br />

axis, if necessary.<br />

Resolving Stereochemistry<br />

To resolve stereochemistry for structures,<br />

1. Select the structures or parts of structures<br />

with stereocenters to be resolved with the<br />

2. Expand the Stereochemistry> submenu<br />

in the Structure menu.<br />

3. Choose the appropriate Assign menu item<br />

to resolve stereocenters of that type.<br />

129<br />

You may also access these functions through<br />

the right-click menu.<br />

Configurations<br />

To force a stereochemical configuration on an<br />

atom or bond, perform the following steps:<br />

1. Hover the atom or bond on which the<br />

configuration will be forced.<br />

2. Right-click on the hovered object.<br />

3. If that object is a potential stereocenter,<br />

then the Stereochemistry> submenu will<br />

be present. Expand this submenu.<br />

4. Choose the appropriate Force menu item<br />

to force the configuration.<br />

Structure Perspective<br />

Even though <strong>ChemDoodle</strong> generates graphics<br />

for structures in two dimensions, the<br />

underlying structures are defined in three<br />

dimensions.<br />

<strong>ChemDoodle</strong> will read in 3D coordinates<br />

from all chemical files and provides functions<br />

for rotating structures in 3D.<br />

NOTE: While <strong>ChemDoodle</strong> has some 3D<br />

editing features, it is not a molecular<br />

modeler and is not the appropriate choice<br />

to build 3D coordinates for structures.<br />

To rotate structures in 3D, perform the<br />

1. Select the structures to be rotated in 3D<br />

using the selection tools.<br />

3. Click the mouse down and drag to rotate<br />

the structure in 3D.<br />

4. Release the mouse to finish the action.

By default, mouse movements while rotating<br />

structures in 3D will rotate the structure<br />

around the x and y axes based on horizontal<br />

and vertical movement respectively. You can<br />

also set the 3D rotations to be defined by a<br />

quaternion trackball in the Preferences<br />

Just like when rotating structures in 2D, there<br />

will also be a rotation anchor present during<br />

3D rotation. Before selecting the 3D rotation<br />

tool, you can move the rotation anchor to a<br />

helpful position than the center, such as over<br />

atom positions. This makes it easy to rotate<br />

structures around atoms in 3D space.<br />

Unique IDs<br />

IDs can be automatically added as attributes<br />

for atoms and bonds. To do so, just select the<br />

appropriate choice in the Unique IDs><br />

submenu in the View menu.<br />

Zero Order/Ionic Bonds<br />

In some cases, a molecule may contain ionic<br />

bonds or you may wish to associate two<br />

atoms that are not connected with a covalent<br />

bond.<br />

<strong>ChemDoodle</strong> contains a zero/ionic bond order<br />

specifically for these cases. You can use this<br />

bond order by selecting the Zero/Ionic bond<br />

type button in the Bonds toolbar. Any<br />

atoms connected with this bond type will be<br />

spatially linked and can be sent to<br />

cheminformatics algorithms such as<br />

molecular formula generation and structure<br />

cleaning.<br />

Note: Most filetypes have no concept of a<br />

zero order bond, so saving these bond<br />

types and loading them into other<br />

applications may not produce desired<br />

results.<br />

Chapter 7:<br />

Reactions<br />

Reactions can be drawn in <strong>ChemDoodle</strong><br />

using structures and arrow shapes. Almost<br />

any type of reaction or mechanism can be<br />

drawn. <strong>ChemDoodle</strong> also contains tools for<br />

explicitly defining reactions for various<br />

purposes.<br />

reactions within <strong>ChemDoodle</strong>. It covers the<br />

• How to draw reactions.<br />

• How to draw mechanisms.<br />

• What types of arrows can be drawn.<br />

• How to build and define reactions and<br />

reaction schemes.<br />

• How to edit reactions.<br />

• How to clean reactions.<br />

Drawing Reaction Arrows<br />

Reaction arrows are created from basic arrow<br />

shapes. Instructions for drawing arrow shapes<br />

are provided in Chapter 4.<br />

Arrow Types<br />

Many different types of arrows can be easily<br />

created using the Arrows toolbar described in<br />

Chapter 2. This section briefly goes over the<br />

different styles and presets.<br />

Arrowhead Styles<br />

Arrowhead styles can be set to both the start<br />

and end of the arrow. Several arrowhead<br />

131<br />

styles (half-heads) can be flipped over the<br />

arrow axis. The following arrowhead styles<br />

are provided:<br />

• Full Indented -<br />

• Full -<br />

• Unfilled Full Indented -<br />

• Unfilled Full -<br />

• Chevron -<br />

• Half Indented -<br />

• Half -<br />

• Unfilled Half Indented -<br />

• Unfilled Half -<br />

• Hook -<br />

Both the arrowhead length and angle can be<br />

changed to match any look. To change the<br />

arrowhead length and angle, perform the<br />

1. Hover the arrow containing the arrowhead<br />

to be edited.<br />

2. Right-click on the arrow and select the<br />

Format Line... menu item.<br />

3. Scroll down to the Reaction section in the<br />

Format Line window that appears.<br />

4. In the Arrow at Start and Arrow at End<br />

sections, use the Length and Angle<br />

sliders to edit the arrowheads.<br />

Quickly Toggle Arrowheads<br />

Instead of opening the shape settings window,<br />

you can easily toggle default arrowheads on<br />

the ends of objects that support arrowheads<br />

by hovering the object and pressing the left

arrow (to toggle start) or right arrow (to<br />

toggle end) keys.<br />

Connector Styles<br />

A connector is the line that connects the start<br />

and end arrows, if any. The following<br />

connector styles are provided:<br />

• Solid -<br />

• Dashed -<br />

• Wavy -<br />

• Doubled -<br />

• No Go (cross) -<br />

• No Go (slash) -<br />

• Rearrangement -<br />

Special Arrow Presets<br />

Many different types of arrows can be drawn<br />

with Arrows toolbar. The following describes<br />

how these tools build common arrow types.<br />

Reaction Arrow - A reaction arrow<br />

is the default style and is drawn with no start<br />

arrow, a Full Indented end arrow and a Solid<br />

connector.<br />

Retrosynthetic Arrow - A<br />

retrosynthetic arrow can be drawn with no<br />

start arrow, a Chevron end arrow and a<br />

Doubled connector. The default arrowhead<br />

angle and length is not aesthetic for this type<br />

of arrow, so use the retrosynthetic preset in<br />

the presets group button to quickly access this<br />

Equilibrium Arrow - An<br />

equilibrium arrow can be drawn with a Half<br />

Indented start arrow, a Half Indented end<br />

arrow and a Doubled connector. The double<br />

line spacing can be edited in the arrow’s<br />

visual specifications.<br />

132<br />

Resonance Arrow - A resonance<br />

arrow can be drawn with a Full Indented<br />

start arrow, a Full Indented end arrow and a<br />

Solid connector.<br />

Electron Pair Shift - A shift of an<br />

electron pair can be drawn with no start<br />

connector. Then select the appropriate arc<br />

angle for the figure.<br />

Single Electron Shift - A shift of a<br />

single electron can be drawn with no start<br />

arrow, a Half Indented end arrow and a Solid<br />

Photon - A photon can be drawn<br />

with a Full end arrow and a Wavy connector.<br />

Bold - A bold arrow can be drawn<br />

with no start arrow, an Unfilled Full end<br />

arrow and a Doubled connector. The default<br />

arrowhead angle and length is not aesthetic<br />

for this type of arrow, so use the<br />

retrosynthetic preset in the presets group<br />

button to quickly access this type.<br />

Bezier Arrow Ideas<br />

In addition to straight and arced arrows, some<br />

pretty complex arrow shapes may be drawn<br />

with the bezier tools. The following are a few<br />

ideas. Just mimic the location of the control<br />

points to match them.

The Chute Arrow<br />

The Loop Arrow<br />

The Escalator Arrow<br />

The Hump Arrow<br />

The Zigzag Arrow<br />

Building Reactions<br />

Reaction figures can be drawn by placing<br />

structures next to arrow shapes to describe<br />

reaction schemes. This method will create a<br />

visual diagram for the reaction, but<br />

133<br />

underlying semantics will not exists. In other<br />

words, there is no formal definition of the<br />

reaction reactants or products.<br />

To address this, <strong>ChemDoodle</strong> provides a<br />

reaction building system to explicitly define<br />

reactions and reaction schemes.<br />

Implicitly<br />

To implicitly define a reaction, perform the<br />

1. Draw the arrow you would like to<br />

represent the reaction arrow.<br />

2. Draw any reactants and place them to the<br />

left of the arrow shape.<br />

3. Draw and products and place them to the<br />

right of the arrow shape.<br />

4. Select the arrow shape and all reactants<br />

and products using the selection tools.<br />

5. Press the Build Implied Reaction menu<br />

item in the Reaction menu to define the<br />

reaction.<br />

All structures with midpoints to the left of the<br />

arrow shape’s midpoint will be defined as<br />

reactants in the reaction while all structures<br />

with midpoints to the right of the arrow<br />

shape’s midpoint will be defined as products<br />

in the reaction.<br />

Explicitly<br />

To explicitly define a reaction, first select the<br />

arrow shape you would like to represent the<br />

reaction arrow using the selection tools. Then<br />

press the Edit Reaction… menu item in the<br />

Reaction menu open the Edit Reaction<br />

window for that selected arrow, as shown in<br />

Figure 7.3.<br />

The Edit Reaction window is a drag and<br />

drop interface. All molecules in the current<br />

document are displayed in the bottom tray,<br />

while the left and right trays correspond to the

constituent reactants and products<br />

respectively. Just drag and drop molecules<br />

from the bottom tray into the other two to set<br />

up the reaction. Once a molecule has been<br />

placed, it will be grayed out in the bottom<br />

tray and no longer selectable. You can transfer<br />

a placed molecule between the products and<br />

reactants by dragging the molecule between<br />

the side trays. You can remove a molecule<br />

from the reaction completely by dragging and<br />

dropping it back in the bottom tray.<br />

Press the Done button in the Reaction<br />

Builder window to set the reaction.<br />

Adding Reaction Conditions<br />

To add reaction conditions above and below<br />

the reaction arrow, first select the arrow shape<br />

you would like to add conditions to using the<br />

selection tools. Then press the Edit<br />

Reaction… menu item in the Reaction menu<br />

open the Edit Reaction window for that<br />

selected arrow, as shown in Figure 7.3.<br />

The Edit Reaction window contains two text<br />

editors for adding text above and below the<br />

reaction arrow. Click on a text area and type<br />

to add text. You can format the text using the<br />

text formatting tools above the text areas.<br />

Use the Symbols widget to input characters<br />

into the reaction condition text areas that are<br />

not present on the keyboard.<br />

Adding Plus Symbols<br />

After building a reaction, plus symbols will<br />

automatically be added at the midpoints<br />

between the constituent reactants and<br />

products. This feature can be turned off in the<br />

under the Reactions tab as shown in Figure<br />

7.2. Just uncheck the Automatically Place<br />

Pluses option.<br />

134<br />

If you want to add your own symbols, just use<br />

Text Area objects. Text Area objects are<br />

discussed in Chapter 4.<br />

Dissolving Reactions<br />

To dissolve a built reaction, just select the<br />

arrow the reaction is defined by with a<br />

selection tool, then select the Dissolve<br />

Reactions menu item in the Reaction menu.<br />

Cleaning Reactions<br />

To clean a reaction, perform the following<br />

1. Define the reaction implicitly or explicitly<br />

using the instructions in the previous<br />

2. Select the arrow shape of the reaction you<br />

would like to clean using the selection<br />

3. Press the Clean menu item in the<br />

Reaction menu to clean it.<br />

The reaction arrow will be horizontally<br />

leveled and resized to its text adhering to the<br />

Text Buffer visual specification. Then the<br />

reaction arrow and constituent molecules will<br />

be aligned according to their vertical centers<br />

and distributed horizontally with a buffer<br />

space. The entire reaction is then centered<br />

horizontally. If the reaction is too wide for the<br />

document, the reactants and arrow are then<br />

stacked above the products so that both<br />

groups are mutually centered as shown in<br />

Figure 7.1.<br />

Figure 7.1: A wide reaction that has been stacked.

The settings for determining how reactions<br />

are laid out can be set in the Preferences<br />

Reactions tab as shown in Figure 7.2.<br />

Figure 7.2: Reaction Visual Specifications<br />

You can adjust the double line spacing for<br />

equilibrium arrows, decide whether or not<br />

pluses should be automatically drawn, set the<br />

text buffer for conditions text and the buffer<br />

between constituent reaction objects. You can<br />

also set the default settings for arrowheads.<br />

<strong>ChemDoodle</strong> can clean multiple reactions at<br />

the same time, but currently can only properly<br />

clean discrete reactions. Cleaning complex<br />

reaction schemes with a given molecule<br />

defined in several different reactions may not<br />

produce desired results.<br />

Figure 7.3: Edit Reaction Window<br />

Reactants<br />

Tray<br />

Text Formatting Tools Reaction Condition Text Areas<br />

136<br />

Products<br />

<strong>ChemDoodle</strong> understands several<br />

spectroscopy and spectrometry techniques.<br />

These spectra can be loaded and edited to<br />

create graphics.<br />

spectra within <strong>ChemDoodle</strong>. It covers the<br />

• What types of spectra are supported.<br />

• How to load spectra.<br />

• How to save spectra.<br />

• How to simulate spectra.<br />

• How to edit spectra.<br />

Inserting Spectra<br />

Spectra can be read in from the JCAMP-DX<br />

format which is the standard defined by<br />

IUPAC. The currently supported JCAMP<br />

formats are for nuclear magnetic resonance<br />

spectroscopy (NMR), infrared spectroscopy<br />

(IR), mass spectrometry (MS) and chemical<br />

To insert spectra from JCAMP files, perform<br />

1. Select the Open... menu item in the File<br />

2. In the file chooser that appears, change<br />

the format filter on the bottom to IUPAC<br />

JCAMP-DX.<br />

3. Find the JCAMP file on your computer<br />

and select it with the file chooser.<br />

137<br />

4. Press the Open button at the bottom-right<br />

of the file chooser to load the spectrum.<br />

The spectrum will be loaded and displayed in<br />

the center of a new document.<br />

Spectra Types<br />

Both continuous and discontinuous spectra<br />

are supported. An example of NMR input is<br />

shown in Figure 8.1. An example of IR input<br />

is shown in Figure 8.2. An example of MS<br />

input is shown in figure 8.3.<br />

Figure 8.1: An NMR spectrum loaded from a<br />

JCAMP file.<br />

Figure 8.2: An IR spectrum loaded from a JCAMP<br />

Figure 8.3: An MS spectrum loaded from a<br />

JCAMP file.

Uninterpretable Spectra<br />

There are many different ways to represent<br />

JCAMP data. Therefore, <strong>ChemDoodle</strong> may<br />

not be able to understand a JCAMP file. If<br />

<strong>ChemDoodle</strong> was not able to interpret any<br />

spectra from the JCAMP file, you will see the<br />

message shown in Figure 8.4. Please send us<br />

the JCAMP file if you see this issue so that<br />

we may improve our compatibility with the<br />

format.<br />

Figure 8.4: <strong>ChemDoodle</strong> could not understand the<br />

spectrum in the JCAMP file.<br />

Saving Spectra<br />

<strong>ChemDoodle</strong> can output spectra in the<br />

following formats:<br />

1. <strong>ChemDoodle</strong> Documents {.icl, .icxml}<br />

2. IUPAC JCAMP-DX {.jdx, .dx}<br />

Be very careful when overwriting spectra to<br />

formats other than the <strong>ChemDoodle</strong><br />

Document. <strong>ChemDoodle</strong> only reads and<br />

writes the information that is relevant to the<br />

display of its graphics, and other data will be<br />

lost. If saving 3rd party spectra files for any<br />

reason, always save them as a new file.<br />

138<br />

Simulating Spectra<br />

<strong>ChemDoodle</strong> can simulate spectra for various<br />

techniques. Currently the following<br />

techniques are implemented:<br />

• 1 H Nuclear Magnetic Resonance<br />

Spectroscopy<br />

• 13 C Nuclear Magnetic Resonance<br />

• Mass Spectrum Parent Peak<br />

To simulate spectra, perform the following<br />

• Select a the chemical structure you would<br />

like to simulate a spectrum for using the<br />

• In the Spectrum menu, hover over the<br />

Generate submenu to view available<br />

techniques.<br />

• Click on the technique you would like to<br />

use.<br />

The generated spectrum will then appear on<br />

the Doodle Board. Some very intense<br />

simulations may take a few seconds to<br />

Editing Spectra<br />

Moving Spectra<br />

To move spectra, use a selection tool, either<br />

spectrum so an open hand mouse cursor<br />

appears and the two spectrum anchor<br />

points are drawn as shown in Figure 8.5.

the spectrum.<br />

Figure 8.5: Hovering over the spectrum will<br />

display its anchor points.<br />

Resizing Spectra<br />

To resize spectra, use a selection tool, either<br />

points are drawn as shown in Figure 8.5.<br />

two anchor points so that anchor point is<br />

filled in with an amber color.<br />

spectrum.<br />

Removing Spectra<br />

Spectra can be removed in a number of ways.<br />

139<br />

pointer over the spectrum so an open hand<br />

mouse cursor appears and the two spectrum<br />

8.5. Then press the backspace or delete key.<br />

pointer over the spectrum so the two<br />

spectrum anchor points are drawn. Then<br />

click with the mouse.<br />

• Select the spectrum using any of the<br />

selection tools. Then press the delete or<br />

backspace key.<br />

Expanding the Perspective<br />

Expanding the spectrum will fit the entire<br />

range and domain of the plot to the display<br />

rectangle. Perform the following steps.<br />

1. Use the selection tools to select any<br />

number of spectra.<br />

2. Click on the Expand Perspective menu<br />

item in the Spectrum menu.<br />

All selected spectra will have their<br />

perspectives expanded.<br />

Editing the Perspective<br />

Editing the perspective will allow you to<br />

modify how the plot fits in the viewing<br />

rectangle and will also allow you to edit the<br />

axes and title. These functions are presented<br />

in the Spectrum Edit window as shown in<br />

Figure 8.8.<br />

To change the plot domain, click and drag the<br />

sliders presented directly under the spectrum.<br />

The sliders display, from left to right, the<br />

minimum domain cutoff, the magnitude of the<br />

domain, and the maximum domain cutoff.<br />

You can also change the plot domain by<br />

clicking and dragging on the main spectrum<br />

panel. Click on the placement where you<br />

would like the domain to begin, then drag to<br />

where you would like the domain to end and

elease the mouse. A dotted grey line will<br />

display while dragging to show you the new<br />

domain. Additionally, holding the shift key<br />

while dragging on the spectrum will translate<br />

the domain of the spectrum.<br />

To change the range scale, click and drag the<br />

vertical slider directly to the right of the<br />

spectrum. You can also change the range scale<br />

by using the mouse scroll gesture on the main<br />

spectrum panel. Scroll up to increase the<br />

range scale and scroll down to decrease the<br />

range scale.<br />

To expand the perspective, double-click on<br />

the main spectrum panel.<br />

Changing the Title<br />

To change the title of the spectrum, in the<br />

Spectrum Edit window shown in Figure 8.8,<br />

click on the Title text field located at the<br />

bottom-left and type in the desired title.<br />

Changing the Axes<br />

There are several options for editing the axes.<br />

X-axis options are presented in the X Axis<br />

section of the Spectrum Edit window shown<br />

in Figure 8.8. You can choose to show or hide<br />

it by clicking the Show check box. You can<br />

choose whether to flip the domain or not by<br />

clicking the Flip check box. You can adjust<br />

the increments for the major and minor tick<br />

spacings using the Major Tick Spacing and<br />

Minor Tick Spacing drop down selections.<br />

The values in the drop down selections are<br />

exponents for base 10. You can change the<br />

title of the X-axis by clicking on the Unit text<br />

field and typing the desired title.<br />

Y-axis options are presented in the Y Axis<br />

it by clicking the Show check box. The<br />

Baseline Bump check box will positively<br />

offset the plot by a small value. You can<br />

140<br />

adjust the increment for the major tick<br />

spacing using the Tick Spacing drop down<br />

selection. The values in the drop down<br />

selection are exponents for base 10. You can<br />

change the title of the Y-axis by clicking on<br />

the Unit text field and typing the desired title.<br />

Showing Grids<br />

Grids can be displayed by performing the<br />

1. Hover the spectrum to display the grid<br />

over.<br />

2. Right-click on the spectrum and select the<br />

Format Spectrum... menu item.<br />

3. Scroll down to the Grid section and select<br />

the Show Grid checkbox.<br />

The color and thickness of the grid lines can<br />

also be set in this format window. A grid<br />

appears as shown in Figure 8.6.<br />

Figure 8.6: A grid is displayed over a spectrum.<br />

Showing Integration Lines<br />

Integration lines can be displayed by<br />

1. Hover the spectrum to display the<br />

integration line over.<br />

3. Scroll down to the Integration Line<br />

section and select the Show for NMR<br />

Spectra checkbox.

