Version History

7.0.1

October 08, 2014

Executive Summary

This is a bugfix update fixing some issues brought to our attention. These issues only affected small groups of users, but we still recommend you update. For changes to version 7, scroll down.

Fixes

  1. Fixed bug in creating ChemDoodle Web Components where integer specifications were not properly set.
  2. Fixed bug in creating ChemDoodle Web Components that prevented spectra from displaying.
  3. Fixed bug where dragging to move content failed on some Macs and a drag and drop action would commence instead.
  4. Fixed issue where some tweets from ChemDoodle were failing.
  5. Resolved graphical glitch where a two token, two line atom label could not be centered.
  6. Tweaked startup memory parameters on Windows as the higher memory allocations were causing issues on older machines.
  7. Fixed issue where another application on Mac could corrupt the Java installation and corrupt ChemDoodle by placing incompatible libraries in the public Java classpath. Be careful of other Java applications that you install!
  8. Some anti-virus software were incorrectly flagging ChemDoodle’s uninstaller. We have made a change to avoid this false positive.

Executive Summary

ChemDoodle 7 is a massive update to ChemDoodle. Included are hundreds of new features and improvements, recommended to us by users like you. Enjoy and please spread the word!

New Features

  1. A new and improved interface based on the feedback from the last 6 years. The new interface is focused on the content and allows you to maximize your drawing areas. Widgets are now floating and can be individually enabled and disabled.
  2. ChemDoodle 3D. A new application for creating 3D graphics and more for the sciences. You have full control over the 3D graphics and animations, including text. Distance, angle and torsion measurements are provided. Also a corresponding builder for 3D ChemDoodle Web Components. There is so much more.
  3. Full multipage document support. Create lists of pages or grids. Draw between all pages and print them out.
  4. BioArt. Large, full color, libraries of new art for use in biological figures, including animals, organs and organelles.
  5. A set of 48 safety symbols included in the glassware set.
  6. Significant performance improvements, in many cases 20x faster than v6. ChemDoodle will now load faster, work faster and respond faster.
  7. New drawing features: collapse fragments to labels, incrementing list attributes (to quickly number or designate parts of structures), new TLC options, rotate atom labels if only a single atom is selected (as opposed to the global option), and more visual specifications among others.
  8. Twitter integration.
  9. Integration with the LabArchives ELN.
  10. Support for both Java 6 and 7 on Mac OS X.
  11. Dozens more improvements and additions.

7.0.0

September 05, 2014

Executive Summary

ChemDoodle 7 is a massive update to ChemDoodle. Included are hundreds of new features and improvements, recommended to us by users like you. Enjoy and please spread the word!

New Features

  1. A new and improved interface based on the feedback from the last 6 years. The new interface is focused on the content and allows you to maximize your drawing areas. Widgets are now floating and can be individually enabled and disabled.
  2. ChemDoodle 3D. A new application for creating 3D graphics and more for the sciences. You have full control over the 3D graphics and animations, including text. Distance, angle and torsion measurements are provided. Also a corresponding builder for 3D ChemDoodle Web Components. There is so much more.
  3. Full multipage document support. Create lists of pages or grids. Draw between all pages and print them out.
  4. BioArt. Large, full color, libraries of new art for use in biological figures, including animals, organs and organelles.
  5. A set of 48 safety symbols included in the glassware set.
  6. Significant performance improvements, in many cases 20x faster than v6. ChemDoodle will now load faster, work faster and respond faster.
  7. New drawing features: collapse fragments to labels, incrementing list attributes (to quickly number or designate parts of structures), new TLC options, rotate atom labels if only a single atom is selected (as opposed to the global option), and more visual specifications among others.
  8. Twitter integration.
  9. Integration with the LabArchives ELN.
  10. Support for both Java 6 and 7 on Mac OS X.
  11. Dozens more improvements and additions.

6.0.1

June 09, 2014

Executive Summary

This is a bugfix update fixing some issues brought to our attention. This update introduces a much more powerful EXE build for Windows, and addresses stability issues related to using grouped objects.

Fixes

  1. A new EXE is built for Windows. This EXE will now use either the 64 bit or 32 bit JRE if available. If both are available, the new executable defaults to the 64 bit JRE.
  2. iChemLabs Updater has been updated to work in mixed Java environments on Mac OS X. Those with both Java 1.7 and 1.6 installed on Mac OS X will notice that ChemDoodle will not automatically open after the update. Ignore this, as this new updater corrects this issue.
  3. Fixed IUPAC naming issue where locants were not correct in ring blocks for stereocenters.
  4. Fixed IUPAC naming where a double dash could occur.
  5. Fixed bug where groups would not always resize all their contents.
  6. Fixed crash if non-recognized colors were present in ChemDoodle Documents.
  7. Colors in groups and reaction area text are now stored correctly in ChemDoodle Documents.
  8. Limited the size of files previewed by the Quicklook plugin to 200MB.

6.0.0

December 01, 2013

Executive Summary

ChemDoodle 6 is a massive update to ChemDoodle. Included are hundreds of fixes and new features, recommended to us by customers. Enjoy and please spread the word!

New Features

  1. IUPAC naming with over 20 options!
  2. Carbon nanotube and prism builders. Both zigzag and armchair nanotubes can be built. These tools quickly produce 3D geometries.
  3. Auto updating labels can now be attached to molecules, so they will update with IUPAC names, molecular formulas and more.
  4. Mac OS X Quick Look plugin. Easily preview all your chemical files in Finder just by pressing the space key.
  5. More Windows support, including a more powerful tool for supporting Windows filetype associations with the option to unassign types, support for the MDLCT and MDLSK clipboard formats for copying and pasting between a wider array of chemical applications, and greatly improved OLE support to allow for double-clicking to edit structures.
  6. More glassware, including a new organized glassware window. You can now also remove liquid from the templates.
  7. Significantly improved graphics. Graphics in ChemDoodle were already very good, but we took a look at all the graphics at very high scales and resolutions. We have made sure to focus on all the little details. Bond join edge cases have been improved. Hashes are now auto centered, making recessed bonds and dashed bonds look much nicer. Other bond types have been scrutinized for the best aesthetics. Convex hull algorithms have been built for better placement of bonds around labels. Cis double bonds will now prefer the inside edge. Circles over charges now only surround the number. Aromatic ring circles now meld to the shape of aromatic circles. Arrows look nicer. You won’t find better graphics in any other application.
  8. 3D coordinate generation.
  9. A new 180° chain angle clean option for easily creating Lewis structures and figures with 90° angles.
  10. Complex embedded ring systems (like corannulene) now clean very well in 2D.
  11. Added resolution controls to the Elemental Analysis widget.
  12. Meso stereochemistry support.
  13. An advanced formatted text system for the system clipboard. You can now copy and paste your molecular formulas, IUPAC names and others into word processing applications with formatting intact.
  14. Many other minor, but useful features: option for the delete key to decrement bonds, nominal mass counter, improvements to the TLC Plate widget, improvements to arc placement previews, alt and shift now modify attribute placement just like placing bonds, improved file chooser previews for data files, more templates for the Templates widget, and more.
  15. Squashing of dozens of bugs.

5.1.0

April 26, 2013

Executive Summary

This update addresses several issues brought to our attention and adds a bunch of minor features. Support is added for ChemDoodle Web Components v5.

Additions

  1. Updated ChemDoodle Web Components support to version 5.
  2. It is now easy to copy/paste ChemDoodle JSON (for easier interaction with the web sketcher on a webpage) directly from the Edit menu.
  3. Added a Paste and Match Style menu item to the Edit menu to paste content and match the current style sheet.
  4. Zero order bonds are now rendered as a line of dots.
  5. Bonds can now easily be drawn between two atoms by just dragging the mouse close to the second atom when drawing.
  6. Half-arrows can now be drawn on bezier curves.
  7. Added 31 new glassware templates.
  8. You can now change the arrow type (full/half) in the shapes settings dialog.
  9. Added rearrangement arrow option to the shapes settings dialog.
  10. In the General panel in Preferences, you can now control the highlight, selected, preview and error colors.
  11. When using the Carbon Chain tool, the carbon chain will now invert in half portions depending on where the mouse is located. More angles are now allowed.
  12. Added a Delocalize menu item to the Structure menu to delocalize a Kekule structure.
  13. Added a menu accelerator for Copy as SMILES and Paste as SMILES.
  14. Improved the bitmap rendering of straight arrows.
  15. Minor graphical improvements inlcuding line highlighting and anchor rendering.

Fixes

  1. Improved PubChem results.
  2. Implicit hydrogens are now preserved in MolGrabber if they help to define stereocenters.
  3. Fixed issue where fusing rings to bonds did not always choose the best orientation in the optimize zone.
  4. Mass calculations now take into account atom charges.
  5. Improved NMR simulation chemical shift accuracy for acetylene and aldehyde protons.
  6. Fixed bug where pasting chemically interpretted atoms would ignore formatting.
  7. Fixed issue where switching to new document when a text field is open reopens the old text field.
  8. Fixed bug where formatting a carbon label caused file corruption.
  9. Fixed bug where closing a blank formatted atom field would cause an error.
  10. Editing arrows using the shape settings window can now be undone.
  11. Reduced the width of the Unicode button in the Symbols widget to facilitate resizing.
  12. Resolved issues where using the shift key on Windows would cause some issues when editing content with a selection tool.
  13. Resolved issues where using the alt key on Windows would cause some issues when selecting content with a selection tool.
  14. Removed the invisible rotation anchor that would be present for single selected atoms.
  15. Decorated reaction arrows now correctly shift text to avoid overlaps.
  16. Fixed issue where using the atom start select tool in the Line Notation Pad widget would cause it to crash on rare occasions.
  17. Selection tools no longer allow the hovering of attributes when selecting single objects.
  18. Fixed issue when url encoding was required to properly query ChemExper.
  19. JCAMP spectra units are now detected regardless of case.
  20. Fixed Kekulizer issue where errors could occur.
  21. Improved detection of MOLFile variations.
  22. Minor textual corrections.

5.0.1

December 06, 2012

Executive Summary

This update addresses several issues brought to our attention since the release of ChemDoodle 5.

Additions

  1. Added a color detection tool to the Quick Color button. This tool will provide you with a magnifying glass to detect colors already in use in the document.
  2. Holding down the slash key while placing carbon chains will invert the chain.
  3. Added molecular diameter descriptor (longest topological distance).

Fixes

  1. Fixed OLE bug that caused pasted ChemDoodle content to print poorly. This will not fix content that has already been pasted. To fix this content, round-trip the data back into ChemDoodle and repaste back into the other application. You can also use the other applications export to PDF, if available, as a workaround.
  2. Fixed bug that prevented ChemDraw files from being written when a text area was present.
  3. Fixed bug where a subscript in long atom labels caused unwanted whitespace to appear.
  4. Fixed label offset issue when previewing certain filetypes in the file chooser.
  5. Resolved issue where the Doodle Board could not be moved on Linux.
  6. Rotating in 3D now correctly checks for atom overlaps.
  7. Chemical SMILES is now off by default for system clipboard content, in order to avoid rare errors where very complex molecules may take a while to evaluate.
  8. Conversion tool success message now includes the number of molecules converted.

5.0.0

October 13, 2012

Executive Summary

ChemDoodle 5 is a massive update to ChemDoodle. Included are hundreds of fixes and new features, recommended to us by customers. Please enjoy and spread the word!

New Features

  1. Round-trip editing on Windows via OLE. (Round-trip editing is already provided on Mac OS X)
  2. Round-trip editing on Linux!
  3. A revamped shape system for much easier and more precise manipulation of shapes, especially in crowded figures. Also a new quick colors button to now quickly change colors of objects.
  4. Bezier curves for complex shapes and mechanisms.
  5. Fragmentation tools.
  6. More functions for handling chemical data on the clipboard.
  7. File chooser previews.
  8. 77 new glassware templates!
  9. Hundreds of other features and improvements.

