iChemLabs | ChemDoodle Version History

12.7.0

October 21, 2024

Executive Summary

Version 12.7.0 is a feature update for ChemDoodle 2D. PubChem searching may now be performed directly from the application. The OLE server for Windows round-trip editing has been greatly improved (please see details below). A number of other options and improvements are included.

Additions

New PubChem searching options in the File>Interfaces menu, as well as in the Chemistry toolbar.
The OLE server has been thoroughly improved, and is much more stable. ChemDoodle OLE objects are now compatible with the Layout and Wrap functions in Word. While much more stable, there is a known issue when activating ChemDoodle OLE objects via double-click or the right-click menu, which may lead to object corruption, but there is a workaround. Please read section 16.7.2 of the user guide before using ChemDoodle OLE objects. Round-trip editing via OLE with the copy/paste functions has no known issues and should work 100% of the time.
There is a new option in Settings>Controls called Default Tool. You may use this option to define which tool is chosen by default when the application is opened and when a new empty document is created or selected from the tabs. Switching between documents where content exists will no longer change the active tool (unless a selection is present).
Sections in the user guide's table of contents are now numbered in PDF viewers.
A message to discuss context sensitive functions is now shown if any of the File>Interfaces submenus are expanded and there is no selection made in the document. This message may be disabled. The same message displayed when expanding the Structure menu will now only occur if no selection is present in the document.

Fixes

Corrected IUPAC naming issues involving cresols. Corrected a number of issues with traditional naming involving trivially substituted benzene derivatives. Corrected several edge cases involving nitrogen base chains. Molecular hydrogen is now named correctly if represented as a single label or as two atoms connected by a bond.
Resolved issue where custom pen shape arrowheads do not point in the correct direction.
When editing text, ctrl-X (command-X on macOS) will now perform a cut action on selected text. Strikethrough is now performed with ctrl-shift-X (command-shift-X on macOS).
Improved rendering of the two electron bond.
SMILES output now correctly includes double bond stereochemistry for bonds in rings.
Corrected output of SMILES reactions if the products were drawn first.
InChI stereochemistry output is now handled directly by the ChemDoodle stereochemistry libraries and is now just as accurate as the leading ChemDoodle system.
Fixed bug where the wrong tab may end up being selected if multiple tabs exist and one is closed.
Fixed issue where Search widget folder chooser is not appearing on Windows.
Corrected the ChemSpider connection in the MolGrabber widget.
Fixed error where PDFs pasted into ChemDoodle would cause a save file to corrupt.

12.6.0

May 25, 2024

Executive Summary

Version 12.6.0 is a feature update for ChemDoodle 2D. Included are new features for EPS file output, new keyboard and tool actions familiar to experienced chemists, a new solubility calculator, the ability to organize content by selections of atoms, and more.

Additions

Alignment, distribution and centering may now be performed on selections of atoms, instead of the whole molecules they are a part of. This will make it much easier to organize figures based on individual atoms within structures. Please see section 11.4 of the ChemDoodle user guide for further instructions.
Improved perspective structure automatic z-ordering with another geometry type.
Added a solubility (logS) calculator based on the Hou algorithm, which can be accessed in the Structure>Descriptors menu, in the Properties widget, and as an auto-updating label.
Condensed labels ending in a radical formula (i.e. OC2H5) are now supported.
Support added for SO3H abbreviation.
When editing text components (atom label or caption), the return/enter key will now confirm and set the text object, while using control+return or control+enter will add a new line. Escape will now cancel and revert the text object to the previous state.
Using the "z" key to flip curved arrows with fishhook end arrowheads will now move the fishhook to the opposite side of that end of the line.
Pressing the system meta key (control on Windows/Linux, command on macOS) and dragging selected content will now duplicate that content. You may also press the system meta key while transforming selected content to copy the current state of that selected content. Use this method to stamp copies of your selected content as you transform it. Please see section 11.3 of the ChemDoodle user guide for further instructions.
Double clicking on an atom or bond using a selection tool will now default to selecting the entire molecule. You may change this behavior back to editing the styles of the object in the Controls settings, by changing the Double Click on Atom/Bond setting.
There are now options in Save Settings to disable the individual output settings window for chemical file and image output, when using the Save/Save As... functions. If disabled, the default settings will be applied. Chemical file settings windows are now provided on save, but are disabled by default.
The Chemical Files settings panel has been reorganized for clarity.
EPS output now includes an option to preserve chemnum tags in output. Such chemnum tags are defaulted as "TMPx", but you may change what the chemnum tag is to be used. These tags, when written in caption labels, will be preserved as unbroken text in EPS output, even if the Render Text as Shapes option is enabled. This way, you can work with chemnum and still have perfect font glyph output to EPS files for your figures.
Bitmap image output is now supported in EPS files.
Bitmap images copied to the system clipboard now adhere to the default application settings for images (scale, resolution, etc.).
Images are now rendered on the fly at the correct native resolution of the image, fixing output scaling issues. Progressive bilinear scaling has been removed.
The precisionFDA integration now has its own submenu in the File>Interfaces submenu. Simply select a structure and then select the precisionFDA>UNIISearch menu item to execute a search. Please see Appendix A.12 of the ChemDoodle user guide for further instructions.

Fixes

Corrected minor tetrahedral stereochemistry perception edge case.
Setting enhanced stereochemistry to an atom now stops the stereochemistry menu from showing options when right clicking on that atom.
Assigning stereochemical configurations for a structure with enhanced stereochemistry present now disregards enhanced stereocenters.
Fixed issue where stereochemical functions were not showing in the context menu and the Structure>Stereochemistry>Resolve functions did not have any effect for centers that are spiro and symmetrical.
Hydrogens connected by a single bond to a chiral center are now removed by the remove hydrogens functions. Only wedge connected hydrogens will be retained on stereocenters.
Added a clearer error message when trying to force a stereo configuration in a projection, when no correct orientation is possible.
Resolved error generating traditional IUPAC names with multiple isotopes.
Hiding a carbon label will now work on carbon atoms when the implicit hydrogen count has been defined to 0.
Undo and redo of the show/hide carbon label action has been corrected to revert back to the previous state of the atom.
The center and distribute on page functions will now keep selected content within the page the center of that content is present on.
Corrected issue when fixed bond angles is disabled and then adding an aromatic ring on using the alt+6 keyboard shortcut lead to a weirdly attached angle.
Corrected a bug where setting a manual attribute wasn't working.
Double click when hovering on a shape in a shape state now opens the styles window for that shape.
Fixed issue where SMILES output does not properly include explicit hydrogens for stereocenters if the option to write explicit hydrogens is enabled.
PDB, PDBML, BCIF, MMCIF and MMTF filetypes all now use the same compatibility warning setting.
Corrected EPS output encoding to enable support of more character glyphs.
For clarity, the "2D Stochastic Build" menu item has been renamed to "Beautify Structure Drawing".
Prevented keyboard tool shortcuts from executing when completing some menu accelerator commands.
Provided a workaround on macOS to reenable the menu bar after the file dialog has been closed without leaving the application.
Provided a workaround for an error in PowerPoint on Windows, where a round-trip copy of an OLE object into PowerPoint and back into ChemDoodle doesn't work.

12.5.0

February 29, 2024

Executive Summary

Version 12.5.0 is a feature update for ChemDoodle 2D. Included is GSRS integration, new MDL SDF features, interface improvements, and more.

Additions

GSRS integration for public and private database searching. You may initiate searches using the File>Interfaces>GSRS menu. Please see Appendix A.7 of the ChemDoodle user guide for further instructions.
Data records from MDL SD files will now be visible in a table when inputting the file in ChemDoodle. In the Settings window, under the Chemical Files tab, scroll down to the MDL Connection Table Files section and enable the Input Data Records as Tables option as you prefer. The data records will be rendered in a table along side each connection table entry. Please note this feature is read-only, and custom data records outside of the file annotations will not be written to SD files.
A new MDL SD file option will output placeholder data records for eCTD data items and submissions. In the Settings window, under the Chemical Files tab, scroll down to the MDL Connection Table Files section and enable the Output eCTD Data Headers option.
Lone atom labels will now have hydrogens left oriented for certain cases, including left HF, HCl, HBr, HI, H2S, H2O, and H3O+. You may still force right orientation using the Label Orientation right-click menu for the atom.
Some adjustments have been made for accepting plus or minus key input when a German keyboard layout is used. The plus and minus keys on the number pad will now mirror the same key functions from the main keyboard.
CTRL + scroll wheel will now zoom in/out in reference to the cursor position.
More options have been added to the auto-updating labels function, including H-Bond Acceptor Count, H-Bond Donor Count, Degree of Unsaturation, Rotatable Bond Count, Molar Refractivity, TPSA and XlogP2.
More improvements to the chemical image recovery algorithm.
The workspace will now remember the window maximized state.

Fixes

Corrected edge cases with atropisomer stereochemical configurations.
Adjusted warnings to be correct involving rare atropisomer cases.
Fixed bug where the Label Orientation right-click menu for atom did not immediately update the graphics.
Stopped a hang when an SD file with invalid data record syntax was input.
Warning states now properly update when you press the Restore Defaults button in the Settings window.
Fixed centering on zoom for multipage documents.
Corrected issue where the font bold/italic settings were not always properly recovered when apply document styles.
The Template widget will now correctly update newly selected templates if the style sheet has been changed.

12.4.0

January 20, 2024

Executive Summary

Version 12.4.0 is a feature update for ChemDoodle 2D. Included is significant work on IUPAC naming output, support for atropisomer stereochemistry, improved and adjustable crosshair background guides, a reaction sprout function, and more.

Additions

Significant updates for IUPAC naming. Much of the focus has been on PIN support and syntax for PINs. Included is advanced support for stereochemistry output, compliant with the latest specification and coverage of more complex stereochemical entities including atropisomers. Also included are new impressive algorithms for resolving indicated hydrogens in mancude ring blocks. Xi symbols used when wavy bonds invalidate a stereochemical configuration. Non-integer support for locants in base templates. Many edge cases have been resolved.
IUPAC naming options in the Settings window have been clarified.
Full support for atropisomer stereochemistry. You may use the full functionality of the ChemDoodle stereochemistry engine for atropisomers, including recognition, configuration setting, flipping, forcing and warnings.
A new Sprout function is included in the Reaction menu. This function will generate a reaction out of any number of selected molecules. The selected molecules will become reactants, and copies will be created as products for further edit.
The crosshair drawing guides have been reworked. You may now move the crosshair location when using a selection tool. Double clicking on the cross hair will recenter it. Crosshair grid breakdown is now optimized for the current rendering scale of the document. Each page within a document will have its own crosshair, which may be moved independently of the others. And you may choose between US and Metric modes for the crosshair rulers.
The Windows installer will now produce a log when run in silent mode. Please see section 1.5.5 of the ChemDoodle user guide for more information.

Fixes

Resolved stereochemistry issues when resonance bonds were present.
Resolved wedge assignment issue for clustered stereocenters when an even numbered cumulene is involved.
Fixed SMILES input issue where tetrehedral geometry was not recognized with a lone electron pair.
Corrected out of SMILES where allenes with implicit hydrogens were mishandled.
Fixed minor issues regarding the rendering of warning descriptions on the document.
The Warnings panel in the Settings window now included subtitles, as intended.
The drawing guides have been improved with thinner lines, which are nicer on high-DPI displays.
Fixed problem where the non-native open file dialog appeared behind the application when using the Recover MS Office Files window.

12.3.0

November 16, 2023

Executive Summary

A number of notable features are included in ChemDoodle 2D v12.3.0. More repeat unit rendering options, context menu controls for changing bond z-orders, a new algorithm for automatically applying bond z-orders based on wedges, subtoken character alignment, conjugated chain resonance curve rendering, a JPEG image quality output option, and more.

Additions

Repeat units can now be rendered as parenthesis, curly brackets and chevrons in addition to square brackets.
Repeat units may now be set to enclose the shortest paths between the two defined bracket bonds, leading to aligned rectangular braces. Aligned bracket graphics may preferable for some users, but this style is not appropriate for all cases. Please see section 9.15.6 of the ChemDoodle user guide for more information.
You may now move overlapping bonds forward, backward, to the front and to the back using the right click menu. The forward and backward options will only be enabled for bonds currently existing in an overlap. See section 11.12.1.1 of the user guide.
There is a new function using the Structure>Auto-layer Bonds by Wedges menu item to automatically correct the z-layout of overlapping bonds in structures containing wedges. Please see section 11.12.1.4.
Subtoken character alignment. ChemDoodle now allows you to align mutli-character tokens by edge characters depending on the attached bonds. There are several modes for this style: Never, Only Terminal, Optimized and Always. Optimized aligns by edge or center depending on the bond environment. This will produce clearer and more attractive graphics in many cases, as more of the bond line is exposed. However, symmetry will be reduced, so the style is set to Never by default. Input ChemDraw CDX/CDXML files will have the style set to Optimized, to match the rendering engine for ChemDraw. See section 4.8.3 of the user guide.
ChemDoodle can now render chains of resonance bonds using a unified dashed curve for more attractive graphics. Please see section 13.15.3.
The auto-updating labels interface now provides a set of checkboxes to add multiple labels at once. The order in which the checkboxes are selected will be the order that the updating labels appear in, from top to bottom.
The atom circle radius style may now be set to 0, excluding the circle rendering from any output images.
You may now control the image quality for output JPEG images. JPEG is a lossy format, so a lower quality will result in a smaller file, but worse image.
Added a Default Document Scale setting (in the Appearance panel of the Settings window) for newly created and opened documents.
Smaller widget title bar interface elements on Windows (macOS widget elements were already in utility mode).
Improvements to CIR/OSR interpretation involving short double bonds.
More 2D clean templates added.
Menu item icons have been updated and are now resolution-less. More menu item icons have been added where multiple choices will benefit from them.

Fixes

Fixed bug where in a document with multiple pages, right-click worked only on the first page.
Shape arrange menu items are now enabled/disabled depending on their z-order for better feedback.
Terminal labels are now also offset around terminal resonance bonds for centered graphics.
Pasting descriptors using the Structure>Descriptor menu items will now appropriately place the resulting labels to avoid overlaps.
Corrected the conversion of pusher shapes into bezier arrows.
Pusher arrowheads now properly adhere to the arrowhead sculpt style.
Arrowables now show the arrowhead sculpt style in the individual styles dialog.
Subtitles in settings panels are now easier to discern.
Placing attributes on bonds can now be modified before releasing the mouse button.
Fixed issue where auto-updating labels for IUPAC names did not update if coordinate changes resulted in a different name, eg. E->Z for an alkene.
The Settings>Styles>Page>Text font size styles will now properly update selections in real time.
Changing style sheet fonts can now be properly cancelled.
Hovering over automatic shapes now shows a pointer cursor instead of an open hand cursor.
Opening the style sheet window is now mapped to the ctrl+L (cmd on macOS) keyboard shortcut.
Fixed issue where some settings dialogs would appear really long, or may cutoff some parts on the right side.
The TLC widget styles button has been changed to the appropriate styles icon.
Corrected issue where the Symbols widget unicode characters insert multiple times into text fields.
Updated OPSIN to v2.8.