Field<br />

X Axis<br />

Options<br />

The color and thickness of the integration line<br />

can also be set in this format window. While<br />

intended for NMR spectra, integration lines<br />

can be added to any plot if desired. An<br />

integration line appears as shown in Figure<br />

8.7.<br />

Figure 8.7: An integration line is calculated over<br />

an NMR multiplet.<br />

Domain Sliders<br />

Main Spectrum Panel<br />

141<br />

Figure 8.8: The Spectrum Edit Window<br />

Range<br />

Slider<br />

Y Axis<br />

Chapter 9: Visual<br />

Specifications<br />

All graphics in <strong>ChemDoodle</strong> are fully<br />

customizable. Visual specifications for the<br />

graphics can be defined for the entire<br />

document, groups of objects or individual<br />

<strong>ChemDoodle</strong> document settings and visual<br />

specifications. It covers the following topics:<br />

• What are document settings, visual<br />

specifications and style sheets.<br />

• How to create and install custom Chemical<br />

Document Settings files.<br />

• Which graphic specifications can be<br />

customized.<br />

• How to customize the graphics of your<br />

figures.<br />

Document Settings<br />

Document settings are the variables that<br />

determine how graphics are rendered in a<br />

document. They are also called visual<br />

specifications when referring to an individual<br />

object. All together, they form the document’s<br />

style sheet.<br />

Style Sheets<br />

Style sheets can be named when creating<br />

formatted documents. The creation of<br />

formatted documents is discussed in Chapter<br />

1.<br />

In addition to creating or conforming<br />

<strong>ChemDoodle</strong> documents to the preset style<br />

142<br />

sheets, you can create your style sheets in<br />

<strong>ChemDoodle</strong> Document Settings files that can<br />

be used later. In the Preferences window,<br />

under the Visuals tab, under the Page tab,<br />

there is a Create Chemical Document<br />

Settings File button at the bottom of the<br />

options. Just perform the following steps to<br />

create a new <strong>ChemDoodle</strong> Document Settings<br />

file with your completed style sheet:<br />

1. Go through the all of the tabs under the<br />

Visuals tab in the Preferences window<br />

and set all of the values in the options to<br />

the preferred values.<br />

2. Click on the Create Chemical Document<br />

Settings File button in the Preferences<br />

Page tab.<br />

3. A new window will appear. Type in the<br />

name of the <strong>ChemDoodle</strong> Document<br />

Settings file.<br />

4. Choose three fonts to cascade through.<br />

This is important because different<br />

operating systems have different font sets<br />

and you may have selected a font not<br />

accessible on another operating system if<br />

you want to use it on that operating<br />

system. Serif and SansSerif will always be<br />

defined on all operating systems, so select<br />

those fonts in the third option as wild<br />

cards.<br />

5. Press the Ok button to save the Chemical<br />

Document Settings file.<br />

All Chemical Document Settings files are<br />

saved to the presets folder in the<br />

<strong>ChemDoodle</strong>Settings folder located in your<br />

folder. Any functions for using <strong>ChemDoodle</strong><br />

Document Settings files or for conforming<br />

documents will now list the new style sheet.

If you want to use Chemical Document<br />

Settings files provided by other users of<br />

<strong>ChemDoodle</strong>, just copy their file into the<br />

presets folder in the <strong>ChemDoodle</strong>Settings<br />

standard Documents folder. If you have<br />

<strong>ChemDoodle</strong> open while copying the file,<br />

close and restart it. They copied style sheet<br />

will then be accessible in <strong>ChemDoodle</strong>.<br />

When you globally change the visual<br />

specifications for a document, <strong>ChemDoodle</strong><br />

will ask you if you would like the changed<br />

settings to become the new default settings.<br />

There are two cases when this happens:<br />

1. After opening the Preferences window and<br />

changing visual specifications.<br />

2. After conforming a document using the<br />

Conform Document... menu item in the<br />

Edit menu.<br />

Just click Yes to set the changed settings as<br />

the default settings. Now when a new<br />

document is opened, the current default<br />

settings will be used to define the graphics.<br />

Alternatively, you may answer No to the<br />

question, and later, if you decide to indeed<br />

use the current document settings as the<br />

default document settings, then select the<br />

Save Document Settings... menu item in the<br />

Restore the Original Default Document<br />

Settings<br />

To restore the original default document<br />

settings, open the Preferences window and<br />

click the Restore Defaults button at the<br />

bottom of the window. Then close the<br />

window and select Yes when asked to set the<br />

current settings as the new default settings.<br />

143<br />

Individual Settings<br />

Setting Types<br />

All visual specifications provided in<br />

<strong>ChemDoodle</strong> are listed in the Preferences<br />

window under the Visuals tab as shown in<br />

Figure 9.1.<br />

Figure 9.1: Visual Specifications<br />

Each visual specification consists of a title to<br />

the left and a component to the right. These<br />

components include:<br />

• On/Off Choices - Click the check box to<br />

choose whether the specification is used or<br />

not. For example, the following check box<br />

will enable or disable the Clear Bond<br />

Overlaps visual specification.<br />

• Single Option Choices - Choose one of the<br />

options from a group exclusively to define<br />

it as the value to use for the specification.<br />

For example one option can be chosen from<br />

the following group set to determine the<br />

value for the Covalent Style specification.

• Number Sliders - Define a number value<br />

by clicking and dragging the slider or by<br />

explicitly typing the value in the text field.<br />

Some number components will be<br />

associated with a dimension drop down<br />

selection to easily set values in other units,<br />

such as centimeters instead of pixels. For<br />

example, slide the slider or type a value into<br />

the text box of the following number<br />

component to define the value for the Bond<br />

Line Thickness specification.<br />

NOTE: Some number components define<br />

angles, and an angle swivel will be<br />

provided instead of a slider. Click and drag<br />

to the angle you want on the swivel to set<br />

the angle.<br />

• Color Buttons - Click on color buttons and<br />

use the color selection window that appears<br />

to select a new color. For example, the<br />

following color button will determine bond<br />

line color.<br />

All objects drawn after changing the visual<br />

specifications in the Preferences window will<br />

conform to the new specifications. All visual<br />

specifications are listed in the following<br />

sections.<br />

Page<br />

144<br />

Background - A color button for the<br />

background color of the document.<br />

Dimensions<br />

Page Size - A specialized component for<br />

setting the page size. Set the width and height<br />

by typing in the text boxes or select a<br />

standard size from the drop down selections.<br />

The button to the left of the text fields will<br />

swap the width and height.<br />

Ångströms / Bond Length - A number slider<br />

for setting the ratio between Ångströms and<br />

the Bond Length specification in pixels. This<br />

specification is useful when finding covalent<br />

bonds and when reading in files with<br />

Ångström coordinates.<br />

Margins<br />

Top - Type in the value for the top page<br />

margin.<br />

Left - Type in the value for the left page<br />

Bottom - Type in the value for the bottom<br />

page margin.<br />

Right - Type in the value for the right page<br />

Text - A color button for the text color of atom<br />

labels.<br />

Buffer Space - A number slider to set the<br />

amount of whitespace between atom text and<br />

the bonds connected to that atom.

Vertical Alignment - A number slider to<br />

control the baseline for rendering text relative<br />

to the center of the atom.<br />

Token Stacking - A single option choice to set<br />

whether atom labels will stack all tokens,<br />

stack only the second token or will never<br />

stack tokens.<br />

Stack Lone/Terminal - An on/off choice to set<br />

whether lone and terminal atoms will stack<br />

their label tokens.<br />

Horizontal Spacing - A number slider to set<br />

the horizontal whitespace between each label<br />

token.<br />

Vertical Spacing - A number slider to set the<br />

vertical whitespace between each label token.<br />

Subscript Reduction - A number slider to set<br />

the size of subscript font relative to the atom<br />

label font.<br />

Subscripts Shift - A number slider to set the<br />

magnitude of the offset from the atom label<br />

font baseline to draw subscripts from.<br />

Superscript Reduction - A number slider to set<br />

the size of superscript font relative to the<br />

atom label font.<br />

Superscript Shift - A number slider to set the<br />

font ascent to draw superscripts from.<br />

Add as - A single option choice to determine<br />

if Hydrogens are added as text to labels or as<br />

atoms with bonds attached.<br />

Add to Carbons - A single option choice to set<br />

how Hydrogens add to Carbons; Hydrogens<br />

can always add to Carbons, can only add to<br />

unsaturated Carbons or will never add to<br />

Carbons.<br />

145<br />

Show Implicit Hydrogens - An on/off choice<br />

to set whether implicit hydrogens are<br />

automatically rendered or not.<br />

Carbons<br />

Display Carbon Labels - A single option<br />

choice to set if Carbon labels display always,<br />

only on lone and hidden Carbons, only on<br />

hidden Carbons, or never show.<br />

Hidden Carbon Angle - An angle number<br />

slider for setting the hidden Carbon angle.<br />

The hidden Carbon angle is the deviation<br />

from 180° between bonds on a Carbon atom<br />

that only has 2 bonds attached to it.<br />

Show Terminal Labels - An on/off choice to<br />

set whether terminal carbon labels are<br />

displayed or not.<br />

Use Circles - An on/off choice for controlling<br />

if element labels are rendered as text or as<br />

circles.<br />

Coloring - A single option choice for<br />

determining whether user chosen colors, CPK<br />

colors, Jmol colors, or PyMOL colors are<br />

used for element labels.<br />

Radius Convention - A single option choice to<br />

control if circles are rendered with a constant<br />

radius, the atomic radius of their element, the<br />

covalent radius of their element or the van der<br />

Waals radius of their element.<br />

Constant Radius - A number slider to set the<br />

constant radius to render element atom circles<br />

with.<br />

Border Width - A number slider to set the<br />

width of the circle outlines when atoms are<br />

rendered as circles.

Fill/Text - A color button for the text color of<br />

attribute labels and graphics.<br />

Logistics<br />

Allowed Distance - A number slider to control<br />

the maximum distance an attribute can be<br />

translated away from the object it defines.<br />

Font Size Reduction - A number slider to<br />

control the font size reduction of attribute text<br />

from its defined font. This is so attribute text<br />

is smaller than the text of the object is<br />

associated with.<br />

Surround with a Circle - An on/off choice to<br />

set whether charges are rendered with a circle<br />

around them.<br />

Diameter - A number slider to set the<br />

diameter of rendered electrons.<br />

Separation - A number slider to set the<br />

separation distance between electrons or<br />

electrons and charges in paired attributes such<br />

as electron pairs and radical cation symbols.<br />

Fill - A color button for the bond line color.<br />

Use Gradient - An on/off choice for rendering<br />

bonds with a gradient between the constituent<br />

atom colors.<br />

146<br />

Split Color - An on/off choice for rendering<br />

bonds that will split the bond color between<br />

the constituent atom colors.<br />

Bond Length - A number slider to define the<br />

optimal length for bonds. This affects<br />

anything that depends on bond length<br />

including drawing bonds and cleaning<br />

Bond Line Thickness - A number slider to<br />

define the width of bond lines.<br />

Bold Bond Thickness - A number slider to<br />

define the width of bold bonds.<br />

Wedge Thickness - A number slider to define<br />

the width of the wide end of wedge bonds.<br />

Unsaturated Spacing (Absolute) - A number<br />

slider to define the spacing between bond<br />

lines in higher order bonds.<br />

Unsaturated Spacing (Relative) - A number<br />

lines in higher order bonds, but relative to the<br />

length of the bond.<br />

Clip Angle - An angle number slider to define<br />

the angle at which non-symmetrical double<br />

bonds will clip the second bond line.<br />

Hash Width - A number slider to define the<br />

width of hashes in bonds rendered with a<br />

hash.<br />

Hash Spacing - A number slider to define the<br />

width the spacing between hashes in bonds<br />

rendered with a hash.<br />

Hash Offset - A number slider to define the<br />

translation from the origin of hashes in bonds<br />

Arrow Length - A number slider to define the<br />

arrowhead length of covalent bonds.

Arrow Angle - An angle number slider to<br />

define the arrowhead angle of covalent bonds.<br />

Wavy Length - A number slider to define the<br />

amplitude of wavy bonds.<br />

Zigzag Length - A number slider to define the<br />

amplitude of zigzag bonds.<br />

Stroke<br />

Style - A drop down selection to set the<br />

default bond stroke style.<br />

Texture - A number slider for setting the<br />

magnitude of texture in stroke styles. For<br />

instance, a higher number will cause Bristle<br />

strokes to look more bristled.<br />

Bond Ends - A single option choice to set how<br />

bond ends are rendered; with no cap, a round<br />

cap or a square cap.<br />

Join Bond Connections - An on/off choice to<br />

define whether the rendering engine will<br />

merge bonds end together for more aesthetic<br />

graphics.<br />

Double Bond Asymmetry - A single option<br />

choice to set when double bonds will be<br />

rendered asymmetrically; always, when<br />

between 2 Carbons, only in rings or never.<br />

Heteroatom Retraction - An on/off choice that<br />

defines whether asymmetric double bonds<br />

will retract the second line from an atom or<br />

not based on that atom being a heteroatom.<br />

Terminal Retraction - An on/off choice that<br />

defines whether terminal double bonds will<br />

retract the second line from a terminal atom<br />

or not.<br />

Unsaturated Spacing - A single option choice<br />

for setting whether unsaturated bonds are<br />

147<br />

rendered with an absolute spacing or with a<br />

relative spacing between bond lines.<br />

Changing this specification will place the<br />

corresponding visual specification in the<br />

Settings section.<br />

Even Hashes - An on/off choice to determine<br />

if the Hash Width and Hash Offset<br />

specifications only affect Bold Dashed and<br />

Recessed bonds.<br />

Clear Bond Overlaps - An on/off choice to<br />

determine if an overlapped bond will erase<br />

the section of overlap.<br />

Overlap Clear Width - A number slider to<br />

define the length of the bond that is erased<br />

when overlapped.<br />

Covalent Style - A single option choice to set<br />

if covalent bonds are rendered as Polar<br />

Covalent bonds with a slash in the stroke, or<br />

as Coordinate Covalent bonds.<br />

Indent Arrow Bond - An on/off choice to set if<br />

covalent bond arrowheads are indented.<br />

Fused<br />

Favor Aromatics - An on/off choice to force<br />

double bonds in fused systems to face<br />

aromatic rings over non-aromatic rings.<br />

Double Bond Orientation - A single option<br />

choice to determine if double bonds in fused<br />

ring systems will face larger rings or smaller<br />

Aromatics<br />

Use Circles - An on/off choice to render<br />

aromatics with a circle instead of in Kekulé<br />

Circle Radius - An number slider to define the<br />

diameter of the aromatic circle relative to the<br />

dimensions of the ring.<br />

Layout<br />

Double Line Spacing - A number slider to<br />

define the spacing between the lines in<br />

equilibrium arrows.<br />

Automatically Place Plusses - An on off<br />

choice to set whether reactions automatically<br />

place plusses between constituent reactants<br />

and products.<br />

Text Buffer - A number slider to define the<br />

buffer between the text set as the reaction<br />

conditions and the ends of the associated<br />

arrow when the text is centered. This value<br />

times 2 will determine the default length that<br />

arrows without associated text are cleaned to<br />

when cleaning reactions.<br />

Constituent Buffer - A number slider to define<br />

the spacing between reaction constituents<br />

Arrowheads<br />

Length - A number slider to define the<br />

arrowhead length of arrow shapes.<br />

Angle - An angle number slider to define the<br />

arrowhead angle of arrow shapes.<br />

Borders and Lines - A color button for the<br />

lines and borders of shapes.<br />

Fill - A color button for the fill color of<br />

shapes.<br />

Text - A color button for the text color of<br />

148<br />

Shapes Add - A single option choice to set<br />

whether shapes are drawn in front of atoms or<br />

behind atoms.<br />

Strokes<br />

Thickness - A number slider to define the<br />

width of solid strokes in shapes.<br />

width of hashes in shapes rendered with a<br />

width the spacing between hashes in shapes<br />

translation from the origin of hashes in shapes<br />

Shadows<br />

Translation - A number slider to define the<br />

distance from the shape the shadow should be<br />

rendered.<br />

angle in relation to the shape to place the<br />

shadow.<br />

Opacity - A number slider to define the<br />

transparency of shadows.<br />

Wideness - A number slider to define the<br />

width of bracket lips relative to the standard<br />

size.<br />

Length Multiplier - A number slider to define<br />

the default extent of orbitals in bond lengths.<br />

So if the length multiplier is 1, then all

orbitals placed will have a length of 1 bond<br />

length.<br />

Stroke Shaded Lobes - An on/off choice to set<br />

whether shaded lobes in orbitals will also be<br />

outlined.<br />

Paths<br />

Close - An on/off choice to set if paths are<br />

closed by default.<br />

Rounded Arc Width - A number slider to<br />

define the width of the corner arcs in rounded<br />

rectangles.<br />

Rounded Arc Height - A number slider to<br />

define the height of the corner arcs in rounded<br />

Show Major Ticks - An on/off choice to set if<br />

major ticks are shown in rulers.<br />

Close - An on/off choice to set if minor ticks<br />

are shown in rulers.<br />

Unit - A drop down selection to set the default<br />

units of ruler objects.<br />

Spectra<br />

Plots - A color button for the spectrum plots.<br />

Grids - A color button for the spectrum grids.<br />

Integration Lines - A color button for the<br />

spectrum integration lines.<br />

Plot Strokes<br />

width of solid strokes in spectrum plots.<br />

149<br />

Hash - An on/off choice to render spectrum<br />

plots with a hashed stroke.<br />

width of hashes in spectrum plots rendered<br />

with a hash.<br />

width the spacing between hashes in spectrum<br />

plots rendered with a hash.<br />

translation from the origin of hashes in<br />

spectrum plots rendered with a hash.<br />

Grids<br />

Show - A on/off switch to set whether<br />

spectrum grids are shown by default.<br />

Thickness - A number slider to define the line<br />

thickness of spectrum grids.<br />

Integration Lines<br />

spectrum integration lines are shown by<br />

default.<br />

thickness of spectrum integration lines.<br />

Editing Visual Specifications<br />

For Single Objects<br />

To edit the visual specifications of a single<br />

object, perform the following steps:<br />

1. Switch to a selection tool and make sure<br />

the current selection is empty.<br />

2. Hover the mouse pointer over the object<br />

of which the visual specifications are to<br />

be changed.<br />

3. Right-click on the object and select the<br />

Format Object... menu item or doubleclick<br />

on the object.