4.1.1

December 05, 2011

Executive Summary

This minor update fixes a number of issues.

Fixes

  1. Fixed rare, but serious, issue where a corrupted autosave would prevent ChemDoodle from loading. Corrupted autosaves are now just renamed so they can be recovered, if possible.
  2. Greatly improved compatibility with ISIS/Sketch files, both SKC and TGF formats. Compressed labels are now read in properly, and various bugs have been fixed.
  3. Fixed bug where TLC plates were not properly read in from ChemDoodle Documents.
  4. Recessed bonds are now properly anti-aliased.
  5. Fixed rare stereochemistry issue where a very complex structure would not be analyzed correctly.
  6. Fixed issue where ODG output would not preserve transform scaling.
  7. Fixed issue where bitmap images from other programs would fail to be pasted, showing an embedded image failure box.
  8. Fixed where formatting was ignored when chemically interpretation was disabled for a single element label.
  9. The parent peak in the Elemental Analysis widget now correctly resizes when the widget is resized.
  10. Improved document shadow resizing, in some rare cases, it would not resize leaving an odd sized shadow behind the document.

4.1.0

November 16, 2011

Executive Summary

This significant update brings dozens of new features and fixes recommended by our users. Included are a significantly improved rendering engine, autosaving, 52 new glassware templates (and the ability to flip them), high-quality bitmap image output control, and other new features. Significant fixes include the disabling of terminal carbon label display by default, the restoration of PubChem functionality in the MolGrabber widget, greatly improved ChemDraw file reading, fixing of all known stereochemistry detection issues, and much more.

Additions

  1. The rendering engine has been upgraded with additional improvements. Bond joins will now look nice regardless of the end cap chosen. The default end cap is now butt for flat bond ends and sharp looking structures. The second line in double bonds will now be placed more appropriately when in constrained structures, such as norbornadiene. Symmetrical double bonds will now extend to connect to the bonds they attach to. Protruding bond merging to multiple single bonds has been improved. Protruding and bold and thin double bonds now merge. Atom labels will now base their vertical alignment on a non superscript or subscript token if a superscript or subscript token is the attachment point. A visual specification to control bond merging is now provided.
  2. Autosaving. Your work is now automatically saved. The defaults can be configured in the Preferences window under the Saving tab. You can turn autosaving on and off, and change the save interval. By default, the save interval is 5 minutes.
  3. 52 new glassware templates.
  4. Glassware templates can now be flipped.
  5. Bitmap image output is improved. The image scale is now definable for each output image. The default scale is 4x. JPEG and PNG output can now define DPI for high quality printing when scalable vector graphics are not an option. The default DPI output is 300dpi. Transparency can now be defined in formats that support it. The defaults can be configured in the Preferences window under the Advanced tab.
  6. A new menu item to optimize a PDB file to ChemDoodle Web Components JSON for fast loading and manipulation.
  7. A new pinwheel color chooser is provided on all platforms. The color chooser is much improved on Windows/Linux, with new panels for more robust color picking.
  8. Arrowheads now shrink when their length is greater than half of the line length.
  9. JCAMP spectra are now written.
  10. Added a new option to control if Hz are automatically converted to PPM from input JCAMP spectra. This is enabled by default.
  11. Line notation formats will now recognize multi-line input.
  12. The widget dock is now movable.
  13. Added a new specification to control the width of the outlines for atoms represented by circle graphics.
  14. EPS and SVG output now includes ChemDoodle metadata for round-trip editing.
  15. The site license configuration now contains master controls to disable/enable updates and expiration notices.

Fixes

  1. PubChem searching in the MolGrabber widget has been restored.
  2. The automatic display of terminal carbon labels is now disabled by default. You can turn them back on in the Preferences window, under the Visuals tab under the Atoms sub-tab in the Carbons section.
  3. ChemDraw files are now read in with finer attention to detail. Text boxes appear correctly and alignments are now read, arrow heads more closely match their size, curved arrow coordinates have been corrected, attribute locations are better calculated, charges and radicals are no longer duplicated graphically, bold and formatted labels are now read, charges will be surrounded with circles if detected, show/hide of carbon labels is now adhered to, wavy bond specifications are set, terminal carbon label and implicit hydrogen settings are read.
  4. Fixed a couple NMR simulation issues. Alcohols are now recognized when connected to aromatic rings. Alcohol shifts next to aromatics are improved.
  5. Fixed bug where stereochemistry in very complex structures with many condensed labels were not being determined correctly.
  6. Stereochemistry will no longer be defined to aromatic bonds like in benzene.
  7. Fixed issue where forcing E/Z stereochemistry did not update atom label positions.
  8. Improved the performance for detecting stereochemistry in complex structures with many condensed labels.
  9. Fixed bug where forcing cis/trans stereochemistry to a non-applicable double bond would cause an error.
  10. Stereochemistry is now detected for double bonds in structures with condensed labels.
  11. Glassware templates now correctly show default stroke colors.
  12. Fixed issue where some glassware templates were not being correctly drawn.
  13. CML output now correctly defines namespaces.
  14. X-axis offsets are now read in from JCAMP files.
  15. SLN input is now read correctly, even if there are atom id clashes.
  16. Fixed issue where the SMARTS matcher was not correctly matching some aromatic bonds.
  17. Improved the maximum activation message to explain how to deactivate/reactivate ChemDoodle.
  18. Fixed bug where XLogP v2.0 calculations were not consistent and were inaccurate.
  19. Bonds no longer withdraw from atoms represented by circle graphics.
  20. The buffer between a reaction arrow and its constituent structures has been reduced by half when cleaning.
  21. ChemExper supplier searches now include explicit hydrogens.
  22. Fixed bug where drawing a double lined arrow would set the default line style to be doubled.
  23. The color button is now clearer when empty colors are defined.
  24. Fixed bug where the template widget would have some issues if it was defined as the default widget.
  25. The Line Notation Pad widget now lays out multiple discrete molecules.
  26. Fixed issue where colors in text areas were not being saved.
  27. Fixed issue where opening a text field/area and then changing tabs caused the text component to remain open.
  28. Fixed issue where sometimes the default document style sheet was being incorrectly overridden by the current style sheet.
  29. Fixed EPS bug where some output would disappear when rotated text areas were present.
  30. Fixed bug where the radical attribute button would place a charge instead.
  31. Fixed issue where MDL CT file output had labels right-aligned, while still valid, some other applications require them to be left-aligned.
  32. Fixed a couple interface issues, such as how drop down menus would close when the mouse scroll was used.
  33. Fixed bug where interface settings were not being stored with the workspace.

4.0.0

August 24, 2011

Executive Summary

ChemDoodle 4 is a massive update to ChemDoodle. This upgrade is free for all customers of ChemDoodle 1, 2 or 3. Included are hundreds of fixes and new features, recommended to us by customers. Enjoy and spread the word!

New Features

  1. A beautifully polished interface.
  2. Laboratory glassware clipart.
  3. New Elemental Analysis widget for calculating masses and formulas, elemental analysis, isotopic distributions and mass spectrometry simulations.
  4. Auto-rendering of implicit hydrogens in atom labels.
  5. New peptide sequence tool.
  6. Integration with your iChemLabs account to transfer structures to and from ChemDoodle Mobile.
  7. Updated Web Components builder to be compatible with version 4.3.0 and to work with spectra.
  8. OpenDocument Graphics output for better support of OpenOffice, especially on Linux.
  9. New rotation anchor for the lasso, to easily rotate around atoms in 2D and 3D.
  10. Improved NMR simulation.
  11. Dozens of new descriptors.
  12. And much more, including hundreds of issue fixes and improvements.

3.3.1

January 27, 2011

Executive Summary

This is a minor bugfix update, addressing minor issues brought to our attention. This update also brings compatibility with ChemDoodle Web Components v4.0.

Additions

  1. Zigzag and Wavy bond amplitudes can now be specified.
  2. Updated ChemDoodle Web Components support to version 4.0. Added the missing visual specification for determining if hidden carbon labels are displayed.

Fixes

  1. Fixed rare issue where widgets were misplaced upon opening ChemDoodle on large monitors.
  2. SVG files are now correctly recognized when dropped on the Doodle Board.
  3. Fixed bug where hydride labels (H-) were not being parsed correctly and caused copy/paste issues.
  4. Fixed bug where monovalent abreviations before a number were not properly parsed.
  5. Fixed the Symbols widget filter.
  6. Corrected the superscript for first order Chi connectivity indices.
  7. Improved dynamic bracket enumeration text positioning and fixed an issue where the enumeration text was clipped.
  8. Dynamic brackets are now correctly saved/opened from ChemDoodle Documents.

3.3.0

October 23, 2010

Executive Summary

ChemDoodle 3.3 is a significant update containing major new features. Notable features include explicit control over atom label formatting, rendered bond merging for aesthetic joins, a simple workspace resizing system so the application does not occupy the entire screen on large resolution devices, new “Kekulize” functionality, dozens of new molecular descriptors, and retrosynthetic arrows.

Additions

  1. Atom label text formatting. ChemDoodle’s default atom label formatting, based on chemical interpretation, can now be overriden. You now have full control to completely format all aspects of the atom label text, from styling, to color and alignment. While very complex labels can now be drawn, this is mainly to allow access to italics and superscripts so common labels can now be easily drawn, such as “iPr”, “iPr” and “R10” for example.
  2. Rendered bond merging for aesthetic bond joins. Wedge-Single, Wedge-Wedge, Wedge-Bold, and Bold-Bold bonds now neatly fit together.
  3. New molecular descriptors are calculated:
    • Degree of Unsaturation
    • Rotatable Bond Count
    • Branching Index
    • Chi Molecular Connectivity Indices – Up to third order for both simple and valence models.
    • Kappa Shape Indices – Up to third order for both simple and alpha models.
    • Critical Pressure
    • Critical Temperature
    • Critical Volume
    • Enthalpy of Formation (ideal gas at 298K)
    • Enthalpy of Fusion
    • Enthalpy of Vaporization (at Tb)
    • Gibbs Enery of Formation (ideal gas, unit fugacity, at 298K)
    • Heat Capacity (ideal gas, at 298K)
    • Liquid Viscocity (at 298K)
    • Normal Boiling Point
    • Normal Freezing Point
  4. New arrow types:
    • Retrosynthetic
    • Bold
    • Rearrangement
  5. A new function to select by SMARTS. ChemDoodle now has a full implementation of the SMARTS matching protocol; further features that access this functionality will be provided as ChemDoodle evolves.
  6. A new SMILES option to preseve bond orders on output. In essense, aromaticity will not be output to SMILES.
  7. The ChemDoodle workspace now sizes appropriately. On smaller screens, ChemDoodle will still expand to the full view, but on larger devices, ChemDoodle will only take as much room as necessary. When resizing the workspace, the widgets will be appropriately placed to the right of the window. The workspace size and location are now preserved between sessions.
  8. A new Kekulize function that assigns double bonds to sets of bonds to maximize pi electron delocalization. If a structure consists of only single bonds, this function will affect the entire structure. If a structure has any resonance bonds assigned, only those bonds will be affected. SMILES input now automatically Kekulizes input.
  9. Text area font colors can now be changed.
  10. Designating all resonance bonds in a ring now forces that ring to be defined as aromatic.
  11. New keyboard shortcuts to add rings to bonds using the shift key. Alternate bond types are now assigned using the alt key.
  12. Adding rings to bonds now automatically selects the most appropriate orientation if the mouse pointer is close to the bond.
  13. A new option to skip the current update. Once chosen, you will no longer be notified of the current update, but will be of subsequent updates. Choosing the Check for Updates menu item in the Help menu will override this choice.
  14. Renovated the keyboard shortcuts PDF.