12.2.1

September 14, 2023
This is a bugfix update to address an issue in v12.2.0 where saved ChemDoodle Documents with arrows may become corrupted. If you are using v12.2.0, please update now. Please visit this link for the full version changelog.

12.2.0

September 09, 2023

Executive Summary

ChemDoodle 2D v12.2 is a feature and maintenance update, correcting a number of issues brought to our attention. The main new feature is atom mapping functionality and input/output of reaction atom-to-atom mapping to a number of chemistry file formats. This update is recommended for all users.

Additions

A new tool is provided in the Arrows toolbar for manually applying atom-to-atom mappings. Most will use this feature for reaction applications. Input and output of reaction atom-to-atom mapping is fully supported in ChemDoodle Documents, ChemDoodle JSON, ChemDraw CDX, ChemDraw CDXML, SMILES, and MDL RXN files. ChemDoodle will display warnings for atom mappings in certain situations. Please see sections 7.8 and 9.12 of the ChemDoodle user guide for more information.
Margin highlights on rulers may now be disabled in the Settings>Appearance panel.

Fixes

The "presets" folder in the user's Documents folder has been renamed to "styleSheets". Simply move the contents of the "presets" folder into the "styleSheets" folder if you wish to continue using any saved style sheets.
The Predefine Measured Mass option for stoichiometry tables has been removed as it did not offer any additional benefit.
Due to performance issues in large documents, all stereochemistry checkers are now disabled by default. You may turn them back on in the Settings>Warnings panel.
Corrected issue with stereochemical wedge application in cyclic bridged systems.
Fixed infinite loop when cleaning certain pinwheel structures.
IUPAC naming using von Baeyer rules is now much faster.
Corrected minor issues with the expansion of abbreviations that match element names.
TLC plate background colors and styles are now properly applied.
v3000 MOL file output now includes the chiral flag in the counts line when appropriate.
Some improvements for MarvinSketch MRV styles.
Fixed round-trip editing issue where EMF data containg both ChemDraw and ISIS/Sketch file information included was not processed.
Corrected rare round-trip editing error when pasting EMF data into ChemDoodle from PowerPoint.
Directly editing OLE objects will no longer center content in pages. Now, the page is centered in the scroll panel view on edit.
Corrected an issue with grouped shapes that could cause fractional metrics to be disabled in vector graphic output, leading to packed text.
Fixed issue where Java file chooser UIs would not update for Light/Dark mode changes.
Fixed issue where the master right-click menu's UI would not update properly for Light/Dark mode changes.
Improved right click menu handling.
Fixed button icons for shapes with shadows.
Fixed bug where before the initial settings file was created, starting a new document would not revert the style sheet.
Fixed issue where changing the application font did not apply to everything.
Fixed bug where the periodic table would fail to print.
Subgrouping is now applied in the Settings>Warnings panel, making it much easier to understand.
Corrected quick start guide typos.

12.1.0

June 25, 2023

Executive Summary

ChemDoodle 2D v12.1 includes a "Dark" mode, new copy abilities in the Elemental Analysis widget, and support for Gaussian Input and Cube files. Reported issues were resolved, including an issue that caused the splash screen to stall for some Windows users.

Additions

The "Light" and "Dark" mode setting is now available in ChemDoodle 2D. This setting is found in the Settings window, under the Appearance tab.
The Elemental Analaysis widget has two new copy features. (1) there is a new button on the top for copying all of the data in the widget (without the spectrum) to the system clipboard and (2) each of the mass and formula label values now allow you to right-click and copy the value to the system clipboard.
An improved pen path smoothing algorithm is implemented.
Gaussian Input and Cube files can now be read and written. Only the structure data will be relevant in ChemDoodle 2D. This is a preview of what is coming to the next update of ChemDoodle 3D.

Fixes

Some Windows users have reported an issue where the splash screen will appear and then stall, with no progress made. This update corrects this issue.
Corrected issue where the tab options in the Window and File menus were not in the proper enabled states.

12.0.0

May 13, 2023

Executive Summary

ChemDoodle 2D v12 presents a new, refreshed interface. We took a close look at every component, icon, window and form inside of the application to optimize and beautify our users' experience. The main interface has been reorganized. Many usability issues have been resolved. Most users will find the changes to be straightforward and the underlying chemistry functionality of the software is unchanged. We have a very quick guide to help you with the bigger changes. In addition to the interface, improvements have been made to our chemical image recovery (CIR or OSR) function, IUPAC naming, the atom and bond joining function, and our user guide.

11.13.0

January 28, 2023

Executive Summary

ChemDoodle 2D v11.13.0 is a feature update wrapping up our latest massive work on stereochemistry. A new advanced CIP descriptor engine is implemented for the most accurate and consistent CIP assignments and the MDL/BIOVIA stereochemical drawing interpretation algorithm is now implemented along side the IUPAC specification. We believe ChemDoodle is now the industry leader for handling stereochemistry, especially in 2D drawings. Several issues have also been corrected, described below.

Additions

A new advanced CIP descriptor engine has been implemented. Based on the work from Hanson et. al., the CENTRES library by John May is included which supports advanced and consistent CIP assignment for all stereochemical features supported by ChemDoodle. Assign "R", "S", "E", "Z", "M", "P" and the pseudo-asymmetric "r", "s", "e", "z", "m" and "p" descriptors with a simple menu function. A new chapter 15 in the user guide focuses solely on stereochemistry discusses all of these features in detail.
The MDL/BIOVIA stereochemical drawing interpretation algorithm is now implemented along side the IUPAC specification for input drawing interpretation only (the IUPAC specification will always be used for output when using ChemDoodle functions). This option is found in the Preferences window, under the Functions tab in the Stereochemistry section.
Significant speed improvements for generating isotopic distributions.
Improvements to congested spiro structure layout.
Minor improvements to JDX spectra input and much faster output to JDX format for simulated NMR spectra.

Fixes

Corrected issue where in certain cases involving double bonds in multiple equivalent rings, the second bond line would be locked in place and could not be flipped to the other side.
Fixed issue where charges were no longer rendered after using the graph reduction functions.
Lewis dot structures were incorrectly output with 60 degree angles for certain atom centers with 4 substituents, this has been rectified.
A rounding error occured when rendering 4 membered rings with double bonds in certain style sheets, leading to only one side being fit correctly, this has been resolved.
Improperly drawn rectangular geometry warnings are no longer flagged in rings of size 3 or 4.

11.12.0

December 14, 2022

Executive Summary

ChemDoodle 2D v11.12.0 is a feature update with a focus on IUPAC naming. Major new abilities include an Attempted PIN (Preferred IUPAC Name) in addition to Traditional IUPAC naming, more nomenclature systems including thorough stoichiometric and additive naming, UTF8 text format output, a lot of new trivial name inclusions and significant new rule and scope support. Additionally, several issues have been corrected, described below.

Additions

IUPAC naming has been upgraded, please see the updated chapter 15 of the ChemDoodle User Guide for detailed instructions:
1. We now include a second type of IUPAC name output, an Attempted Preferred IUPAC Name (PIN) in addition to the Traditional IUPAC name. Traditional IUPAC names will be modified by the options in ChemDoodle, while the PIN will not be. ChemDoodle will try its best to generate the PIN, but is not guaranteed to, which is why it is called an Attempted PIN. The Structure>Structure to IUPAC Name menu item will now display both name types. Auto-updating labels will display the Attempted PIN, but can be changed to show the Traditional IUPAC name instead in the Functions panel of the Preferences window. Please see chapter 14 of the ChemDoodle User Guide for further explanation.
2. More nomenclature systems, including stoichometric and additive naming for polyatomic or metal complexes. Hydrate naming is supported. ChemDoodle will attempt to intelligently name your structures as clearly as possible using the best nomenclature system, and will respect zero-order bonds when separating structures. ChemDoodle will automatically split a structure to better name complexes if it feels this will lead to a clearer name (such as NaCl drawn with a single bond, ChemDoodle will split it and name it as sodium chloride). Dative bonds may be used to specify coordination centers, and ChemDoodle will default to naming those centers additively.
3. Added an option to prefer chain length over unsaturations, which is compliant with P-44.0 of the 2013 Blue book.
4. IUPAC names may now be output into pure UTF8 characters to preserve most formatting without markup languages.
5. Ring assemblies now use parenthesis if the base name starts with a number. Fixed issue affecting complex ring assemblies.
6. Improved efficiency for generating von Baeyer names regarding structures with multiple complex ring systems connected by chains.
7. Made error clearer when there is no defined maximum coordination for an element, but one is required.
8. Stopped infinite loop involving a rare substructure.
9. Fixed bug involving pentavalent Pnictogen functional groups.
10. Many new options have been added. These options are described in the ChemDoodle User Guide, chapter 14.
11. Most of the common names from the Principles of Chemical Nomenclature and Red book tables are now included.
12. Better support for replacement chain nomenclature in small structures containing no carbon atoms.
13. Aluminium is now used instead of aluminum, caesium now used instead of cesium.
14. Improvements to lambda notation when charges are present.
15. Individual isotopic elements are now correctly designated.
2D cleaning improvements for bulky spiros.

Fixes

Improved coordinate covalent bond rendering to better represent a plus on the non-arrow end.
Fixed bug where stereochemical projections were not recognized if a condensed label existed in the structure.
Some users experienced application hanging on macOS when accessibility features or 3rd party applications using macOS accessibility APIs are enabled. This update stops the hanging and allows the software to continue to function. There will still be an issue with the file chooser, as that is a compatibility issue on the Java side that we cannot control. But in ChemDoodle 2D and 3D, you may switch to the non-native file chooser which will not be affected if you wish to use such accessibility software and ChemDoodle 2D at the same time. Do this by going into Preferences for the ChemDoodle 2D application, selecting the Files tab, and then unchecking “Use Native Filechooser” in the Filechooser settings. Then restart the ChemDoodle 2D application.
LabArchives posting has been fixed.
Linux KDE URL launches are not functional with Java, so we included a workaround to launch URLs when running ChemDoodle 2D on Linux with KDE.

11.11.0

October 23, 2022

Executive Summary

ChemDoodle 2D v11.11 is another feature update focusing on our main topic this year, stereochemistry. Stereochemical projections will now be automatically recognized and stereochemical features will be analyzed. Fischer, Haworth and chair projections are supported.

Additions

Projections drawn in ChemDoodle will now be automatically recognized and stereochemical features may be analyzed. Fischer, Haworth and chair projections are supported. Projection drawing warnings are flagged. You may use the force stereochemistry functions on properly drawn projections, and a helpful error message will display if ChemDoodle cannot force the desired configuration. Projection interpretation may be disabled in the Preferences window under the Functions>Tools>Stereochemistry section. For thorough information, please see section 13.17 of the ChemDoodle user guide.
Added option to output MDL CT atom stereo parity. This option is found in the Preferences window, under the Files>Formats>Chemical>MDL Connection Table Files section.
Added support for dative bond types in MDL/BioVia formats.
Improvements for the input/output of implicit hydrogens in labels concerning ChemDraw files.

Fixes

Corrected bug where molecules with condensed labels were displaying stereo descriptors on the wrong atoms/bonds.
Corrected elemental analysis m/z calculations when multiple isotopes of the same type are present.
Fixed error where copying text from labels sometimes did not work.
When copying text, plain text output will now properly include spaces.

11.10.0

July 11, 2022

Executive Summary

ChemDoodle 2D v11.10 includes further advancements to our cheminformatics functions along with some new features. The stereochemistry engine has seen a complete rewrite, with a brand new system for evaluating stereogeometries in OD/2D/3D, leading to accurate generation and interpretation of wedge drawings and full support for stereochemistry in SMILES protocol. Further advancements in our industry-leading 2D coordinate layout algorithm are provided. New features include ring coloring for highlights, support for group objects in ChemDraw files, checking bonds for drawing warnings, new periodic table options and more. For macOS users, the QuickLook plugin is now functional on the latest macOS versions.

Additions

Further advances for the 2D structure layout algorithm. Added more templates. Better ring embedding. Better overlap untangling. Standard molecule type orientations (amino acids, steroids, etc.). Try your hardest structures and let us know what you think!
The stereochemistry engine has been rewritten from the ground up. It now works closely with the 2D layout algorithm and produces accurate wedge diagrams according to IUPAC rules, even in complex cases. Interpretation of wedge drawings is also accurate via IUPAC rules. More stereochemistry warnings are now shown, including on bonds, to check your work. Please see section 13.17 of the ChemDoodle User Guide for more information.
Significant SMILES improvements. Atom properties are now interpreted as best as possible if not in the correct order as defined by Daylight. Reaction SMILES are now read and written. Reworked and full support for advanced stereochemistry in SMILES input and output. Allene and cumulene configurations are now supported. Advanced parsing of all configuration types, even those not supported by ChemDoodle. Unsupported configuration types will just be ignored, but will show a warning in the Line Notation Pad widget. Corrected all known issues.
Improvements to the automatic chain drawing tools. When using shortcuts to add chains, if the origin is an end of a triple bond, the angle will be made 180 degrees. Using shortcut keys to add chains will also look for the least congested area, like the optimize zone does.
Support for the input and output of group objects to ChemDraw CDX and CDXML files. On input, non-integral groups from ChemDraw are not fully compatible with the z-indexing system in ChemDoodle, so there is a new option in Files Preferences for ChemDraw files to breakup groups on input, preserving the intended z-indexing.
Highlight shapes now allow you to color in rings. This ability is off by default when creating a highlight. Please see section 9.13.3 of the ChemDoodle User Guide for more information.
Lewis dot structures now can be generated from skeleton structures containing condensed labels.
Added new warnings, and warnings are now shown on bonds. Please see section 13.5 of the ChemDoodle User Guide for more information.
Historic IUPAC group classifications can now be displayed on the periodic table.

Fixes

Corrected an issue where 2D clean didn't preserve double bond geometry if a condensed label was present.
Flipped stereo wedge bonds are now correctly considered when updating stereochemical configurations.
Brown frame surrounding template additions when drawing has been removed.
Fixed issue in ICXML files where path and bezier fill states were not saved.
The QuickLook plugin is now functioning on the latest macOS versions.
Typographical fixes.

11.9.0

March 01, 2022

Executive Summary

ChemDoodle 2D v11.9 focuses on improvements to our cheminformatics functions, specifically a new blazing fast ring search algorithm for very fast performance when editing very large and complex structures, further advancements in our 2D layout algorithm for really nice structure cleaning of very complex systems, and the handling of isotopes that have no abundance on Earth in our molecular mass/elemental analysis/molecular formula tools.