4. Change the visual specifications in the<br />

window that appears. You will see the<br />

graphics update in real-time on the<br />

5. Click the Done button in the window to<br />

set the changes.<br />

You can also press the Cancel button to<br />

cancel all changes.<br />

For a Group of Objects<br />

To edit the visual specifications of a group of<br />

objects, perform the following steps:<br />

1. Switch to a selection tool.<br />

2. Select all of the content of which the<br />

visual specifications are to be changed.<br />

3. Open the Preferences window and click<br />

on the Visuals tab.<br />

4. Change all the visual specifications in the<br />

Visuals tab to your preference. You will<br />

see the graphics update in real-time on the<br />

5. Click the Done button in the Preferences<br />

window to set the changes.<br />

Current Style Sheet<br />

To conform a group of objects to the current<br />

style sheet, perform the following steps:<br />

3. Press the Conform to Document<br />

Settings menu item in the Content menu.<br />

All content will conform to the visual<br />

specifications defined in the document’s style<br />

sheet. This function will also change fonts<br />

150<br />

and scale structures to match the defined bond<br />

Different Style Sheet<br />

To conform the entire document to a different<br />

1. Press the Conform Document... menu<br />

2. In the window that appears, choose the<br />

style sheet you prefer from the drop down<br />

3. You will be asked if you would like to<br />

conform atom text by changing fonts;<br />

choose Yes or No.<br />

4. If the bond length has changed, you will<br />

be asked if you would like the structures<br />

to be scaled to match the new value;<br />

The entire document will now conform to<br />

your choice of style sheet.<br />

3D Graphics<br />

<strong>ChemDoodle</strong> is a tool for generating 2D<br />

graphics. However, <strong>ChemDoodle</strong> handles 3D<br />

input and you can create orthographic 2D<br />

scenes of your 3D data. That being said, with<br />

all of the bond types and atom labels<br />

showing, the figure may not be very aesthetic.<br />

To create better looking 2D orthographic<br />

scenes of your 3D data, perform the following<br />

suggestions.<br />

• Change all bonds to plain single bonds, and<br />

include double bonds if necessary.<br />

• Change the visual specifications to show all<br />

atoms as circles instead of as text labels.<br />

• Change the visual specifications to render<br />

atoms with their Jmol colors.

• Increase the bond line width visual<br />

specification.<br />

bonds with a gradient between their<br />

• Increase the bond overlap buffer visual<br />

specification to clearly show bond overlaps.<br />

We have provided a sample style sheet to<br />

quickly create 2D orthographic scenes from<br />

3D data that can be accessed when creating a<br />

formatted document or conforming a given<br />

document as is described in the previous<br />

section called Orthographic 3D Scene.<br />

Bond Stroke Styles<br />

<strong>ChemDoodle</strong> provides several bond stroke<br />

styles to casually style your structures for<br />

presentations, posters and more casual media.<br />

To change bond stroke styles, select the bonds<br />

to be changed with a selection tool and use<br />

the Stroke toolbar.<br />

The default bond line stroke width is 1.2<br />

pixels. This is not sufficient to see some<br />

stroke styles and the value will need to be<br />

increased. Other stroke styles, such as the<br />

Brush style, will not display well for really<br />

short bonds and structures rendered with<br />

those styles should be expanded.<br />

The following bond stroke styles are currently<br />

provided:<br />

• Basic -<br />

• Bristle -<br />

151<br />

• Brush -<br />

• Calligraphy -<br />

• Charcoal -<br />

• Scribble -<br />

• Wobble -<br />

Advanced Document<br />

Rendering<br />

The graphics defined by <strong>ChemDoodle</strong> are<br />

always exact and based on very precise<br />

coordinates. However, the screen that you use<br />

to display <strong>ChemDoodle</strong> and bitmap images<br />

that are output will need to define the<br />

graphics in a much less precise resolution.<br />

Algorithms have been developed to minimize<br />

the perception of this loss of resolution and<br />

<strong>ChemDoodle</strong> provides full access to control<br />

how the graphics are rendered. Note that<br />

scalable vector graphics are also exact and<br />

based on precise coordinates and are therefore<br />

resolution-less. The following settings will<br />

only affect the display of graphics on your<br />

computer monitor and the output of bitmap<br />

graphics; scalable vector graphics will not be<br />

Advanced document rendering settings can be<br />

defined in the Preferences window under the<br />

Advanced tab.<br />

Anti-Aliasing<br />

Anti-aliasing controls whether or not the<br />

geometry rendering methods will attempt to<br />

reduce aliasing artifacts along the edges of<br />

shapes. Anti-aliasing is enabled by default.<br />

A typical antialiasing algorithm works by<br />

blending the existing colors of the pixels<br />

along the boundary of a shape with the<br />

requested fill paint according to the estimated<br />

partial pixel coverage of the shape. This<br />

function reduce the appearance of jagged<br />

edges. Figure 9.2 is a structure rendered<br />

without anti-aliasing enabled, while Figure<br />

9.3 is a structure rendered with anti-aliasing<br />

enabled.<br />

Figure 9.2: Anti-aliasing is disabled.<br />

Figure 9.3: Anti-aliasing is enabled.<br />

152<br />

Font Fractional Metrics<br />

Font fractional metrics controls whether the<br />

positioning of individual character glyphs<br />

takes into account the sub-pixel accuracy of<br />

the scaled character advances of the font or<br />

whether such advance vectors are rounded to<br />

an integer number of whole device pixels.<br />

This hint only recommends how much<br />

accuracy should be used to position the<br />

glyphs and does not specify or recommend<br />

whether or not the actual rasterization or pixel<br />

bounds of the glyph should be modified to<br />

match. Font fractional metrics are disabled by<br />

default to produce better graphics for bitmap<br />

images and for the computer screen. In<br />

<strong>ChemDoodle</strong>, this property does not affect<br />

printing. Since printing is usually with a high<br />

resolution device, <strong>ChemDoodle</strong> will always<br />

enable font fractional metrics for printer<br />

rendering.<br />

Rendering text to a low resolution device like<br />

a screen will necessarily involve a number of<br />

rounding operations as the high quality and<br />

very precise definition of the shape and<br />

metrics of the character glyphs must be<br />

matched to discrete device pixels. Ideally the<br />

positioning of glyphs during text layout<br />

would be calculated by scaling the design

metrics in the font according to the point size,<br />

but then the scaled advance width will not<br />

necessarily be an integer number of pixels. If<br />

the glyphs are positioned with sub-pixel<br />

accuracy according to these scaled design<br />

metrics then the rasterization would ideally<br />

need to be adjusted for each possible subpixel<br />

Unfortunately, scaling each glyph customized<br />

to its exact subpixel origin during text layout<br />

would be prohibitively expensive so a<br />

simplified system based on integer device<br />

positions is typically used to lay out the text.<br />

The rasterization of the glyph and the scaled<br />

advance width are both adjusted together to<br />

yield text that looks good at device resolution<br />

and has consistent integer pixel distances<br />

between glyphs that help the glyphs look<br />

uniformly and consistently spaced and<br />

readable.<br />

This process of rounding advance widths for<br />

rasterized glyphs to integer distances means<br />

that the character density and the overall<br />

length of a string of text will be different from<br />

the theoretical design measurements due to<br />

the accumulation of a series of small<br />

differences in the adjusted widths of each<br />

glyph. The specific differences will be<br />

different for each glyph, some being wider<br />

and some being narrower than their<br />

theoretical design measurements. Thus the<br />

overall difference in character density and<br />

length will vary by a number of factors<br />

including the font, the specific device<br />

resolution being targeted, and the glyphs<br />

chosen to represent the string being rendered.<br />

As a result, rendering the same string at<br />

multiple device resolutions can yield widely<br />

varying metrics for whole strings.<br />

When font fractional metrics are enabled, the<br />

true font design metrics are scaled by the<br />

153<br />

point size and used for layout with sub-pixel<br />

accuracy. The average density of glyphs and<br />

total length of a long string of characters will<br />

therefore more closely match the theoretical<br />

design of the font, but readability may be<br />

affected since individual pairs of characters<br />

may not always appear to be consistent<br />

distances apart depending on how the subpixel<br />

accumulation of the glyph origins<br />

meshes with the device pixel grid. Enabling<br />

this hint may be desirable when text layout is<br />

being performed that must be consistent<br />

across a wide variety of output resolutions.<br />

Specifically, this hint may be desirable in<br />

situations where the layout of text is being<br />

previewed on a low resolution device like a<br />

screen for output that will eventually be<br />

rendered on a high resolution printer or<br />

typesetting device.<br />

When disabled, the scaled design metrics are<br />

rounded or adjusted to integer distances for<br />

layout. The distances between any specific<br />

pair of glyphs will be more uniform on the<br />

device, but the density and total length of<br />

long strings may no longer match the<br />

theoretical intentions of the font designer.<br />

Disabling this hint will typically produce<br />

more readable results on low resolution<br />

devices like computer monitors.<br />

Dithering<br />

Dithering controls how closely to<br />

approximate a color when storing into a<br />

destination with limited color resolution.<br />

Dithering is enabled by default<br />

Some rendering destinations may support a<br />

limited number of color choices which may<br />

not be able to accurately represent the full<br />

spectrum of colors that can result during<br />

rendering operations. For such a destination,<br />

dithering controls whether rendering is done<br />

with a flat solid fill of a single pixel value

which is the closest supported color to what<br />

was requested, or whether shapes will be<br />

filled with a pattern of colors which combine<br />

to better approximate that color.<br />

Rendering Algorithm<br />

This setting provides a high level<br />

recommendation as to whether to bias<br />

algorithm choices more for speed or quality<br />

when evaluating tradeoffs. This hint could be<br />

consulted for any rendering or image<br />

manipulation operation, but decisions will<br />

usually honor other, more specific settings in<br />

preference to this setting. The rendering<br />

algorithm is set to Quality by default.<br />

Alpha Interpolation Algorithm<br />

The alpha interpolation setting is a general<br />

setting that provides a high level<br />

recommendation as to whether to bias alpha<br />

blending algorithm choices more for speed or<br />

quality when evaluating tradeoffs. The alpha<br />

interpolation algorithm is set to Quality by<br />

This setting controls the choice of alpha<br />

blending calculations that sacrifice some<br />

precision to use fast lookup tables or lower<br />

precision SIMD instructions. This hint could<br />

also control whether or not the color and<br />

alpha values are converted into a linear color<br />

space during the calculations for a more linear<br />

visual effect at the expense of additional perpixel<br />

calculations.<br />

Color Rendering Algorithm<br />

The color rendering algorithm controls the<br />

accuracy of approximation and conversion<br />

when storing colors into a destination image<br />

or surface. The color rendering algorithm is<br />

set to Quality by default.<br />

When a rendering or image manipulation<br />

operation produces a color value that must be<br />

stored into a destination, it must first convert<br />

154<br />

that color into a form suitable for storing into<br />

the destination image or surface. Minimally,<br />

the color components must be converted to bit<br />

representations and ordered in the correct<br />

order or an index into a color lookup table<br />

must be chosen before the data can be stored<br />

into the destination memory. Without this<br />

minimal conversion, the data in the<br />

destination would likely represent random,<br />

incorrect or possibly even unsupported<br />

values. Algorithms to quickly convert the<br />

results of rendering operations into the color<br />

format of most common destinations are well<br />

known and fairly optimal to execute.<br />

Simply performing the most basic color<br />

format conversion to store colors into a<br />

destination can potentially ignore a difference<br />

in the calibration of the color space of the<br />

source and destination or other factors such as<br />

the linearity of the gamma correction. Unless<br />

the source and destination color space are<br />

identical, to correctly perform a rendering<br />

operation with the most care taken for the<br />

accuracy of the colors being represented, the<br />

source colors should be converted to a device<br />

independent color space and the results then<br />

converted back to the destination color space.<br />

Furthermore, if calculations such as the<br />

blending of multiple source colors are to be<br />

performed during the rendering operation,<br />

greater visual clarity can be achieved if the<br />

intermediate device independent color space<br />

is chosen to have a linear relationship<br />

between the values being calculated and the<br />

perception of the human eye to the response<br />

curves of the output device.<br />

Stroke Control<br />

Stroke control defines whether a rendering<br />

implementation should or is allowed to<br />

modify the geometry of rendered shapes for<br />

various purposes. Stroke control is set to Best<br />

Compromise by default.

Some implementations may be able to use an<br />

optimized platform rendering library which<br />

may be faster than traditional software<br />

rendering algorithms on a given platform, but<br />

which may also not support floating point<br />

coordinates. Some implementations may also<br />

have sophisticated algorithms which perturb<br />

the coordinates of a path so that wide lines<br />

appear more uniform in width and spacing.<br />

If an implementation performs any type of<br />

modification or "normalization" of a path, it<br />

should never move the coordinates by more<br />

than half a pixel in any direction.<br />

When stroke control is set to Normalize,<br />

geometry will be altered to improve<br />

uniformity or spacing of lines and overall<br />

aesthetics. The compromise is that geometry<br />

will be offset to fit to the pixel resolution of<br />

the rendering device. A consequence is that<br />

lines that are parallel may not appear exactly<br />

parallel, such as in double bonds.<br />

When stroke control is set to Pure, geometry<br />

will be left unmodified and rendered with<br />

sub-pixel accuracy. There will be noticeable<br />

lightness and bolding in straight lines that are<br />

vertical or horizontal.<br />

Figure 9.5 shows a rectangle and structure<br />

displayed with stroke control set to Pure,<br />

while Figure 9.6 shows the same objects with<br />

stroke control set to Normalize.<br />

Figure 9.5: A structure and rectangle rendered<br />

with stroke control set to Pure. Notice the bolding<br />

and blurring of the horizontal and vertical lines.<br />

155<br />

Figure 9.6: A structure and rectangle rendered<br />

with stroke control set to Normalize. Notice that<br />

parallel lines are not preserved.<br />

For even better graphics, a third option is<br />

provided called Best Compromise. This<br />

option will use pure stroke control for all<br />

chemical structures. All other shapes will first<br />

be analyzed for vertical and horizontal lines,<br />

and any found will be rendered with<br />

normalized stroke control while the rest of the<br />

graphics will be rendered with pure stroke<br />

Image Scaling<br />

Image scaling controls how image pixels are<br />

filtered or resampled during an image<br />

rendering operation. This will have noticeable<br />

affects on images that are not rendered in<br />

their natural scale. The image scaling<br />

algorithm is set to Progressive Bilinear by<br />

Implicitly images are defined to provide color<br />

samples at integer coordinate locations. When<br />

images are rendered upright with no scaling<br />

onto a destination, the choice of which image<br />

pixels map to which device pixels is obvious<br />

and the samples at the integer coordinate<br />

locations in the image are transferred to the<br />

pixels at the corresponding integer locations<br />

on the device pixel grid one for one. When<br />

images are rendered in a scaled, rotated, or<br />

otherwise transformed coordinate system,<br />

then the mapping of device pixel coordinates<br />

back to the image can raise the question of<br />

what color sample to use for the continuous<br />

coordinates that lie between the integer<br />

locations of the provided image samples.<br />

Interpolation algorithms define functions<br />

which provide a color sample for any<br />

continuous coordinate in an image based on<br />

the color samples at the surrounding integer<br />

coordinates.<br />

Progressive Bilinear is better than Bicubic<br />

which is better than Bilinear which is better<br />

than Nearest-Neighbor at producing<br />

reasonable graphics of stretched or shrunken<br />

bitmap images. The better the algorithm used,<br />

the worse the runtime will get.<br />

Chapter 10:<br />

Sharing<br />

Information<br />

<strong>ChemDoodle</strong> has advanced functions for<br />

interacting with other applications on your<br />

computer. This is essential for inputting<br />

graphics into word processors or for<br />

transferring chemical data into modeling<br />

applications.<br />

<strong>ChemDoodle</strong>’s system clipboard capabilities.<br />

It covers the following topics:<br />

• Introducing the system clipboard.<br />

• How to copy data and graphics from<br />

<strong>ChemDoodle</strong> into other applications.<br />

• How to copy data and graphics from other<br />

applications into <strong>ChemDoodle</strong>.<br />

• What types of data can be transferred.<br />

• What image formats are supported.<br />

• How to save images.<br />

• How to insert images.<br />

• How to take advantage of round trip editing.<br />

The System Clipboard<br />

The system clipboard is a construct of the<br />

operating system that contains data for<br />

sharing between applications. Only one<br />

application can place data on the system<br />

clipboard at a time. Other applications can<br />

then see that data and load it. This system<br />

forms the basis for copy and paste<br />

157<br />

functionality. <strong>ChemDoodle</strong> will place a wide<br />

range of chemical and graphic data on the<br />

system clipboard as well as associate that data<br />

with the correct MIME types for other<br />

applications to use.<br />

MIME Types<br />

A MIME type is an identifier to define the<br />

data it is associated with. For example, a<br />

structure can be represented in MDL<br />

MOLFile format. The MDL MOLFile format<br />

is a plain text format and can be associated<br />

with the MIME type, text/plain. However, this<br />

is a very generic description and other<br />

applications will only recognize it as plain<br />

text, rather than as a chemical structure.<br />

Therefore a different MIME type is associated<br />

with this data, chemical/x-mdl-molfile, to<br />

define it as a structure in the MDL MOLFile<br />

format. In this manner, other applications will<br />

recognize this data as a chemical.<br />

<strong>ChemDoodle</strong> follows the MIME standards put<br />

forth by the Chemical MIME Project (http://<br /> This should be<br />

regarded as the standard, however, many<br />

chemical software developers do not follow<br />

these rules, thereby causing issues when<br />

transferring data between chemical<br />

Additionally, since many items can be present<br />

on the system clipboard at once, applications<br />

may paste a certain data type by default that<br />

may not be the data you want to paste. For<br />

instance, Microsoft Word can paste both text<br />

data types and image data types. If both are<br />

present on the system clipboard, Microsoft<br />

Word will automatically select the text data<br />

type when pasting, even if you wanted the<br />

image to be pasted. There can even be<br />

different image types, confusing the situation<br />

Therefore, <strong>ChemDoodle</strong> allows you to define<br />

how data and which data is placed on the<br />

system clipboard to work with the<br />

applications that you use.<br />

Clipboard Settings<br />

<strong>ChemDoodle</strong> can transfer data to almost any<br />

application that has been created. But it is<br />

impossible for <strong>ChemDoodle</strong> to determine<br />

which data should be transferred. Therefore,<br />

you need to set the appropriate Copy Settings<br />

to make sure any ambiguities are resolved<br />

with the application you are pasting to. Copy<br />

Settings can be set in the Preferences<br />

window under the Advanced tab as shown in<br />

Figure 10.1. These settings will allow you to<br />

explicitly control what data <strong>ChemDoodle</strong> will<br />

transfer to other applications.<br />

Figure 10.1: Copy Settings<br />

There are three main types of data that may<br />

be transferred:<br />

• Text Types - Contains a line or lines of text<br />

that will be interpretable by other<br />

applications. Some chemical formats are<br />

also listed here to be pasted as text into<br />

other applications. All text data will be<br />

interpreted as text by other applications and<br />

158<br />

any chemical significance will be lost. Only<br />

one text data type will be placed on the<br />

system clipboard at a time.<br />

• Image Types - This group contains both<br />

bitmap and vector images. Bitmap images<br />

are not scalable in resolution. Vector images<br />

are much more versatile and will remain<br />

crisp and clear regardless of resizing or<br />

transformation. Bitmap and vector images<br />

are discussed in detail in the next section.<br />

• Chemical Types - Chemical types include<br />

structure information. Only chemical<br />

programs will see these.<br />

Therefore, to work with other applications,<br />

first decide what type of data you would like<br />

to transfer and what types of data the other<br />

application accepts. Then set the appropriate<br />

copy settings to continue.<br />

Scalable Vector Graphics<br />

There are two types of images, bitmap and<br />

vector. Bitmap images are traditional images<br />

and define a rectangle of pixels and their<br />

colors, while vector images define drawing<br />

instructions for recreating it. When resizing,<br />

the bitmap will become blurry, pixelated and<br />

lose its quality while the vector image will<br />

remain crisp and clear. Figure 10.2 shows a<br />

bitmap image of a structure, while Figure<br />

10.3 shows a vector image of the same<br />

structure. Both were created by <strong>ChemDoodle</strong>.<br />

Try zooming in on both images using your<br />

PDF reader and you can see the difference in<br />

quality for yourself.<br />

Figure 10.2: A Bitmap Image

Figure 10.3: A Vector Image<br />

Bitmap images will suffer from this issue<br />

with any change of resolution, including<br />

printing to a printer. Because of this, we<br />

recommend you insert vector images into<br />

your documents. The only downside to using<br />

vector graphics is that some programs may<br />

not support them. <strong>ChemDoodle</strong> compatibility<br />

with 3rd party applications is discussed in<br />

Appendix C.<br />

If you must use a bitmap image, then<br />

<strong>ChemDoodle</strong> provides high resolution options<br />

(such as scaling and DPI control) for a few<br />

bitmap formats as discussed in the Image<br />

Output Options section later in this chapter.<br />

159<br />

Copying Data to Other<br />

Applications<br />

Using the Copy Function<br />

To copy data from <strong>ChemDoodle</strong> into other<br />

applications, perform the following steps:<br />

1. Determine which data you would like to<br />

transfer and the types of data that the<br />

other application can accept and configure<br />

the copy settings in the Preferences<br />

window under the Advanced tab<br />

accordingly.<br />

2. Select the objects on the Doodle Board<br />

that you would like to copy using the<br />

content selection tools.<br />

3. Click on the Copy menu item in the Edit<br />

menu or press its menu accelerator<br />

keyboard shortcut which is ctrl-C<br />

(command-C on Mac OS X).<br />

4. Use the paste function present in the other<br />

application to paste the content. If the<br />

other application has a Paste Special...<br />

function, you may use that to specify<br />

which data type to paste.<br />

Using the Copy As Function<br />

The copy as functions are preset shortcuts for<br />

placing certain data forms on the system<br />

clipboard without changing the data types to<br />

be copied in the Advanced tab of the<br />

Preferences window.<br />

Just select the content in the document to be<br />

copied and then select one of the menu items<br />

in the Copy As... submenu of the Edit menu.<br />

The most popular data types are supported.<br />

These functions will place both text and<br />

chemical data on the system clipboard for<br />

maximum compatibility with 3rd party<br />

applications. No image data will be placed on<br />

the system clipboard.