Fixes

  1. Fixed bug on Linux, where EMF output was missing atom labels.
  2. Fixed bug where EPS clipping was not preserved correctly.
  3. Provided a workaround for a Mac bug caused by the latest Mac Java updates, where the Preferences… menu item did not appear in the ChemDoodle menu.
  4. Fixed SMILES bug where double digit ring indexes were not written.
  5. SMILES reading no longer places explicit hydrogens on chiral centers.
  6. Explicit Hydrogens are now output to SMILES.
  7. Emptying the lasso now updates the Properties widget.
  8. Fixed issue where reaction text areas were not properly accounted for when distributing objects.
  9. Fixed bug where using parenthesis incorrectly in condensed notations caused problems during label expansion.
  10. A Linux natural serif font is now used to correctly show font icons on Linux.
  11. Hydrogen counts are now modified by radicals.
  12. Attributes now rotate with structures instead of preserving their distance vector from the atom they describe.
  13. Menu items to calculate descriptors now warn when the structure cannot be sensibly expanded.
  14. Changing fonts to bold/italic now resizes the lasso.
  15. Fixed issue where completely undoing all actions in a text area did not allow you to redo anything.
  16. Underline and strikethrough rendering in text areas now always draws a 1 pixel solid line.
  17. Using the font edit buttons in the text area toolbar no longer steals focus from the text area.
  18. Fixed issue where arc angles could not be set to 0 in the Format Arc… window.
  19. Arrows now correctly conform to document settings.
  20. Charges are now appropriately assigned to the nitro group abbreviation.
  21. Aromaticity detection is significantly improved, especially for fused ring systems.
  22. Changing bond orders in rings now reassesses aromaticity.
  23. Fixed rare bug where sometimes dragging a structure from the MolGrabber widget caused undo/redo issues.
  24. An informative error is now displayed by the MolGrabber widget if a database is inaccessible.
  25. Fixed bug where certain visual aids were saved to the workspace, but upon a new session, the View menu was not properly updated to show they were enabled.

3.2.1

September 05, 2010

Executive Summary

ChemDoodle 3.2.1 is primarily a bug fix release. While few, the added features are powerful and improve the drawing system. Site licensees must upgrade to 3.2.1 prior to activating with a renewed activation code.

Additions

  1. A new setting has been added to turn off the starting atom requirement. The starting atom setting is intended for users new to chemical drawing programs. More experienced users find they can more quickly draw figures if they turn off this starting atom requirement. This option is provided in the General tab of the Preferences window.
  2. A new right-click menu item has been added to quickly show/hide Carbon labels without opening preferences. This option only appears for “C” labels.
  3. A new option has been added to show/hide borders on Rectangles, Ovals, Text Areas and HTML Areas. This option is disabled by default for Text Areas and HTML Areas so they are now borderless by default.
  4. A new spectrum mouse gesture, shift+drag, will translate the spectrum along the x-axis.
  5. Integration lines can now be rendered for NMR spectra. Color and thickness are editable.
  6. Grids can now be rendered for spectra. Color and thickness are editable.
  7. ChemDoodle Web Components v3.5 is included.

Fixes

  1. Fixed major issue when renewing a Site License activation where an innocuous error is displayed, making it seem like an error had occured when really everything renewed correctly.
  2. Fixed bug where the Line Notation Pad widget would go blank if an atom with an isotope defined was input.
  3. Isotopes are now supported in ChemSketch files.
  4. Improved the interpretation of coordinates from JCAMP-CS files.
  5. Fixed the reading of negative abscissa values from JCAMP-DX files.
  6. Fixed issue reading element types from SKC files with atomic numbers greater than 107.
  7. Improved the performance of line notation readers.
  8. Line notation readers now warn of multiline input.
  9. Fixed SMILES input issue where the ring closing bond type is specified before a ring declaration.
  10. Improved ROSDAL reading.
  11. Fixed the reading of mass numbers and radicals from InChI strings.
  12. Fixed the writing of radicals to InChI strings.
  13. Fixed bug where changing the bond width or texture thickness to values not available in the Strokes toolbar had no effect.
  14. Single bonds in condensed labels are no longer superscripted.
  15. Charges are now set when expanding condensed labels with charges defined.
  16. Abbreviations now trump elements, so “Ac” is interpreted as an acetyl group instead of Actinium.
  17. Improved condensed notation interpretation to recognize abbreviations at the beginning of atom labels.
  18. Improved handling of abbreviations with different interpretations depending on connectivity, for instance “CO2″ can be either carbon dioxide or part of a ester or carboxyl group.
  19. Fixed rendering of orbitals and ovals in PICT output.
  20. Fixed shape rotation issues in PICT output.
  21. Fixed bug where SSSR linear independence was incorrectly determined by atom sets. The linear independence is now correctly determined by bonds.
  22. Keyboard atom shortcuts alt+3 and alt+8 now correctly place cyclopropene and cyclooctatetraene, respectively.
  23. Fixed bug where the window would go blank when trying to determine the stereochemistry of a fully substituted double bond.
  24. Fixed bug where text input components remained and could not be removed if clearing the Doodle Board while a text input component was active.
  25. Fixed bug where zooming in on a flipped x-axis spectrum in the Spectrum Edit window caused the spectrum to incorrectly flip and display crossing tails.
  26. Removed the rendering of infinite tails at the end of spectra that may be incorrectly interpreted as data. The spectrum now stops at its ends.
  27. Fixed the display of the Degree of Unsaturation descriptor in the Properties widget.
  28. Improved the calculation of the Hydrogen Bond Acceptor descriptor.
  29. Improved small case issues in aromaticity detection.
  30. Fixed bug in calculating Morgan indices.
  31. Fixed issue where the main window sometimes lost focus when trying to use keyboard accelerators and shortcuts.
  32. Fixed minor issues where modifier keys didn’t show immediate feedback when transforming lasso content.
  33. Slightly improved Statistics widget scrolling and selecting.
  34. Raster image output now correctly conforms to the advanced specifications for document rendering.
  35. Removed HTML Area highlight decorations from appearing in image output.
  36. Fixed bug where second token in superatoms didn’t stack if that superatom is the first entity in a label.
  37. Dragging after placing an atom will now correctly hover/dehover it.
  38. The atom the mouse is under is now automatically hovered after a template or ring is placed.
  39. Fixed minor issue when searching ChemExper where results without coordinates were displayed.
  40. Fixed issue when searching ChemSpider where short bonds to Hydrogens were being considered when scaling structures to the preferred bond length causing structures to be somewhat larger than preferred.
  41. Fixed minor issue where shadow settings were displayed for shapes that did not support shadows.
  42. Fixed issue where some spectrum visual specifications were mistakenly global.
  43. Expanding the spectrum to fit in the Spectrum Edit dialog now refreshes the tick spacing controls.
  44. Negative values in spectra no longer offset the baseline.
  45. Closing the Preferences window by using the top bar’s close icon will now work just like the Done button.
  46. Fixed bounds calculation for rotated label shapes.
  47. Enabling/disabling chemical warnings now give immediate visual feedback.
  48. Added lasso decorations for orbitals.
  49. Removed lag when checking for updates when no internet connection is found.
  50. Displaying the update changelog when new updates are announced is now instantaneous.

3.2.0

July 30, 2010

Executive Summary

ChemDoodle 3.2 is a significant update containing major new features and improvements. Notable features include orbital objects, the expansion of condensed formulas in atom labels (allowing for the automatic proper handling of condensed formulas by the Properties widget and other algorithms), a more robust abbreviations system (that can be used in atom labels for all atom models) and integration with the ChemSpider database. Notable improvements include an evolution of the ChemDoodle rendering engine for improved rendering and performance as well as full control over the low level graphics settings, a new table layout for the Properties widget that conveniently updates when drawing a single molecule, and full compatibility to directly paste scalable vector graphics into the entire Microsoft Office suite on Windows and Mac OS X.

Additions

  1. Orbitals can now be added to structures. These are 2D graphics that can be attached to atoms or bonds or can be standalone. A gradient is used to give them a 3D appeal. Supported are atomic orbitals (s, p, d, f), hybrid orbitals (sp lobe, sp3), and bonding orbitals (σ, π). Orbitals can also be read from and written to ChemDraw files. There are two visual specifications for orbitals in the Preferences window under the Visuals tab under the Shapes subtab: Length Multiplier – Sets the default size of orbitals relative to the current bond length; Stroke Shaded Lobes – Sets whether or not outlines are drawn around shaded orbital lobes.
  2. The graphics engine in ChemDoodle has seen a significant upgrade and graphics rendering has significantly improved. Performance has also been significantly improved. Graphics controls for low level rendering are now exposed in the Preferences window under the Advanced tab. Change these only if necessary to favor speed or to affect how graphics are rendered. These rendering options will only affect devices with resolutions, such as bitmap images and monitors; scalable vector graphics remain perfect and unchanged.
  3. Added a new option to simulate soft clipping for bitmap images in the Advanced tab of the Preferences window. This makes Recessed bonds look much nicer.
  4. A new system for expanding condensed formulas and abbreviations in atom labels to their all atom models. There are several features that benefit from this:
    1. All calculations based on structures (properties, NMR spectra, etc.) will first expand the molecule, so proper results will now be obtained when using condensed formulas.
    2. Atom label errors are improved. ChemDoodle will alert you of unknown tokens and will properly evaluate atom valencies. For instance, a terminal label of CH3 will be approved while a terminal label of CH4 will not.
    3. Abbreviations can now be expanded. So Ph, Et, COOH, etc. will be properly expanded to the corresponding all atom models and can be used in condensed formulas. You can add your own custom abbreviations.
    4. Atom label token stacking is more intelligent and will now stack based on token groups. For instance, the label CH2CH2COOCH2CN will stack as (CH2)(CH2)(COO)(CH2)(CN).
    5. Complex shorthand notations are also supported, so C(CH3)3 will be expanded as a t-butyl fragment and CPh3 will be expanded as a triphenylmethyl fragment.
  5. The ChemSpider database has been integrated into the MolGrabber widget.
  6. The Properties widget now has a second mode that will be automatically activated when a single molecule, and only a single molecule, is being edited in the current document. The display will change to a table that will list the most important properties and will automatically update if allowed. There is a new checkbox at the top of the widget to disable automatic updating of the data, which will be useful for less powerful computers.
  7. Scalable vector graphics can now be directly pasted into the entire Microsoft Office suite, including Powerpoint and Excel.
  8. Added a Save Selection as Image… menu item to the File menu to quickly save just the selected content to an image.
  9. Added a Copy As submenu to the Edit menu to quickly copy selected structures as various datatypes at maximum compatibility on the system clipboard.
  10. Added a new drag erase gesture when using the Eraser tool. Press and drag over any objects to be removed and they will be highlighted. Release the mouse to delete all highlighted objects. If you drag over a previously highlighted object, it will be unhighlighted.
  11. ChemDoodle Web Components v3.1 is now included. The ChemDoodle Web Component generator has been updated accordingly. New default sizes are provided for standard iOS device resolutions.
  12. Molar Refractivity can now be calculated for structures.
  13. Some widget settings are now saved in the workspace, including the last selected widget and the database choice in the MolGrabber widget.
  14. The MolGrabber widget now provides a direct link to the chosen database’s website for the selected molecule. Press the Show Associated Data button and the top item will show the database’s compound id. Click on the compound id to visit the webpage for that molecule.
  15. Menu items for unrepresented keyboard shortcuts have been added: Flip Bond, Align Bond and Add Attribute.
  16. A new keyboard shortcut for adding attributes to hovered objects, Shift-A.
  17. Added a new visual specification to set whether the second bond line in double lined bonds are shrunken when next to an atom label.
  18. Radial gradient rendering is greatly improved for shapes to better portray 3D appeal.