Additions

Isotope data is now included for isotopes with no natural abundance on Earth. This allows for the calculation of masses and elemental analysis on structures drawn with a wide range of isotope mass values, including tritium (³H). If no mass data is available for the specified isotope, the elemental analysis and isotopic distribution functions will display an appropriate error to notify you of the missing information. Mass calculations on isotopes with no mass values will display a "NaN" value. Molecular formulas will now properly handle any isotope definitions, even if no mass data is available.
A much faster smallest set of smallest rings algorithm (SSSR, RP-Path) is now used by ChemDoodle, allowing for very fast handling of even large and complex embedded structures in a short amount of time. Because the new SSSR algorithm is so fast, the Ring Search Cutoff performance option is no longer necessary and has been removed.
Vastly improved structure cleaning. Better handling of macrocycles, embedded systems containing macrocycles and better overlap resolution. Partial cleaning has been improved and will be more flexible when selecting parts of ring blocks. The templates used for cleaning have been curated for better graphics.
Improvements to SMARTS matching performance.

Fixes

Sorted rings by size when coloring in rings, so each ring could be clearly seen.
Fixed problem where bezier curves read in from older ChemDoodle Documents would not load properly.

11.8.0

January 16, 2022

Executive Summary

ChemDoodle 2D v11.8 includes significant improvements to many features, including excellent chain replacement nomenclature in IUPAC naming, support for allene/cumulene stereochemistry, improved bezier curve tools, current InChI support and more file options.

Additions

Excellent IUPAC naming support for chain replacement nomenclature. There are two new options as well: (1) to enable/disable chain replacement nomenclature (on by default) and (2) to allow a minimum of 2 replacements (3 required by default).
Updated InChI support to the current v1.06. Full support for InChI stereochemistry, including allenes and cumulates.
Stoichiometry tables can now be generated from typed chemical equations, in addition to drawn chemical reactions. Simply select the Reaction>Stoichiometry... menu item with no reaction selected, and a form will appear for you to input the typed chemical equation.
Full support for allene and cumulene stereochemistry, both for odd numbers of bonds (E/Z) and even numbers of bonds (M/P). There is a style to change M/P displays to Ra/Sa instead.
Allene and cumulene coordinates are now properly assigned by the 2D structure cleaning function. Stereochemistry is preserved for these centers.
Double bonds in ring sizes of 7 or smaller are no longer designated stereochemical configurations by default, as designated by the IUPAC Blue Book 2013. You may turn these double bond configurations back on in the Functions panel.
Users now have control over the CIP ligand cutoff length.
Bezier curve editing has been vastly improved. You are now able to change the locations of control points independently of their mirror, but the default behavior is to keep them symmetrical. All micro edits can now be undone and redone. The first intersect point's first anchor will now appear and be editable if the custom shape is closed. Better handling of cases where a bezier curve drawing is cancelled.
Perfect support for bezier curve objects in ChemDraw CDX/CDXML files.
Added support for mmCIF, BinaryCIF and PDBML.
Added option to add PAIR headers to SDF file output in the Files panel.

Fixes

Corrected issue where stereochemical configurations were not automatically resolving for meso centers.
Fixed the automatic updating of cis/trans stereochemical configurations.
Corrected issue where an implicit hydrogen and explicit hydrogen on the same side of a double bond would not disqualify the stereochemical configuration.
Adjusted the handling of isotopes in the CIP algorithm to match the latest Hanson paper.
Included a check for corrupted bond spacing output from ChemDraw CDX/CDXML files and corrected the values.

11.7.0

August 23, 2021

Executive Summary

ChemDoodle 2D v11.7 is a feature update. The main new feature is expert IUPAC naming support for ions, as well as other IUPAC naming features.

Additions

IUPAC naming support for ions, including radical ions. Both positive and negative, with differences in electrons or protons, as well as combinations of charge centers on a single molecule are supported. This is by traditional rules with IUPAC Red Book 2005 clarifications.
Support for naming neutral and charged elements, as defined by the 2005 Red Book.
Full support for ring assemblies (up to 10 units, max for traditional naming). Over 10 repeating units will be named substitutively. Previously, only 2 unit ring assemblies were supported.
Revised support for hydros and H locants. Also support for oxo fused H locants.
Added the following new traditional IUPAC naming options: (1) detach hydros from the front of of base names, which will instead be treated as substituents, (2) exclude H locants on predefined heterocyclic trivial and semi-trivial systems where the hydrogen is on an unabiguous pnictogen atom as defined in the '79 Blue Book, (3) whether or not to always force the radical suffix as the final suffix, (4) disable functional group mapping, (5) use explicit cation/anion naming.

Fixes

Reconcilled radical IUPAC naming support with the 2005 Red Book.

11.6.0

July 23, 2021

Executive Summary

ChemDoodle 2D v11.6 is a feature update. Of significant interest is the ability to define, edit, input and output enhanced stereochemistry definitions to a handful of compatible file formats. Windows users should also consider this update, as we have rebuilt our OLE server, which is now without any known issues, and fixed filetype associations for 64 bit registry systems. Additionally, you may now recover SKC data embedded in Microsoft Office documents on all operating systems.

Additions

Enhanced Stereochemistry. You may now define enhanced stereochemistry for chemical structures, using or and & modifiers. All stereocenters are absolute (abs) by default. Groupings will be automatically determined via incrementation, but you may also manually define group numbers for more advanced stereochemistry queries. Enhanced stereochmistry definitions are read and written from ChemDoodle Documents, ChemDoodle JSON, ChemDraw files, ChemAxon Marvin Documents and MDL CT files (limited in v2000, full support in v3000). Please see section 13.17.6 of the ChemDoodle User Guide for more information.
The ChemDoodle OLE server has been rewritten and is now vastly improved. All known issues we have been able to reproduce have been resolved. Copying very large images into MS Office now works without issue. Resolved problems when cancelling OLE edit changes in ChemDoodle. Printing issues should no longer occur. A new x64 build is now provided. Improved efficiency.
MS Office extraction will now recognize and recover embedded SKC data. This is data pasted in from BIOVIA Draw (formerly known as ISIS/Sketch, Symyx Draw and Accelrys Draw).
Updated OPSIN to version 2.5.
Updated Batik to version 1.14.

Fixes

File type associations on Windows are again properly handled (handling 64 bit registry edits).
Corrected the handling of custom MOL2 records on file input.
Resolved issue where SVG embedding in ChemDoodle Documents would be corrupted on rare occasions on Windows.
Prevented file load error when a corrupted image is encountered on reading a ChemDoodle Document. Now, the rest of the file will be read in, and the corrupted image will be shown in the document with an error display.

11.5.0

May 28, 2021

Executive Summary

ChemDoodle 2D v11.5 is a feature update. This update is all about databases. Google Patents is integrated to allow you to search the Google Patents and non-patent literature databases using structures drawn in ChemDoodle. The SciFinder-n interface has been improved and updated. A new PubChem protocol, PUG, replaces the old Entrez protocol for better results from the MolGrabber widget. RCSB PDB database connections have been switched to HTTPS.

Additions

Google Patents searching is integrated. You may perform structure, substructure and similarity searching into the Google Patents and non-patent literature databases at Google using structures drawn in ChemDoodle.
The SciFinder-n interface has been updated and improved for better usability and with a UI matching the current SciFinder-n product.
PubChem access now uses the PUG REST protocol, which results in more stable communication with the PubChem database and higher quality results when using the MolGrabber widget.
Updated import of MMTF/PDB data from the RCSB.
There is now an option to disable the native file choosers used by ChemDoodle in the Preferences window, under the Files tab. Disable the native file choosers if you are having issues with them, for instance if you have a problem with iCloud on macOS and cannot get the file choosers to load.

Fixes

Corrected issue which prevented the socket communication port from being changed if a current instance of ChemDoodle was currently open.
Fixed issue which caused CurvePoint3D input from CDX files to fail.

11.4.0

April 02, 2021

Executive Summary

ChemDoodle 2D v11.4 is a feature and stability update. The main new feature is chemical image recovery, allowing you to recover chemical drawings for further edit from chemical images.

Additions

ChemDoodle now has the ability to recreate a chemical drawing from an image of a molecule, recovering the original chemical data. This function is performed using the File>Recover from Image... menu item. This function is different from inserting the image as inserting an image provides you with just a graphic, while recovering the chemical drawing allows you to regain access to the chemical information to use or edit further. We call this function Chemical Image Recovery (CIR). Some may also refer to this function as Optical Structure Recognition (OSR). For more information, please see section 15.10 of the ChemDoodle 2D User Guide.
Improved handling of implicit/explicit hydrogens in condensed labels. Handling of hydrogens with a plus immediately after in condensed labels are now properly understood.
Page counts are now handled in CDX/CDXML output.
When creating ChemDoodle Web Components, you now have the option of including all compatible content in the current document, if applicable.
Updated the ChemDoodle Web Components library to v9.2.

Fixes

The user guide is no longer provided in the product download to reduce bandwidth. You may still access the user guide at any time online, and if you download it and place it in the docs folder in the ChemDoodle installation folder, ChemDoodle will open the downloaded file instead of forwarding you to the website to download again.
Fixed bug where formula cells in stoichiometry forms continued to duplicate label content on every table update.
Editing stoichiometry forms now shows an eraser icon to clear the cell, instead of a close icon.
Corrected the tolyl abbreviation definition.
Corrected autoconnect issues when using chain tools and shortcuts.
Corrected the display of red circles to indicate autoconnections in some overlap cases for the optimize zone.
Fixed error when an image is saved of a blank document, now a default 1x1 dimension will be used for automatically sized output. For custom sized output, the custom size will be used. Corrected errors that occured when the preview components attempted to render an empty image.
Fixed bug where border buffer considerations were not being doubled for preview dimensions.
Labels are now expanded when querying SciFinder-n. Recent connection issues to SciFinder-n have been resolved.
Adjusted the Window>Collect Windows menu item to not push widgets off screen.
Corrected issue where the default file dialog location was the present working directory, it has been corrected to the user Documents folder; workspace reset now resets the file dialog locations to the Documents folder.
Corrected issue where if a file dialog was cancelled, and no file saved, the default file dialog location would revert to the present working directory; now, no change will occur with the location memory.

11.3.0

January 18, 2021

Executive Summary

ChemDoodle 2D v11.3 is a feature update. The main new feature is expert IUPAC naming support for free radicals. Other major features include new image output sizing options with previews, and stoichiometry table options.

Additions

Free radicals are now expertly handled by our IUPAC naming algorithms. These are by traditional rules. Monovalent and multivalent radical centers, as well as multiple radical centers within the same structure are supported. Both trivial and systematic naming is supported. Options are provided, including Section A vs Section D naming rules and carbene naming.
New image output options to manually define image size, instead of the default behavior of automatically sizing the image based on the graphics content measurements. You will be able to choose whether graphics content is scaled to fit custom dimensions. A new preview component is shown in the image settings window to make clear how the final image is laid out. Please see section 15.8.6 of the ChemDoodle 2D User Guide for more information
An option for stoichiometry forms to automatically predefine the measured mass. If you would like undefined experimental reactant measured mass values to be predefined to the defined theoretical reacting mass values, then select this option. This option may help to speed up your use of the stoichiometry form. The predefined measured mass values will be considered as user defined explicit values, which can be further edited. These options are found in the Functions panel of the Preferences window under the Calculations section.
Shadows, gradients and fills can now be applied to bezier curves, pens and polylines, even if they are not closed.

Fixes

Further CDX and CDXML file support: Fixed the incorrect input of the ElementList data type, better support for styled curves and arrowhead sizing on curves, automatic line feeds from fixed width labels are now properly handled, line type properties on arrowheads are now read in, fixed issue resolving final bezier point in inconsistent files, elliptical arcs can now be written.
Free radicals are now appropriately accounted for in aromaticity detection.
Saving ODG output now correctly displays output options.

11.2.0

December 11, 2020

Executive Summary

ChemDoodle 2D v11.2 is a feature and stability update and is recommended for all users. The focus of this update is chemical data recovery. You can now copy and paste chemical figures (regardless of the chemical software use to create the figures) from applications on Windows and macOS into ChemDoodle to recover the original chemical drawings for extraction and further editing. We also have a new tool in ChemDoodle for scanning Microsoft^® Office files to extract chemical drawings if you do not have access to the original operating system or Microsoft Office anymore. This update includes significant work on CDX and CDXML file support with a goal of reproducing graphics in a pixel-perfect manner.

Additions

Recover chemical figures and drawings pasted into 3rd party applications, like a word processor, by other chemical software where chemical data was embedded. Simply copy the figure in the 3rd party application and paste into ChemDoodle to recover the original drawing for further editing. This works on both Windows and macOS, as long as the original image was embedded on the same operating system. See section 15.7 of the ChemDoodle 2D User Guide for more information.
The ability to scan Microsoft Office documents for chemical data has been completed and is no longer an experimental feature. On any operating system you run ChemDoodle on, you will now be able to extract chemical data from Microsoft Office files, even if you do not have access to the original chemical program or Microsoft Office. You can finally collaborate with chemists in creating documents even if they use a different operating system.
You can now copy and paste CDX and CDXML data directly into ChemDoodle on both Windows and macOS.
CDX and CDXML data can now be recovered from EMF and PDF files, regardless of operating system, by opening them in ChemDoodle.
A significant amount of work has been invested in our already very thorough CDX and CDXML file handling, with a focus on pixel-perfect interpretation. Better support for all kinds of arrows, including bold, equilibrium and retrosynthetic; also improved arrowhead sizing. Support for faded colors in shapes. Improved adherence to double bond orientations. Text placement has been made much more accurate, including rotated text. Much better handling of symbol attributes. Isotope mass values are no longer added for deuterium and tritium labels, as they are not present in the original render. Arc input has been fixed with end points and angles now correctly interpreted, and elliptical arcs are input as well.
There is a new CDX and CDXML file option to suppress the load of invisible atoms (no labels or bonds attached). This option is enabled by default and can be disabled in the Preferences window, under the Files tab.
CDX and CDXML pages are now combined on load by default. You may still have pages separated on load by changing the settings in the Preferences window, under the Files tab.
Monoisotopic mass is now the default calculation for mass fragmentation tools.

Fixes

On macOS, PDF was not recognized from the system clipboard until an initial copy was executed from ChemDoodle. This has been corrected.
Fixed problem where unknown CDX objects would stop CDX file reading, leading to missing data from the file.
Fixed error where molecule highlight shapes with no fills or borders rendered would cause selection problems.
Fixed bug where ChemDoodle JSON query variables were incorrectly negated on read.
Corrected rare issue where stoichiometry tables were being corrupted on input, leading to the containing file not being read properly. This update fixes the issue and those files should now open without problems.

Microsoft is a registered trademark of Microsoft Corporation.

11.1.0

September 24, 2020

Executive Summary

ChemDoodle 2D v11.1 is a feature and stability update and is recommended for all users. The major new feature is advanced repeat unit support, both in graphical drawing and cheminformatics interpretation and expansion. Other notable features include improved reaction building interfaces and feedback, arc-length controls, and smaller EPS file output. This update also corrects an issue introduced by macOS 10.15.6, leading to corrupted and missing windows. So if you are experiencing these issues, make sure to install this update.