Pasting Data from Other<br />

To paste data from other applications into<br />

<strong>ChemDoodle</strong>, perform the following steps:<br />

1. Use the copy function present in the other<br />

2. Click on the Paste menu item in the Edit<br />

keyboard shortcut which is ctrl-V<br />

(command-V on Mac OS X) to paste the<br />

highest priority data to the Doodle Board.<br />

Where Content is Pasted<br />

The pasted content will be located according<br />

to the following rules:<br />

1. If your mouse pointer is hovering over the<br />

document, the center of the pasted content<br />

will be located at the mouse pointer.<br />

2. If the mouse pointer is not hovering over<br />

the document, and the lasso is active, then<br />

the pasted content will appear to the<br />

bottom-right of the lassoed content.<br />

3. If the mouse pointer is not hovering over<br />

the document and the lasso is inactive,<br />

then the pasted content will appear at the<br />

top left of the document.<br />

Paste Special...<br />

Since an application can place different data<br />

types on the system clipboard, the data that<br />

<strong>ChemDoodle</strong> pastes may not always be the<br />

desired type. In general, <strong>ChemDoodle</strong> pastes<br />

chemical data over images and images over<br />

text. If you would like to paste alternate data,<br />

click on the Paste Special... menu item in the<br />

Edit menu. A window will appear listing all<br />

<strong>ChemDoodle</strong> compatible data as shown in<br />

Figure 10.4. Just select the list item you<br />

would like to paste and press the Paste<br />

160<br />

Figure 10.4: Paste Special Window<br />

Pasting Text as Chemical Data<br />

Sometimes it may be necessary to handle text<br />

data from the system clipboard. For instance,<br />

a chemical application may paste the<br />

MOLFile format in plain text, or you may be<br />

copying a SMILES string from a web browser.<br />

<strong>ChemDoodle</strong> provides a Paste Text as<br />

Chemical function to conveniently handle<br />

this.<br />

To paste text content from another application<br />

as chemical data, perform the following steps:<br />

application to place the text on the system<br />

clipboard.<br />

2. Expand the Paste Text As Chemical...<br />

submenu in the Edit menu.<br />

3. Depending on the type of data being<br />

represented by the text, select the<br />

appropriate menu item in the submenu to<br />

paste.<br />

Using this method, any of the line notations<br />

that <strong>ChemDoodle</strong> understands can be pasted<br />

as chemical data. Additionally, there is a

XYZ-Like Data menu item for pasting text<br />

as chemical data in an XYZ-like format. This<br />

option will automatically scan the text to<br />

extract atom labels and positions. The final<br />

menu item is Guess Chemical Format. This<br />

will detect the chemical format of the text<br />

data on the system clipboard and paste the<br />

chemical data accordingly, which is perfect<br />

for ASCII or XML data types, such as<br />

MOLFiles or CML. This function will alert<br />

you if not chemical format could be<br />

associated with the text data.<br />

Chemical Format<br />

Compatibility<br />

<strong>ChemDoodle</strong> supports one of the largest<br />

chemical format libraries in the industry and<br />

can interpret various chemical formats for<br />

input to and output from other chemical<br />

applications. Chemical formats are discussed<br />

in detail in Appendix B.<br />

Image Format Compatibility<br />

<strong>ChemDoodle</strong> supports the input and output of<br />

a wide range of bitmap and vector images.<br />

Supported Input Formats<br />

<strong>ChemDoodle</strong> can read the following bitmap<br />

image formats:<br />

• Joint Photographic Experts Group<br />

{.jpg, .jpeg, .jpe, .jfif, .jfi, .jif}<br />

• Microsoft Bitmap {.bmp, .dib}<br />

• Tagged Image File Format {.tiff, .tif}<br />

• Wireless Bitmap {.wbmp}<br />

• CompuServ Graphics Interchange Format<br />

{.gif}<br />

• Portable Network Graphics {.png}<br />

161<br />

• UNIX Portable PixMap<br />

{.ppm, .pnm, .pbm, .pgm}<br />

• Photoshop Document {.psd}<br />

<strong>ChemDoodle</strong> can read the following vector<br />

• Adobe Portable Document Format {.pdf}<br />

• Web Scalable Vector Graphics {.svg, .svgz}<br />

Supported Output Formats<br />

<strong>ChemDoodle</strong> can write the following bitmap<br />

• UNIX Portable PixMap {.ppm, pnm, pbm,<br />

pgm}<br />

<strong>ChemDoodle</strong> can write the following vector<br />

• Encapsulated Postscript<br />

{.eps, .epi, .epsi, .epsf}<br />

• Macintosh Vector Pict {.pict}<br />

• OpenDocument Graphics {.odg}<br />

• Windows Enhanced Metafile {.emf}

Images<br />

<strong>ChemDoodle</strong> will automatically embed<br />

chemical data in certain image formats. When<br />

these images are inserted into <strong>ChemDoodle</strong>,<br />

they will be checked for chemical information<br />

and that chemical information will be loaded<br />

if found.<br />

<strong>ChemDoodle</strong> embeds chemical information<br />

into the following image formats:<br />

• Encapsulated Postscript {.eps}<br />

• Web Scalable Vector Graphics {.svg}<br />

To export all of the objects in the current<br />

document to an image, perform the following<br />

1. Select the Save As Image... menu item<br />

from the File menu.<br />

2. A file chooser will appear. Select the<br />

location you would like to have the<br />

document saved in and type in a name for<br />

the file if you do not like the default<br />

name. You do not need to type in an<br />

3. After you are satisfied with a location and<br />

name, select the image type of the image<br />

to be exported.<br />

4. After selecting the file type to be used,<br />

press the Save button to export your<br />

document as an image.<br />

5. If options are available, a window will be<br />

shown to allow you to set the options.<br />

Define the settings to your preference and<br />

then click the Done button.<br />

162<br />

Image<br />

To export specific objects in the current<br />

1. Use a selection tool to select the objects to<br />

be exported to an image.<br />

2. Select the Save Selection As Image...<br />

menu item from the File menu.<br />

3. A file chooser will appear. Select the<br />

4. After you are satisfied with a location and<br />

5. After selecting the file type to be used,<br />

press the Save button to export the<br />

selected objects to an image.<br />

6. If options are available, a window will be<br />

Image Output Options<br />

There are several options that you can define<br />

for output images. Some options are only<br />

available for bitmap or vector types, while<br />

some options will be available for both.<br />

Image Border Buffer<br />

You can control the image border buffer, or<br />

the amount of space surrounding the graphics<br />

in an image, by changing the Border Buffer<br />

setting in the Preferences window under the<br />

Advanced tab. The default image border<br />

buffer is 3 pixels.

Image Scale (bitmap only)<br />

This setting will determine the scale of the<br />

output image. The larger the scale, the larger<br />

the output image. Vector graphics can be<br />

rescaled at any time, and therefore this setting<br />

is only available for bitmap images. You will<br />

need to scale bitmap images to a larger size if<br />

you want to use a higher resolution, but retain<br />

the same dimensions.<br />

Resolution (bitmap only)<br />

This setting will instruct printers and other<br />

renderers how to scale the image. The higher<br />

the DPI setting, then the crisper the image<br />

will look, but the smaller it will appear. By<br />

default, the DPI setting is 300dpi. Currently,<br />

only the JPEG and PNG output support this<br />

option. Vector graphics are resolution-less,<br />

and therefore this setting is only available for<br />

bitmap images.<br />

Transparency (bitmap only)<br />

If the bitmap image type supports<br />

transparency, this option will be available.<br />

Render Text as Shapes (PDF)<br />

In vector graphics, text is output as shapes, so<br />

they are no longer recognized as text by other<br />

applications. If you prefer to preserve the<br />

characters for editing in other applications,<br />

then select this option. Note that the font you<br />

use for the text must be present on the system<br />

that you open the PDF in, or the font you<br />

used will be replaced with something similar,<br />

but not identical.<br />

Inserting Images<br />

For any of the image formats that<br />

<strong>ChemDoodle</strong> can read, you can import files<br />

of that format into your documents. To do so,<br />

163<br />

1. Select the Insert Image... menu item in<br />

the File menu.<br />

2. In the file chooser that appears, navigate<br />

to and select the image you would like to<br />

insert.<br />

3. Select the Open button to insert the<br />

image.<br />

If you selected an image file type that is not<br />

understood by <strong>ChemDoodle</strong>, a message will<br />

appear to notify you of the issue.<br />

In addition to inserting images via the File<br />

menu, you may also simply drag compatible<br />

images from your file system or from other<br />

applications on the Doodle Board.<br />

Round Trip Editing<br />

Round trip editing is a very advanced feature<br />

for allowing <strong>ChemDoodle</strong> content to transfer<br />

between applications by embedding it into<br />

images. In most cases, <strong>ChemDoodle</strong> will<br />

automatically perform this embedding for<br />

you. Through round trip editing, you can copy<br />

<strong>ChemDoodle</strong> content into your word<br />

processor for instance, and then later copy<br />

that content back into <strong>ChemDoodle</strong> for reediting.<br />

NOTE: Make sure you always save your<br />

drawings and figures in a <strong>ChemDoodle</strong><br />

Document and never rely on a third party<br />

application to save your <strong>ChemDoodle</strong> data.<br />

That third party application may change<br />

how it works and you may lose your data!<br />

Support<br />

Round trip editing requires that both<br />

<strong>ChemDoodle</strong> and the application you are<br />

inserting the <strong>ChemDoodle</strong> content into work<br />

together. Currently, <strong>ChemDoodle</strong> supports<br />

round trip editing with any applications that<br />

understand Object Linking and Embedding<br />

(OLE) on Windows, that preserve PDF

comments on Mac OS X, or with OpenOffice<br />

on Linux. This covers a large number of<br />

applications that most scientists use, however<br />

there will always be that one application it<br />

does not work with. We are actively working<br />

to expand the range of applications<br />

<strong>ChemDoodle</strong> can provide round trip editing<br />

functionality with.<br />

Setup<br />

No additional setup is required for round trip<br />

editing on Windows. The OLE server is<br />

automatically registered when <strong>ChemDoodle</strong><br />

is installed.<br />

By default, in Advanced Preferences, OLE is<br />

enabled. OLE is required to be enabled for<br />

round trip editing to work on Windows.<br />

Procedure<br />

Round trip editing is very simple on<br />

Windows. Just copy in <strong>ChemDoodle</strong> and<br />

paste into the receiving application. To edit<br />

the content, copy the embedded object from<br />

the receiving application and paste back into<br />

<strong>ChemDoodle</strong> to recover the objects. Once you<br />

have finished editing, again copy in<br />

<strong>ChemDoodle</strong> and paste back into the<br />

receiving application to replace the original<br />

object.<br />

Some applications may not paste the OLE<br />

object by default. In this case, make sure to<br />

use a provided Paste Special function in the<br />

receiving application to choose the OLE<br />

Not all applications on Windows support<br />

OLE, and round trip editing is not possible<br />

with those applications.<br />

164<br />

editing on Mac OS X.<br />

By default, in Advanced Preferences, PDF is<br />

enabled. PDF is required to be enabled for<br />

round trip editing to work on Mac OS X.<br />

Round trip editing is very simple on Mac OS<br />

X. Just copy in <strong>ChemDoodle</strong> and paste into<br />

the receiving application. To edit the content,<br />

copy the image from the receiving application<br />

and paste back into <strong>ChemDoodle</strong> to recover<br />

the objects. Once you have finished editing,<br />

again copy in <strong>ChemDoodle</strong> and paste back<br />

into the receiving application to replace the<br />

original image.<br />

Some applications may not paste the PDF by<br />

default. In this case, make sure to use a<br />

provided Paste Special function in the<br />

receiving application to choose the PDF.<br />

Not all applications on Mac OS X preserve<br />

PDF comments, and round trip editing is not<br />

possible with those applications.<br />

Workaround for iWork Pages<br />

iWork Pages corrupts PDF comments, so<br />

round-trip editing will fail directly from<br />

Pages. There are two workarounds for this:<br />

1. Copy the figure from Pages into Keynote<br />

and then copy in Keynote and paste into<br />

<strong>ChemDoodle</strong> to recover the data.<br />

2. Use the Inspector to retrieve the unaltered<br />

PDF directly from Pages.<br />

To perform the second procedure, please<br />

follow these steps:

1. When working with figures pasted into<br />

Pages from <strong>ChemDoodle</strong>, open the<br />

Inspector by clicking on the Inspector<br />

button in Pages top toolbar.<br />

2. In the Inspector, click on the Metrics icon<br />

, and then click on the <strong>ChemDoodle</strong><br />

figure so that droppedImage.pdf appears as<br />

in Figure 10.5.<br />

3. Drag the droppedImage.pdf onto the<br />

Doodle Board in <strong>ChemDoodle</strong> to recover<br />

the data.<br />

Figure 10.5: Inspector showing the<br />

droppedImage.pdf <strong>ChemDoodle</strong> embedded<br />

165<br />

Forward<br />

Round trip editing on Linux is only possible<br />

with OpenOffice/LibreOffice and other<br />

variants and only on Linux. We did our best to<br />

provide as simple a procedure as possible, but<br />

given the lacking state of these projects, there<br />

are some inconveniences to deal with. We<br />

will do our best to continue to improve this<br />

procedure, but your help is required to submit<br />

issues to the OpenOffice/LibreOffice<br />

development teams and urge them to improve<br />

their software and APIs.<br />

Round trip editing on Linux requires that the<br />

user install our <strong>ChemDoodle</strong> OpenOffice<br />

plugin. The plugin is named <strong>ChemDoodle</strong>.oxt<br />

and can be found in the resources folder in<br />

the <strong>ChemDoodle</strong> installation folder.<br />

To install the plugin, perform the following<br />

1. Launch OpenOffice/LibreOffice.<br />

2. In the Tools menu, select Extension<br />

Manager...<br />

3. Click the Add... button.<br />

4. In the file chooser that appears, locate the<br />

<strong>ChemDoodle</strong>.oxt file in the resources<br />

folder and select it.<br />

If the plugin is successfully registered, it will<br />

appear in the Extension Manager as shown<br />

in Figure 10.6.<br />

Figure 10.6: The Extension Manager with the<br />

<strong>ChemDoodle</strong> plugin properly registered

In Advanced Preferences, both PNG (720dpi)<br />

and <strong>ChemDoodle</strong> Collage are required to be<br />

enabled for round trip editing to work on<br />

Linux. Other raster image types should be<br />

disabled.<br />

To insert a <strong>ChemDoodle</strong> object into<br />

OpenOffice/LibreOffice, perform the<br />

1. Ensure the clipboard settings are correct<br />

as stated above.<br />

2. Select the content you wish to copy and<br />

use a copy function in <strong>ChemDoodle</strong>.<br />

3. In the Office application you want to<br />

insert the object into, open the Object<br />

submenu in the Insert menu and select<br />

OLE Object... (Figure 10.7)<br />

4. In the window that appears, select<br />

<strong>ChemDoodle</strong> Embedded Object and<br />

select the OK button. (Figure 10.8)<br />

Figure 10.7: The OLE Object... menu item<br />

166<br />

Figure 10.8: Selecting the <strong>ChemDoodle</strong><br />

Embedded Object to insert<br />

To edit the inserted <strong>ChemDoodle</strong> object,<br />

1. Select the inserted <strong>ChemDoodle</strong> object<br />

that you wish to edit, and double-click on<br />

it.<br />

2. Use a copy function with the<br />

<strong>ChemDoodle</strong> object still selected.<br />

3. In <strong>ChemDoodle</strong>, use a paste function to<br />

paste the <strong>ChemDoodle</strong> Objects.<br />

4. Edit the content.<br />

5. Reselect the content and follow the<br />

procedure for inserting the <strong>ChemDoodle</strong><br />

object into OpenOffice/LibreOffice above<br />

to replace the previous object.