Fixes

  1. Improved how the default style sheet is saved. The default style sheet will no longer be affected when ChemDoodle is closed. Both changing preferences and conforming a document will now ask if the new settings should be default. A new menu item, Save Document Settings…, is present in the Window menu for explicit saving the current document style sheet as the default settings.
  2. Fixed a bug where structures could not be dragged into the Line Notation Pad widget.
  3. Fixed bug where changing tabs when content was selected would change the colors of the selected content.
  4. Selected content is now properly remembered when switching between tabs.
  5. Fixed issue where a molecule still appeared selected if it was deselected using the alt+shift keyboard shortcut.
  6. Fixed bug where reading a lone atom from a file will have its label misplaced.
  7. Fixed issue where the SSSR finder was not enforcing linear independence.
  8. Fixed issue where the Euler facet ring finder was skipping rings.
  9. Colored in ring guides no longer appear in output.
  10. Fixed bug where an infinite loop started when cleaning complex multi-ring-substituted ring systems.
  11. Fixed bug where some structures were not being cleaned.
  12. Improved the cleaning of complex ring systems.
  13. When cleaning structures, triple bonds are now aligned parallel to their substituents.
  14. Improved boundary conditions for token alignment to favor the horizontal alignments.
  15. Fixed bug where some counters were not being calculated in the Properties widget.
  16. The Calligraphy stroke skew angle has been offset by 15 degrees to avoid ghosting effects with vertical bonds.
  17. The arrow size for the ACS Document 1996 chemical document settings has been set to 8 pixels by default.
  18. Changing the arrow specifications now will apply to arrows without having to reselect an arrow tool.
  19. ISIS Sketch files that are missing the closing tag are now read properly.
  20. Fixed conversion issues with ChemSketch files.
  21. Fixed PDB file issue where files that incorrectly contain 0′s in inappropriate places were not being read.
  22. Fixed issue with aromaticity detection where some 5 membered aromatic rings were not being properly detected. Changing any atom labels in rings will now recheck their aromaticity.
  23. Fixed issue when adding hydrogens as text to some structures, where nonexistent hydrogens were being found and “removed” so nothing would be added.
  24. Fixed slowdown when custom fonts were used.
  25. Changing the atom label vertical alignment now updates bond buffers.
  26. Aligning bonds now takes into account if the bond has been flipped.
  27. Attributes now move correctly in grouped content.
  28. Fixed bug where holding alt+shift to select a molecule would incorrectly move the hovered atom.
  29. Negative coordinates in CDX files are now properly read.
  30. Inserting a PDF or dropping it on the Doodle Board will search first for ChemDoodle metadata.
  31. There is no longer a clash on the system clipboard between the PICT and PDF formats on Mac OS X. Both should now always remain selected. You can now work with both Microsoft Office and iWork without having to change the clipboard settings.
  32. Macintosh Vector PICT output has been improved.
  33. Macintosh Vector PICT clips have been improved to remove the residual effect on clip borders.
  34. Windows Enhanced Metafile output has been improved.
  35. Removed small rectangle that appeared in EMF output to the top left of the origin that was only visible if content was offscreen.
  36. EPS output is now smaller.
  37. Improved ruler tracking when moving the Doodle Board scrollbars.
  38. Fixed issue with text input components where text would appear to “jiggle”.
  39. Fixed rare lasso repaint issue that would stop certain sides from displaying the crawling ants effect.
  40. Fixed issue that caused a crash when reading a corrupted workspace file.
  41. Fixed bug where some right-click menu items were displayed but were disabled.
  42. Fixed problem where stacking of off-document content was performed when clicking on the blue background, when stacking should only be performed by clicking on the red strips.
  43. Document rendering and application rendering have been separated.
  44. Missing references have been added.
  45. Fixed minor issues.
  46. Minor text fixes.

3.1.0

June 17, 2010

Executive Summary

ChemDoodle 3.1 provides three new file formats: ACD/ChemSketch Document, MDL RXNFile (both V2000 and V3000) and MDL RDFile. ChemDoodle now reads and writes the formats of all chemical sketchers. Also implemented is a complete interface to the ChemExper database providing structures and properties from the MolGrabber widget and access to chemical suppliers for structures that you draw. The NMR simulation algorithms have been greatly improved. Many bugs have been fixed.

Additions

  1. Incorporated the input and output of the ACD/ChemSketch Document format.
  2. Incorporated the input and output of the MDL RXNFile format for storing single reactions. Both V2000 and V3000 connection tables are supported
  3. Incorporated the input and output of the MDL RDFile format for storing reaction schemes.
  4. Integration of the ChemExper database.
    1. Access to structures and properties provided in the MolGrabber widget.
    2. Access to to chemical suppliers for the chemicals drawn by clicking the Chemical Suppliers menu item in the Structure menu.
  5. Search widget now displays a drop box for placing the search structure in, replacing the spinner that was previously there and making the use of the widget much more intuitive.
  6. More restriction options have been added for the Search widget, and those options are now accessible right from the widget.
    1. Restricting result set size.
    2. Excluding PDB files.
  7. NMR simulation algorithms greatly improved.
    1. 1H: anisotropic effects, ring strain, hydrogen bonding effects, rapid exchange, diastereocenters, heteroaromatics
    2. 13C: alkane improvements, alkene improvements, alkyne improvements, decreased quaternary peak intensities, heteroaromatics
  8. When atoms are hovered, the enter key will now set the hovered atom’s label to the last typed atom label. Opening a previously typed atom label will set the enter key text to that label.
  9. When bonds are hovered, the arrow keys will orient the bond in the pressed direction from start atom to end atom, rotating the entire molecule it is contained in.
  10. When objects are hovered, pressing the comma key will open that object’s visual specifications formatting window.
  11. Added a visual specification for reactions to set the padding for reaction condition text if that text is centered. When cleaned, reaction arrows will now fit their text based on this padding. Reaction arrows with no text will have a length equal to twice this value; 30px by default.
  12. Added a visual specification for attributes to determine the amount of reduction for font text size in attributes that contain text.
  13. Included a new file specification for MDL connection tables to include/exclude Hydrogen counts.
  14. Added a style sheet to quickly produce 2D graphics for 3D data and scenes.

Fixes

  1. Fixed issue that caused a flashing of the mouse cursor when using the lasso tool and hovering over shape anchors.
  2. Fixed issue where the close icons weren’t being rendered on tabs on Windows/Linux.
  3. Fixed issue where clicking on a terminal atom didn’t select it.
  4. Atom Label Tool icon has been changed to stick out more.
  5. Fixed bug where nothing happened when deducing the stereochemistry of an ambiguous stereocenter.
  6. Structure cleaning algorithm runtime has been greatly improved when complex embedded rings are present. Previously, this runtime lasted about 30 seconds, it is now instantaneous.
  7. Added more preset templates to the structure cleaning algorithm.
  8. The cleaning of very wide reactions has been greatly improved.
  9. The default reaction constituent buffer has been halved to 20px.
  10. Fixed problem where the File menu would temporarily disappear if reading a file in ChemDoodle that wasn’t recognized.
  11. Fixed issue where rarely a file will be duplicated on the recent files list on Windows.
  12. Delete key properly removes all attribute objects selected, regardless of type.
  13. Radical attributes can now be properly deleted.
  14. Attribute fonts can now be changed properly.
  15. Nudging content with the arrow keys now properly moves attributes.
  16. The quote character is no longer stacked in atom labels.
  17. Pasted molecular properties from the Descriptors submenu in the Structure menu all now paste a title description as well.
  18. Fixed bug where choosing empty colors in the color choosers on Windows/Linux caused errors.
  19. Removed duplicated ChemDoodle Document checkbox in the Windows Filetype Association window.
  20. Fixed NMR SignalSeek widget bug in the peak breakdown that displayed duplicated peak labels.
  21. Heteroatoms that split nuclei are now properly highlighted in breakdowns from the NMR SignalSeek widget.
  22. Shift contributions are now right-aligned to align the decimal points in the shift explanations from the NMR SignalSeek widget.
  23. Fixed 13C NMR shift explanations in the NMR SignalSeek widget.
  24. The NMR SignalSeek widget temperature is now properly described in Kelvins.
  25. Fixed bug in the NMR simulation algorithms where some functional groups were being defined past their bounds.
  26. Bond breakers are now rendered properly.
  27. Bond z-order is now preserved when copying and pasting structures.
  28. Fixed issue where changing the bond stroke styles could not be undone.
  29. Fixed issue where valency warnings were incorrectly displayed on cations.
  30. Fixed issue where files that were opened and changed the size of the page didn’t do so according to the selected viewing scale.
  31. Fixed issue where opening multiple files didn’t immediately perform checks.
  32. Fixed certain checks after using keyboard shortcuts.
  33. Fixed issue where changing tabs may not have reset the out-of-bounds warnings.
  34. ChemDoodle Documents can now be recognized by ChemDoodle even if the extension is changed.
  35. Fixed minor issues related to reading files that do not have the correct extensions.
  36. The Format Atom window is now restricted to 500px in height.
  37. Improved the look of file choosers on Mac OS X.
  38. Improved warning message that is displayed on Windows when open files are locked by another application and cannot be saved.
  39. Greatly improved the rendering of tabs on Windows/Linux.
  40. Fixed bug where tab titles in the Preference window were cutoff on Windows.
  41. Minor graphical and text improvements.

3.0.0

May 24, 2010

Executive Summary

ChemDoodle 3 is a complete overhaul of the ChemDoodle application. This update provides performance improvements, graphical improvements and a long list of new features; major features are listed below. All known ChemDoodle 2 bugs have been fixed.

New Features

  1. New operating system specific installers (Windows Installer, Mac DMG, Linux BIN)
  2. A thorough user guide
  3. Performance enhancements
  4. New intuitive keyboard drawing controls
  5. Greatly improved lasso system
  6. Improved graphics (Atom label token stacking, robust text bounds calculations, improved bonds, more graphical preferences)
  7. Create chemical images, animations and interactive components for webpages
  8. NMR simulation
  9. Handling of spectra
  10. Improved arrows system
  11. Handling of reactions
  12. Search your hard drives for chemicals
  13. New chemical file formats
  14. New cheminformatics descriptors and functions
  15. Incorporated elemental database
  16. New references system
  17. and so much more …

2.0.5

December 19, 2009

Executive Summary

This is an emergency bugfix update to rectify an issue where EMF vector graphics on Windows/Linux were missing text. This bug was introduced in the 2.0.4 bugfix update on 12/18. This update fixes this issue. For the fixes introduced in 2.0.4, please click here. We apologize for any inconvenience.

2.0.4

December 18, 2009

Executive Summary

This is a minor bugfix update to patch a few issues. This will most likely be the last bugfix update before ChemDoodle 3 is released. ChemDoodle 3 is a free upgrade for all customers that have purchased ChemDoodle 1 or 2.

Fixes

  1. Fixed problem where rotated shapes would disappear when pasting vector graphics in Microsoft Word on Macs.
  2. Fixed issue where text was sometimes cutoff if near the edge of images on Windows/Linux. A new Preferences setting has been added in the Advanced tab to set the image border buffer for more control over image output.
  3. Molecular mass calculations (and others in the Properties widget) now use the correct number of Hydrogens when Hydrogens are added as text and suppressed on Carbons.
  4. The missing Reaction Arrow option in Condensed Mode has been added.
  5. Look and feel has been corrected on Mac OSX 10.6.

2.0.3

September 12, 2009

Executive Summary

This is a minor bugfix update to patch a few issues.