Additions

Full and advanced repeat unit support. You may now easily draw brackets with repeating unit values; see section 9.14 of the ChemDoodle 2D User Guide. You may place in any text you desire, but 0 and positive integers will be recognized by the cheminformatics engine in ChemDoodle 2D and will be expanded accordingly; see section 13.13. Repeat units can be adjacent and fully embedded. You may also expand repeat units to their all atom models. Errors in repeat unit drawing (for instance if you draw a repeat unit between bonds in two separate molecules) will be shown by the warning system in ChemDoodle 2D; see section 13.5.
The reaction editor has been improved, making it easier to see what your actions are doing and how molecules will participate in the reaction. If you hover molecules in the reaction editor, the molecule in the document will now be highlighted. Centering of reaction text in the editor is now the default. If you have defined a selection of molecules when you edit a reaction, only those molecules (and any molecules already assigned to the reaction) will be present in the reaction editor.
Hovering over a reaction now visually describes its interpretation. Reactants will be highlighted in a cyan color while products are highlighted in a magenta color.
You can now control the arc-length of an arc or curved arrow by using the two new control points that flank the endpoints of the arc using a selection tool or any arc tool.
Made adding attributes a little quicker by automatically choosing the last attribute name, and updating the list order when a previous name is selected and used.
EPS shortcuts have been implemented for smaller EPS image files.
You can now paste IUPAC name text directly as a chemical structure by using the Edit>Paste Text as Chemical>IUPAC Name menu item, also found in the right-click menu.
Both the menu item for generating an IUPAC name and the auto-updating label for IUPAC names will display more relevant error information when an IUPAC name cannot be generated.

Fixes

macOS 10.15.6 exposed a bug in Java, causing some windows to be corrupted or not appear. This may prevent users from saving new files or opening windows such as the Preferences window. This update corrects this issue.
Fixed issue where highlighted text in the reaction editor would result in highlighted text in the document.
Fixed issue with stereochemistry where the depth search picked the highest priority difference, not the closest difference; this mainly affected centers in evenly sized symmetrical rings, where a heteroatom is opposite the center.
SMARTS now properly catches lowercase "p" for aromatic phosphorus.
Transform statistics are now shown when editing shapes using shape tools.
Corrected issue where editing a shape using a shape tool would incorrectly move any current selection.
Corrected issue of rare artifacts in EMF output, mainly in spectra and arrowheads.
Corrected issue where tables were not properly output to several vector image formats.
The quick-start guide will now be placed in a scroll pane if the screen height is not suitable. Some Windows users will small screens or increased resolution were not able to close the quick-start window easily.
Corrected issue where the workspace could corrupt if an external monitor where ChemDoodle 2D was being displayed was disconnected.
Minor text corrections.

11.0.0

June 14, 2020

Executive Summary

Version 11 is a major update to ChemDoodle 2D and a direct result of the support we have received from all of our customers. Major additions include a fully chemically aware and self-calculating stoichiometry table, automatic electron pushing arrows mirroring the functionality of the ChemDoodle Web Components that can also be manually edited, and a new experimental feature to recover chemical data embedded in Microsoft Office files, regardless of the originating program or operating system (you can now share your chemical Word files with users on different operating systems, and even Linux users can now work with chemical data in Microsoft Office files). Many improvements are also provided in this update, including significant performance improvements, most noticeable on macOS and when editing multipage documents. This update is free and recommended for all ChemDoodle subscription, Lifetime and Site licenses.

Additions

Stoichiometry tables: ChemDoodle 2D now includes an industry leading stoichiometry table. This stoichiometry table is a form where you input theoretical and experimental values from your experiment and you will get accurate calculations for your input and results. ChemDoodle 2D's stoichiometry tables are fully chemically aware and are self-calculating. Input reactions are automatically balanced (however you can override these stoichiometric ratios with the Equivalents row) and the limiting component is automatically inferred based on the input values. ChemDoodle 2D enforces the credibility of the calculations for the entire table, and will even warn you if your input is suspicious, for instance, if you have a percent yield greater than 100%. Please read section 7.9 of the ChemDoodle User Guide before using this function.
Automatic electron pushing arrows: following the functionality from the ChemDoodle Web Components, you can now have single electron, electron pair and bond forming pushing arrows automatically drawn by setting a starting and ending atom or bond. You can also convert these pushing arrows into bezier shapes, to fully control the graphics. See section 9.13 of the ChemDoodle User Guide for more information. You can also copy/paste these pushers in ChemDoodle JSON format.
Chemical data recovery from Microsoft Office files: (experimental feature) ChemDoodle 2D can now search and extract chemical data embedded in Microsoft Office files, regardless of the program they were created from, including ChemDoodle, ChemDraw, ChemSketch and Biovia Draw. See section 15.8.5 of the ChemDoodle User Guide for more information. If you have issues with your Microsoft Office file, please send it to us so we can correctly handle it.
Cleaning reactions can now be implicitly done based on a selection. You no longer need to explicitly define a reaction to clean it.
New quick start guides are high resolution, and include controls directly in the guide for easier use and instruction.
A message about context sensitive menus is now displayed when the Structure menu is expanded, as many users were confused that you need to select a molecule to use many of these functions. This message can be disabled.
Significant performance improvements, especially on macOS, and when dealing with multipage documents.
New experimental features can now be enabled through the application.config file.

Fixes

Corrected autosave issue where page row and column counts were not stored.
Resolved issues involving secondary monitors.
Fixed issue where decimal formatting was not properly set for US locale, causing issues with some functions in countries where non-US formatting of numbers is used.
Several reaction based issues have been resolved: deleted reaction components no longer causes the balance reaction function to fail; fixed the centering of loaded reactions from files; fixed the cleaning of reactions in multipage documents; balancing reactions no longer commits the implied reaction as an explicit reaction; better placement of balanced reaction output below the bounds of the reaction; balanced equation warnings are now properly displayed for drawn reaction input.
Fixed padding issue in tables, where padding was doubled when content was not center aligned.
Increased table cell colspan and rowspan limits.
ChemDraw file input improvements: reactions read in should suppress plus symbol display; read in of degree symbol from CDX only shows unrecognized character, this has been corrected.
Stopped multiple quick start guides from appearing.
Editing OLE objects now correctly centers content after opening in ChemDoodle 2D.

10.4.0

May 10, 2020

Executive Summary

This update includes a number of features, and improves several aspects of the application. We continue to improve our 2D structure cleaning algorithm, this time with a focus on structures with unavoidable overlaps when standard angles and lengths are used. ChemDoodle can now accept pastes of ChemDraw PDF on macOS, recovering the original ChemDraw data; this essentially allows you to recover chemical data from ChemDraw images pasted into programs like Microsoft Office on macOS. A number of other smaller features is included based on customer feedback. This update is recommended for all users.

Additions

Significant improvements to the 2D structure cleaning algorithm. Mainly, much better output for structures where regular angles and lengths would lead to overlaps.
Recover chemical data from ChemDraw images pasted into other applications (such as Microsoft Office) on macOS by directly copying and pasting that image into ChemDoodle.
You can now insert the output from the Elemental Analysis widget into the document as a table object.
Domain and range parameters for spectra can now be manually entered when editing spectrum perspectives, in addition to the slider controls.
When placing bonds on atoms, the Optimize Zone now favors the least hindered option when there are several best angles.
Better label centering on terminal double bond ends when rendered asymmetrically.
The resolution of calculations in auto-updating labels can now be controlled in the Preferences window, in the Functions tab, in the Calculations section.
Units for calculations in auto-updating labels can now be excluded in the Preferences window, in the Functions tab, in the Calculations section.
Improved scroll speed sensitivity, and added a new setting to control this sensitivity in the Preferences window, in the General tab, in the Accessibility>Interface section.

Fixes

Continued refinement of ChemDraw file interpretation: corrected negative absolute bond spacing values from input files, corrected incorrect interpretation of bold width settings on shapes, improvements reading in rotated text, improvements for bond overlap buffers, corrected error related to blank labels.
Greatly improved PDF support for inserting PDF images, as well as resolved issues with copy/paste and save/load of PDF files.
EPS support of fonts with spaces (if applicable).
Resolved issue where double bonds stereochemistry was not retained when cleaning structures where a double bond connected to a ring.
Cleaning now resets attribute auto-placement on lone atoms.
Fixed issue where ignoring stereochemistry when cleaning had no effect.
Moving auto-updating labels and undoing now sets it back to recentering again.
Moving autoplaced attribute and undoing now sets it to automatic layout again.
Fixed issue where centering atoms and bonds with attributes that were not autoplaced would not be able to be undone (just attribute location).
Cleaning structures and resetting attributes now correctly remembers autoplace values for undo/redo.
Aligning and centering label shapes now correctly takes into account bounds, not just the start point, regardless of label alignment.
Improved table hovering with selection tools where separators interfered with centers of cells with column and row spans greater than 1.
Copying tables now properly rechecks graphics.
Resolved issue where cyclobutadiene double bonds were not rendered symmetrically.
Conform document and changing document size actions now correctly recheck object out-of-bounds warnings.
Formatting label shapes no longer shows irrelevant properties.
Fixed the incorrect layout of settings in the Preferences Functions pane.
Undo and redo actions now cancel the current drawing action if performed mid-action.

10.3.0

March 06, 2020

Executive Summary

This update brings further advances to our 2D structure cleaning algorithm and includes the latest ChemDoodle Web Components 9 library. Several issues are corrected, improving the stability of ChemDoodle 2D v10. This update is recommended for all users.

Additions

The 2D structure cleaning algorithm has seen further advancement. Spiro systems are now expertly handled and a better relaxation algorithm is used when there are inevitable overlaps with standard angles and lengths.
Improved rendering of multiple order bond lines in acute angles.
The built-in ChemDoodle Web Components library has been updated to v9.1.0, along with the necessary changes to the component builder.

Fixes

Corrected the application of style sheets with page counts, where a change in page count would cause an error. Page counts are now properties of the document, and not of style sheets.
Fixed double bond spacing value in J. Het. Chem style sheet.
Fixed page size loading from autosaves.
EPS output now properly defines font families with spaces.
Fixed the output of ChemDoodle metadata in EPS, which caused the file to be improperly written on Windows.
Tweaked automatic charge placement when overlaps with label subscripts would occur.
Reduced the Twitter tweet allowed length to 270 from 280. Twitter uses text weight, not character count and this is a safer value.
The DMG icon for macOS is now properly displayed.
Fixed other minor issues reported.

10.2.0

January 25, 2020

Executive Summary

This is a significant feature update to ChemDoodle 2D v10. This update is recommended for all ChemDoodle 2D users. Major changes include an updated shape system allowing you to edit shapes while you draw them, greatly speeding up figure drawing. A significant amount of work has culminated in a brand new and powerful table tool for creating rich data graphics. ChemDoodle 2D can also now balance any drawn reactions or typed chemical equations. Please tell your friends, colleagues and students about ChemDoodle!

Additions

Tables - Tables are very powerful shapes for creating organized groupings of content in grid patterns. You can control the table grid and its formatting as well as the content that appears within each table cell and cell formatting. Tables can be drawn in several styles and are defined and controlled by an intuitive anchor box set. While the large number of anchors may at first seem overwhelming, each anchor performs a specific function for the table and provides instant feedback for edits you may want to perform. Rowspans, colspans, padding and alignment are supported. Tables can be fit to contained content. This is a great way of creating really attractive and informative figures of data. Please first read section 9.10 of the user guide for instructions.
Fast Shape Editing - The shape system has been expanded and you can now edit shapes while drawing shapes. There is a new General Preferences option to determine whether you can edit all shapes, only the same shape type, or no shapes while drawing shapes. This dramatically speeds up the drawing of figures in ChemDoodle 2D as you no longer need to switch to a selection tool to edit shapes.
Reaction Balancing - Complete reactions can be balanced by ChemDoodle 2D, either when drawn using structures and arrows, or typed as a reaction equation. ChemDoodle 2D will be able to balance any reaction equation that can be balanced. Drawn reactions will be converted into reaction equations. Keep in mind not all equations can be balanced, and some equations have an infinite number of irreducible solutions. For infinitely irreducible solutions, a solution that minimizes positive integers for coefficients has been deduced to balance your equation. In some cases, there may be a solution if a reactant is moved to the product side or a product moved to the reactant side. In these cases a negative number will be provided for the coefficient. If there is more information to convey, a message will be presented upon balancing. See section 7.8 of the user guide for more information.
Lone chemically interpreted linear formulas can be placed in the document. Click within the document where you want the formula to go without anything hovered using the Text for Atoms and Captions tool. Before setting the label, turn on chemical interpretation by pressing the Interpret Chemically button and a chemically interpreted atom label will be placed instead of a caption shape. This is useful for quickly writing and parsing a molecular formula to calculate a molecular mass, for instance.
Resolving stereochemistry configurations has been made more efficient.
Improved the loading of SVG files where no height or width was provided. Also handled the loading of SVG files if no height, width or viewBox attributes are defined.

Fixes

Resolved IUPAC naming issues with pyrolle type hydrogens.
Fixed valence warnings for implicit hydrogen overrides for elements that have multiple valence levels via MDL valence theory.
Structures viewed and bound to ChemDoodle 3D are now first expanded from ChemDoodle 2D.
Stopped erroneous stereochemistry detection when ligand depths hit the CIP cutoff distance. See section 13.15.1.3 of the user guide for more information.
Stereochemical configurations now correctly update as structure coordinates are changed.
Corrected freeze that occurred if an oxidation state was contained in an interpreted atom label.
Fixed Statistics widget issue where hovering atoms didn't fit in the widget interface.
Fixed issue where releasing the shift modifier key when drawing shapes did not reset the aspect ratio for the shape being edited.
Shapes that are drawn outside of the bounds of the document now immediately display a warning.
Resolved issue where automatic shapes could not be properly copied after being grouped.
Resolved issues where loaded grouped content did not correctly preserve z-order information.
Bond z-order information is now correctly preserved through undo and redo commands.
Fixed issue with Preferences Styles on Windows where the Spectra tab was cut off.
Fixed bug where double clicking on a file to open on Windows did not work properly.
Included missing executable details for Windows.
Included more application registry keys on installation for Windows, including DisplayVersion, which is required for many management systems.
Quicklook plugin works again and has been rebuilt with the latest version of Xcode on Catalina.
On macOS, using the file dialog now disables menu items and accelerators.

10.1.0

December 18, 2019

Executive Summary

This is a feature update to ChemDoodle 10. Major changes include the introduction of a new feature to query SciFinder-n from ChemDoodle and improvements to the stereochemistry engine.

Additions

SciFinder-n integration. We have been working with our partners from the CAS to initiate SciFinder-n queries from ChemDoodle. Draw your query in ChemDoodle and search SciFinder-n by Substances, Suppliers, Reactions or References. These features require a SciFinder-n account.

Fixes

Improvements to molecular and radical formula interpretation, making sure to preserve implicit hydrogen counts and charge.
Fixed a bug when interpreting wedge diagrams for chiral stereochemistry that affected some complex ring system cases.
Double bond stereochemistry is no longer resolved when two substituents on one side of the double bond have the same angle (they overlap) to the double bond.
Double bond stereochemistry is no longer resolved when one side has only one substituent and it is collinear with the double bond.