Troubleshooting<br />

Common error boxes may appear,<br />

troubleshoot them as follows.<br />

The following warning means that you should<br />

enable the PNG (720dpi) option and disable<br />

the PNG option in Advanced Preferences for<br />

the best quality images.<br />

The following warnings means that you<br />

should enable <strong>ChemDoodle</strong> Collage in<br />

Advanced Preferences.<br />

The following warning means that PNG<br />

(720dpi) needs to be enabled in Advanced<br />

The following warning means you need to<br />

read the Clipboard Settings section above<br />

again.<br />

Other Issues<br />

Why is bitmap image used instead of a vector<br />

graphic?<br />

167<br />

OpenOffice/LibreOffice does not support<br />

vector graphics through their Embedded<br />

Object insertion. Please contact the<br />

appropriate Office development teams to urge<br />

them to improve this. For now, we use a 720<br />

dpi image so print quality will still be<br />

excellent.<br />

Why can’t I paste the object directly between<br />

Office applications?<br />

This is apparently a bug in OpenOffice/<br />

LibreOffice, please contact the appropriate<br />

Office development teams to urge them to fix<br />

Why do I have to double click the object to<br />

round trip it?<br />

This is just what OpenOffice/LibreOffice<br />

requires to execute the object. Please contact<br />

the appropriate Office development teams to<br />

urge them to improve this.<br />

Why can’t I just paste the object? Why do I<br />

need to go through the menu to insert it?<br />

Implementing direct pasting of the object<br />

exhibits many inconsistencies which make it<br />

unsuitable for regular use. This is something<br />

we are trying to work around. Please contact<br />

urge them to fix this.<br />

Printing<br />

The document can be printed from<br />

<strong>ChemDoodle</strong>. In most cases, this procedure is<br />

identical to other applications you use on your<br />

operating system. You can define settings,<br />

preview, and print.<br />

Page Setup<br />

By selecting the Page Setup... menu item in<br />

the File menu, you will be able to set the<br />

printer settings. The window that appears will<br />

be identical to the same window that appears

in other applications on your operating<br />

system. Here, you can determine which<br />

printer to print to and set up the page<br />

Flipping the Page Orientation<br />

In some cases, you may desire that your<br />

document is printed in landscape mode. To do<br />

this, perform the following steps:<br />

1. Select the Page Setup... menu item in the<br />

File menu.<br />

2. In the window that appears, find the<br />

appropriate setting for page orientation,<br />

and change it to landscape.<br />

3. Press the confirm button in the window to<br />

save your settings and close it.<br />

4. A question will appear asking if you<br />

would like to swap the width and height<br />

of <strong>ChemDoodle</strong>. If this is appropriate for<br />

your document, select Yes, otherwise,<br />

select No.<br />

It is important that the direction that the<br />

printer prints your document, and the size of<br />

your document are distinct. Printing in<br />

landscape mode only means that the printer<br />

prints your content at a 90 degree angle. It<br />

does not alter your document in any way. So<br />

in some cases, you may want to flip the<br />

dimensions of your document and reorient<br />

your figures such that they will better fit on a<br />

landscape orientation.<br />

This procedure gives you the most control<br />

over your documents, by allowing you to<br />

control the dimensions of your document and<br />

separately to control the orientation that your<br />

document is printed to the printer.<br />

Print Preview<br />

To preview your document before you print,<br />

select the Print Preview menu item in the<br />

File menu. Click the Ok button to the bottom<br />

168<br />

right when you are finished to close the<br />

preview. Only the content that should appear<br />

in the printing will appear in the preview, no<br />

warnings, highlights or other interface<br />

decorations will be present.<br />

Printing a Document<br />

To print a document, perform the following<br />

1. Select the Print... menu item in the File<br />

2. In the window that appears, confirm or<br />

change any available settings.<br />

3. Press the Print button to print your<br />

Appendix A:<br />

Managing<br />

The chapters in this user guide explain how to<br />

use <strong>ChemDoodle</strong> to draw and work with<br />

chemical figures. There are other functions<br />

for managing the application itself.<br />

This section shows the new user how to<br />

manage <strong>ChemDoodle</strong>. It covers the following<br />

• Updating <strong>ChemDoodle</strong>.<br />

• Deactivating and restoring <strong>ChemDoodle</strong>.<br />

• Using your iChemLabs account.<br />

• Making use of provided media and<br />

resources.<br />

Application and File Icons<br />

You may wish to associate file icons and<br />

application icons with <strong>ChemDoodle</strong> if<br />

<strong>ChemDoodle</strong> does not already do this for you,<br />

such as on Linux. In the resources folder in<br />

the main <strong>ChemDoodle</strong> installation folder,<br />

operating system specific graphics will be<br />

provided for <strong>ChemDoodle</strong> and recognized<br />

chemical file types. Use you operating<br />

system’s documentation to associate those<br />

icons with the application and file types.<br />

Updating <strong>ChemDoodle</strong><br />

<strong>ChemDoodle</strong> will check for official<br />

iChemLabs updates and will automatically<br />

169<br />

update to the latest available version for you<br />

if you allow it to do so.<br />

To check for updates, just click the Check<br />

For Updates menu item in the Help menu. If<br />

no update is available, you will see a<br />

confirmation message stating that your copy<br />

of <strong>ChemDoodle</strong> is up to date. If there is an<br />

update available, you will see an Update<br />

Available window appear listing all the<br />

changes introduced by the update. Just click<br />

the Update button to proceed. <strong>ChemDoodle</strong><br />

will close to perform the update, so make sure<br />

to save your files before continuing.<br />

NOTE: You must have administrator<br />

privileges to update <strong>ChemDoodle</strong>. If you<br />

see a message stating that you cannot<br />

update because you do not have the<br />

necessary permissions, please double<br />

check that you ran <strong>ChemDoodle</strong> as<br />

administrator (on Windows for instance) or<br />

contact your system administrator to help<br />

The auto-updater will then open. It will<br />

download the latest <strong>ChemDoodle</strong> updates,<br />

verify the contents with our server, and then<br />

proceed to update <strong>ChemDoodle</strong>. The updater<br />

can be seen in Figure A.1. It may take several<br />

minutes to complete. After the updater<br />

completes, it will notify you that it is ready<br />

and that <strong>ChemDoodle</strong> will be reopened. Just<br />

click the Ok button to close the updater and<br />

continue. Your version of <strong>ChemDoodle</strong> has<br />

now been updated. Enjoy!<br />

Figure A.1: The iChemLabs Updater

By default, <strong>ChemDoodle</strong> will automatically<br />

check for updates while loading. You can<br />

disable this feature in the Preferences<br />

window under the Online tab. You may<br />

always manually check for updates by using<br />

the menu item mentioned above.<br />

Windows Administrator Privileges<br />

A common issue on Windows Vista/7+ is to<br />

enable administrator privileges for<br />

<strong>ChemDoodle</strong> to update. If <strong>ChemDoodle</strong> states<br />

that you do not have the necessary<br />

administrator privileges on these platforms,<br />

1. Exit <strong>ChemDoodle</strong>.<br />

2. Locate the <strong>ChemDoodle</strong> icon (shortcut or<br />

actual application).<br />

3. Right-click on the icon and select Run as<br />

administrator.<br />

4. Accept the security request.<br />

You will then be able to update <strong>ChemDoodle</strong>.<br />

If this process does not work, you will need to<br />

consult with a system administrator to update<br />

Skipping Updates<br />

If you wish to ignore the current update, when<br />

the Update Available window is displayed,<br />

just select the Skip this Version button as<br />

shown in Figure A.2. You will no longer be<br />

notified that this update is available. You will<br />

170<br />

still be notified of subsequent updates, which<br />

you may also skip.<br />

To obtain an update that was skipped, select<br />

the Check For Updates menu item in the<br />

Help menu.<br />

Figure A.2: The Update Available window with the<br />

Skip this Update button.<br />

Purchasing Upgrades<br />

Major version upgrades to <strong>ChemDoodle</strong> must<br />

be purchased. When a major version upgrade<br />

becomes available, you will still be presented<br />

with the Update Available window.<br />

However, instead of an Update button, a<br />

Purchase Upgrade button will be presented.<br />

Click on the Purchase Upgrade button to be<br />

directed to the upgrade purchase page. After<br />

purchasing the upgrade, again check for<br />

updates. The Update button will then be<br />

showing and you may proceed with the<br />

update as described in the previous sections.<br />

Moving your Activated Copy<br />

to a New Computer<br />

At some point, you may want to switch to a<br />

different computer. Your purchased

<strong>ChemDoodle</strong> activation code is restricted by<br />

the number of computers <strong>ChemDoodle</strong> is<br />

activated on. Therefore, we provide you the<br />

ability to deactivate <strong>ChemDoodle</strong> and<br />

reactivate it on a new computer. To begin, just<br />

click the Deactivate <strong>ChemDoodle</strong> menu item<br />

in the Help menu.<br />

NOTE: When deactivating <strong>ChemDoodle</strong><br />

and switching to a new computer, your<br />

custom preferences and other user settings<br />

will be lost. If you have settings files<br />

(templates, chemical document settings),<br />

those can be copied to the new<br />

<strong>ChemDoodle</strong>Settings folder that will appear<br />

after <strong>ChemDoodle</strong> is activated on the new<br />

computer.<br />

Once the deactivation procedure has begun, it<br />

cannot be cancelled. Make sure you record<br />

your activation code, which will be displayed<br />

in the Details section of the deactivation<br />

confirmation message, so you can use it<br />

again. You should also have a record of your<br />

code from the email receipt you received<br />

upon purchasing it.<br />

Once you accept the confirmation message,<br />

<strong>ChemDoodle</strong> will close and your copy will be<br />

deactivated. You may now use your activation<br />

code to activate <strong>ChemDoodle</strong> on a new<br />

Preparing for a System<br />

Restore<br />

If you do anything to your system that will<br />

remove or eliminate the <strong>ChemDoodle</strong> license<br />

file, such as performing a system restore or<br />

installing your operating system from scratch,<br />

you will need to first deactivate your copy of<br />

<strong>ChemDoodle</strong>. Instructions for deactivating<br />

<strong>ChemDoodle</strong> can be found in the previous<br />

171<br />

Using iChemLabs Cloud<br />

Services<br />

With an iChemLabs account, you have the<br />

ability to save files online so you can open<br />

them anywhere or send them to other<br />

iChemLabs applications as well as access<br />

relevant cloud services from within<br />

You may log into your iChemLabs account at<br />

anytime in <strong>ChemDoodle</strong> by choosing the<br />

Sync with Online Account... menu item in<br />

the File menu. The login window will also<br />

have an option to link your iChemLabs<br />

account with your copy of <strong>ChemDoodle</strong>. If<br />

selected, <strong>ChemDoodle</strong> will automatically log<br />

into your iChemLabs account while it starts<br />

up. You can then change these settings at any<br />

time in the Preferences window under the<br />

Online tab.<br />

All customers receive a free account to use<br />

this feature. Your username is the email<br />

address your activation code is associated<br />

with, and your password is the last 4<br />

characters of your activation code. The<br />

password must be either in all uppercase or<br />

all lowercase.<br />

Currently, the following iChemLabs<br />

applications integrate with your iChemLabs<br />

account:<br />

• <strong>ChemDoodle</strong><br />

• <strong>ChemDoodle</strong> Mobile

Appendix B:<br />

Chemical File<br />

Types<br />

<strong>ChemDoodle</strong> can currently read and write 24<br />

different chemical file types. This section<br />

discusses the following issues:<br />

• What chemical file types are supported.<br />

• <strong>ChemDoodle</strong>’s adherence to third party file<br />

type specifications.<br />

• The extent of support for third party<br />

chemical file types.<br />

• Warnings about saving your documents in a<br />

format other than the <strong>ChemDoodle</strong><br />

Document format.<br />

• How to annotate your files.<br />

• How to use <strong>ChemDoodle</strong>’s file conversion<br />

tool.<br />

Adherence to Third Party<br />

File formats implemented in <strong>ChemDoodle</strong><br />

strictly follow their published specifications.<br />

<strong>ChemDoodle</strong> does not take liberties with their<br />

rules or inject <strong>ChemDoodle</strong>-only content into<br />

them. All file format objects and properties<br />

are mapped as closely as possible to objects<br />

and properties in <strong>ChemDoodle</strong>. Thorough<br />

implementation details are also provided in<br />

the following sections. Specification<br />

references can be found by selecting the<br />

References menu item in the Help menu.<br />

172<br />

<strong>ChemDoodle</strong> will try to interpret all 3rd party<br />

files as best as possible, so if you do find a<br />

file that doesn’t read well, please send it to us<br />

so we can improve our compatibility.<br />

Be Careful Saving 3rd Party<br />

Formats<br />

<strong>ChemDoodle</strong> does its best to preserve the data<br />

it reads in from third party formats, however<br />

it may not be perfect as those formats may<br />

have been intended for systems that are very<br />

different from <strong>ChemDoodle</strong>. For instance,<br />

one program may define a charge by placing<br />

a text box near an atom, while <strong>ChemDoodle</strong><br />

defines a charge by associating a charge<br />

attribute with that atom. When read,<br />

<strong>ChemDoodle</strong> may decide to convert that text<br />

box to a charge attribute, thereby changing<br />

the data that is in the file.<br />

That being said, it is very important that you<br />

carefully consider whether to allow<br />

<strong>ChemDoodle</strong> to save over 3rd party data files<br />

as <strong>ChemDoodle</strong> may not retain all essential<br />

information that the other program requires.<br />

When saving 3rd party files, <strong>ChemDoodle</strong><br />

will display this warning as a reminder before<br />

allowing you to continue. These warnings can<br />

be disabled in the Preferences window under<br />

the Saving tab.<br />

Instead, we recommend that you first save a<br />

copy of that file to edit, instead of saving over<br />

files created in other applications.<br />

Testing 3rd Party File Type<br />

Output<br />

If you are unsure about whether your<br />

document will be saved in its entirety to a 3rd<br />

party format, first check with this<br />

documentation. If you are still concerned,<br />

save a test file in <strong>ChemDoodle</strong>, close the

document you just saved, and then reopen the<br />

file in <strong>ChemDoodle</strong>. If some content is<br />

missing or any object properties have<br />

changed in some way, then the format you are<br />

trying to save to does not support those<br />

objects and/or properties or <strong>ChemDoodle</strong><br />

does not yet support the output of those<br />

objects and/or properties for that format.<br />

Supported Chemical File<br />

1. <strong>ChemDoodle</strong> Documents (.icl)<br />

2. <strong>ChemDoodle</strong> Javascript Data (.cwc.js)<br />

3. ACD/ChemSketch Document (.sk2)<br />

4. Beilstein ROSDAL (.ros)<br />

5. CambridgeSoft ChemDraw Exchange<br />

(.cdx)<br />

6. CambridgeSoft ChemDraw XML (.cdxml)<br />

7. CHARMM CARD File (.crd)<br />

8. ChemAxon Marvin Document (.mrv)<br />

9. Chemical Markup Language (.cml)<br />

10. Daylight SMILES (.smi, .smiles)<br />

11. IUPAC InChI (.inchi)<br />

12. IUPAC JCAMP-DX (.jdx, .dx)<br />

13. ISIS Sketch File (.skc)<br />

14. ISIS Sketch Transportable Graphics File<br />

(.tgf)<br />

15. MDL MOLFiles, both V2000 and V3000<br />

connection tables (.mol, .mdl)<br />

16. MDL RXNFiles, both V2000 and V3000<br />

connection tables (.rxn)<br />

17. MDL RDFiles (.rdf, .rd)<br />

18. MDL SDFiles (.sdf, .sd)<br />

173<br />

19. Molinspiration JME String (.jme)<br />

20. RCSB Protein Data Bank Files<br />

(.pdb, .ent)<br />

21. Schrödinger MacroModel (.mmd, .mmod)<br />

22. Schrödinger Maestro (.mae)<br />

23. Standard Molecular Data (.smd)<br />

24. Tripos Mol2 (.mol2, .ml2, .sy2)<br />

25. Tripos Sybyl Line Notation (.sln)<br />

26. XYZ Files (.xyz)<br />

File Annotations<br />

Annotations can be read and written to files<br />

where possible. Each document has its own<br />

set of annotations. To view previously defined<br />

annotations, edit them or create your own,<br />

select the Annotations... menu item in the<br />

File menu. Then edit the fields shown in<br />

Figure B.1.<br />

Figure B.1: File Annotations Window<br />

All data associated with a file will be saved in<br />

<strong>ChemDoodle</strong> Documents. Other users that<br />

open your annotated <strong>ChemDoodle</strong><br />

Documents files will be able to easily access<br />

them. Other file types may be able to save<br />

annotations as well, read their documentation<br />

in the following sections for the extent of<br />

annotation functionality.

File Conversion Tool<br />

<strong>ChemDoodle</strong> contains robust functionality for<br />

easily and quickly converting files between<br />

different formats. This tool is accessed by<br />

clicking the Convert... menu item in the File<br />

menu and is shown in Figure B.2. Unlike<br />

other chemical conversion utilities,<br />

<strong>ChemDoodle</strong> converts all document objects<br />

and properties in addition to just atoms and<br />

bonds; this including shapes, fonts, colors,<br />

annotations, document settings, etc.<br />

Figure B.2: Chemical File Conversion Utility<br />

Perform the following steps to convert a file:<br />

1. Choose a recognized input file with the<br />

file chooser that appears after clicking the<br />

Choose Input button. Use the file format<br />

filter at the bottom of the file chooser to<br />

select different file formats.<br />

2. Choose the location to store the output by<br />

clicking the Choose Location button or<br />

by manually typing in the path to the file.<br />

You can change the name of the output<br />

file this way.<br />

3. Choose an output format and extension<br />

from the drop down selection below the<br />

output location.<br />

174<br />

4. Click the Convert button.<br />

When complete, <strong>ChemDoodle</strong> will display<br />

statistics about the conversion or any issues<br />


iChemLabs <strong>ChemDoodle</strong><br />

About<br />

The <strong>ChemDoodle</strong> Document format is the<br />

native <strong>ChemDoodle</strong> format. Everything<br />

created in <strong>ChemDoodle</strong> can be stored in a<br />

<strong>ChemDoodle</strong> Document.<br />

Versions<br />

• any<br />

Extensions<br />

• .icl<br />

• .icxml<br />

Format<br />

XML<br />

Annotations<br />

All annotations are saved.<br />

All document settings are stored.<br />

• Embed Images - Embedding images will<br />

result in larger save files, but the documents<br />

will open on other computers without<br />

needing to first find the images. If there are<br />

pasted images in a document (rather than<br />

loaded from a file), allow the embedding of<br />

images to save them properly.<br />

175<br />

Javascript Data<br />

The <strong>ChemDoodle</strong> Javascript Data format is a<br />

Javascript file containing JSON data for<br />

native objects that can be handled by the<br />

<strong>ChemDoodle</strong> Web Components.<br />

• .cwc.js<br />

Javascript with JSON<br />

No annotations are saved.<br />

No document settings are stored.<br />

Currently, there are no options.

ACD/ChemSketch Document<br />

This is a binary format for storing chemical<br />

figures and is the main format for the ACD/<br />

ChemSketch application. Non-chemical<br />

objects are not yet supported. Most chemical<br />

objects and properties that are mutually<br />

inclusive between ChemSketch and<br />

<strong>ChemDoodle</strong> are supported.<br />

Version<br />

2+<br />

• .sk2<br />

Binary<br />

No annotations are stored.<br />

Styles for objects are stored but there is no<br />

global style sheet.<br />

Currently, there are no options.<br />

Supported Formats<br />

• ACD_ChemSketch_2_0_DocumentFormat<br />

• DocumentDescriptionFormat<br />

• PageDescriptionFormat<br />

• PictureFormat<br />

• StyleListFormat<br />

• BaseGraphStyleFormat<br />

• PenStyleFormat<br />

• FontStyleFormat<br />

• AtomStyleFormat<br />

• BondStyleFormat<br />

176<br />

• ObjectsListFormat<br />

• MoleculeFormat<br />

• AtomDataFormat<br />

• BondDataFormat<br />

• PageInfoDescriptionFormat<br />

• EnvironmentDescriptionFormat<br />

Notes<br />

• Most mutually inclusive chemical objects<br />

between ChemSketch and <strong>ChemDoodle</strong> are<br />

supported.<br />

• Shapes are not yet supported.<br />

• There is a serious issue with how<br />

superatoms are stored in ChemSketch files<br />

that renders them impossible to recover. In<br />

these cases, <strong>ChemDoodle</strong> will replace the<br />

superatom with a Carbon atom.<br />

• All bond types are mapped to the closest<br />

supported bond type.