Fixes

  1. Fixed issue where SMILES strings would incorrectly contain lowercase letters for non-aromatic heteroatoms in the defined “organic subset”.
  2. Reading of ISIS Sketch skc files now ignores obfuscated tags (as defined by the version 4 specification) if present, which prevented the files from being loaded.
  3. Fixed bug where non-element symbols caused issues with the Properties widget.

2.0.2

June 22, 2009

Executive Summary

Apple released Java Update 4 on 6/15 that caused issues with ChemDoodle on Mac. This release fixes those issues on Mac as well as a few other minor issues for all platforms.

Additions

  1. Added a new Calligraphy stroke style for bonds.

Fixes

  1. After Apple’s Java Update 4 on Mac OSX, popups cause the main menu to disappear until another popup appears. This issue has been resolved.
  2. After Apple’s Java Update 4 on Mac OSX, a few widget icons appeared dark. This issue has been resolved.
  3. On Mac OSX 10.5, the file chooser windows will now display the associated Leopard file icons.
  4. Fixed issue when placing templates with atoms close to the pivot would fuse those proximate atoms together when short bond length settings were selected.
  5. Cyclohexane chair conformer buttons in the Rings toolbar now select their corresponding template in the Templates widget for further manipulation.
  6. One new tutorial page has been added concerning Carbon labels.
  7. Opening files and new tabs now update the Stroke toolbar.
  8. All Chemical Document Settings files have been remade for the current selection of Preferences settings.
  9. In rings, the Flip Bond Orientation right-click menu item will now control whether Double and Resonance bonds point inside or outside of that ring. If the bond is a fused bond between two rings, this function will change which ring it faces.
  10. The stroke settings in the Strokes toolbar no longer become clear on Windows and Linux when hovering over them. Mac was always working.
  11. Proxy settings can now be cleared.
  12. The updater has been updated to version 1.2.1 to fix minor issues.

2.0.1

June 14, 2009

Executive Summary

This bugfix update fixes the most recent issues discovered.

Fixes

  1. OpenOffice has a bug where clips are incorrectly interpreted from metadata. ChemDoodle now simulates clips before sending the data to OpenOffice. This is mainly so recessed bonds render correctly in OpenOffice.
  2. The MOL format is now selectable as a text output option for placing on the system clipboard. You must enable this option in the Advanced tab of the Preferences window. This is necessary for copying into certain 3rd party applications that incorrectly ignore chemical MIME types.
  3. Two new tutorial pages have been added: chains and Lewis structures.
  4. ChemDoodle now checks and warns you on Linux if it has been opened without use of the essential shell script.
  5. Index numbers are now stripped from older PDB file formats, where ids are sometimes appended to atom element symbols.
  6. The covalent radius tolerance is increased, allowing easier calculation of covalent bonds.
  7. The sheet size choosers now show the correctly selected choices when initialized, rather than the default US Letter.
  8. Fixed issue where atom label text was sometimes being cutoff by a pixel on Windows XP when printing.
  9. Fixed issue where the cyclohexane chair buttons were incorrectly drawn adhering to specific settings in Preferences.

2.0.0

May 27, 2009

Executive Summary

This release is a major version upgrade to ChemDoodle 2. In thanks for the support received from everyone, this upgrade is free to all customers. This release provides the ability to transfer scalable vector graphics into Microsoft Office, OpenOffice, iWork, Adobe Products, and most other applications. ChemDoodle 2 also fully reads/writes 16 popular chemical formats, becoming one of the most robust chemical conversion tools available. Also provided are two new widgets, TLC Canvas and Properties, plus an updated widget, Line Notation Pad. Other new features such as different stroke styles, a condensed mode for netbooks, and many others have been incorporated.

Additions

  1. ChemDoodle can now transfer scalable vector graphics into Microsoft Office, OpenOffice, iWork, Adobe Products, and almost any other application. iChemLabs has written this functionality as a proprietary library. No other Java application can transfer scalable vector graphics, and only ChemDoodle can transfer scalable vector graphics into OpenOffice on Linux! You may read more about this feature here.
  2. Different bond stroke styles can now be used to create chemical art. This is perfect for posters and other less formal occasions. Currently provided are brush, bristle, charcoal, scribble and wobble stroke styles. You may read more about this feature here.
  3. A new TLC Canvas widget has been added for digitally reproducing your TLC plates. Gradients and transparency are supported for photorealism. You may read more about this feature here.
  4. A new Properties widget for calculating various properties of selected molecules. More properties will be provided in the future. This widget updates to changes within the selected molecules.
  5. The SMILES widget has been upgraded to the Line Notation Pad widget and can parse and generate Daylight SMILES, Beilstein ROSDAL, SYBYL SLN and IUPAC InChI. Added a new option to explicitly control the starting point for line notations. Note that this setting is ignored for canonicalized line notations. You may read more about this feature here.
  6. File annotations are now read and written in chemical documents for your records and so others can see your notes.
  7. Several new chemical filetypes can now be read and written. All objects and properties are handled, including fonts, colors, shapes, annotations, settings, etc., if applicable.
    1. ISIS Sketch File (.skc)
    2. ISIS Sketch Transportable Graphics File (.tgf)
    3. Protein Data Bank Files (.pdb, .ent)
    4. Standard Molecular Data (.smd)
    5. Tripos Mol2 (.mol2)
    6. Daylight SMILES (.smi, .smiles)
    7. Sybyl Line Notation (.sln)
    8. IUPAC InChI (.inchi)
    9. Beilstein ROSDAL (.ros)
  8. MDL v3000 connection tables are now written.
  9. CML arrays can now be written as well as read. You can choose whether to use arrays or not.
  10. Many chemical file type options improved.
  11. Full support documentation is provided for all recognized chemical file types.
  12. Added icons for ChemDoodle Template files.
  13. The structure beautifier has been significantly upgraded.
  14. New condensed mode for netbooks and other low-resolution workstations. All toolbars are condensed, and only 1 widget appears at a time in this mode. All recently opened files will be located in a submenu of the File menu. The main scale starts at 75%. All windows will now display properly on small resolutions including preferences and the periodic table of elements. The desktop will scroll if very small dimensions are used.
  15. Added a cyclohexane chair conformer button and its mirror image counterpart to the Rings toolbar.
  16. Added four new bond types: Zero/Ionic, Double Dashed, Any and Unknown.
  17. Added a deactivation procedure for those wishing to move their installation to a different computer. This procedure begins by selecting the Deactivate ChemDoodle menu item in the Help menu. This option is only present for activated copies of ChemDoodle.
  18. New ruler shapes measure and display dimensions in various units.
  19. Added polyline/polygon and freeform shapes. Control points are anchors for further connections and closing shapes. Pen shapes can now be closed as well.
  20. New Remove Selected Bonds and Calculate Covalent Bonds menu functions have been added to the Structure menu. Calculate covalent bonds when reading in corrdinate files without explicit topology.
  21. A new Flatten menu item has been added to the Content menu and sets all the z-coordinates of atoms to 0.
  22. New Fisher projection chain and random chain tools for drawing chains quickly.
  23. A much improved color chooser is provided on Windows and Linux.
  24. Page dimensions can now be exchanged in all page dimension input panels.
  25. Added additional grid background guides at 1/2 and 1/4 inches. All grids are now aligned to the top-left.
  26. Added crosshair background guides.
  27. Atom circle radii can now be specified as atomic, covalent, van der Waals or constant. You can set the constant radius.
  28. Added an Angstrom-to-Bond Length ratio in the Preferences window so you may control the scale of real coordinates that are read in from files. This ratio controls all measurements performed in ChemDoodle.
  29. Atom text can now be rotated.
  30. Morgan indices can now be assigned to atoms as identifier objects. This function is accessible in the View menu.
  31. Choosing all zeros in the Multiplet Tool widget now clears it.
  32. Horizontal scrolling is now supported on Macs.
  33. Format guessing is now more robust than ever.
  34. A complete Unicode selector has been added to the Symbols widget.
  35. Symbols widget symbols have been updated, reorganized and cleaned up.
  36. Added bracket lip width property.
  37. All object properties are now individually modifiable.
  38. Unit selectors have been added to all measurements.
  39. The Join function will now also join two distinct bonds.
  40. New arbitrary zoom option in the Formatting toolbar’s zoom combobox.
  41. Keyboard shortcuts have been intuitively assigned to almost all menu items. The docs folder in the main ChemDoodle folder will contain a pdf will all the keyboard shortcuts presented in a table.
  42. A thorough navigatable and searchable (in pdf form) user’s guide has been written and has replaced the tutorial.
  43. Linux icons provided in the /ChemDoodle/resources folder are now 48x48px in dimension and are better quality.
  44. The iChemLabs Emender application is now provided in the /ChemDoodle/resources folder to easily repair a corrupted ChemDoodle installation.

Fixes

  1. Runtime performance improved dramatically for large amounts of content.
  2. Containing rectangles are now properly calculated for all shapes, even when rotated.
  3. Fixed various line notation issues.
  4. Adobe PDF output is now saved at the correct scale and size. When pasting into iWork, scalable vector images will now be the correct size.
  5. Adding labels as substuents will now default to placing a starting atom if no starting atom is selected.
  6. Adding labels as substuents now correctly overrides the last chosen drawing mode.
  7. Fixed issue where Unicode was not being properly saved to ChemDoodle Documents.
  8. Fixed various issues associated with undo/redo when adding labels as substuents.
  9. Identifiers set by ChemDoodle functions can no longer be incorrectly altered.
  10. If an error is encountered during a file load, no new tab appears. The first tab is not modified if it is the only one present.
  11. Symbol font from ChemDraw files is now converted to Unicode upon read. Output will also be in Unicode, which is the correct practice.
  12. Fixed problem where linear atom centers with non-Carbon labels could not be edited to become Carbons.
  13. Fixed error where specific identifiers weren’t being saved properly.
  14. Fixed a few issues when setting filetype associations to the Windows registry. On Vista, you must install the file associations as administrator.
  15. Fixed cutoff layout for line notation popups on Windows.
  16. The Doodle Board is now correctly placed and sized upon startup on all resolutions.
  17. Now correctly calculates scaling parameters during transforms.
  18. Page margins now explicity set margin settings when printing. Note that you cannot print outside of the intrinsic printer margins. To use all the area the printer can print to, set all margins in ChemDoodle to 0.
  19. Text components are now properly closed when switching between Doodle Sheets.
  20. Empty content from widgets can no longer be dragged.
  21. Removed gray lines that were bordering some bitmap images copied to the system clipboard.
  22. Fixed issue where modifier keys were not registering if the mouse pointer was not located above the Doodle Sheet.
  23. Fixed issue where documents printed with missing content when an image was present on Windows and Linux.
  24. Fixed error that occured when a history action was performed while using the pen tool.
  25. Fixed error when only a single atom was conformed to preferences.
  26. Fixed issue where purging the history prevents the save data warning from appearing when closing a Doodle Sheet.
  27. Fixed issue where the transform tool doesn’t select the previously last placed objects on the Doodle Board if the last object placed was deleted.
  28. Fixed issue where shape orientations would sometimes flip when scaled.
  29. Fixed minor issue where converting to CDX reported a non-existent problem.
  30. Corrected issue where certain ChemDoodle Document properties were implied booleans instead of explicit booleans.
  31. Fixed bug where forcing stereochemistry with no identifier set, but with wedge bonds present, caused errors if a bond was facing the wrong direction.
  32. Fixed issue where text areas would act weird at scales other than 100%.
  33. Fixed issue where not inputting a number into the mass number input window caused an error.
  34. Corrected issue where the mass warning display wouldn’t disappear, even if the warning was followed.
  35. Fixed bug where overlapping atoms weren’t being copied correctly.
  36. On Macs, ChemDoodle will now check if it has been incorrectly removed from its parent folder.
  37. Binary file read errors now display properly.
  38. An empty file warning is now displayed when attempting to open a blank file.
  39. Activation code failures are now unambiguously described.
  40. Activation now fails if the preferences file cannot be written.
  41. Error panes are now displayed if there was a problem encountered during activation, after the activation code is validated.
  42. XYZ files are now interpreted in Angstroms.
  43. Multiplets can now be correctly loaded back into the Multiplet Tool widget when using the right-click menu function.
  44. Fixed issue with the Symbols widget where some symbols were not correctly correlated with an identical glyph in the hover preview.
  45. Fixed problem encountered when saving files with dots in the paths causing some files to be saved in a parent directory of the chosen location with incorrect filenames.
  46. 3D coordinates are now centered and scaled properly.
  47. Cancelling preferences changes to selected objects now works properly.
  48. The last set printing orientation is now correctly remembered.
  49. Corrected image rendering issue with significant bond overlap.
  50. Solved tiff and bmp saving issues.
  51. Fixed issue where drag and drop completion didn’t reset the main cursor.
  52. Fixed problem where a rejected drag and drop gesture caused poor UI responsiveness.
  53. Fixed widescreen print centering issue that existed on Macs.
  54. Fixed issue where plist changes were not being recognized in Mac apps.
  55. Colors and fonts saved in preferences no longer affect toolbar buttons.
  56. Correctly added trailing ‘…’ to the end of certain right-click menu items.
  57. All input and output streams are now buffered to improve performance.
  58. The second ’26′ in the font size combobox is now correctly labeled ’36′.
  59. A monospaced font is now used when displaying plain text in ChemDoodle, such as the README file.
  60. Minor graphical improvements.
  61. Minor lexical corrections.
  62. Eliminated several minor errors.