10.0.2

December 03, 2019

Executive Summary

This is a bug-fix update to improve the stability of ChemDoodle 10, and is recommended for all users.

Fixes

Fixed issue that caused license corruption issues to occur after prolonged use of the software.
IUPAC naming no longer incorrectly names charged functional groups that are not supported. An unable to name message will be shown. Charges and radicals support for IUPAC naming is currently under development.
Atom overlap warning has been relaxed to now show warnings when atoms are too close together rather than just having identical x and y coordinates.
SMILES reader now provides better coordinates if the input contains a lot of stereochemical double bond configuration that lead to overlaps.
ChemDoodle now remembers which color chooser was last used, and will default to that picker the next time a color needs to be chosen.
Resolved errors in ChemDoodle Web Components output.

10.0.1

November 16, 2019

Executive Summary

This is a minor bug-fix update to improve the stability of ChemDoodle 10 and fixes an issue related to loading fonts on some machines as well as resolving issues with the update announcement window. This update is recommended for all users of ChemDoodle 10.

10.0.0

November 13, 2019

Executive Summary

ChemDoodle 10 is a significant update to ChemDoodle. Major improvements include new IUPAC naming work, improvements to the structure cleaning system, inter-application communication with ChemDoodle 3D and SciFinder-n integration (see full description below). Additionally, we continue to improve the infrastructure of our applications and provide support on the latest operating systems while correcting any known issues. Enjoy and please tell your friends, colleagues and students about us! Your support helps us continue to provide the highest quality chemistry software in the market that is affordably priced.

New Features

A significant amount of work has been invested in our IUPAC naming algorithms. The functional group system has been completely overhauled to expertly handle advanced, multivalent functional groups. Support is now provided for functional groups containing phosphorus, silicon, boron and many other elements. Complex support has been added for handling unique base chains (heteroatoms and siloxanes for instance) and better automatic choosing of base chains. Support for functional groups as base chains if there is no better carbon based option. Support for isotopes, including both modern and Boughton principle rules. Fixed all known IUPAC naming issues reported to us.
SciFinder-n integration. We have been working with our partners from the CAS to initiate SciFinder-n queries from ChemDoodle. These features require a SciFinder-n account. While the features are implemented, it will be a few more weeks before the service is functional and accessible. A new update will be available to enable the features when the service becomes available.
The structure cleaning algorithm has been significantly updated. New systems are in place for generating much better large or complex ring systems. A 3D embedding of very congested structures is now applied. The stochastic method is much more flexible allowing for better output in the most un-ideal structures.
Inter-application communication between ChemDoodle and ChemDoodle 3D. Load 3D molecules of your 2D structures in ChemDoodle 3D with a single menu item click in ChemDoodle. Hot link your structure in ChemDoodle to ChemDoodle 3D, to draw in 2D and watch the molecule build in real-time in ChemDoodle 3D.
ChemDraw reaction schemes can now be input and output from ChemDoodle.
Accurate IUPAC locants can now be easily shown on structures as you draw them for increased clarity when analyzing IUPAC names or for other purposes.
Twitter output now allows up to 280 characters and outputs a much higher quality image.
New BioArt graphics with a space theme, including planets, moons and other interstellar objects.

Fixes

Fixed issue where reading in some stereo bonds from SMILES strings would lead to 180 degree angles.
Fixed problem where cleaning structures did not adjust bond attribute placements.
Resolved issue where changing isotopic mass numbers did not trigger an update to the molecule.
Corrected custom mass number form where the number field was too small.
Adding a highlight and cancelling styles customization can now be correctly undone.
Fixed issue where the recent files cache could get corrupted, leading to a crash on startup on Windows.
Resolved issues generating IUPAC InChI on Windows.
Fixed issue where ChemDoodle could not be hidden on later versions of macOS.
Improvements to z-ordering on macOS.

9.1.0

April 28, 2019

Executive Summary

This is a minor update to ChemDoodle 9, to fix reported issues and tweak a few features.

Features

Mass numbers now show relative abundance values in parenthesis for naturally occurring isotopes when setting this value in the right-click menu for atoms.
A new option, Selection Tools Auto-select Last Object is now present in General Preferences to disable the automatic selection of content when a selection tool is activated.
Superscript and subscript editing in text fields can now be accessed via the keyboard shortcuts ctrl+shift+= and ctrl+=, respectively.
Strikethrough editing in text fields can now be accessed via the keyboard shortcut ctrl+X.
Improved pasting placement location from the right-click menu.
Updated isotopic mass data to the latest references available.

Fixes

The option to minimize space between lines in labels now is specific to atom labels, and will not affect captions.
Fixed bug where captions would lose their hover ability when grouped and ungrouped.
Fixed issue where individual atoms and captions could not be rotated.
Fixed bug where manually placed charges would turn into automatically placed charges when copied and pasted.
Fixed an issue where toolbar shortcuts were not saved properly.
Corrected problem where formatting buttons did not update properly when moving the caret in text fields for atom labels and captions.
Fixed Windows/Linux issue where formatting shortcuts were not being executed in text fields.
Performance improvements for the rendering of spectra.
Improvements to the structure cleaning algorithm.
Fixed Elemental Analysis widget issue when calculating for structures containing uranium.
Fixed isotopic mass for 59Co.
Fixed a minor issue involving the output of text areas to ChemDraw files.
Fixed bug where black outlines for rectangles were missing in output ChemDraw files.
Fixed macOS issue where the native file chooser sometimes used the wrong extension in the name field when saving files.
Fixed Windows/Linux issue where the cursor hotspot was not properly defined for label tools.
Resolved issues involving null colors from files.
Fixed issue where modified hydrogen type SMARTS [HX1] were not being read correctly.
Update messages are now clearer, with the ability to skip updates restored.
Interface access to the online account has been removed as it is no longer available.

9.0.3

July 27, 2018

Executive Summary

This is a minor bug-fix update to improve the stability of ChemDoodle 9 and fix an issue related to reading some older ChemDoodle Documents. This update also turns off advanced stereochemistry checking by default, as it is an intensive algorithm and may cause performance issues with some users. If you are experiencing performance issues, go into ChemDoodle's Preferences, and in the Warnings tab, deselect the 3 checks for stereochemistry. Thank you again for choosing ChemDoodle!

9.0.2

May 16, 2018

Executive Summary

This is a bug-fix update to improve the stability of ChemDoodle 9. This update is free and recommended for all users of ChemDoodle 9.

Fixes

Resolved tool shortcut clashes with drawing tools, such as the peptide tool.
Spectrum backgrounds can now be disabled.
Better handling of organic subset elements in aromatic SMILES.
Fixed macOS issue where ChemDoodle was unable to find the installation folder.
Fixed the Quicklook plugin on macOS.

9.0.1

May 03, 2018

Executive Summary

This is a bug-fix update to improve the stability of ChemDoodle 9. This update is free and recommended for all users of ChemDoodle 9.

Fixes

Reported crashes have been resolved.
Fixed a bug where removing all templates from a group would cause a template file corruption.
Avoided a translocation issue on macOS.
Fixed issue on macOS where text field formatting disappears behind the application when text is selected.
Double clicking on associated files on macOS now properly opens those files in ChemDoodle.
Windows installer now prevents the installation over a previous installation of ChemDoodle, which may sometimes result in a corrupted installation.
Improved low resolution and cut-off drag gesture images.

9.0.0

April 24, 2018
ChemDoodle 9 is a major revision of every aspect of the software. We spent over 2 years overhauling and improving the cheminformatics engine, interface, drawing controls, image and chemical file types, graphics, and operating system compatibility. In addition to the new features, the entire codebase has been refactored for the current best standards to take advantage of the latest performance, memory and security features of the operating system.

Features

Drawing and Graphics-
1. A new system was developed in ChemDoodle that automatically places attributes (charges, radicals, stereocenter configurations, etc.) for you. It does a really good job, simply place your attribute and it and any other attributes will be automatically placed in optimal positions. You can override this system by manually dragging your attribute to the preferred spot, and use the right-click menu to reset it. You can also use the new Structure>Clean>Reset Attributes menu item.
2. A new function for collapsing chemical structures to labels (Structure>Auto-Collapse to Labels). This will use your current abbreviations library to intelligently condense structures into smaller images.
3. Electron counts in resonance rings can now be calculated and displayed.
4. Captions now have their own font setting. The atom text tool is incredibly smart and will know when you are trying to edit an atom label or writing a caption. The caption font can be set in Preferences>Visuals>Shapes. The text tool is now the only text tool in ChemDoodle (the text area has been removed), simplifying the drawing of advanced figures. Using the tab key while editing a caption will now create new equally spaced captions.
5. In addition to armchair and zigzag carbon nanotubes, chiral nanotubes can now be drawn by holding down a number to define m while using the nanotube tool. Calculations for radius sizes have been made incredibly accurate.
6. Highlights can now be added to entire and partial structures with a range of options for controling size and many other visual specifications expected in ChemDoodle.
7. The dynamic bracket has been redone to allow for better graphics and multiple brackets on an individual bond. They can now be controlled like other shapes.
8. Graphics for cumulenes have been greatly improved with many new options for controlling how double bonds orient themselves.
9. Multiple updating labels can now be stacked for a single structure. You can move them to override this behavior or reset them back to being stacked. If settings are changed in Preferences>Functions (IUPAC options for instance), all updating labels will now automatically update.
10. A much better system for showing hovered and selected shapes and calculating bounds for rotated shapes.
11. More statistics are now shown when drawing bonds, rings, chains and templates, especially at non-standard angles and lengths.
12. The escape key will now work for canceling current drawing actions.
13. Many smaller improvements and features: use alt+tab to select backwards through molecules and shapes (add shift), vast improvements across the entire hover and selection system, improved implicit hydrogen placement and isotope labels, individual control over dot sizes in zero order bonds, better adherence to turning off bond hovering across the application, tweaks to structure cleaning, improved format editing of non-chemical text, improved rotating of 3D coordinates, better feedback for drawing rulers.
Chemistry -
1. The CIP stereochemistry system has been rebuilt from the ground up, and is a state-of-the-art implementation of CIP rules. Even the most advanced stereocenters are now properly resolved, in accordance with the work from NextMove Software. ChemDoodle now is much better equiped to make stereochemistry suggestions in the right-click menu. A new option in the Stereocenter menu will now allow you to define all CIP stereocenters, instead of having to manually define each group.
2. The warning system has been redone to show clearer warnings and multiple warnings on the same object. Better stereochemistry warnings are now available including marking incorrectly drawn stereocenters, drawn stereocenters that are not stereocenters, and unspecified stereocenters.
3. The implicit hydrogen system is now easier to use than ever, allowing for the automatic or manual setting of implicit hydrogens based on advanced valence rules. Resonance systems can now resolve implicit hydrogen locations based on SMILES aromatic types. Aromaticity detection has been dramatically improved as well as Kekulization of advanced resonance systems.
4. Full support for the latest elements as defined by IUPAC.
5. Many more improvements to the cheminformatics engine, including radical support for masses in condensed labels, improved NMR simulation and spectrum rendering, fixes to some complex von Baeyer system IUPAC naming, properties caching for improved performance and more.
Interface -
1. A brand new cursor system that looks nice and is customizable. Control the contrast mode, drawing cursor and rendering options. Left handed users now have access to a left handed mode for cursors.
2. The IUPAC name-to-structure interface has been significantly improved and the latest OPSIN version is used.
3. Improved color palettes, now with Rasmol and CPK color sets. Your own custom color set can now also be defined from scratch or from other sets and saved.
4. HTTPS support for PubChem is now implemented for access in MolGrabber.
5. Added more icons for menu items. Better Preferences icons.
6. A new and improved color chooser across all platforms, including alpha support.
7. You can now control which file and image types appear in the save file choosers through the Preferences>Files pane. This is helpful to all users that need to lessen the time spent saving files.
8. Improvements to the left floating toolbar.
Chemical Files -
1. The Nature style sheet has been added to ChemDoodle for quickly creating documents in Nature style.
2. SMILES interpretation has seen significant work, with a focus on very advanced cheminformatics techniques. You can now control the behavior for explicit hydrogen output andcontrol whether implied double bond stereo characters should be output. Implicit vs explicit hydrogens in SMILES strings is now expertly handled, as well as OpenSMILES recommendations such as explicit bond types.
3. Added support for the RCSB MacroMolecular Transmission Format (MMTF), including for small molecules.
4. Added more support for text formatting and improved label alignments from ChemDraw files. Old ChemDraw files (<v8) can now also be loaded. Better support for the output of single and pairs of brackets. We have also added advanced support for the vast majority of header settings.
5. MDL CT files have improved headers on output and V3000 readers have been improved.
6. ISIS/Sketch file improvements and better arrow handling. We have also added support for some corrupted SKC files coming from 3rd party producers that were missing important tags. Most header settings are now handled for ChemDoodle style sheets.
7. Fixed the import of corrupted MRV files from ChemAxon products.
8. Vast improvements to the default centering and scaling of single molecule and multiple molecule structure files.
9. Many more minor improvements for small concerns in molecule/reaction formats.
Images - TIFF images can now be exported with custom DPI settings. GIF image output can now have semi-transparent pixels merged with white. Image settings have now been moved into the Preferences>Files pane. Default options for individual image types can now be defined here. Added viewBox attribute for SVG. When saving files, you can now use alternate extensions and other image file chooser improvements.
Vector Art - New glassware graphics have been added as well as dozens of new BioArt.
Customizability - The keyboard and tools shortcuts are now fully customizable by the user, using the Window>Edit Shortcuts menu item (note that some keyboard shortcuts have been changed). The user settings folder location can now be controlled by editing the ChemDoodle/config/application.config file. Custom attribute names and values are now persisted through ChemDoodle restarts.
Windows - Full support for high-DPI screens, without the manual scaling required in the past. Text sizes are also improved across the application and images updated in most places for higher reoslutions. The OLE plugin has been rebuilt for the most current compliance with Windows libraries. The auto-updater is now supported for Windows 10 (you will need to manually update to ChemDoodle 9 first).
macOS - Improved and full Retina support. The UI has been improved signiifcantly and there are no longer any blurry interface elements. Text sizes are also improved across the application and images updated in most places for higher reoslutions. Improvements to recognizing control+click as a right-click action across the entire application. Better support for handling open file actions from the system.

8.1.0

July 10, 2016

Executive Summary

This is a significant minor update to ChemDoodle 8. A number of issues brought to our attention have been addressed and several new features have been added.