Beilstein ROSDAL<br />

Beilstein ROSDAL is a chemical line notation<br />

format. ROSDAL stands for Representation<br />

Of Structure Description Arranged Linearly.<br />

The documentation on this format is quite<br />

sparse and most programs will not support it.<br />

Unknown<br />

• .ros<br />

Line Notation, plain text<br />

• All non-elemental atom labels are converted<br />

to Carbon labels.<br />

supported bond type.<br />

• Line notation formats do not contain<br />

coordinates. They will have to be generated<br />

by the application that reads the ROSDAL<br />

• Shapes will not be stored.<br />

• ROSDAL shorthands, charges and<br />

stereochemical bonds are supported.<br />

• Based on the sparse documentation,<br />

ROSDAL is completely implemented in<br />

177<br />

CambridgeSoft ChemDraw<br />

Files<br />

CDX Files<br />

figures. Non-chemical objects are supported.<br />

Most objects and properties that are mutually<br />

inclusive between ChemDraw and<br />

<strong>ChemDoodle</strong> are supported. This is a<br />

common format for manuscript submission,<br />

but we recommend that you use CDXML<br />

instead as CambridgeSoft suggests it.<br />

CDXML Files<br />

ChemDraw XML files are identical to their<br />

CDX counterparts, except they are XML<br />

format instead of binary. We recommend that<br />

you use CDXML for manuscript submission<br />

if <strong>ChemDoodle</strong> Documents are not an option.<br />

8+<br />

• cdx<br />

• cdxml<br />

CDX is binary while CDXML is XML<br />

Most document settings are stored.<br />

Supported Objects and Properties<br />

• kCDXProp_CreationProgram<br />

• kCDXProp_Name<br />

• kCDXProp_PrintMargins

• kCDXProp_ChainAngle<br />

• kCDXProp_BondLength<br />

• kCDXProp_BoldWidth<br />

• kCDXProp_LineWidth<br />

• kCDXProp_MarginWidth<br />

• kCDXProp_HashSpacing<br />

• kCDXProp_FractionalWidths<br />

• kCDXProp_InterpretChemically<br />

• kCDXProp_BondSpacing<br />

• kCDXProp_LabelStyle<br />

• kCDXProp_MacPrintInfo<br />

• kCDXProp_ColorTable<br />

• kCDXProp_FontTable<br />

• kCDXObj_Page<br />

• kCDXProp_BoundingBox<br />

• kCDXProp_HeightPages<br />

• kCDXProp_WidthPages<br />

• kCDXObj_Fragment<br />

• kCDXObj_Node<br />

• kCDXProp_2DPosition<br />

• kCDXProp_3DPosition<br />

• kCDXProp_Node_Element<br />

• kCDXProp_Atom_Isotope<br />

• kCDXProp_Atom_Charge<br />

• kCDXProp_Atom_Radical<br />

• kCDXProp_Atom_ShowSter<br />

eo<br />

• kCDXProp_Atom_CIPStere<br />

ochemistry<br />

178<br />

• kCDXProp_IgnoreWarnings<br />

• kCDXObj_Text<br />

• kCDXProp_Text<br />

• kCDXProp_RotationAng<br />

le<br />

• kCDXObj_Bond<br />

• kCDXProp_Bond_Begin<br />

• kCDXProp_Bond_End<br />

• kCDXProp_Bond_Order<br />

• kCDXProp_Bond_Display<br />

• kCDXProp_Bond_Display2<br />

• kCDXProp_ForegroundColo<br />

r<br />

• kCDXProp_Bond_ShowSter<br />

• kCDXProp_Bond_CIPStere<br />

• kCDXObj_Graphic<br />

• kCDXProp_Graphic_Type<br />

• kCDXProp_ForegroundColor<br />

• kCDXProp_Arrow_Type

• kCDXProp_Arrow_HeadSize<br />

• kCDXProp_SupersededBy<br />

• kCDXObj_Arrow<br />

• kCDXProp_ArrowShaftSpac<br />

ing<br />

• kCDXProp_ArrowheadTail<br />

• kCDXProp_ArrowheadHead<br />

• kCDXProp_Arrow_HeadSiz<br />

e<br />

• kCDXProp_Tail3D<br />

• kCDXProp_Head3D<br />

• kCDXProp_Arc_AngularSize<br />

• kCDXProp_CornerRadius<br />

• kCDXProp_Rectangle_Type<br />

• kCDXProp_Center3D<br />

• kCDXProp_MajorAxisEnd3D<br />

• kCDXProp_MinorAxisEnd3D<br />

• kCDXProp_Oval_Type<br />

• kCDXProp_Orbital_Type<br />

• kCDXProp_Bracket_Type<br />

• kCDXObj_BracketedGroup<br />

• kCDXObj_BracketAttachme<br />

nt<br />

• kCDXProp_Bracket_Gra<br />

phicID<br />

• kCDXProp_Symbol_Type<br />

179<br />

• kCDXProp_LineStarts<br />

• kCDXObj_EmbeddedObject<br />

• kCDXProp_GIF<br />

• kCDXProp_TIFF<br />

• kCDXProp_PNG<br />

• kCDXProp_JPEG<br />

• kCDXProp_BMP<br />

• kCDXProp_RotationAngle<br />

• kCDXProp_EndObject<br />

• Most mutually inclusive objects between<br />

ChemDraw and <strong>ChemDoodle</strong> are<br />

• ChemDraw formats do not use Unicode<br />

characters, which has become the standard.<br />

Upon read, <strong>ChemDoodle</strong> will convert<br />

Symbol font characters to their<br />

corresponding unicode characters, however,<br />

the reverse is not done. Greek characters<br />

(and other non-Latin Unicode characters)<br />

may not be displayed correctly in<br />

ChemDraw for this reason.

CHARMM CARD File<br />

CHARMM CARD files describe cartesian<br />

coordinates for molecules. These files are<br />

typically used with the CHARMM software.<br />

c36b2<br />

• .crd<br />

ASCII, plain text<br />

• All coordinates are in Ångströms and are<br />

centered around the origin.<br />

180<br />

ChemAxon Marvin<br />

Marvin Documents extend chemical markup<br />

language with additional objects and<br />

properties representing the graphical abilities<br />

of ChemAxon products.<br />

5.3.2<br />

• .mrv<br />

Inherits CML annotations.<br />

Inherits CML options.<br />

Supported Tags and Attributes<br />

*inherits CML objects and properties<br />

• MDocument<br />

• MChemicalStruct<br />

• MTextBox<br />

• MField<br />

• MPoint<br />

• x<br />

• y<br />

• MEllipse<br />

• thickness<br />

• lineColor<br />

• MRectangle<br />

• MRoundedRectangle<br />

• arcWidth<br />

• arcHeight<br />

• Bracket<br />

• type<br />

• MPolyline<br />

• headLength<br />

181<br />

• tailLength<br />

• arcAngle<br />

MarvinSketch and <strong>ChemDoodle</strong> are<br />

• Output is always in arrays.<br />

• Inherits CML notes.

Chemical Markup Language<br />

Chemical Markup Language stores a wide<br />

range of chemical objects and properties<br />

utilizing XML protocol. It is only a secondary<br />

format, most useful for embedding chemical<br />

content in webpages.<br />

• 2<br />

• 1 (Read-only)<br />

• .cml<br />

If provided, annotations are read and written<br />

with the logically corresponding attributes in<br />

the metadataList element: dc:creator, dc:date,<br />

dc:description, dc:rights, dc:title.<br />

• Dimension: Either 2 dimensions can be<br />

save with coordinates in pixels (for<br />

drawings), or 3 dimensions can be saved<br />

with coordinates in Ångströms (for exact<br />

structural coordinates).<br />

• Arrays: You may store all atoms and bonds<br />

as arrays to save space. Child objects of<br />

atoms and bonds will be excluded.<br />

• cml<br />

• list<br />

• metadataList<br />

• metadata<br />

182<br />

• molecule<br />

• formula<br />

• title<br />

• name<br />

• content<br />

• atomArray<br />

• atom<br />

• id<br />

• elementType<br />

• formalCharge<br />

• isotope<br />

• x2<br />

• y2<br />

• xy2<br />

• x3<br />

• y3<br />

• z3<br />

• xyz3<br />

• bondArray<br />

• bond<br />

• atomRefs2<br />

• order<br />

• bondStereo<br />

to Carbon labels. "Du", "Dummy" and "R"<br />

are allowed.<br />

• All 2D coordinates are in pixels.<br />

• All 3D coordinates are in Ångströms and<br />

are centered around the origin.<br />

• CML array formats can be read and written.<br />

• The older version 1 format of CML can also<br />

be read, but it cannot be written.<br />

183<br />

Daylight SMILES<br />

Daylight SMILES is a chemical line notation<br />

format. SMILES stands for Simplified<br />

Molecular Input Line Entry Specification.<br />

4.9<br />

• .smi<br />

• .smiles<br />

• Output Aromaticity: If selected, then an<br />

aromatic model will be imposed on the<br />

output SMILES string with lower case<br />

letters, such that a Kekulé structure of<br />

benzene will be output as c1ccccc1 instead<br />

of C1=CC=CC=C1.<br />

• Kekulize Input: If selected, input data that<br />

contains aromatic information will be<br />

Kekulized and that aromatic information<br />

will be lost.<br />

• Isotopes and charges are handled.<br />

coordinates. They will have to be generated

y the application that reads the SMILES<br />

184<br />

IUPAC InChI<br />

IUPAC InChI is a unique and unambiguous<br />

chemical line notation format. InChI stands<br />

for International Chemical Identifier. It is<br />

quickly becoming a standard identifier in<br />

databases.<br />

1.02<br />

• .inchi<br />

• Auxiliary Information: Include the<br />

auxiliary information with each InChI<br />

string.<br />

• InChI Key: Include a unique InChI key<br />

with each InChI string.<br />

• InChI files do not contain coordinates<br />

unless they are provided in an Auxiliary<br />

information string. They will have to be<br />

generated by the application that reads the<br />

InChI file.<br />

• Shapes will not be stored.

• <strong>ChemDoodle</strong> utilizes JNI-InChI, which is a<br />

wrapper around the official IUPAC source<br />

for generating InChI files.<br />

185<br />

IUPAC JCAMP Data<br />

JCAMP is primarily for storing spectroscopic<br />

data, but can also store low resolution<br />

chemical structure data. The supported<br />

techniques are mass spectrometry, infrared<br />

spectroscopy, nuclear magnetic resonance<br />

spectroscopy and ion mobility spectrometry.<br />

JCAMP data stands for the Joint Committee<br />

on Atomic and Molecular Physical data.<br />

While spectra and chemical structures are<br />

read, currently only chemical structures are<br />

written, but support for spectra output will be<br />

provided in the future.<br />

• IR - 4.24<br />

• MS - 5.00<br />

• NMR - 5.00<br />

• Chemical Structures - 3.7<br />

• .jdx<br />

• .dx<br />

Plain text<br />

from appropriate records. Title, author and<br />

copyright status are supported.<br />

• Convert Hz to PPM: If enabled and an<br />

NMR spectrum is read in with Hz as the xunit,<br />

<strong>ChemDoodle</strong> will automatically<br />

convert the domain to ppm.

Supported Records<br />

• TITLE<br />

• JCAMP-CS<br />

• ORIGIN<br />

• OWNER<br />

• MOLFORM<br />

• ATOMLIST<br />

• BONDLIST<br />

• DATE<br />

• TIME<br />

• CHARGE<br />

• RADICAL<br />

• MAX_RASTER<br />


• XY_RASTER<br />

• Spectra are read, but not written. Be careful<br />

not to overwrite your data.<br />

• This format is typically for the storage of<br />

spectra, but chemical structures can be<br />

included.<br />

186<br />

MDL ISIS Sketch Files<br />

SKC Files<br />

This is the default format for storing chemical<br />

drawings in ISIS Sketch and Symyx Draw.<br />

Non-chemical objects are supported. All<br />

inclusive between ISIS Sketch and<br />

<strong>ChemDoodle</strong> are supported. This format was<br />

designed to be platform dependent (for some<br />

unknown reason), so SKC files written on<br />

Windows will not work on Macs and vice<br />

versa. However, <strong>ChemDoodle</strong> can recognize<br />

all SKC files and will correctly read them<br />

regardless of what platform they were<br />

generated on. You may choose which SKC<br />

output format to use if necessary.<br />

TGF Files<br />

ISIS Sketch transportable graphics files are<br />

identical to their SKC counterparts, except<br />

they are ASCII format instead of binary.<br />

Symyx seems to have discontinued support<br />

for this format, so most applications will<br />

probably not read them.<br />

• .skc<br />

• .tgf<br />

SKC is binary, TGF is plain text<br />

No document settings are stored.

• SKC Binary Output Format: ISIS Sketch<br />

SKC files are platform dependent, as per<br />

MDL's specification. SKC files written on<br />

versa. You may modify how the files are<br />

saved with this setting. Upon read,<br />

<strong>ChemDoodle</strong> will determine which format<br />

is used, and report any problems.<br />

Supported Blocks and Properties<br />

• rect<br />

• Obj_coords<br />

• Pen_width<br />

• Pen_style_token<br />

• Fill_style<br />

• Transparent<br />

• Pen_RGB2Color<br />

• Fill_RGB2Color<br />

• Pen_widthUnit<br />

• RxnAtch<br />

• rounded_rect<br />

• Roundrect_curve<br />

187<br />

• line<br />

• ArrowDir<br />

• ArrowStyle<br />

• ArrowSize<br />

• polygon<br />

• Poly_points<br />

• Poly_smoothed<br />

• ellipse<br />

• Pen_style_token

• arc<br />

• Arc_endpts<br />

• spline<br />

188<br />

• text<br />

• MDLEdittext<br />

• subsketch<br />

• mol<br />

• Begsketch<br />

• Endsketch<br />

• Totobjs<br />

• rxnarrow<br />

• bracket_rect<br />

• circ_arc<br />

189<br />

• smooth_spline<br />

• Bond_atoms<br />

• Bond_type<br />

• Bond_stereo_type<br />

• Bond_hash_spacing<br />

• Bond_bond_spacing<br />

• Bond_crossed<br />

• Bond_alt_stereo<br />

• Atom_coords<br />

• Atom_zcoord

• Atom_type<br />

• Atom_symbol<br />

• Atom_chg<br />

• Atom_rad<br />

• Atom_msdif<br />

• Font<br />

• Atom_margin_width<br />

• All mutually inclusive objects between ISIS<br />

Sketch and <strong>ChemDoodle</strong> are supported.<br />

190<br />

MDL Connection Table Files<br />

MOL Files<br />

MOL files have become one of the most<br />

popular formats for storing chemical<br />

information, especially in drawing programs.<br />

It typically stores only a single molecule. It<br />

consists of a header followed by an MDL<br />

connection table. All connection table formats<br />

follow ASCII standards.<br />

SD Files<br />

A SD (structure-data) file stores any number<br />

of molecules and other annotations. SD files<br />

are simply concatenated MOL files with<br />

additional data records.<br />

RXN Files<br />

RXN file is a very popular format for storing<br />

a single discrete chemical reaction. If consists<br />

of connection tables for the reactants and<br />

RD Files<br />

A RD (reaction-data) file stores any number<br />

of reactions and molecules and other<br />

annotations. RD files are simply concatenated<br />

RXN and MOL files with additional data<br />

records.<br />

• v3000<br />

• v2000<br />

• v1000 (Read only)<br />

• .mol<br />

• .mdl<br />

• .sd<br />

• .rxn<br />

• .rdf<br />

• .rd<br />

Only a title and the first comment is stored in<br />

the header if provided (80 characters each<br />

max). All annotations are stored as data<br />

records in SD files. Since the data headers are<br />

not specifically standardized, other programs<br />

will probably not be able to read them, but<br />

anyone can view the file in a text editor to see<br />

the information.<br />

• Bond Length Conversion: Coordinates are<br />

in bond lengths. When saving, coordinates<br />

can be converted using the standard bond<br />

length (30px) or the currently selected bond<br />

• Force v3000 Connection Tables: v2000<br />

connection tables are standard and used by<br />

default; V3000 connection tables must be<br />

and will be automatically used if a<br />

connection table contains more than 999<br />

• Output Hydrogen Counts: If this option is<br />

selected, the query values for Hydrogen<br />

counts will be provided in both v2000 and<br />

v3000 connection tables..<br />

v2000<br />

• Atom<br />

• Bond<br />

191<br />

• Properties<br />

v3000<br />

• Atom Alias<br />

• Charge<br />

• Radical<br />

• Isotope<br />

• End of Block<br />

• CTAB<br />

• COUNTS<br />

• ATOM<br />

• CHG<br />

• RAD<br />

• MASS<br />

• HCOUNT<br />

• BOND<br />

• CFG<br />





to Carbon labels in v2000 connection<br />

tables, but the Alias property is used for<br />

those programs that read it. All labels are<br />

retained in v3000 connection tables, with<br />

blanks as '*'.<br />

• All coordinates are in bond lengths and are<br />

192<br />

Molinspiration JME String<br />

JME Strings are technically a line notation,<br />

but do not compress connection tables. This<br />

format is mainly for input and output from<br />

Molinspiration’s Java Molecular Editor<br />

(JME).<br />

• .jme<br />

• Charges are stored.<br />

RCSB Protein Data Bank<br />

The Protein Data Bank format is one of the<br />

most popular formats for storing 3D chemical<br />

data. A large database of Protein Data Bank<br />

files is hosted at the RCSB website for public<br />

use. The RCSB also hosts a large set of<br />

monomer units which describe the topology<br />

in PDB files. Since most of the data is based<br />

on crystallographic information, bond orders<br />

are vague and only single bonds are<br />

recognized. PDB files are not recommended<br />

for the storage of 2D chemical drawings.<br />

• 3.20<br />

• earlier (read only)<br />

• .pdb<br />

• .ent<br />

If provided, the authors, keywords and title<br />

will be stored.<br />

• HEADER<br />

• KEYWDS<br />

• AUTHOR<br />

• REVDAT<br />

193<br />

• HETATM<br />

• CONECT<br />

• MASTER<br />

• END<br />

• When read, the PDB monomer database is<br />

contacted to determine topology. If there are<br />

no bonds found, then <strong>ChemDoodle</strong> will<br />

attempt to calculate all bonds by covalent<br />

Schrödinger Files<br />

MMD Files<br />

The MacroModel format is the primary<br />

format for the MacroModel application. It is a<br />

modeling format and contains information on<br />

atom types.<br />

MAE Files<br />

The Maestro file format is the standard<br />

exchange format for Schrödinger products.<br />

Technically, it extends the MMD format.<br />

• MMD-7.0<br />

• MAE-8.0<br />

• .mmd<br />

• .mmod<br />

• .mae<br />

Both MMD and MAE files are plain text<br />

MMD<br />

The Macromodel format is supported fully<br />

and in accordance with the official<br />

documentation.<br />

MAE<br />

• root<br />

194<br />

• m_atom<br />

• m_bond<br />

• p_m_ct<br />

• Atom types are mapped as closely as<br />

possible.<br />

• Multiple molecules can be stored as<br />

compound files or movies.

Standard Molecular Data<br />

Standard Molecular Data is an older ASCII<br />

format for storing chemical data. It is mainly<br />

dependent on Fortran Format specification.<br />

This format is fairly obsolete and most<br />

programs will not support it.<br />

• 4.3<br />

.smd<br />

A title is stored with the STRT block if<br />

provided. Otherwise the filename is used. The<br />

first comment will be stored in the TEXT<br />

block if provided.<br />

Supported Blocks<br />

• >STRT<br />

• >DTCR<br />

• >DTUP<br />

• >CT<br />

• >CO<br />

• >LB<br />

• >FORM<br />

195<br />

• All coordinates are in pixels.<br />

• Morgan indices are output in the Labels<br />

Tripos Mol2<br />

A Tripos Mol2 file is a complete, portable<br />

representation of a SYBYL molecule. This is<br />

a modeling format.<br />

7.1<br />

• .mol2<br />

• .ml2<br />

• .sy2<br />

If provided, annotations are written as<br />

comments at the beginning of the file. Title<br />

and author annotations are read.<br />

• @ATOM<br />

• @BOND<br />

• @MOLECULE<br />


196<br />

• This format is typically for the storage of a<br />

single molecule, but multiple molecules can<br />

be saved in a single Mol2 file.