1.4.0

December 19, 2008

Executive Summary

  • This release contains full access to the PubChem database, stereochemistry functions, new identifier objects, 3D functions, an enhanced menu system, improved widget controls, new object properties, and much more. Please refer to the complete list below for details.

Additions

  1. The MolGrabber widget has been completely redone and now contains a full and direct connection to PubChem. You may now search through a database of over 20 million predrawn structures to use in your documents. The ability to handle large numbers of results has also been improved. Properties from PubChem can also be displayed with the new Show Associated Data button. All work is now multi-threaded for excellent performance while a spinner keeps you updated of the progress. You may read more about this feature here.
  2. Stereochemistry can now be discovered and assigned. These functions are accessable in the new Structure menu and in the right-click menu after lassoing structures. You may search structures for chiral carbons and assign CIP R/S identifiers to them. You may also search structures for asymmetrical double bonds and assign CIP E/Z or cis/trans identifiers to them. You can also force stereochemistry on potential and assigned stereocenters. You may read more about this feature here. All stereochemistry objects have been included in our CDX/CDXML interpreters.
  3. New objects called Identifiers can now be associated with objects. Identifiers are both logically and spatially associated to an object so that they can be moved only within a certain radius of the object they describe. You may add bulk identifiers with some of the chemical functions provided in ChemDoodle. You may also add individual identifiers by right-clicking on an object and selecting the Add Identifier menu item. Each identifier has display content and a name. A name should be unique to a group of identifiers so you may use more advanced queries and functions later. The identifier binding distance can be changed in the Preferences window under the Visuals tab. You may read more about this feature here.
  4. 3D coordinates for structures are now supported. There is a new button in the Functions toolbar for allowing you to rotate structures in three dimensions. ChemDoodle will read and write 3D coordinates to all chemical filetypes. You may read more about this feature here.
  5. Bond angles and bond lengths can now be separately locked. The shift key toggles bond length locking, while the alt key toggles bond angle locking. The Preferences window contains options for the default behavior for adding bonds. You may read more about this feature here.
  6. The alt key, when held, will allow you to select an entire molecule in select-one mode when a constituent atom is clicked. It can be used in conjunction with the shift key to add and remove entire molecules from the lasso.
  7. Menu System:
    1. The menu system has been dramatically improved. There are two new menus, Content and Structure. The Options menu has been removed and its functions redistributed. The Content menu contains functions for manipulating objects on the Doodle Sheet while the Structure menu contains chemical functions.
    2. A new Convert menu item has been included for converting chemical files between the formats recognized by ChemDoodle. (File)
    3. A new Actual Size function for negating zoom effects. (View)
    4. A new Current Selection function for centering the currently selected objects in the view of the Doodle Board. (View)
    5. Added a new Doodle Sheet guide to specify the boundaries of the page margins. (View)
    6. There are new functions for aligning and distributing objects on the page. The distribution functions can also be done with more precision by specifying certain parameters if you choose to supply them. (Content)
    7. There are new functions for selecting objects on the page. You may select the previously lassoed objects, the next molecule, or the inverse of the currently lassoed objects. (Content)
    8. New Deselect and Reselect menu items. (Content)
    9. A new Join function for combining two atoms into one. (Content)
    10. New Add Frame functions for surrounding the currently selected objects with various frames. (Content)
    11. The Add Hydrogens function can now be applied to specifically lassoed structures or to the entire contents of the Doodle Sheet. (Structure)
    12. The Generate SMILES String function of the right-click menu is now mirrored in the Structure menu. (Structure)
    13. The Add Abbreviation function of the right-click menu is now mirrored in the Structure menu. (Structure)
  8. Object Properties:
    1. Atoms, bonds and identifiers now have their own formatting window, just like shapes. You may access this window in the right-click menu or by double-clicking on the object.
    2. Atoms and bonds now contain their own set of properties, so they do not need to match the currently assigned chemical document settings. When an object is first placed, it will inherit all of the properties of the currently assigned chemical document settings. You may then alter the object’s properties by right-clicking on it and then selecting the Format Object menu item.
    3. There is a new button located in the Functions toolbar that will conform lassoed objects to the currently selected chemical document settings.
    4. There is now a new Atom Label Buffer property in the Preferences window under the Visuals tab. This buffer controls how closely bonds will draw to an atom’s text.
    5. There is now a new bond Overlap Buffer Space property in the Preferences window under the Visuals tab. This buffer controls how much whitespace will be “erased” from bonds located underneath other bonds. This property can also be disabled.
    6. Added a new Double Bond Asymmetry option to allow double bonds to be rendered off-center if that bond connects two Carbons.
    7. ChemDoodle Documents now save the Ignore Warnings property of atoms. Object warnings can be rechecked again if you select the new right-click menu item, Check for Warnings.
    8. All compatible properties have been included in our CDX/CDXML interpreters.
  9. The XYZ format can now be read and written. Several options are included for this format, such as which atom identifier to use and whether to buffer this identifier. These options can be specified in the Preferences window under the Saving tab.
  10. SVG and Adobe PDF graphics can now be displayed so you may add vector graphics to your figures.
  11. Added a new Snap to Grid option in the Preferences window. You can snap to either a 5 pixel or 10 pixel grid (or none, of course).
  12. Widgets are now resizable. The maximize button will now expand the widget to the largest practical size, or reduce it and replace it to its starting position and size. Windows and Linux frame icons have been changed to more naturally match their native look and feel.
  13. Specific image types can now be placed onto and retrieved from the System Clipboard in addition to the generic java image. These types include png, gif, jpg, ppm, tiff and bmp. The only ones pasted by default are the generic java image and bmp (for OpenOffice compatibility). You may change these options in the Preferences window under the Advanced tab.
  14. When conforming objects to chemical document settings, you will now be asked if you would like to change the fonts of the objects along with being asked if you would like to scale them.
  15. When zooming in and out, the currently lassoed objects will be centered in the view of the Doodle Board. If no objects are lassoed, all objects will be centered in the view of the Doodle Board.
  16. If either of the affine transformation tools or the lasso tools are selected, the last object or structure added to the Doodle Sheet will be selected. If you double-click on the Doodle Sheet in the 2D affine transformation mode, the lasso will now be emptied.
  17. Templates now auto-connect to nearby atoms just like rings do. Auto-connect can now be disabled in the Preferences window under the General tab.
  18. XML file parsing errors are now displayed in an error message pane when trying to load XML chemical filetypes.
  19. Added more greek symbols to the Symbols widget. Increased the size of the symbol preview box. Elements will now also display a preview.
  20. Added symbols that are added to objects as identifiers. The symbols include lone electron, electron pair, radical cation and radical anion. You can use these to help you create Lewis Dot Structures.
  21. Added a nucleotide template pack.
  22. Colors may now be set separately to different text types. There are new choices governed by the Color Selection button for Shape Text, Atom Text and Identifier Text.
  23. Colors are now associated with Chemical Document Settings files.
  24. ChemDoodle’s main color may now be changed in the Preferences window under the General tab. Pale colors lead to better results. You must restart ChemDoodle for this change to take full effect.
  25. Updated README.txt and the tutorial.

Fixes

  1. Linux Issues:
    1. Fixed text field widths in the Login window.
    2. Fixed text field widths in the Image Formatting Options windows.
    3. Fixed improperly condensed text in the Preferences window that causes some options to not be displayed.
    4. Fixed the JPG problem where no image was saved with the default settings.
    5. Backgrounds have been removed from button groups.
    6. ChemDoodle is now copy/paste compatible with OpenOffice.
  2. SMILES Issues:
    1. Fixed problematic SMILES generation when molecules contained complex fused rings.
    2. Fixed problem where non-organic group elements were incorrectly written.
    3. Removed some uneccesary parenthesis in results.
    4. Results now displayed in a scrolling text pane so long results are not cut off when selecting the Generate SMILES String menu items.
    5. Fixed problem where no string would be generated if a single atom had an unreasonably large number of bonds connected to it.
    6. Fixed SMILES widget issue where warnings were not being reset if a new molecule was dragged into it.
  3. ChemDoodle now asks before setting itself as the default editor for chemical filetypes on Windows. You will be presented with a checklist of all compatible chemical filetypes. Uncheck all you do not want to have associated with ChemDoodle.
  4. Doublet radicals combined with a + or - charge will be merged into a radical cation or radical anion respectively for ChemDraw files.
  5. The Format toolbar’s font chooser is now updated when loading CDX/CDXML files.
  6. Fixed a few problems regarding property parsing in MDL SDFiles. Added the alias property to the MDL MOLFile.
  7. Improved CML interpretation. Compatible stereochemistry is now read and written. Data arrays attributes are now read. Added support for a few less common attributes.
  8. Switching between portrait and lanscape modes for printing no longer affects the Doodle Sheet.
  9. The wavy line property for reaction arrows now has the appropriate affect.
  10. Some infrequent problems with the Stack function have been fixed. Shapes can also be stacked now. The stack page padding is now the margins of the Doodle Sheet.
  11. Fixed problem where dropping objects on the Doodle Sheet when zoomed placed the object in that corresponding place if the sheet was not zoomed. Dragging objects off of a zoomed Doodle Sheet has also been fixed.
  12. Fixed issue where the Paste functions were not being enabled if the System Clipboard was blank while ChemDoodle was loading.
  13. Fixed the 180° rotation function.
  14. Fixed default size of the Doodle Board on small screen resolutions.
  15. Scaling now only affects lassoed objects if conforming only those objects.
  16. Fixed the calculation of the number of hydrogens to add into a label if in strict hydrogen mode and Add Hydrogens as Text is selected.
  17. Fixed problem where Guideline options did not mirror the actual display if the current preferences were reset.
  18. Conforming chemical document settings actions to objects and the Doodle Sheet can now be undone.
  19. Applying CSS to HTML areas can now be undone.
  20. Fixed problem where changing a bond’s color was not undone properly.
  21. Improved the algorithm for calculating the optimal angle to add bonds too. Fixed issue where the optimal angle was incorrect for horizontal bonds.
  22. File extensions containing capitals are now handled correctly.
  23. The About ChemDoodle window has been dramatically improved.
  24. Fixed problem where removing hydrogens couldn’t be undone when removing from a lassoed structure.
  25. Fixed issue where sometimes the shift key wasn’t recognized when pressed.
  26. Fixed dimension issues for bonds and atoms.
  27. Double-clicking on a label will now open its editor.
  28. Fixed problem where the hash properties of objects weren’t being loaded properly in the Format Bond window.
  29. Improved the look of bond breakers by centering them correctly.
  30. Page dimensions for postscript files are now set properly.
  31. Fixed problem where selecting the Use Circles option for atoms did not result in the desired effects if User Chosen colors was selected.
  32. Fixed problem where rarely an object would be focused in an image.
  33. Fixed problem where copying a single shape did not work. Chemical types are no longer placed on the System Clipboard if selected objects do not contain chemical objects.
  34. Improved drag-and-drop compatibility with files from the file system.
  35. Image border properties are now set properly.
  36. Changed the Multiplet Tool widget’s icon so that it’s more recognizable.
  37. Scale anchors for the lasso are now only displayed in the 2D affine transformation state.
  38. Improved Application loading speed.
  39. Updated all CDS files.
  40. Minor graphical enhancements and fixes.
  41. Minor textual fixes.

