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ChemDoodle Changelog

What's new in ChemDoodle 7.0.2

Dec 20, 2014
  • Fixes:
  • 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.

New in ChemDoodle 7.0.1 (Oct 9, 2014)

  • 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.

New in ChemDoodle 7.0.0 (Oct 9, 2014)

  • 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.

New in ChemDoodle 6.0.1 (Jun 9, 2014)

  • 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.
  • 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.

New in ChemDoodle 6.0.0 (Dec 2, 2013)

  • 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.
  • 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.

New in ChemDoodle 5.1.0 (Sep 28, 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.

New in ChemDoodle 5.0.1 (Sep 28, 2013)

  • 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.

New in ChemDoodle 5.0.0 (Sep 28, 2013)

  • ChemDoodle 5 is a massive update to ChemDoodle. Included are hundreds of fixes and new features.
  • 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.

New in ChemDoodle 4.1.1 (Sep 28, 2013)

  • 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.

New in ChemDoodle 4.1.0 (Sep 28, 2013)

  • 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.

New in ChemDoodle 4.0.0 (Sep 28, 2013)

  • 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.

New in ChemDoodle 3.3.1 (Sep 28, 2013)

  • 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.

New in ChemDoodle 3.3.0 (Nov 1, 2010)

  • 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 Tb)
  • Gibbs Enery of Formation (ideal gas, unit fugacity, at 298K)
  • Heat Capacity (ideal gas, at 298K)
  • Liquid Viscocity (at 298K)
  • Normal Boiling Point
  • Normal Freezing Point
  • 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 where EPS clipping was not preserved correctly.
  • 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.

New in ChemDoodle 3.2.1 (Nov 1, 2010)

  • 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.

New in ChemDoodle 3.2.0 (Nov 1, 2010)

  • 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 (s, p). 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:
  • 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.
  • 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.
  • 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.
  • 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).
  • 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.
  • 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.

New in ChemDoodle 3.1.0 (Nov 1, 2010)

  • 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.
  • Access to structures and properties provided in the MolGrabber widget.
  • 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.
  • Restricting result set size.
  • Excluding PDB files.
  • NMR simulation algorithms greatly improved.
  • 1H: anisotropic effects, ring strain, hydrogen bonding effects, rapid exchange, diastereocenters, heteroaromatics
  • 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 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.

New in ChemDoodle 3.0.0 (Nov 1, 2010)

  • 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

New in ChemDoodle 2.0.5 (Dec 20, 2009)

  • 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.

New in ChemDoodle 2.0.4 (Dec 19, 2009)

  • 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. 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.

New in ChemDoodle 2.0.3 (Nov 7, 2009)

  • 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.

New in ChemDoodle 2.0.2 (Jul 16, 2009)

  • Additions:
  • Added a new Calligraphy stroke style for bonds.
  • Fixes:
  • 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 when hovering over them.
  • Proxy settings can now be cleared.
  • The updater has been updated to version 1.2.1 to fix minor issues.

New in ChemDoodle 2.0.1 (Jun 15, 2009)

  • 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.