Tripos Sybyl Line Notation<br />

SLN is a chemical line notation format. It is<br />

derived from SMILES but contains additional<br />

explicit information such as Hydrogen counts.<br />

• .sln<br />

by the application that reads the SLN file.<br />

• Macroatoms are read on input.<br />

197<br />

XYZ<br />

The XYZ chemical filetype is a very basic<br />

data format for storing atom types and<br />

coordinates. There is no official<br />

documentation for this format, so other<br />

applications may define it differently.<br />

• .xyz<br />

If a comment is provided, it will be output in<br />

the second line of the file. The second line of<br />

the file is also read in as a comment.<br />

• Atom Identifier: The element type can be<br />

specified with either the element's symbol<br />

or its atomic number.<br />

• Identifier Buffer: The identifier can be<br />

buffered to 3 columns so programs that read<br />

it can expect a certain column width.<br />

• Only atom symbol and coordinate data are<br />

stored.<br />

• Bonds will not be stored.<br />

centered around the origin.

• Single spaces are used to delimit tokens in<br />

the atom table.<br />

• All coordinates are rounded and recorded to<br />

the fifth decimal place.<br />

Appendix C:<br />

Compatibility with<br />

3rd Party<br />

<strong>ChemDoodle</strong> works with many 3rd party<br />

applications. The most common applications<br />

are discussed in this section. It is not an<br />

inclusive list. This section lists:<br />

• Common applications that are used with<br />

• Which types of data are transferred to<br />

common 3rd party applications.<br />

• Any solutions to issues involved with the<br />

3rd party applications.<br />

• Round trip editing compatibility.<br />

Microsoft Office<br />

Word<br />

On Windows and Mac OS X, text, images and<br />

scalable vector graphics can be transferred.<br />

For scalable vector graphics, if using Word on<br />

Windows, Windows Enhanced Metafile must<br />

be selected in the copy settings. For scalable<br />

vector graphics, if using Word 2004 on Mac<br />

OS X, Macintosh Vector PICT must be<br />

selected in the copy settings; Word 2008<br />

requires PDF to be selected in the copy<br />

settings. Make sure all bitmap image types<br />

are deselected.<br />

Round trip editing is functional on Windows<br />

with Microsoft Office using <strong>ChemDoodle</strong>’s<br />

OLE library. Round trip editing is functional<br />

199<br />

on Mac OS X with Microsoft Office 2011 (at<br />

update 14.0.1 or more recent).<br />

Powerpoint<br />

Same as Word.<br />

Excel<br />

Apple iWork<br />

Pages<br />

Text, images and scalable vector graphics can<br />

be transferred. For scalable vector graphics,<br />

PDF must be selected in the copy settings.<br />

Round trip editing is supported via the<br />

workaround detailed in the Round Trip<br />

Editing section of Chapter 10.<br />

Keynote<br />

Same as Pages. Round trip editing is<br />

supported directly supported.<br />

Same as Pages. Round trip editing is not<br />

OpenOffice<br />

Writer<br />

On all operating systems, text, images and<br />

For scalable vector graphics, if using Writer<br />

on Windows, Windows Enhanced Metafile<br />

must be selected in the copy settings. For<br />

scalable vector graphics, if using Writer on<br />

Mac OS X, Macintosh Vector PICT must be<br />

selected in the copy settings. For scalable<br />

vector graphics, if using Writer on Linux,<br />

OpenDocument Graphics must be selected in<br />

the copy settings.<br />

Round trip editing is supported on Linux by<br />

using <strong>ChemDoodle</strong> UNO plugin.

Calc<br />

On all platforms, text, images and scalable<br />

vector graphics can be transferred.<br />

For Mac OS X, first save <strong>ChemDoodle</strong><br />

content as Macintosh Vector PICTs and then<br />

insert or drag and drop the file into Calc.<br />

using <strong>ChemDoodle</strong> UNO plugin.<br />

Impress<br />

Same as Calc.<br />

Adobe Products<br />

Photoshop<br />

Images and scalable vector graphics can be<br />

transferred. For scalable vector graphics, PDF<br />

must be selected in the copy settings.<br />

Illustrator<br />

Scalable vector graphics can be transferred.<br />

First, save content as PDF and then open,<br />

insert or drag and drop the file into Illustrator.<br />

For direct pasting, make sure all vector<br />

graphics are disabled except for Windows<br />

Enhanced Metafile on Windows or Macintosh<br />

Vector Pict on Mac OS X.<br />

Browsers<br />

Most browsers will support image and<br />

scalable vector graphic output from<br />

<strong>ChemDoodle</strong> for display in web pages. The<br />

best scalable vector graphic formats to use are<br />

SVG and PDF.<br />

For information of <strong>ChemDoodle</strong> Web<br />

Components browser compatibility, visit the<br />

<strong>ChemDoodle</strong> Web Components website:<br />

Other<br />

<strong>ChemDoodle</strong> is compatible with any<br />

application that supports the data<br />

200<br />

<strong>ChemDoodle</strong> places on the system clipboard.<br />

Because <strong>ChemDoodle</strong> expertly handles<br />

Windows Enhanced Metafiles, Macintosh<br />

Vector PICT 2, PDF and OpenDocument<br />

Graphics, scalable vector graphics can be<br />

directly pasted into all native applications.<br />

Round trip editing will be supported with any<br />

application that supports OLE on Windows,<br />

or that will preserve PDF comments on Mac<br />

Appendix D:<br />

Elemental Data<br />

<strong>ChemDoodle</strong> has access to an extensive<br />

database of elemental data compiled from<br />

published resources. This section introduces<br />

the new user to <strong>ChemDoodle</strong>’s chemical data.<br />

• The elemental and chemical data provided<br />

in <strong>ChemDoodle</strong>.<br />

• How to view the chemical data.<br />

• Where to find references for the data.<br />

• How to use the interactive periodic table.<br />

Elemental Database<br />

The elemental database allows <strong>ChemDoodle</strong><br />

to perform many tasks, from filling the<br />

dynamic periodic table to deducing covalent<br />

bonds to calculating a molecular mass. The<br />

data itself can be viewed by opening various<br />

data tables in <strong>ChemDoodle</strong> or by using the<br />

dynamic periodic table. The data tables are<br />

found in the View menu. Currently<br />

<strong>ChemDoodle</strong> provides 3 data tables:<br />

• Elemental Data - Displays all data in the<br />

elemental database not contained in other<br />

tables.<br />

• Ionization Energies - Displays all<br />

published ionization energies for the<br />

elements.<br />

• Isotopes - Displays all published isotopes,<br />

their masses, natural abundances and halflives.<br />

201<br />

Each table is interactive, and you can click on<br />

a column header to reorder the content by that<br />

column. By clicking again you can reverse<br />

the order of that column. By pressing down<br />

and dragging, you can reorder the columns to<br />

more easily correlate different columns.<br />

References<br />

All data within <strong>ChemDoodle</strong>’s databases are<br />

associated with a unit (if not unit-less) and the<br />

reference source it originated from so you<br />

may assess its quality. The entire set of<br />

references can be viewed at any time by<br />

selecting the References menu item in the<br />

Help menu as shown in Figure D.1. Non-data<br />

related references are also displayed in this<br />

list, including filetype specifications and<br />

Figure D.1: <strong>ChemDoodle</strong>ʼs References List<br />

Interactive Periodic Table<br />

<strong>ChemDoodle</strong> contains an interactive periodic<br />

table of elements for reference, printing and<br />

demonstrations. It is viewable by selecting the<br />

the Interactive Periodic Table menu item in<br />

the View menu. The window that opens is<br />

shown in Figure D.2.<br />

Figure D.2: The Interactive Periodic Table

You may hover over elements and click on<br />

them for additional information. There may<br />

also be groups listed in the top region.<br />

Hovering over a group will desaturate all<br />

other groups. This is shown in Figure D.3<br />

when the mouse pointer hovers over the<br />

Other Non-Metals group.<br />

Figure D.3: Focusing on a group.<br />

The table is customizable and you can choose<br />

from several format options, including the<br />

display of Atomic Mass, Names and Electron<br />

configurations in addition to the element<br />

Symbol. The block in the bottom-left corner<br />

of the periodic table will display the current<br />

format of each element as shown in Figure D.<br />

4.<br />

Figure D.4: Element Format<br />

202<br />

You can also customize graphical options,<br />

such as the element border colors and text<br />

In addition to the traditional classifications<br />

display, you can also choose to display these<br />

other features of the elements:<br />

• CPK Colors - Displays each element with<br />

its CPK (Corey, Pauling, Koltun) color.<br />

• Jmol Colors - Displays each element with<br />

its Jmol color.<br />

• PyMOL Colors - Displays each element<br />

with its PyMOL color.<br />

• State of Matter - Each element is colored<br />

based on its state of matter at the set<br />

temperature. Solids are black, liquids are<br />

blue and gases are red. Unknown states are<br />

grey. A temperature slider will appear in the<br />

controls to set the temperature which is<br />

displayed on the top right of the figure.<br />

• Years of Discovery - Each element is<br />

colored if discovered before the set year of<br />

discovery. A year slider will appear in the<br />

controls to set the year of discovery which<br />

is displayed on the top right of the figure.<br />

Each display format shows off interesting<br />

properties and makes for great in-class<br />

demonstrations, such as the State of Matter<br />

display shown in Figure D.5.

Figure D.5: States of Matter Display<br />

To print the periodic table, click the Print<br />

button at the bottom-right of the window. The<br />

References button will display<br />

<strong>ChemDoodle</strong>’s references and the Close<br />

button will close the Interactive Periodic<br />

Table window.<br />

Appendix E: How<br />

NMR is Simulated<br />

Algorithms<br />

The NMR simulation algorithms are a free<br />

and experimental feature provided in<br />

<strong>ChemDoodle</strong>. The algorithms are<br />

continuously developed and improved.<br />

Shift Prediction<br />

<strong>ChemDoodle</strong> estimates chemical shifts for all<br />

hydrogen or carbon atoms for which<br />

incremental constants are available. The<br />

algorithm is an empirical approach and begins<br />

by identifying key functional groups in a<br />

structure. The identified functional groups are<br />

used to determine base values for the<br />

estimated shifts of the nuclei.<br />

After determining a base shift, a breadth-first<br />

algorithm is employed to look at the chemical<br />

environment surrounding each nucleus. Based<br />

on the functional groups around it,<br />

incremental constants are added to the base<br />

shift to calculate the estimated shift. Other<br />

contributions may be included such as ring<br />

strain and other algorithms.<br />

Splitting<br />

Splitting is determined by a table of typical jconstant<br />

magnitudes and the spin of the<br />

interacting nuclei. Splitting is calculated for<br />

all spins. Splitting magnitudes are determined<br />

from Pascal’s triangle.<br />

Roof Effects<br />

The magnitude for roof effects are determined<br />

by the resolution of the spectrum, set by the<br />

Pulse Frequency parameter, and the relative<br />

adjacency of the interacting peaks. The<br />

simulated roof effects will show a leaning of<br />

204<br />

the split peak towards the peak that is<br />

splitting it. Peaks split by multiple peaks will<br />

lean towards all of them.<br />

Solvent Peaks<br />

Solvent peaks are simulated using the same<br />

algorithms. Splitting from deuterium occurs.<br />

The magnitude ratio for solvent to solute<br />

peaks is determined by the Dilution<br />

parameter.<br />

1 H Rapid Exchange<br />

If the temperature is above 273K, rapid<br />

exchange will occur for hydrogen bonded<br />

protons. These peaks will merge into a single<br />

broadened peak with a shift calculated at their<br />

weighted average. The shift will then be<br />

moved downfield relative to the magnitude of<br />

the temperature.<br />

1 H Anisotropic Effects<br />

If the solvent or solute contain aromatic or<br />

antiaromatic rings, then 1 H nuclei will be<br />

appropriately shielded or deshielded based on<br />

the solvent/solute ratio and the types of rings<br />

involved.<br />

1 H Diastereotopic Pairs<br />

If a methylene is adjacent to a stereocenter,<br />

then the two methylene protons will be<br />

separated into individual peaks. The peaks<br />

will be separated by .3 ppm centered around<br />

the predicted shift for the methylene group.<br />

The choice of nucleus to be shifted upfield or<br />

downfield is random.<br />

13 C Quaternary Carbon Intensity<br />

Reductions<br />

To simulate a lack of Overhauser effects,<br />

quaternary carbons have their peak intensities<br />

reduced by 33%.<br />

Limitations<br />

<strong>ChemDoodle</strong> can only predict shifts for<br />

nuclei where environments are well described

in its database. Functional groups that are not<br />

described well will have poorly calculated<br />

shifts and may result in values around 0 ppm,<br />

which should be ignored.<br />

Since incremental constants do not take into<br />

account structure topography, 3D<br />

conformations will be poorly analyzed. It is<br />

essential that you fully scrutinize all NMR<br />

simulation results from <strong>ChemDoodle</strong>.<br />

To learn more about the algorithms<br />

implemented in <strong>ChemDoodle</strong> and their<br />

accuracy, obtain the references listed under<br />

the Algorithms > Spectroscopy > Nuclear<br />

Magnetic Resonance section of<br />

<strong>ChemDoodle</strong>’s reference list. The reference<br />

list can be viewed by selecting the<br />

Appendix F:<br />

<strong>ChemDoodle</strong> Web<br />

In addition to creating graphics and chemical<br />

files, <strong>ChemDoodle</strong> can also create dynamic<br />

web components. This feature utilizes another<br />

iChemLabs technology, the <strong>ChemDoodle</strong><br />

Web Components library. This section lists:<br />

• Creating <strong>ChemDoodle</strong> Web Components in<br />

• <strong>ChemDoodle</strong> rendering features that are<br />

available in the <strong>ChemDoodle</strong> Web<br />

Components library.<br />

• Other functions for working with<br />

• Learn how generated components work for<br />

both desktop and mobile browsers.<br />

• Restrictions on using <strong>ChemDoodle</strong> Web<br />

Components in your webpages.<br />

Generating <strong>ChemDoodle</strong><br />

Web Components<br />

To generate a <strong>ChemDoodle</strong> Web Component,<br />

1. In the File menu, select the Generate<br />

Web Component... menu item. Make<br />

sure to first have drawn or loaded any<br />

content you wish to be displayed on the<br />

2. If you had selected a Molecule or<br />

Spectrum before opening this window,<br />

then an appropriate viewer will be<br />

206<br />

selected. Otherwise, choose the Type of<br />

component you would like to create.<br />

3. If the Type of component chosen requires<br />

content, then click on the Select button<br />

and choose the content to be displayed in<br />

the component.<br />

4. As is shown in Figure F.1, set the size of<br />

the component and the component name<br />

(a random name is generated for you to<br />

avoid name clashes).<br />

Figure F.1: Generate <strong>ChemDoodle</strong> Web<br />

Component Window<br />

5. Define any visual specifications for the<br />

component. It will inherit compatible<br />

visual specifications from the current<br />

document style sheet in <strong>ChemDoodle</strong>.<br />

6. In the Relevant Startup Parameters<br />

tree, select any Javascript variables or<br />

functions you would like to define.<br />

Placeholders for them will be generated in<br />

the Javascript code.<br />

7. Press the Preview button to preview your<br />

<strong>ChemDoodle</strong> Web Component in your<br />

main browser as shown with Apple Safari<br />

in Figure F.2.<br />

Figure F.2: Previewing the Web Component<br />

(Apple Safari shown)

8. Make any changes, if necessary.<br />

9. Click the Generate button to generate the<br />

Javascript for the component.<br />

Paste the generated Javascript directly in<br />

your webpage (in the tag) in the<br />

location you prefer the component to appear.<br />

You must first install the <strong>ChemDoodle</strong> Web<br />

Components library for your webpage for<br />

these components to work. Installation<br />

instructions are provided on the official<br />

<strong>ChemDoodle</strong> Web Components website at<br /><br />

download.<br />

Generating Javascript Data<br />

Files for Use with<br />

If you are displaying several Web<br />

Components with the same molecule/<br />

spectrum or are doing advanced development,<br />

it may be more efficient to generate the data<br />

first in a Javascript data file to be loaded into<br />

your webpage. To do this, perform the<br />

1. Draw all structures and spectra to be used<br />

in your webpage on the Doodle Board.<br />

207<br />

2. In the File menu, select the Save as...<br />

3. In the file chooser that appears, select the<br />

location and the name of the file to be<br />

4. In the drop down selection for the file<br />

type, choose iChemLabs <strong>ChemDoodle</strong><br />

Javascript Data.<br />

5. Press the Save button.<br />

All structures and spectra on the Doodle<br />

Board will be saved to the <strong>ChemDoodle</strong> Web<br />

Component JSON format in Javascript. To<br />

use this file, link it into the HTML page as a<br />

Javascript resource or copy and paste the<br />

source of the file into your Javascript code.<br />

Use the variable names declared in that file to<br />

use them.<br />

Molecules begin with 'molecule' and spectra<br />

begin with 'spectrum'. You should rename<br />

these variables to not clash with other<br />

declared Javascript variables if necessary.<br />

These data structures can be used as is, such<br />

as for immediate loading into Canvases via<br />

load functions.<br />

Optimizing PDB Files<br />

The <strong>ChemDoodle</strong> Web Components can<br />

handle many of the features in PDB files.<br />

Unfortunately, reading and processing all of<br />

the data in a PDB file can be very time<br />

consuming in Javascript. <strong>ChemDoodle</strong><br />

contains a special Optimize PDB to JSON...<br />

function in the File menu to predigest PDB<br />

content into the native <strong>ChemDoodle</strong> Web<br />

Components JSON format. To do this,<br />

1. In the File menu, select the Optimize<br />

PDB to JSON... menu item.