1.3.1

October 19, 2008

Fixes

  1. Fixed a bug where no standardized locale was set, causing interpretation problems when reading and writing files in some locales where commas are used to denote decimals. Users in the US were not affected by this bug. All files are now standardized to the US locale. This change will not fix previously saved files. To manually fix previously corrupted files, just open them in a text editor and use a replace all function to convert all commas to periods. We apologize for any inconveniences this problem has caused.

1.3.0

August 17, 2008

Additions

  1. ChemDraw files (*.cdx) and ChemDraw XML files (*.cdxml) can now be flawlessly read and written. Share your documents with ChemDraw users with ease or submit ChemDraw documents with publication manuscripts if required! Mutually exclusive objects cannot be save or read such as ChemDoodle multiplet simulations. You may read more about this feature here.
  2. Added read and write support for Chemical Markup Language (*.cml).
  3. A message now appears when saving formats that cannot describe all ChemDoodle objects. This messasge will describe the format and any possible changes to your document when you save. These messages can be disabled in the Save tab in the Preferences dialog.
  4. SMILES strings are now generated. You can access this feature by dragging a selected molecule or group of objects onto the SMILES Palette or its icon. You may also select a molecule and group of objects and select the Generate SMILES String menu item in the right-click menu. The SMILES Palette now contains a new button to copy the contents of the text field directly to the system clipboard. Added a new option in the Advanced tab of the Preferences dialog to control SMILES copying/pasting behavior.
  5. Added 5 new bond types: wavy, two-electron, bond and thin double, quintuple and sextuple.
  6. Renovated the shape system in ChemDoodle (all properties are now instance specific):
    1. Shape groups have been implemented. New button groups contain various preset settings for common shapes and can be recognized by a small arrow in the bottom-right corner of the button. Click, as usual, to use the object. Press down and hold for a second to display a sub-toolbar with other presets for that shape. Just drag and release over the new presets to select them.
    2. Added an arc shape type.
    3. Mechanism arrows may now be preset at 120°. Arcs and mechanism arrows can now be altered to display at any arc angle.
    4. Added a new shape properties dialog that can be accessed by selecting the Format Shape menu item in the shape’s right-click menu.
    5. Added shadow property.
    6. Added shaded property.
    7. Added stroke thickness property.
    8. Added hash properties.
    9. Added parenthesis and curly bracket types.
    10. Added wavy line type.
    11. Added rounded rectangle type.
    12. Added many new arrowhead options with complete control over their look.
    13. Added reaction arrow types: towards products, towards reactants.
    14. Changing shape properties can be undone and redone.
  7. Added a new Hidden Carbon Angle property to govern the angle at which “hidden” carbons will display their label between two near parallel single bonds. Added an option to turn hidden carbons off. This can all be accessed in the Visuals tab in the Preferences dialog.
  8. There is a new Page tab in the Preferences dialog. This tab now holds the Create Chemical Document Settings File button. New sections are added to control the page dimensions and margins.
  9. Added and option to the Multiplet tool to govern which direction the scale is oriented.
  10. Added a feature to display unique atom and bond ids. These options can be selected under the Unique IDs submenu in the View menu.
  11. Added an iChemLabs Newsfeed menu item to the Help menu for easy access to stories and information regarding ChemDoodle.

Fixes

  1. Optimized file reading and writing.
  2. Current values are now displayed properly in page size dialogs.
  3. Shape rotation system has been fixed. Shapes no longer loose their position after rotation. All rotations are now saved and copied accurately.
  4. Minor HTML Area text changes can now be undone and redone.
  5. Fixed problem where multiple consecutive returns in a label caused it to incorrectly calculate its bounds.
  6. Labels and multiplets are now highlighted when lassoed.
  7. Multiplets can now be rotated.
  8. Removed rounding errors associated with brackets, zigzag bonds, wedge bonds, bond breakers and the pen tool.
  9. Fixed an issue where copying a shape sometimes did not copy all of its properties correctly.
  10. Removed redundant copy function from image right-click menus.
  11. Fixed problem where both a selected group of objects and a hovered object could be right-clicked at the same time.
  12. Symbols Widget now checks if the default font can display a given symbol before using the packaged unicode font.
  13. Symbols Widget now checks the entire string to match abbreviation searches, and those searches are no longer case-sensitive.
  14. Fixed Symbols Widget problem where some abbreviations were not appearing.
  15. Fixed problem where MolGrabber LITE widget contents would temporarily disappear on mac if the area surrounding the text fields was clicked.
  16. Saving MDL MOLFiles and SDFiles no longer changes the current opened document.
  17. MDL MOLFiles and SDFiles are no longer saved with non-elemental atom labels.
  18. MDL MOLFiles .mol extention is now used by default over .mdl.
  19. Fixed problems where atom fonts were altered if switching between tabs while those atoms were selected.
  20. Fixed mac problem where control+click did not initiate a right-click action.
  21. Added a mouse pointer spinner to notify you if ChemDoodle is taking a very long time to load a file.
  22. Fixed a few inconsistencies with the official Chemical Document Settings files.
  23. Chemical Document Settings changes can now be undone and redone.
  24. Fixed how reaction arrows were drawn weirdly if the direction was reversed.
  25. More magnification scales have been added.
  26. Fit Page to Width and Fit Page to Window scales have been improved.
  27. Added font sizes 6 and 7.
  28. Updated tutorial to any changes.
  29. Includes iChemLabs Updater v1.2 which fixes Windows bug that stopped it from performing its task.
  30. Fixed minor errors.
  31. Fixed minor textual inconsistencies.

1.2.3

July 19, 2008

Fixes

  1. Fixed major problem where ChemDoodle Documents saved with ChemDoodle v1.2.2 could not be opened. They will be able to be opened after this update. We apologize for any inconvenience.

News

The next big update of ChemDoodle will provide the ability to flawlessly read and write ChemDraw CDX and CDXML files! This means you can work with anyone using ChemDraw, and even submit your ChemDoodle Documents to publishers without any issues as ChemDraw files (if they don’t accept ChemDoodle’s main format). Visit www.ichemlabs.com for a new story to be posted about this great feature later in the week!

1.2.2

July 13, 2008

Additions

  1. Greatly improved the tutorial. The tutorial is now 17 pages long, consisting of all of the main features of ChemDoodle. You may view the tutorial at any time by selecting the ChemDoodle Tutorial menu item in the Help menu. There are still some lesser or more specific features not covered in the tutorial, and those will be covered in future videos posted on the main iChemLabs website.
  2. Multiple fonts can now be associated with a chemical document settings file. ChemDoodle will check down the list and select the first font present on the users computer. If none of the specified fonts are present, a message is displayed explaining the situation. All other settings will still be applied. All official chemical document formats have been updated accordingly.
  3. Added a static bracket set object that acts like a rectangle.
  4. Added more menu accelerators.
  5. The iChemLabs Updater has been upgraded to version 1.1.0. When downloading files, the updater will now display a progress indicator of the number of Kb downloaded under the spinner. You will not observe this change until the following update.

Fixes

  1. When placing rings and templates, a lone carbon now follows the mouse if no starting atom is selected.
  2. Fixed problem where Label objects didn’t appear after being set.
  3. Fixed problem where radicals were not read properly from ChemDoodle Documents.
  4. Fixed how the lasso measures the dimensions of different bonds. The bounding box will now resize itself based on bond properties.
  5. Fixed problem where copying vector images to the system clipboard copied all objects on the sheet, and not just those selected.
  6. Removed the vertical alignment property from chemical document settings files that was causing unintended text alignment effects across different operating systems.
  7. Chemical document settings files now add a new Doodle Sheet to the Doodle Board with their properties set if opened in ChemDoodle. This is an alternative way to apply chemical document settings other than through the menus.
  8. Text areas now update appropriately when they are resized by the lasso.
  9. Fixed problem where the Doodle Sheet was cleared and the Single Bond button was selected, but the bond order was not being set properly.
  10. Fixed problem where the Preferences dialog claims some chemical document settings properties have been changed, but really were not.
  11. Fixed various issues associated with stacking objects.
  12. Fixed problem where imported files were not displayed on rare occasions.
  13. Fixed problem where sometimes preview lines showed up for placing rectangle objects after dynamic brackets were set.
  14. Fixed problem where messages displayed white backgrounds instead of clear backgrounds on Windows.
  15. Fixed minor issue where reaction arrows were converted to equilibrium arrows, but the History widget states a mechanism arrow action.
  16. Fixed minor graphical and textual inconsistencies.
  17. Fixed minor errors.

1.2.1

June 29, 2008

Additions

  1. New advanced methods for creating, setting, and altering chemical document settings and formats. Bond preferences have been redone with many more options and are all 100% accurate. Preferences are now document dependent and will be retained when saved or when switching between tabs. Font and sheet size are now saved with preferences. To find out more, click here.
  2. Added many chemical document formats including: ACS Document 1996, Helvetica Chimica Acta, RSC (1 and 2 Columns), and many others.
  3. Doodle Sheets can now be resized.
  4. Added more template packs: Cycloalkanes, Functional Groups, Hexoses, Polycycles, Stereocenters and more Ring Conformers. A separator now appears between official and unofficial template packs.
  5. Drag and drop has now been implemented. To find out more, click here.
  6. Radicals have been fixed, and are now separate from charge decorations. Radical properties can be changed in the Preferences menu, and radicals now automatically orient themselves according to the angle from the parent atom.
  7. New advanced affine transforms have been included. The added arbitrary rotate and advanced scaling functions are precise and intuitive. To find out more, click here.
  8. New menu items have been added including (not mentioned elsewhere): Clear, Purge History, Close and Close Others.
  9. Dragging slightly outside of the Doodle Sheet will cause the scroll bars to scroll, if appropriate.
  10. Added circular atom guides in the View menu that draw circular guides around atoms with a radius equal to the bond length.
  11. Base64 encoding is now used to embed images in ChemDoodle Documents. This allows for larger files to be embedded, and therefore the size restriction has been removed.
  12. Widget buttons now display tool tips.
  13. Added a new Purchase menu for easy access to the Permanently Activate ChemDoodle menu item. This menu disappears after ChemDoodle is permanently activated.
  14. Added a new filetype and icon for ChemDoodle Chemical Document Settings Files (.cds).