Additions

New bitmap colorspace output options: Color, Greyscale, Monochrome. The images are not just in the colorspace, but the image data is correctly defined, so that monochrome images are much smaller than grayscale, which will be smaller than color.
Added Functions setting to use either the Bondi or current literature value for the van der Waals radius in the VABC calculator.
Added support for implicit hydrogen overrides to all capable formats.
Added some more recent elemental data.
Updated and expanded vdW values.
Added the latest new element names from IUPAC, completing the last row.
Alpha colors are now stored in ChemDoodle Documents.
Chain tool now merges with previous drawn structures in the same manner as rings and templates. Red rings will be shown for auto-connect overlaps and this behvior can be controlled in General Preferences. All issues involving drawing chains on top of previous structures have been resolved.
Auto-connect range when drawing rings, chains and templates is now controllable in General Preferences.
Added option to suppress implicit hydrogens from groups 1-12.
Functional hydrogen settings have been moved from Atom Visuals Preferences to Functions Preferences.
Added more refined options for controlling double bond symmetry. Now terminal double bonds connected to a ring can be made symetrical as a case.
Updated to OPSIN 2.1.
OPSIN warnings now still produce a result and display an appropriate warning instead of failing.
Added templates for tetroses.
Keyboard shortcuts have been added for the atom label tool, so you can bold, italicize and underline text via the keyboard.

Fixes

Added HTTPS support for NIH Cactus, returning functionality to the 3D clean tool.
Corrected Elemental Analysis and Mass Parent Peak simulation results for structures with multiple charges.
Addressed a number of issues for implicit hydrogen calculations in resonance systems.
Fixed issue where arbitrary rings and and crown ethers drawn to a bond of length that was different from the standard length didn't work properly.
Fixed bug where Preferences boolean button sets were flagging visuals changes for non-visual settings.
Fixed incorrect behavior where General or Advanced Preferences settings were falsely notifying the user of style sheet changes.
Fixed issue where output ChemDoodle 3D Scene (ic3) files from ChemDoodle were flipped on the y-axis.
Corrected a number of minor graphical glitches with vertical connections and wedge/bold bonds.
Closing the color select window no longer conforms colors, but does update the color button.
Using the color scrubber of the Quick Colors button now also sets the selection to that color after choosing.
Quick Colors button now correctly adjusts an entire label, even if chemical interpretation is off.
Minor updates to the Periodic Table.
The Center>Selection menu items are now correctly context sensitive.
iChemLabs extensions to JCAMP DX files have been removed and are no longer necessary. Note that older JCAMP spectra written from ChemDoodle that used these extensions (typically simulation output) will not be able to be read anymore.
Fixed rare crash that occured when Preferences bounds somehow ended up out of the defined bounds.
Fixed some minor IUPAC naming issues.
Isotopes from ChemDraw files are now displayed correctly.
Isotope labels are now correctly accounted for in bond retraction.
Ring, chain and template actions that don't actually change the document are now ignored in history.
Minor text sizing considerations and corrections.
Kekulizer now ignores zero order bonds.
Improved text layout in tabs not to overlap with close buttons.
Restoring the document now correctly updates the History widget.
Restoring the document now correctly clears the selection if there is one defined.
Fixed issue where loading an autosave didn't correctly enable the Restore menu item.
Fixed issue where dialogs were not reappearing after being deiconified.
Carbon labels will now be displayed in the implicit hydrogen count is overridden to 0.
Fixed the Login window cutoff.
Completely uppercase element symbols are now correctly handled when reading in MDL CT files.

8.0.1

February 14, 2016

Executive Summary

This is a minor update fixing issues brought to our attention since the ChemDoodle 8 launch. For changes to version 8, scroll down.

Fixes

Periodic table should now open again from the View menu.
Fixed the interpretation of deuterium and tritium in complex condensed labels.
Charges in left oriented labels are now located in better positions.
Default cyclopentadiene and cycloheptatriene tools now place saturation on the sprout point unless not chemically feasible.
Adding rings and templates will no longer merge multiple atoms into a single point if multiple adding atoms are within the merging distance of a present atom.
Fixed rendering of Bold and Thin double bonds when in perspective merges.
Improved the vitamin templates.
Added feature to lock polyline drawing to the horizontal and vertical positions if the shift key is held down.
Flipping while retaining stereochemistry now accounts for meso centers.
Torsion bond function now preserves stereochemistry if set to do so by the option under the Functions tab in Preferences.
Search widget will no longer execute a search when the drop panel is empty.
Fixed issue where single atom results were not rendered in the Search widget.
Search widget results are now sorted with hits appearing first.
Search widget searches with stereochemistry defined in query structures now work properly.
Fixed bug where the Search widget could not be manually stopped.
Fixed bug where query labels would disappear in the document after being dropped in the Search widget.
Fixed minor SKC import issues with text labels.

8.0.0

January 19, 2016

Executive Summary

ChemDoodle 8 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

The graphics system has been improved even beyond current industry standards for graphics. Every bond merge and pixel was scrutinized. Chemical structures have never looked better. ChemDoodle provides the best graphics in chemistry, everything else is a waste of money.
Major IUPAC naming improvements, including very advanced ring systems.
Full support for Retina display Macs and support for high-DPI Windows hardware.
A new query structure system for defining sets of molecules and for searching partner services.
New powerful tools for drawing arbitrary rings and crown ethers to atoms and bonds.
Superscript and subscript merging to easily create atomic notations and other chemical text.
More specific cleaning tool for adjusting only a selection of a structure.
Text output options and improvements for EPS and SVG files in addition to PDF.
A dramatically improved Templates widget with new and more aesthetic templates.
Read in NTUPLES (multiple spectra) from JCAMP files.
Added support for both the SketchEl (el) and Crystallographic Information Format (cif) filetypes.
More support for working with the ChemDoodle Web Components.
Dozens of new BioArt graphics.
Performance improvements for faster work.
Dozens more new features: two new bond types, implicit hydrogen control, automatic IUPAC locant labelling, vastly improved condensed labels, search files based on query structures, recursive SMARTS, metric support for document aids and rulers, a new precise form for scaling a specific bond, many interface improvements and so much more.

7.0.2

December 19, 2014

Executive Summary

This is a bugfix update fixing a number of issues brought to our attention. The majority of issues improve stability of ChemDoodle on Mac OS X Yosemite, and with the Oracle JRE. Please also note that we are ending support for Java 6 soon. This also means that ChemDoodle v7 will be the last version to work on Mac OS X 10.6 (Snow Leopard). We recommend upgrading to more recent versions of Java on all platforms, and specifically to Java 8 on Mac OS X platforms. Java 8 for Mac OS X is considerably more stable than Java 7 for Mac OS X.

Fixes

The ChemDoodle application on Mac OS X will now favor Oracle Java over Apple Java. We recommend using Java 1.8 from Oracle for Mac OS X, instead of 1.7.
Full screen mode is reenabled for Java 1.8 on Mac OS X.
Fixed bug where clicking on individual objects did not select content. (Oracle Java on Mac OS X)
Fixed flickering drop down buttons. (Oracle Java on Mac OS X)
Fixed crash when dragging and placing a bond and atom to another bond corrupted the history stack.
Fixed issue where restoring defaults on selected content was not working properly.
Fixed bug where the atom label toolbar disappears when the bracket label tool is used.
Fixed issue where the periodic table could not be printed.
Fixed issue where some warnings were appearing for formatted labels.
Fixed missing button selected cues on Yosemite.
Fixed Linux issue where the default text color in editors was a dark gray instead of a black.
Fixed issue with the document shadows when the document page size was altered.
3D files with only a single atom are now correctly centered in ChemDoodle 3D.
Improved text rendering for ChemDoodle 3D.
Fixed PDB issue where some malformatted files placed indexes in the charge column. These charge values are now ignored if they are determed to be malformatted.
QuickLook plugin now works with the Oracle JRE on Mac OS X.
iChemLabs Updater now works with the Oracle JRE on Mac OS X.

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

Fixed bug in creating ChemDoodle Web Components where integer specifications were not properly set.
Fixed bug in creating ChemDoodle Web Components that prevented spectra from displaying.
Fixed bug where dragging to move content failed on some Macs and a drag and drop action would commence instead.
Fixed issue where some tweets from ChemDoodle were failing.
Resolved graphical glitch where a two token, two line atom label could not be centered.
Tweaked startup memory parameters on Windows as the higher memory allocations were causing issues on older machines.
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!
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

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.
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.
Full multipage document support. Create lists of pages or grids. Draw between all pages and print them out.
BioArt. Large, full color, libraries of new art for use in biological figures, including animals, organs and organelles.
A set of 48 safety symbols included in the glassware set.
Significant performance improvements, in many cases 20x faster than v6. ChemDoodle will now load faster, work faster and respond faster.
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.
Twitter integration.
Integration with the LabArchives ELN.
Support for both Java 6 and 7 on Mac OS X.
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

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.
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.
Full multipage document support. Create lists of pages or grids. Draw between all pages and print them out.
BioArt. Large, full color, libraries of new art for use in biological figures, including animals, organs and organelles.
A set of 48 safety symbols included in the glassware set.
Significant performance improvements, in many cases 20x faster than v6. ChemDoodle will now load faster, work faster and respond faster.
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.
Twitter integration.
Integration with the LabArchives ELN.
Support for both Java 6 and 7 on Mac OS X.
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

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.
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.
Fixed IUPAC naming issue where locants were not correct in ring blocks for stereocenters.
Fixed IUPAC naming where a double dash could occur.
Fixed bug where groups would not always resize all their contents.
Fixed crash if non-recognized colors were present in ChemDoodle Documents.
Colors in groups and reaction area text are now stored correctly in ChemDoodle Documents.
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

IUPAC naming with over 20 options!
Carbon nanotube and prism builders. Both zigzag and armchair nanotubes can be built. These tools quickly produce 3D geometries.
Auto updating labels can now be attached to molecules, so they will update with IUPAC names, molecular formulas and more.
Mac OS X Quick Look plugin. Easily preview all your chemical files in Finder just by pressing the space key.
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.
More glassware, including a new organized glassware window. You can now also remove liquid from the templates.
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.
3D coordinate generation.
A new 180° chain angle clean option for easily creating Lewis structures and figures with 90° angles.
Complex embedded ring systems (like corannulene) now clean very well in 2D.
Added resolution controls to the Elemental Analysis widget.
Meso stereochemistry support.
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.
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.
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

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

Fixes

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

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.
Holding down the slash key while placing carbon chains will invert the chain.
Added molecular diameter descriptor (longest topological distance).

Fixes

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.
Fixed bug that prevented ChemDraw files from being written when a text area was present.
Fixed bug where a subscript in long atom labels caused unwanted whitespace to appear.
Fixed label offset issue when previewing certain filetypes in the file chooser.
Resolved issue where the Doodle Board could not be moved on Linux.
Rotating in 3D now correctly checks for atom overlaps.
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.
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

Round-trip editing on Windows via OLE. (Round-trip editing is already provided on Mac OS X)
Round-trip editing on Linux!
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.
Bezier curves for complex shapes and mechanisms.
Fragmentation tools.
More functions for handling chemical data on the clipboard.
File chooser previews.
77 new glassware templates!
Hundreds of other features and improvements.

4.1.1

December 05, 2011

Executive Summary

This minor update fixes a number of issues.

Fixes

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.
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.
Fixed bug where TLC plates were not properly read in from ChemDoodle Documents.
Recessed bonds are now properly anti-aliased.
Fixed rare stereochemistry issue where a very complex structure would not be analyzed correctly.
Fixed issue where ODG output would not preserve transform scaling.
Fixed issue where bitmap images from other programs would fail to be pasted, showing an embedded image failure box.
Fixed where formatting was ignored when chemically interpretation was disabled for a single element label.
The parent peak in the Elemental Analysis widget now correctly resizes when the widget is resized.
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

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.
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.
52 new glassware templates.
Glassware templates can now be flipped.
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.
A new menu item to optimize a PDB file to ChemDoodle Web Components JSON for fast loading and manipulation.
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.
Arrowheads now shrink when their length is greater than half of the line length.
JCAMP spectra are now written.
Added a new option to control if Hz are automatically converted to PPM from input JCAMP spectra. This is enabled by default.
Line notation formats will now recognize multi-line input.
The widget dock is now movable.
Added a new specification to control the width of the outlines for atoms represented by circle graphics.
EPS and SVG output now includes ChemDoodle metadata for round-trip editing.
The site license configuration now contains master controls to disable/enable updates and expiration notices.

Fixes

PubChem searching in the MolGrabber widget has been restored.
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.
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.
Fixed a couple NMR simulation issues. Alcohols are now recognized when connected to aromatic rings. Alcohol shifts next to aromatics are improved.
Fixed bug where stereochemistry in very complex structures with many condensed labels were not being determined correctly.
Stereochemistry will no longer be defined to aromatic bonds like in benzene.
Fixed issue where forcing E/Z stereochemistry did not update atom label positions.
Improved the performance for detecting stereochemistry in complex structures with many condensed labels.
Fixed bug where forcing cis/trans stereochemistry to a non-applicable double bond would cause an error.
Stereochemistry is now detected for double bonds in structures with condensed labels.
Glassware templates now correctly show default stroke colors.
Fixed issue where some glassware templates were not being correctly drawn.
CML output now correctly defines namespaces.
X-axis offsets are now read in from JCAMP files.
SLN input is now read correctly, even if there are atom id clashes.
Fixed issue where the SMARTS matcher was not correctly matching some aromatic bonds.
Improved the maximum activation message to explain how to deactivate/reactivate ChemDoodle.
Fixed bug where XLogP v2.0 calculations were not consistent and were inaccurate.
Bonds no longer withdraw from atoms represented by circle graphics.
The buffer between a reaction arrow and its constituent structures has been reduced by half when cleaning.
ChemExper supplier searches now include explicit hydrogens.
Fixed bug where drawing a double lined arrow would set the default line style to be doubled.
The color button is now clearer when empty colors are defined.
Fixed bug where the template widget would have some issues if it was defined as the default widget.
The Line Notation Pad widget now lays out multiple discrete molecules.
Fixed issue where colors in text areas were not being saved.
Fixed issue where opening a text field/area and then changing tabs caused the text component to remain open.
Fixed issue where sometimes the default document style sheet was being incorrectly overridden by the current style sheet.
Fixed EPS bug where some output would disappear when rotated text areas were present.
Fixed bug where the radical attribute button would place a charge instead.
Fixed issue where MDL CT file output had labels right-aligned, while still valid, some other applications require them to be left-aligned.
Fixed a couple interface issues, such as how drop down menus would close when the mouse scroll was used.
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

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

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

Fixes

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

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.
Rendered bond merging for aesthetic bond joins. Wedge-Single, Wedge-Wedge, Wedge-Bold, and Bold-Bold bonds now neatly fit together.
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 T_b)
- 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
New arrow types:
- Retrosynthetic
- Bold
- Rearrangement
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.
A new SMILES option to preseve bond orders on output. In essense, aromaticity will not be output to SMILES.
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.
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.
Text area font colors can now be changed.
Designating all resonance bonds in a ring now forces that ring to be defined as aromatic.
New keyboard shortcuts to add rings to bonds using the shift key. Alternate bond types are now assigned using the alt key.
Adding rings to bonds now automatically selects the most appropriate orientation if the mouse pointer is close to the bond.
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.
Renovated the keyboard shortcuts PDF.