2. A window will appear. Select the Choose<br />

Input button and locate the PDB file you<br />

would like to optimize.<br />

3. The output file path will be automatically<br />

generated for the same containing folder<br />

and name, but with an extension of .js.<br />

Click the Choose Location button to<br />

change the location of the output file.<br />

<strong>ChemDoodle</strong> will automatically change<br />

the extension to .js.<br />

4. When satisfied with the paths, select the<br />

Optimize button. Depending on the size<br />

of the PDB file, this function may take<br />

several seconds to complete.<br />

5. To use the Javascript file with the<br />

<strong>ChemDoodle</strong> Web Components, just<br />

include it in your web project, and import<br />

it as a URI resource on the HTML page it<br />

is used. The PDB will be represented as a<br />

Molecule data structure with the same<br />

name as the input file, prepended by the<br />

string “pdb_”. For instance, if you<br />

optimized the file “1BNA.pdb”, then you<br />

can load the variable pdb_1BNA directly<br />

into your component with the<br />

loadMolecule() function.<br />

Generating Components for<br />

Mobile Devices<br />

<strong>ChemDoodle</strong> Web Components will work in<br />

all browsers including those on mobile<br />

devices, notably iPhone OS (iPhone, iPod<br />

Touch, iPad) and Android devices. All<br />

rendering is supported on the mobile devices<br />

and touch events and gestures are recognized<br />

by the components.<br />

There is no difference between generating<br />

components for desktop browsers versus for<br />

mobile browsers. The only consideration<br />

would be the size of the component. The<br />

208<br />

<strong>ChemDoodle</strong> Web Component generator<br />

contains a drop down selection to the right of<br />

the dimension panel containing preset sizes<br />

for mobile devices. Use it to quickly set<br />

standard sizes if preferable.<br />

Rendering Compatibility<br />

Even though <strong>ChemDoodle</strong> and the<br />

<strong>ChemDoodle</strong> Web Components library are in<br />

the same family of products, their feature sets<br />

are not identical. Many graphical features and<br />

visual specifications provided in<br />

<strong>ChemDoodle</strong> are not yet available in<br />

Use the <strong>ChemDoodle</strong> Web Component<br />

window in <strong>ChemDoodle</strong> to help guide you<br />

through the available visual specifications in<br />

the <strong>ChemDoodle</strong> Web Components library.<br />

Use the Preview button to ensure your<br />

graphics will be correctly represented to your<br />

satisfaction.<br />

License<br />

The <strong>ChemDoodle</strong> Web Components library is<br />

licensed under version 3 of the GNU<br />


following exception:<br />

As a special exception to the GPL, any<br />

HTML file in a public website or any free<br />

web service which merely makes function<br />

calls to this code, and for that purpose<br />

includes it by reference, shall be deemed a<br />

separate work for copyright law purposes. If<br />

you modify this code, you may extend this<br />

exception to your version of the code, but<br />

you are not obligated to do so. If you do not<br />

wish to do so, delete this exception<br />

statement from your version.<br />

This means that your websites do NOT need<br />

to be released under GPL if you call the<br />

<strong>ChemDoodle</strong> Web Components library,

unless that HTML page is part of a<br />

commercial product or service.<br />

Am I allowed to use this?<br />

The license protects the code if one changes it<br />

or integrates it with a proprietary product. If<br />

you are concerned about how the license will<br />

affect you, then you should contact us. If you<br />

do not fully understand the GPL license or<br />

you answer yes to any of the questions listed<br />

next, then you should contact us before using<br />

this library.<br />

• Will you be changing this library’s source<br />

code?<br />

• Will you be integrating this library with<br />

another product that you will be distributing<br />

to the public in any form?<br />

• Are you part of a commercial organization?<br />

• Will you need access to iChemLabs cloud<br />

services (using the<br />

<strong>ChemDoodle</strong>.iChemLabs package)?<br />

Attributions on webpages for the use of<br />

<strong>ChemDoodle</strong> and <strong>ChemDoodle</strong> Web<br />

Components are greatly appreciated, but not<br />

required.<br />

Several <strong>ChemDoodle</strong> Web Component<br />

badges are provided for this purpose if you<br />

choose to use them at http://<br /><br />

Further Information<br />

For further information regarding the<br />

<strong>ChemDoodle</strong> Web Components, including<br />

webpage installation instructions, the most<br />

recent version and updates, advanced<br />

programming and use of the API, examples<br />

209<br />

and browser compatibility, visit the official<br />

Appendix G:<br />

Mobile<br />

<strong>ChemDoodle</strong> Mobile is the mobile<br />

companion to <strong>ChemDoodle</strong>. <strong>ChemDoodle</strong><br />

Mobile is free for all customers of<br />

<strong>ChemDoodle</strong>. This section lists:<br />

• What <strong>ChemDoodle</strong> Mobile is.<br />

• How to log into <strong>ChemDoodle</strong> Mobile.<br />

• The features in <strong>ChemDoodle</strong> Mobile.<br />

• Transferring structure data between<br />

<strong>ChemDoodle</strong> and <strong>ChemDoodle</strong> Mobile.<br />

Supported Platforms<br />

<strong>ChemDoodle</strong> Mobile is supported on both<br />

iOS and Android.<br />

iOS<br />

<strong>ChemDoodle</strong> Mobile can be installed on<br />

iPhones, iPod Touches and iPads via the<br />

iTunes AppStore. You can find <strong>ChemDoodle</strong><br />

Mobile for iOS here: <strong>ChemDoodle</strong> Mobile on<br />

the iTunes AppStore<br />

Android<br />

phones running the Android operating system<br />

via the Android Marketplace here:<br />

<strong>ChemDoodle</strong> Mobile on Google Play<br />

Logging in to <strong>ChemDoodle</strong><br />

All <strong>ChemDoodle</strong> customers receive free<br />

accounts to log into <strong>ChemDoodle</strong> Mobile.<br />

210<br />

This is the same account you use to sync with<br />

your online account in <strong>ChemDoodle</strong> desktop.<br />

Your username is the email address your<br />

activation code is associated with, and your<br />

password is the last 4 characters of your<br />

activation code. The password must be either<br />

in all uppercase or all lowercase.<br />

<strong>ChemDoodle</strong> Mobile<br />

Features<br />

<strong>ChemDoodle</strong> Mobile is a calculator for drawn<br />

organic structures. There are four main<br />

windows: Draw, Calculate, Spectra and<br />

Help. The Draw window shows a typical<br />

<strong>ChemDoodle</strong> sketcher, where you can draw<br />

and store your structures. The Calculate page<br />

calculates properties and the Spectra page<br />

simulates NMR spectra. All spectra are<br />

interactive. The Help page contains a<br />

thorough help guide.<br />

Calculations<br />

• Molecular Mass<br />

• Monoisotopic Mass<br />

• Average Molecular Polarizability<br />

• Polar Surface Area<br />

• logP<br />

• Mass Parent Peak (Isotopic Distribution)<br />

• 1H NMR<br />

Transferring Data between<br />

<strong>ChemDoodle</strong> Desktop and<br />

Data saved to your online account can be<br />

accessed from any iChemLabs application<br />

that uses that account.<br />

To create data in <strong>ChemDoodle</strong> for use in<br />

<strong>ChemDoodle</strong> Mobile, perform the following<br />

1. Draw the structure to be loaded into<br />

<strong>ChemDoodle</strong> Mobile in a new document<br />

2. Log into your online account by using the<br />

Sync with Online Account... menu item<br />

3. Select the Save as Online File... menu<br />

item in the File menu.<br />

4. Choose a name for your structure and<br />

save it.<br />

5. Log into <strong>ChemDoodle</strong> Mobile.<br />

6. Press the Load button in <strong>ChemDoodle</strong><br />

Mobile and then select From Account.<br />

7. Choose the file you just saved from<br />

<strong>ChemDoodle</strong> to load it.<br />

In the reverse manner, structures you saved in<br />

<strong>ChemDoodle</strong> Mobile can be edited in<br />

NOTE: <strong>ChemDoodle</strong> Mobile can only<br />

handle one molecule a time. If you load a<br />

large document with many molecules and<br />

shapes, only the first molecule will be used.<br />

If you then save that file in <strong>ChemDoodle</strong><br />

Mobile, you will override the original file and<br />

lose the additional structures and shapes<br />

present in that file.<br />

Appendix ICL-1:<br />

Technical Support<br />

When to Contact Customer<br />

Service<br />

While we do our best to debug and test<br />

<strong>ChemDoodle</strong>, a few bugs will always slip<br />

past us. Because of this, you may have<br />

encountered an issue with <strong>ChemDoodle</strong>. We<br />

certainly want your experience with<br />

iChemLabs software to be as enjoyable and<br />

hassle free as possible and we will do our best<br />

to address any issues you bring to our<br />

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Figure ICL-1.1: Contact Customer Service Menu<br />

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  • Recommendations

The Future of Scientific Software <strong>ChemDoodle</strong> ® <strong>v5.0</strong> <strong>User</strong> <strong>Guide</strong> iChemLabs

  • Page 2 and 3: Copyright © 2006-2012 iChemLabs, L
  • Page 4 and 5: Drawing Controls ..................
  • Page 6 and 7: Charges ...........................
  • Page 8 and 9: Removing individual Objects .......
  • Page 10 and 11: Image Format Compatibility ........
  • Page 12 and 13: Introduction This User Guide provid
  • Page 14 and 15: will still have to individually act
  • Page 16 and 17: • The only chemical data format y
  • Page 18 and 19: Toolbars Toolbars Figure 1.2: ChemD
  • Page 20 and 21: Ruler Guides There are two rulers a
  • Page 22 and 23: • Phytomedicine Document • RSC
  • Page 24 and 25: Saving Documents To save your docum
  • Page 26 and 27: The Workspace The ChemDoodle worksp
  • Page 28 and 29: • Open - Open a recognized chemic
  • Page 30 and 31: • Clear - Remove all content from
  • Page 32 and 33: • SMARTS... - A textfield will ap
  • Page 34 and 35: • Add Frame> - Contains various f
  • Page 36 and 37: structures to embed them in 3D. Thi
  • Page 38 and 39: of formation of a molecule at the s
  • Page 40 and 41: • Select Tab Left - This function
  • Page 42 and 43: Files + Formatting Toolbar Figure 1
  • Page 44 and 45: • cyclooctane ring • cyclobutad
  • Page 46 and 47: • Brackets - Square (pair), paren
  • Page 48 and 49: allow new bonds to be placed with a
  • Page 50 and 51: Figure 2.4: An expanded widget Widg

Elemental Analysis Widget Purpose T

Button Function The Choose Start Po

the structure from the main structu

copyrighted materials, consult your

the Multiplet Tool widget button or

Lastly, the widget is initially sma

Search Widget Purpose The Search wi

it low and providing smaller root s

If you set an atom's label to one t

TLC Canvas Widget Purpose The TLC C

the control points that appear, and

you have located where to place the

e the Interpret Chemically button,

place the bond in the preferred ori

To change the z-order of bonds when

Placing Rings with Fixed Lengths an

Placing Templates at Non-fixed Leng

2. Right-click on the hovered attri

6. Positive Dipole 7. Negative Dipo

Placing Orbitals at Non-fixed lengt

1. Select a line tool by expanding

Changing Arc Angles Arc angles can

5. Release the mouse to set the new

Drawing Ovals To draw an oval, perf

emptying the current selection. Per

4. Release the mouse to set the pai

1. Select the content to be measure

Chapter 5: Editing Content Overview

Select the Inverse of the Current S

Stacking Stacking will place all co

Fonts To change the fonts of atom l

platforms. The pinwheel color choos

Chapter 6: Advanced Chemistry and C

you want to search for a substructu

• Exhaustive Ring Count - The tot

• Critical Volume - Estimates the

Flipping Glassware To flip the clip

implicit hydrogen auto-rendering, j

Several constructs are supported by

• Euler Facet Rings - The Euler f

By default, mouse movements while r

arrow (to toggle start) or right ar

constituent reactants and products

Figure 7.3: Edit Reaction Window Re

Uninterpretable Spectra There are m

elease the mouse. A dotted grey lin

Chapter 9: Visual Specifications Ov

• Number Sliders - Define a numbe

Attributes Colors Fill/Text - A col

Circle Radius - An number slider to

4. Change the visual specifications

Advanced document rendering setting

which is the closest supported colo

Image Scaling Image scaling control

Therefore, ChemDoodle allows you to

Pasting Data from Other Application

Importing Chemical Content from Ima

comments on Mac OS X, or with OpenO

Clipboard Settings In Advanced Pref

in other applications on your opera

By default, ChemDoodle will automat

Appendix B: Chemical File Types Ove

File Conversion Tool ChemDoodle con

ACD/ChemSketch Document About This

• kCDXProp_ChainAngle • kCDXPro


Chemical Markup Language About Chem

y the application that reads the SM

Supported Records • TITLE • JCA

• arc • Fill_style • Transpar

• Atom_type • Atom_symbol • A

• All coordinates are in bond len

Schrödinger Files About MMD Files

Tripos Mol2 About A Tripos Mol2 fil

• Single spaces are used to delim

Calc On all platforms, text, images

You may hover over elements and cli

Appendix E: How NMR is Simulated Al

Appendix F: ChemDoodle Web Componen

2. A window will appear. Select the

Appendix G: ChemDoodle Mobile Overv

Appendix ICL-1: Technical Support W

4. When a feature is completed, it

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how to add formal charges on chemdoodle

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how to add formal charges on chemdoodle

#Chemdoodle help formal charge plus#

#chemdoodle help formal charge professional#.

To complete this exercise, try drawing both of the representations of the sulfate ion shown above. Note that the overall charge on this ion is -2. This is done by setting up the data and a few styles for the Canvas. The center-left number defines the multiple count. You can create renderings of Lewis Dot Structures with the ChemDoodle Web Components.

chemdoodle help formal charge

The bottom-right number defines the repeat count. The top-right number defines the charge amount. Pressing the up and down arrows will increment and decrement the values at these positions. Drag diagonally to the opposite corner of the rectangle defined by the brackets and release the mouse, In this mode, up and down arrows will be displayed at various positions on the bracket. ZINC ensuring physical similarity of six properties (molecular weight, formal charge. To show the formal charge on an atom in ChemDoodle, use the + or - tools that have.

For example, in the drawing of the sulfate ion (SO42-) shown on the left, each oxygen atoms is assigned a formal charge of minus one and the sulfur atom is assigned a formal charge of plus two. Add a structure to the canvas and then add brackets around it by pressing the mouse down where the first corner of the bracket will start. DUD-E is designed to help test docking algorithms by providing. Formal charges may be associated with atoms in Lewis structures. To place brackets a structure, use the bracket from the toolbar.

To show the charge on an ion in ChemDoodle, use the bracket tool described below. Check out ChemDoodle 3D Get both now for only 15 ChemDoodle 3D 3D Chemical Graphics, Animations and Modeling Professional Quality, Affordable Prices Trusted by thousands of institutions in over 100 countries Chemistry World Review (Win/Mac/Linux v7) Dr. In a Lewis structure, the charge on an ion is placed as a superscript on surrounding square brackets, as shown for the sulfate ion in the drawing to the right. The overall ion charge is a property of an ion as a hole and is not associated with a particular atom.

chemdoodle help formal charge

One can calculate the formal charges for any given atom with the help of the following formula: F. These charges help in knowing if the given structure of the molecule is stable or not. To show the formal charge on an atom in ChemDoodle, use the + or - tools that have been described previously. Formal charge is the individual electric charges on the atoms in a given polyatomic molecule. For example, in the drawing of the sulfate ion (SO_4^2-) shown on the left, each oxygen atoms is assigned a formal charge of minus one and the sulfur atom is assigned a formal charge of plus two. Transcribed image text: Formal charges may be associated with atoms in Lewis structures.

how to add formal charges on chemdoodle


Tutorial > Lewis Dot Structures

You can create renderings of Lewis Dot Structures with the ChemDoodle Web Components . This is done by setting up the data and a few styles for the Canvas .

For atoms, it is important to show lone pairs by setting the Atom.numLonePair variable as shown in the following examples. The sketcher also has tools to allow the drawing of lone pairs. The lone pairs will automatically be placed in the optimal positions. You can change how lone pairs appear with the following styles:

  • atoms_lonePairDistance_2D - This is the distance between the lone pair and the atom.
  • atoms_lonePairSpread_2D - This is the distance between the electrons in the pair.
  • atoms_lonePairDiameter_2D - This is the diameter of the dots that represent the electrons.

Additionally, you will want to display all carbon labels by setting the atoms_displayAllCarbonLabels_2D style to true, and by turning off the display of implicit hydrogens by setting the atoms_implicitHydrogens_2D style to false.

Neither the MDL MOLFile or Daylight SMILES formats support lone pairs, so validation must be done programmatically by accessing the Molecule data structure, by visual analysis, or by using the ChemDoodle JSON format .

For bonds, set the bonds_lewisStyle_2D style to true for traditional Lewis Dot Structures. You may also want to set up the atom coordinates longer bond lengths to clearly show off multiple bonds and at 90° angles.

You can also use the ChemDoodle.iChemLabs.createLewisDot() function from iChemLabs Cloud services . This function creates a Molecule that represents the input molecule as a Lewis Dot Structure using 90° angles and appropriately place lone pairs to satisfy the octet rule (charges will need to be present on the input molecule).

Just a simple one to start, Neon with 8 electrons:

Chloroform, showing carbon labels and with implicit hydrogens off:

Hydrogen sulfate anion:

Get your work done with our popular desktop software.

how to add formal charges on chemdoodle

ChemDoodle 2D

how to add formal charges on chemdoodle

ChemDoodle 3D


  1. Solved Add formal charges. Consider the incomplete

    how to add formal charges on chemdoodle

  2. Solved Add formal charges to each resonance form of HCNO.

    how to add formal charges on chemdoodle

  3. Solved Draw I with three lone pairs and add formal charges,

    how to add formal charges on chemdoodle

  4. Draw I with three lone pairs and add formal

    how to add formal charges on chemdoodle

  5. Solved Add formal charges to each resonance form of HCNO.

    how to add formal charges on chemdoodle

  6. OneClass: Add formal charges to a,b and c ..and which structure would be favored? Add formal

    how to add formal charges on chemdoodle


  1. ChemDoodle 2D to 3D Coordinates demo

  2. Calculation of Oxidation no of Central Metal Atom in a Complex

  3. How To Add Formal Attire to Rush ID Pictures

  4. ChemDoodle Shorts: Functional Groups

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  6. Cheryl Tweedy & Kimberley Walsh with Frank Skinner (P1)


  1. What Is the Formal Charge on Nitrogen in NO3?

    The formal charge of nitrogen in the compound NO3 is plus 1. The whole nitrate ion carries a total charge of minus 1 when combining the charges of the one nitrogen atom and three oxygen atoms.

  2. What Is the Charge on a Sulfate Ion?

    The formal charge of the sulfate ion, which has the molecular formula (SO4)2-, is -2. Ions that have a negative charge are called anions, and positively charged ions are called cations.

  3. What Is the Ionic Charge of SO4?

    The ionic charge of SO4 is -2. Ionic, or formal, charge is not an actual charge of the chemical, but rather an estimate of electron distribution within a molecule or ion, based on a simplified model.

  4. Answer ChemDoodle Sketcher Questions

    Click the down arrow next to the attributes button. options for changing the attributes of an atom · Click increase charge to increase the charge, or decrease

  5. Chemdoodle help formal charge

    To show the formal charge on an atom in ChemDoodle, use the + or - tools that have been described previously. This sum does equal the overall

  6. ChemDoodle 3D Chemoodie Sketcher. Formal charge, ion

    To show the formal charge on an atom in ChemDoodle, use the + or -tools ... add brackets around it by pressing the mouse down where the first

  7. ACHIEVE: How to add formal charges and find “missing” molecules

    ACHIEVE: How to add formal charges and find “missing” molecules. 3.4K views · 2 years ago ...more. Roxi Hulet. 17.2K. Subscribe.

  8. ChemDoodle Shorts: Lewis Dot Structures

    Comments. thumbnail-image. Add a comment... 4 ... Lewis Structures, Introduction, Formal Charge, Molecular Geometry, Resonance, Polar or Nonpolar.

  9. ChemDoodle Shorts: Lewis Dot Structures

    In this #ChemDoodle Short, we will be discussing #Lewis dot structures. The focus is on drawing Lewis structures for simple molecules.

  10. ChemDoodle v5.0 User Guide

    Adding Charges ................................ 84<br />. Incrementing and ... <strong>ChemDoodle</strong> guess formal charges for a<br />.

  11. Demos > 2D Sketcher

    Charges - After a charge sign has been selected, hover an atom and click the mouse to add or subtract from that atom's charge amount. Lone Pairs - After a

  12. Chemdoodle help formal charge

    You can create renderings of Lewis Dot Structures with the ChemDoodle Web Components. chemdoodle help formal charge. The bottom-right number

  13. Tutorial > Lewis Dot Structures

    (charges will need to be present on the input molecule). Examples. Just a

  14. ChemDoodle 3D Version History

    The major new feature is the ability to add charges, radicals