Fixes

  1. Sliders in Preferences now contain a number field, and the units can be changed.
  2. Fixed bug where scale edges in the Multiplet Widget were incorrectly calculated when a simulation was showing.
  3. SMILES Widget now displays an appropriate message when empty content is input.
  4. MolGrabber LITE Widget and SMILES Widget lists have been improved for easier reading.
  5. Template Widget no longer loses focus when traversing template lists.
  6. Symbols Widget now works with label objects.
  7. Label objects can now be edited by double-clicking on them.
  8. Shift now properly locks the aspect ratio for all shapes when resizing or placing, except for lines. Lines will align vertically or horizontally when shift is held. Shift now causes the screen to update for immediate feedback.
  9. Fixed problem where rounding errors would occur when editing objects at scales other than 100%.
  10. Fixed small bug where the cyclopropane button actually places cyclobutanes.
  11. Cut/copy/paste and undo/redo buttons and menu items have been overhauled so that they remain consistent. Paste now always appears in the right-click menu if there is something to paste. Images can be directly copied to the clipboard. Undoing the “New Doodle Sheet” item in the History widget no longer removes it.
  12. Radicals now appear properly.
  13. Fixed problem where HTML areas were not being properly read from save files.
  14. Fixed problem when saving transparent images, where the transparent property was not being set.
  15. Fixed problem where documents beginning with “Untitled” could be duplicated in the system.
  16. The appropriate tab will be selected when prompted to save a file that is not the currently selected tab.
  17. Fixed problem where closing a tab also closed the tab to its right.
  18. Fixed problem where Unacceptable Oxidation State warnings lingered even after they were addressed.
  19. Fixed message that was displayed when checking for updates could not continue because ChemDoodle could not connect to the internet. Added a timeout to URL connections. Improved internet connection errors.
  20. Fixed problem where Preferences dialog did not appear when requested to in message popups.
  21. Splash screen now notes when OpenBabel is queried.
  22. Template menu items no longer appear if shapes are selected.
  23. Improved the window shrinking special effect when windows are hidden.
  24. Lasso modes are now appropriately handled when switching between tabs.
  25. Fixed minor graphical and textual inconsistencies. Improved the layouts of most dialogs.
  26. Fixed minor errors.

1.2.0

May 23, 2008

Additions

  1. Added a brand new widget, Multiplet Tool. This widget simulates and displays multiplets and their splitting trees. Both ESR and NMR can be simulated based on input parameters. Both Gaussian and Lorentzian linewidths can be used. Spectra can be displayed in the function, the first derivative or the second derivative. A slider panel is included for easy tweaking of the parameters when fitting. Everything is customizable.
  2. A new Label shape has been added. Unlike text or HTML areas, the label has no border or background, and automatically fits its text. Use these with ease for figure titles, equation labels for reactions, etc.
  3. The display of textual atom labels has been completely redone. Support for styles such as subscript and superscript are now independent of font. Centering of the labels has also been improved. In addition, the Preference menu now has a new property for atom label vertical alignment. If the chosen font has unconventional ascents or descents from the font baseline, use this property to adjust the vertical alignment.
  4. A unicode font is now provided, so that all systems can support the characters displayed in the Symbols Widget.
  5. When adding carbon chains, the preview now looks exactly like the product.
  6. ChemDoodle can now determine the filetype of an input file, and will describe errors that occur if unrecognized filetypes are opened.
  7. Bitmap image support has been standardized and greatly improved. ChemDoodle will discribe how to use images that are not of the recognized filetypes.
  8. Image components can now be directly copied to the system clipboard with a right-menu function.
  9. CSS can now be easily applied to HTML areas by selecting the appropriate right-menu function. Additional CSS files can be added to the ChemDoodle/settings/css folder.
  10. Templates can now be separated into groups. These templates are located in the ChemDoodle/settings/templates folder for easy inclusion and distribution.
  11. Added more abbreviations to the Symbols Widget.

Fixes

  1. The registration of Windows filetypes has been fixed. Now, filetypes associated with ChemDoodle display their appropriate icon, open in ChemDoodle when double-clicked, and have appropriately defined descriptions and MIME-types.
  2. Symbol Widget characters now correctly fit in their buttons.
  3. Carbon chain preview now correctly displays the number of bonds being added if starting on an unsubstituted carbon.
  4. Error dialogs now fit details better.
  5. Bicubic image scaling is better for rotations, and this is now stated in the Preferences menu.
  6. Periodic Table now greyscales when an element is selected, instead of blurring.
  7. The splashscreen progress is more thorough.
  8. Message dialogs now allow for buttons and other components to obtain focus.
  9. The mouse position refreshes after a right-menu has been closed.
  10. Landscape documents now reopen properly.
  11. The Periodic Table’s Electrons checkbox now properly displays the Bohr electron configurations on the right side.
  12. README.txt and tutorial have been updated.
  13. Fixed concurrent modification error when saving while overriding a currently opened file.
  14. Subscripts are now properly displayed in the abbreviations panel of the Symbols Widget.
  15. Fixed problem where ruler caret disappears in certain areas.
  16. Fixed problem where widget buttons were not obtaining focus.
  17. Fixed problem where redo function caused bond mode to begin.
  18. Bond highlights are now still drawn, even if the bond color is empty.
  19. Fixed minor graphical inconsistencies and improved a few button icons.
  20. Fixed minor errors.

1.1.3

April 23, 2008

Additions

  1. Added a beautiful, printable, customizable interactive periodic table of elements with physical properties. More elemental data will be added in subsequent updates.
  2. Brackets now have an associated label that will automatically place itself in the correct position.
  3. Bond color and border/line color have been separated in the color chooser for easier color management.
  4. Double bonds can be customized to be symmetrical always, never or only when not part of a ring.
  5. Labels can now be added as substituents instead of just changing the highlighted atom’s label. (A single bond will be added with the new atom displaying the current label)
  6. New content added to the Symbols widget including “Arrows”, “Constants and Units”, and “Punctuation”. A new preview popup appears in the upper-left corner of the Symbols widget when hovering over a symbol. Additional content will be added in subsequent updates.

Fixes

  1. Splashscreen performance greatly improved. Flashing has been eliminated.
  2. After a trial expires, a popup will appear describing the situation before asking for another activation code.
  3. ChemDoodle now recognizes HTTP redirects and reports them in an error dialog.
  4. ChemDoodle now alerts you to image warnings, such as trying to load a file that is not a recognized filetype or trying to load an image that is too large.
  5. Logouts due to session expirations are now easily handled, continuing with the current function after re-authentication.
  6. Text area now retains style information if a symbol is inserted. The inserted symbol will now conform to the surrounding style. The font and size choosers in the format bar now correctly display the style at the cursor position.
  7. Brackets copy correctly.
  8. Doodle sheets now remember which lasso mode they were in. An error where open text inputs would sometimes remain on screen when switching sheets has been corrected.
  9. Select one mode error corrected.
  10. SMILES widget now counts ‘*’ labels in aromatics as instructed in SMILES documentation.
  11. Fixed template scaling problem. Text in templates are now oriented and centered correctly.
  12. Widget button drawing has been optimized to improve performance.
  13. Lasso optimized to improve refresh rate.
  14. Nudging has been fixed; the Doodle Board’s scrollbar no longer responds to arrow keys.
  15. Copying and pasting no longer crops off long atom labels.
  16. Fixed error where the clean tool would incorrectly align some triple bonds.
  17. Object flipping now causes the doodle sheet to repaint.
  18. Atom lock-on distance is now a function of the current bond length.
  19. Labels now orient correctly regardless of whether or not atoms are being checked for chemical correctness.
  20. Resolution of Mac icons increased to 512×512 pixels.
  21. Fuzziness has been removed from Windows cursors.
  22. Resolution of Windows icons increased to 240×240 pixels. The ChemDoodle Windows executable has been recreated with many improvements.
  23. Fixed Linux problem where message dialogs would appear behind the splash screen.
  24. Failing to connect to the internet, after logging in, will log you off.
  25. Fixed minor graphical inconsistencies and aberrations.
  26. Fixed minor errors.

1.1.2

March 19, 2008

Additions

  1. Preferences now contains an option for displaying carbon labels on carbons with three modes: never, on lone carbons or always.
  2. A new drawing warning for unacceptable oxidation states has been added.
  3. CPK and Jmol color sets completed.

Fixes

  1. Brackets between discrete molecules are drawn correctly.
  2. Corrected minor issues concerning the abbreviation management panel.
  3. Updated oxidation state database.
  4. Fixed minor graphical and textual issues.

1.1.1

March 10, 2008

Additions

  1. The messaging and error system has been recreated from the ground up. Error and message windows now fit the Look-and-Feel of ChemDoodle as well as providing much more information on a given situation and how to troubleshoot certain scenarios.
  2. ChemDoodle will carefully check files upon opening them. If any errors are encountered, an error pane will describe the exact problem, where in the file that error is encountered, and suggestions to fix it.
  3. SMILES widget now parses reactions as defined by the SMILES documentation with correct 2D layout.
  4. Tables are now included in the View menu to list chemical data, including atomic properties and isotope distributions.
  5. Any mass number can now be associated with an atom, not just the known ones. An error for checking this property has also been added.
  6. Added templates pack #2 containing polycyclic aromatic hydrocarbons.
  7. Aromatic ring size is now definable in the Preferences window.
  8. Preferences now contains an option for filling or not filling arrowheads.
  9. Preferences now contains advanced options for what data flavors are placed on the system clipboard during copying to other applications to ease pasting ambiguities.
  10. The Preferences window has been completely redone, with more functions for restoring defaults and cancelling changes.
  11. New iChemLabs login screen containing a check box for linking your account information with your copy of ChemDoodle.
  12. New components improve the aesthetic and functional nature of ChemDoodle, including drop shadow borders and shrinkable task panes.

Fixes

  1. A new widget management system to get rid of the less appropriate “scrolling” system. The Statistics and History widgets are always displayed, but only one other widget is visible. The selected widget can be chosen from graphical widget buttons that appear below the History widget.
  2. Fixed undo problem where rotations were being “unrotated” around a differet center point.
  3. Reaction arrows and mechanism arrows now copy and paste correctly.
  4. Fixed ring problem where single bonds incorrectly change to the selected bond order when placed.
  5. Fixed multiple molecule optimization problems with the SMILES widget.
  6. Templates now save without retaining more specific information hampering user defined color and font choices. Current templates have been fixed.
  7. The text area margin window has been improved.
  8. Fixed highlighting ambiguity on some objects when the lasso is active.
  9. Fixed minor graphical and textual problems.

1.1.0

February 01, 2008

Version 1.1.0 is the official market release version of ChemDoodle.


1.0.7

January 20, 2008

  1. Added a Templates widget which stores templates for adding to the Doodle Board. You may also create your own templates. Current templates include amino acids and ring conformers.
  2. The Symbol widget now also adds to text areas and reaction arrow texts.
  3. Fixed mac list cell rendering problem where some list items would become white or invisible.
  4. Fixed MolGrabber LITE.
  5. MDL MOLFiles and SDFiles now center around the origin for each molecule. Further options have been added for normalizing coordinates by the standard bond length or the currently selected bond length.
  6. Fixed various minor errors.

1.0.6

January 06, 2008

  1. OpenBabel is now integrated for flawless interpretation of over 80 chemical file types. Import, Export and Convert between them.
  2. An auto-update function has been added so you no longer need to update ChemDoodle manually.
  3. More image types have been supported. In all there are 7 supported bitmap image types and 6 supported vector image types. All have support for all of their specifications.
  4. Images can now be embedded in ChemDoodle Documents.
  5. The 2D structure cleaner has been improved.
  6. MDL SDFiles have become a native format for ChemDoodle.
  7. Doodle Sheets now recognize when work has been done, and empty sheets will now close without requesting approval.