Fixes

Fixed bug on Linux, where EMF output was missing atom labels.
Fixed bug where EPS clipping was not preserved correctly.
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.
Fixed SMILES bug where double digit ring indexes were not written.
SMILES reading no longer places explicit hydrogens on chiral centers.
Explicit Hydrogens are now output to SMILES.
Emptying the lasso now updates the Properties widget.
Fixed issue where reaction text areas were not properly accounted for when distributing objects.
Fixed bug where using parenthesis incorrectly in condensed notations caused problems during label expansion.
A Linux natural serif font is now used to correctly show font icons on Linux.
Hydrogen counts are now modified by radicals.
Attributes now rotate with structures instead of preserving their distance vector from the atom they describe.
Menu items to calculate descriptors now warn when the structure cannot be sensibly expanded.
Changing fonts to bold/italic now resizes the lasso.
Fixed issue where completely undoing all actions in a text area did not allow you to redo anything.
Underline and strikethrough rendering in text areas now always draws a 1 pixel solid line.
Using the font edit buttons in the text area toolbar no longer steals focus from the text area.
Fixed issue where arc angles could not be set to 0 in the Format Arc... window.
Arrows now correctly conform to document settings.
Charges are now appropriately assigned to the nitro group abbreviation.
Aromaticity detection is significantly improved, especially for fused ring systems.
Changing bond orders in rings now reassesses aromaticity.
Fixed rare bug where sometimes dragging a structure from the MolGrabber widget caused undo/redo issues.
An informative error is now displayed by the MolGrabber widget if a database is inaccessible.
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

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.
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.
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.
A new spectrum mouse gesture, shift+drag, will translate the spectrum along the x-axis.
Integration lines can now be rendered for NMR spectra. Color and thickness are editable.
Grids can now be rendered for spectra. Color and thickness are editable.
ChemDoodle Web Components v3.5 is included.

Fixes

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.
Fixed bug where the Line Notation Pad widget would go blank if an atom with an isotope defined was input.
Isotopes are now supported in ChemSketch files.
Improved the interpretation of coordinates from JCAMP-CS files.
Fixed the reading of negative abscissa values from JCAMP-DX files.
Fixed issue reading element types from SKC files with atomic numbers greater than 107.
Improved the performance of line notation readers.
Line notation readers now warn of multiline input.
Fixed SMILES input issue where the ring closing bond type is specified before a ring declaration.
Improved ROSDAL reading.
Fixed the reading of mass numbers and radicals from InChI strings.
Fixed the writing of radicals to InChI strings.
Fixed bug where changing the bond width or texture thickness to values not available in the Strokes toolbar had no effect.
Single bonds in condensed labels are no longer superscripted.
Charges are now set when expanding condensed labels with charges defined.
Abbreviations now trump elements, so "Ac" is interpreted as an acetyl group instead of Actinium.
Improved condensed notation interpretation to recognize abbreviations at the beginning of atom labels.
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.
Fixed rendering of orbitals and ovals in PICT output.
Fixed shape rotation issues in PICT output.
Fixed bug where SSSR linear independence was incorrectly determined by atom sets. The linear independence is now correctly determined by bonds.
Keyboard atom shortcuts alt+3 and alt+8 now correctly place cyclopropene and cyclooctatetraene, respectively.
Fixed bug where the window would go blank when trying to determine the stereochemistry of a fully substituted double bond.
Fixed bug where text input components remained and could not be removed if clearing the Doodle Board while a text input component was active.
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.
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.
Fixed the display of the Degree of Unsaturation descriptor in the Properties widget.
Improved the calculation of the Hydrogen Bond Acceptor descriptor.
Improved small case issues in aromaticity detection.
Fixed bug in calculating Morgan indices.
Fixed issue where the main window sometimes lost focus when trying to use keyboard accelerators and shortcuts.
Fixed minor issues where modifier keys didn't show immediate feedback when transforming lasso content.
Slightly improved Statistics widget scrolling and selecting.
Raster image output now correctly conforms to the advanced specifications for document rendering.
Removed HTML Area highlight decorations from appearing in image output.
Fixed bug where second token in superatoms didn't stack if that superatom is the first entity in a label.
Dragging after placing an atom will now correctly hover/dehover it.
The atom the mouse is under is now automatically hovered after a template or ring is placed.
Fixed minor issue when searching ChemExper where results without coordinates were displayed.
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.
Fixed minor issue where shadow settings were displayed for shapes that did not support shadows.
Fixed issue where some spectrum visual specifications were mistakenly global.
Expanding the spectrum to fit in the Spectrum Edit dialog now refreshes the tick spacing controls.
Negative values in spectra no longer offset the baseline.
Closing the Preferences window by using the top bar's close icon will now work just like the Done button.
Fixed bounds calculation for rotated label shapes.
Enabling/disabling chemical warnings now give immediate visual feedback.
Added lasso decorations for orbitals.
Removed lag when checking for updates when no internet connection is found.
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

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.
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.
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.
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.
The ChemSpider database has been integrated into the MolGrabber widget.
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.
Scalable vector graphics can now be directly pasted into the entire Microsoft Office suite, including Powerpoint and Excel.
Added a Save Selection as Image… menu item to the File menu to quickly save just the selected content to an image.
Added a Copy As submenu to the Edit menu to quickly copy selected structures as various datatypes at maximum compatibility on the system clipboard.
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.
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.
Molar Refractivity can now be calculated for structures.
Some widget settings are now saved in the workspace, including the last selected widget and the database choice in the MolGrabber widget.
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.
Menu items for unrepresented keyboard shortcuts have been added: Flip Bond, Align Bond and Add Attribute.
A new keyboard shortcut for adding attributes to hovered objects, Shift-A.
Added a new visual specification to set whether the second bond line in double lined bonds are shrunken when next to an atom label.
Radial gradient rendering is greatly improved for shapes to better portray 3D appeal.

Fixes

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.
Fixed a bug where structures could not be dragged into the Line Notation Pad widget.
Fixed bug where changing tabs when content was selected would change the colors of the selected content.
Selected content is now properly remembered when switching between tabs.
Fixed issue where a molecule still appeared selected if it was deselected using the alt+shift keyboard shortcut.
Fixed bug where reading a lone atom from a file will have its label misplaced.
Fixed issue where the SSSR finder was not enforcing linear independence.
Fixed issue where the Euler facet ring finder was skipping rings.
Colored in ring guides no longer appear in output.
Fixed bug where an infinite loop started when cleaning complex multi-ring-substituted ring systems.
Fixed bug where some structures were not being cleaned.
Improved the cleaning of complex ring systems.
When cleaning structures, triple bonds are now aligned parallel to their substituents.
Improved boundary conditions for token alignment to favor the horizontal alignments.
Fixed bug where some counters were not being calculated in the Properties widget.
The Calligraphy stroke skew angle has been offset by 15 degrees to avoid ghosting effects with vertical bonds.
The arrow size for the ACS Document 1996 chemical document settings has been set to 8 pixels by default.
Changing the arrow specifications now will apply to arrows without having to reselect an arrow tool.
ISIS Sketch files that are missing the closing tag are now read properly.
Fixed conversion issues with ChemSketch files.
Fixed PDB file issue where files that incorrectly contain 0's in inappropriate places were not being read.
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.
Fixed issue when adding hydrogens as text to some structures, where nonexistent hydrogens were being found and "removed" so nothing would be added.
Fixed slowdown when custom fonts were used.
Changing the atom label vertical alignment now updates bond buffers.
Aligning bonds now takes into account if the bond has been flipped.
Attributes now move correctly in grouped content.
Fixed bug where holding alt+shift to select a molecule would incorrectly move the hovered atom.
Negative coordinates in CDX files are now properly read.
Inserting a PDF or dropping it on the Doodle Board will search first for ChemDoodle metadata.
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.
Macintosh Vector PICT output has been improved.
Macintosh Vector PICT clips have been improved to remove the residual effect on clip borders.
Windows Enhanced Metafile output has been improved.
Removed small rectangle that appeared in EMF output to the top left of the origin that was only visible if content was offscreen.
EPS output is now smaller.
Improved ruler tracking when moving the Doodle Board scrollbars.
Fixed issue with text input components where text would appear to "jiggle".
Fixed rare lasso repaint issue that would stop certain sides from displaying the crawling ants effect.
Fixed issue that caused a crash when reading a corrupted workspace file.
Fixed bug where some right-click menu items were displayed but were disabled.
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.
Document rendering and application rendering have been separated.
Missing references have been added.
Fixed minor issues.
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

Incorporated the input and output of the ACD/ChemSketch Document format.
Incorporated the input and output of the MDL RXNFile format for storing single reactions. Both V2000 and V3000 connection tables are supported
Incorporated the input and output of the MDL RDFile format for storing reaction schemes.
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.
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.
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.
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
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.
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.
When objects are hovered, pressing the comma key will open that object's visual specifications formatting window.
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.
Added a visual specification for attributes to determine the amount of reduction for font text size in attributes that contain text.
Included a new file specification for MDL connection tables to include/exclude Hydrogen counts.
Added a style sheet to quickly produce 2D graphics for 3D data and scenes.

Fixes

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

New operating system specific installers (Windows Installer, Mac DMG, Linux BIN)
A thorough user guide
Performance enhancements
New intuitive keyboard drawing controls
Greatly improved lasso system
Improved graphics (Atom label token stacking, robust text bounds calculations, improved bonds, more graphical preferences)
Create chemical images, animations and interactive components for webpages
NMR simulation
Handling of spectra
Improved arrows system
Handling of reactions
Search your hard drives for chemicals
New chemical file formats
New cheminformatics descriptors and functions
Incorporated elemental database
New references system
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

Fixed problem where rotated shapes would disappear when pasting vector graphics in Microsoft Word on Macs.
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.
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.
The missing Reaction Arrow option in Condensed Mode has been added.
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

Fixed issue where SMILES strings would incorrectly contain lowercase letters for non-aromatic heteroatoms in the defined "organic subset".
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.
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

Added a new Calligraphy stroke style for bonds.

Fixes

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.
After Apple's Java Update 4 on Mac OSX, a few widget icons appeared dark. This issue has been resolved.
On Mac OSX 10.5, the file chooser windows will now display the associated Leopard file icons.
Fixed issue when placing templates with atoms close to the pivot would fuse those proximate atoms together when short bond length settings were selected.
Cyclohexane chair conformer buttons in the Rings toolbar now select their corresponding template in the Templates widget for further manipulation.
One new tutorial page has been added concerning Carbon labels.
Opening files and new tabs now update the Stroke toolbar.
All Chemical Document Settings files have been remade for the current selection of Preferences settings.
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.
The stroke settings in the Strokes toolbar no longer become clear on Windows and Linux when hovering over them. Mac was always working.
Proxy settings can now be cleared.
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

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.
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.
Two new tutorial pages have been added: chains and Lewis structures.
ChemDoodle now checks and warns you on Linux if it has been opened without use of the essential shell script.
Index numbers are now stripped from older PDB file formats, where ids are sometimes appended to atom element symbols.
The covalent radius tolerance is increased, allowing easier calculation of covalent bonds.
The sheet size choosers now show the correctly selected choices when initialized, rather than the default US Letter.
Fixed issue where atom label text was sometimes being cutoff by a pixel on Windows XP when printing.
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

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.
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.
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.
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.
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.
File annotations are now read and written in chemical documents for your records and so others can see your notes.
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)
MDL v3000 connection tables are now written.
CML arrays can now be written as well as read. You can choose whether to use arrays or not.
Many chemical file type options improved.
Full support documentation is provided for all recognized chemical file types.
Added icons for ChemDoodle Template files.
The structure beautifier has been significantly upgraded.
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.
Added a cyclohexane chair conformer button and its mirror image counterpart to the Rings toolbar.
Added four new bond types: Zero/Ionic, Double Dashed, Any and Unknown.
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.
New ruler shapes measure and display dimensions in various units.
Added polyline/polygon and freeform shapes. Control points are anchors for further connections and closing shapes. Pen shapes can now be closed as well.
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.
A new Flatten menu item has been added to the Content menu and sets all the z-coordinates of atoms to 0.
New Fisher projection chain and random chain tools for drawing chains quickly.
A much improved color chooser is provided on Windows and Linux.
Page dimensions can now be exchanged in all page dimension input panels.
Added additional grid background guides at 1/2 and 1/4 inches. All grids are now aligned to the top-left.
Added crosshair background guides.
Atom circle radii can now be specified as atomic, covalent, van der Waals or constant. You can set the constant radius.
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.
Atom text can now be rotated.
Morgan indices can now be assigned to atoms as identifier objects. This function is accessible in the View menu.
Choosing all zeros in the Multiplet Tool widget now clears it.
Horizontal scrolling is now supported on Macs.
Format guessing is now more robust than ever.
A complete Unicode selector has been added to the Symbols widget.
Symbols widget symbols have been updated, reorganized and cleaned up.
Added bracket lip width property.
All object properties are now individually modifiable.
Unit selectors have been added to all measurements.
The Join function will now also join two distinct bonds.
New arbitrary zoom option in the Formatting toolbar's zoom combobox.
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.
A thorough navigatable and searchable (in pdf form) user's guide has been written and has replaced the tutorial.
Linux icons provided in the /ChemDoodle/resources folder are now 48x48px in dimension and are better quality.
The iChemLabs Emender application is now provided in the /ChemDoodle/resources folder to easily repair a corrupted ChemDoodle installation.

Fixes

Runtime performance improved dramatically for large amounts of content.
Containing rectangles are now properly calculated for all shapes, even when rotated.
Fixed various line notation issues.
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.
Adding labels as substuents will now default to placing a starting atom if no starting atom is selected.
Adding labels as substuents now correctly overrides the last chosen drawing mode.
Fixed issue where Unicode was not being properly saved to ChemDoodle Documents.
Fixed various issues associated with undo/redo when adding labels as substuents.
Identifiers set by ChemDoodle functions can no longer be incorrectly altered.
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.
Symbol font from ChemDraw files is now converted to Unicode upon read. Output will also be in Unicode, which is the correct practice.
Fixed problem where linear atom centers with non-Carbon labels could not be edited to become Carbons.
Fixed error where specific identifiers weren't being saved properly.
Fixed a few issues when setting filetype associations to the Windows registry. On Vista, you must install the file associations as administrator.
Fixed cutoff layout for line notation popups on Windows.
The Doodle Board is now correctly placed and sized upon startup on all resolutions.
Now correctly calculates scaling parameters during transforms.
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.
Text components are now properly closed when switching between Doodle Sheets.
Empty content from widgets can no longer be dragged.
Removed gray lines that were bordering some bitmap images copied to the system clipboard.
Fixed issue where modifier keys were not registering if the mouse pointer was not located above the Doodle Sheet.
Fixed issue where documents printed with missing content when an image was present on Windows and Linux.
Fixed error that occured when a history action was performed while using the pen tool.
Fixed error when only a single atom was conformed to preferences.
Fixed issue where purging the history prevents the save data warning from appearing when closing a Doodle Sheet.
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.
Fixed issue where shape orientations would sometimes flip when scaled.
Fixed minor issue where converting to CDX reported a non-existent problem.
Corrected issue where certain ChemDoodle Document properties were implied booleans instead of explicit booleans.
Fixed bug where forcing stereochemistry with no identifier set, but with wedge bonds present, caused errors if a bond was facing the wrong direction.
Fixed issue where text areas would act weird at scales other than 100%.
Fixed issue where not inputting a number into the mass number input window caused an error.
Corrected issue where the mass warning display wouldn't disappear, even if the warning was followed.
Fixed bug where overlapping atoms weren't being copied correctly.
On Macs, ChemDoodle will now check if it has been incorrectly removed from its parent folder.
Binary file read errors now display properly.
An empty file warning is now displayed when attempting to open a blank file.
Activation code failures are now unambiguously described.
Activation now fails if the preferences file cannot be written.
Error panes are now displayed if there was a problem encountered during activation, after the activation code is validated.
XYZ files are now interpreted in Angstroms.
Multiplets can now be correctly loaded back into the Multiplet Tool widget when using the right-click menu function.
Fixed issue with the Symbols widget where some symbols were not correctly correlated with an identical glyph in the hover preview.
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.
3D coordinates are now centered and scaled properly.
Cancelling preferences changes to selected objects now works properly.
The last set printing orientation is now correctly remembered.
Corrected image rendering issue with significant bond overlap.
Solved tiff and bmp saving issues.
Fixed issue where drag and drop completion didn't reset the main cursor.
Fixed problem where a rejected drag and drop gesture caused poor UI responsiveness.
Fixed widescreen print centering issue that existed on Macs.
Fixed issue where plist changes were not being recognized in Mac apps.
Colors and fonts saved in preferences no longer affect toolbar buttons.
Correctly added trailing '...' to the end of certain right-click menu items.
All input and output streams are now buffered to improve performance.
The second '26' in the font size combobox is now correctly labeled '36'.
A monospaced font is now used when displaying plain text in ChemDoodle, such as the README file.
Minor graphical improvements.
Minor lexical corrections.
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

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.
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.
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.
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.
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.
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.
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)
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.
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.
SVG and Adobe PDF graphics can now be displayed so you may add vector graphics to your figures.
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).
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.
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.
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.
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.
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.
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.
XML file parsing errors are now displayed in an error message pane when trying to load XML chemical filetypes.
Added more greek symbols to the Symbols widget. Increased the size of the symbol preview box. Elements will now also display a preview.
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.
Added a nucleotide template pack.
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.
Colors are now associated with Chemical Document Settings files.
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.
Updated README.txt and the tutorial.

Fixes

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.
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.
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.
Doublet radicals combined with a + or - charge will be merged into a radical cation or radical anion respectively for ChemDraw files.
The Format toolbar's font chooser is now updated when loading CDX/CDXML files.
Fixed a few problems regarding property parsing in MDL SDFiles. Added the alias property to the MDL MOLFile.
Improved CML interpretation. Compatible stereochemistry is now read and written. Data arrays attributes are now read. Added support for a few less common attributes.
Switching between portrait and lanscape modes for printing no longer affects the Doodle Sheet.
The wavy line property for reaction arrows now has the appropriate affect.
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.
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.
Fixed issue where the Paste functions were not being enabled if the System Clipboard was blank while ChemDoodle was loading.
Fixed the 180° rotation function.
Fixed default size of the Doodle Board on small screen resolutions.
Scaling now only affects lassoed objects if conforming only those objects.
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.
Fixed problem where Guideline options did not mirror the actual display if the current preferences were reset.
Conforming chemical document settings actions to objects and the Doodle Sheet can now be undone.
Applying CSS to HTML areas can now be undone.
Fixed problem where changing a bond's color was not undone properly.
Improved the algorithm for calculating the optimal angle to add bonds too. Fixed issue where the optimal angle was incorrect for horizontal bonds.
File extensions containing capitals are now handled correctly.
The About ChemDoodle window has been dramatically improved.
Fixed problem where removing hydrogens couldn't be undone when removing from a lassoed structure.
Fixed issue where sometimes the shift key wasn't recognized when pressed.
Fixed dimension issues for bonds and atoms.
Double-clicking on a label will now open its editor.
Fixed problem where the hash properties of objects weren't being loaded properly in the Format Bond window.
Improved the look of bond breakers by centering them correctly.
Page dimensions for postscript files are now set properly.
Fixed problem where selecting the Use Circles option for atoms did not result in the desired effects if User Chosen colors was selected.
Fixed problem where rarely an object would be focused in an image.
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.
Improved drag-and-drop compatibility with files from the file system.
Image border properties are now set properly.
Changed the Multiplet Tool widget's icon so that it's more recognizable.
Scale anchors for the lasso are now only displayed in the 2D affine transformation state.
Improved Application loading speed.
Updated all CDS files.
Minor graphical enhancements and fixes.
Minor textual fixes.

1.3.1

October 19, 2008

Fixes

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

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.
Added read and write support for Chemical Markup Language (*.cml).
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.
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.
Added 5 new bond types: wavy, two-electron, bond and thin double, quintuple and sextuple.
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.
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.
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.
Added and option to the Multiplet tool to govern which direction the scale is oriented.
Added a feature to display unique atom and bond ids. These options can be selected under the Unique IDs submenu in the View menu.
Added an iChemLabs Newsfeed menu item to the Help menu for easy access to stories and information regarding ChemDoodle.

Fixes

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

1.2.3

July 19, 2008

Fixes

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

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.
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.
Added a static bracket set object that acts like a rectangle.
Added more menu accelerators.
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

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

1.2.1

June 29, 2008

Additions

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.
Added many chemical document formats including: ACS Document 1996, Helvetica Chimica Acta, RSC (1 and 2 Columns), and many others.
Doodle Sheets can now be resized.
Added more template packs: Cycloalkanes, Functional Groups, Hexoses, Polycycles, Stereocenters and more Ring Conformers. A separator now appears between official and unofficial template packs.
Drag and drop has now been implemented. To find out more, click here.
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.
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.
New menu items have been added including (not mentioned elsewhere): Clear, Purge History, Close and Close Others.
Dragging slightly outside of the Doodle Sheet will cause the scroll bars to scroll, if appropriate.
Added circular atom guides in the View menu that draw circular guides around atoms with a radius equal to the bond length.
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.
Widget buttons now display tool tips.
Added a new Purchase menu for easy access to the Permanently Activate ChemDoodle menu item. This menu disappears after ChemDoodle is permanently activated.
Added a new filetype and icon for ChemDoodle Chemical Document Settings Files (.cds).

Fixes

Sliders in Preferences now contain a number field, and the units can be changed.
Fixed bug where scale edges in the Multiplet Widget were incorrectly calculated when a simulation was showing.
SMILES Widget now displays an appropriate message when empty content is input.
MolGrabber LITE Widget and SMILES Widget lists have been improved for easier reading.
Template Widget no longer loses focus when traversing template lists.
Symbols Widget now works with label objects.
Label objects can now be edited by double-clicking on them.
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.
Fixed problem where rounding errors would occur when editing objects at scales other than 100%.
Fixed small bug where the cyclopropane button actually places cyclobutanes.
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.
Radicals now appear properly.
Fixed problem where HTML areas were not being properly read from save files.
Fixed problem when saving transparent images, where the transparent property was not being set.
Fixed problem where documents beginning with "Untitled" could be duplicated in the system.
The appropriate tab will be selected when prompted to save a file that is not the currently selected tab.
Fixed problem where closing a tab also closed the tab to its right.
Fixed problem where Unacceptable Oxidation State warnings lingered even after they were addressed.
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.
Fixed problem where Preferences dialog did not appear when requested to in message popups.
Splash screen now notes when OpenBabel is queried.
Template menu items no longer appear if shapes are selected.
Improved the window shrinking special effect when windows are hidden.
Lasso modes are now appropriately handled when switching between tabs.
Fixed minor graphical and textual inconsistencies. Improved the layouts of most dialogs.
Fixed minor errors.

1.2.0

May 23, 2008

Additions

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.
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.
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.
A unicode font is now provided, so that all systems can support the characters displayed in the Symbols Widget.
When adding carbon chains, the preview now looks exactly like the product.
ChemDoodle can now determine the filetype of an input file, and will describe errors that occur if unrecognized filetypes are opened.
Bitmap image support has been standardized and greatly improved. ChemDoodle will discribe how to use images that are not of the recognized filetypes.
Image components can now be directly copied to the system clipboard with a right-menu function.
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.
Templates can now be separated into groups. These templates are located in the ChemDoodle/settings/templates folder for easy inclusion and distribution.
Added more abbreviations to the Symbols Widget.

Fixes

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.
Symbol Widget characters now correctly fit in their buttons.
Carbon chain preview now correctly displays the number of bonds being added if starting on an unsubstituted carbon.
Error dialogs now fit details better.
Bicubic image scaling is better for rotations, and this is now stated in the Preferences menu.
Periodic Table now greyscales when an element is selected, instead of blurring.
The splashscreen progress is more thorough.
Message dialogs now allow for buttons and other components to obtain focus.
The mouse position refreshes after a right-menu has been closed.
Landscape documents now reopen properly.
The Periodic Table's Electrons checkbox now properly displays the Bohr electron configurations on the right side.
README.txt and tutorial have been updated.
Fixed concurrent modification error when saving while overriding a currently opened file.
Subscripts are now properly displayed in the abbreviations panel of the Symbols Widget.
Fixed problem where ruler caret disappears in certain areas.
Fixed problem where widget buttons were not obtaining focus.
Fixed problem where redo function caused bond mode to begin.
Bond highlights are now still drawn, even if the bond color is empty.
Fixed minor graphical inconsistencies and improved a few button icons.
Fixed minor errors.

1.1.3

April 23, 2008

Additions

Added a beautiful, printable, customizable interactive periodic table of elements with physical properties. More elemental data will be added in subsequent updates.
Brackets now have an associated label that will automatically place itself in the correct position.
Bond color and border/line color have been separated in the color chooser for easier color management.
Double bonds can be customized to be symmetrical always, never or only when not part of a ring.
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)
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

Splashscreen performance greatly improved. Flashing has been eliminated.
After a trial expires, a popup will appear describing the situation before asking for another activation code.
ChemDoodle now recognizes HTTP redirects and reports them in an error dialog.
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.
Logouts due to session expirations are now easily handled, continuing with the current function after re-authentication.
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.
Brackets copy correctly.
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.
Select one mode error corrected.
SMILES widget now counts '*' labels in aromatics as instructed in SMILES documentation.
Fixed template scaling problem. Text in templates are now oriented and centered correctly.
Widget button drawing has been optimized to improve performance.
Lasso optimized to improve refresh rate.
Nudging has been fixed; the Doodle Board's scrollbar no longer responds to arrow keys.
Copying and pasting no longer crops off long atom labels.
Fixed error where the clean tool would incorrectly align some triple bonds.
Object flipping now causes the doodle sheet to repaint.
Atom lock-on distance is now a function of the current bond length.
Labels now orient correctly regardless of whether or not atoms are being checked for chemical correctness.
Resolution of Mac icons increased to 512x512 pixels.
Fuzziness has been removed from Windows cursors.
Resolution of Windows icons increased to 240x240 pixels. The ChemDoodle Windows executable has been recreated with many improvements.
Fixed Linux problem where message dialogs would appear behind the splash screen.
Failing to connect to the internet, after logging in, will log you off.
Fixed minor graphical inconsistencies and aberrations.
Fixed minor errors.

1.1.2

March 19, 2008

Additions

Preferences now contains an option for displaying carbon labels on carbons with three modes: never, on lone carbons or always.

A new drawing warning for unacceptable oxidation states has been added.

CPK and Jmol color sets completed.

Fixes

Brackets between discrete molecules are drawn correctly.

Corrected minor issues concerning the abbreviation management panel.

Updated oxidation state database.

Fixed minor graphical and textual issues.

1.1.1

March 10, 2008

Additions

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.

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.

SMILES widget now parses reactions as defined by the SMILES documentation with correct 2D layout.

Tables are now included in the View menu to list chemical data, including atomic properties and isotope distributions.

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.

Added templates pack #2 containing polycyclic aromatic hydrocarbons.

Aromatic ring size is now definable in the Preferences window.

Preferences now contains an option for filling or not filling arrowheads.

Preferences now contains advanced options for what data flavors are placed on the system clipboard during copying to other applications to ease pasting ambiguities.

The Preferences window has been completely redone, with more functions for restoring defaults and cancelling changes.

New iChemLabs login screen containing a check box for linking your account information with your copy of ChemDoodle.

New components improve the aesthetic and functional nature of ChemDoodle, including drop shadow borders and shrinkable task panes.

Fixes

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.

Fixed undo problem where rotations were being "unrotated" around a differet center point.

Reaction arrows and mechanism arrows now copy and paste correctly.

Fixed ring problem where single bonds incorrectly change to the selected bond order when placed.

Fixed multiple molecule optimization problems with the SMILES widget.

Templates now save without retaining more specific information hampering user defined color and font choices. Current templates have been fixed.

The text area margin window has been improved.

Fixed highlighting ambiguity on some objects when the lasso is active.

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

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.

The Symbol widget now also adds to text areas and reaction arrow texts.

Fixed mac list cell rendering problem where some list items would become white or invisible.

Fixed MolGrabber LITE.

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.

Fixed various minor errors.

1.0.6

January 06, 2008

OpenBabel is now integrated for flawless interpretation of over 80 chemical file types. Import, Export and Convert between them.

An auto-update function has been added so you no longer need to update ChemDoodle manually.

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.

Images can now be embedded in ChemDoodle Documents.

The 2D structure cleaner has been improved.

MDL SDFiles have become a native format for ChemDoodle.

Doodle Sheets now recognize when work has been done, and empty sheets will now close without requesting approval.

End Users

End Users

ChemDoodle 2D

ChemDoodle 3D

ChemDoodle Mobile

Developers

Developers

ChemDoodle Web Components

ChemStack

ChemDoodle Version History

12.7.0

Executive Summary

Additions

Fixes

12.6.0

Executive Summary

Additions

Fixes

12.5.0

Executive Summary

Additions

Fixes

12.4.0

Executive Summary

Additions

Fixes

12.3.0

Executive Summary

Additions

Fixes

12.2.1

12.2.0

Executive Summary

Additions

Fixes

12.1.0

Executive Summary

Additions

Fixes

12.0.0

Executive Summary

11.13.0

Executive Summary

Additions

Fixes

11.12.0

Executive Summary

Additions

Fixes

11.11.0

Executive Summary

Additions

Fixes

11.10.0

Executive Summary

Additions

Fixes

11.9.0

Executive Summary

Additions

Fixes

11.8.0

Executive Summary

Additions

Fixes

11.7.0

Executive Summary

Additions

Fixes

11.6.0

Executive Summary

Additions

Fixes

11.5.0

Executive Summary

Additions

Fixes

11.4.0

Executive Summary

Additions