ChemDoodle 2.0.0

ChemDoodle is a fully functional chemical drawing application that works on every operating system including Linux, and works well! In addition to being multiplatform, ChemDoodle also natively reads and writes many common file formats including ChemDraws CDX and CDXML. You can write ChemDraw files for submitting journal manuscripts or share these files with your rich friends who purchased ChemDraw. No longer do you need to worry if your colleages are using compatible applications or operating systems.
Main features:
- A professional program for professional scientists.
ChemDoodle doesnt just look good, it also works well. ChemDoodle allows you to easily produce any chemical figure imaginable. All objects (atoms, bonds and shapes) are easily created and can be associated with various properties to specify their appearance. ChemDoodle also comes with a number of preset chemical document settings files, such as ACS Document 1996 and Helvetica Chimica Acta, or you may create your own. ChemDoodle also has advanced systems for loading and saving images, creating and displaying text, as well the ability to read and write important chemical file formats. And ChemDoodles functionality is only rivaled by its ease of use; it allows you to manipulate all of your items with efficient menu items or quick mouse clicks.
- Widgets - many applications for the price of one!
One of the great things about ChemDoodle is that its not just a program for creating chemical structures or molecule drawings. It is a 2D chemical environment where anything chemistry can be incorporated. ChemDoodles widgets are a great example of this freedom. These mini-applications perform various unique tasks such as interfacing with databases, generating and interpreting SMILES strings, and simulating multiplets. The output from these widgets can be easily dragged right onto your document. We are always looking to add more widgets, so you may be pleasantly surprised after updating ChemDoodle, to see a new widget that appears for you to play with!
- A variety of native file formats.
In addition to ChemDoodles own format (ICL) and chemical document settings format (CDS), ChemDoodle can flawlessly read and write ChemDraws CDX and CDXML, MDL MOLFiles and SDFiles, and chemical markup language (CML). If journals do not accept ChemDoodles ICL format or any of the vector image formats provided, just save your document as a ChemDraw file and submit that as well. All mutually inclusive objects, including shapes and images, can be saved with almost all properties preserved. This story at iChemLabs describes the reading and writing of ChemDraw files in more detail. You may also want to use structures created in ChemDoodle with other chemical applications. ChemDoodle fully supports MDLs formats, which have become the standard chemical file formats, and almost every chemical application will be able to load them. A wide range of native formats allows for ease in using ChemDoodle for any task.

Version restrictions:
- 14 days trial period

Enhancements
Additions:
- ChemDoodle can now transfer scalable vector graphics into Microsoft Office, OpenOffice, iWork, Adobe Products, and almost any other applicationiChemLabs has written this functionality as a proprietary libraryNo 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 artThis is perfect for posters and other less formal occasionsCurrently provided are brush, bristle, charcoal, scribble and wobble stroke stylesYou may read more about this feature here.
- A new TLC Canvas widget has been added for digitally reproducing your TLC platesGradients and transparency are supported for photorealismYou may read more about this feature here.
- A new Properties widget for calculating various properties of selected moleculesMore properties will be provided in the futureThis 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 InChIAdded a new option to explicitly control the starting point for line notationsNote that this setting is ignored for canonicalized line notationsYou 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 writtenAll objects and properties are handled, including fonts, colors, shapes, annotations, settings, etc., if applicable.
- ISIS Sketch File (.skc)
- ISIS Sketch Transportable Graphics File (.tgf)
- Protein Data Bank Files (.pdb, .ent)
- Standard Molecular Data (.smd)
- Tripos Mol2 (.mol2)
- Daylight SMILES (.smi, .smiles)
- Sybyl Line Notation (.sln)
- IUPAC InChI (.inchi)
- Beilstein ROSDAL (.ros)
- MDL v3000 connection tables are now written.
- CML arrays can now be written as well as readYou 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 workstationsAll toolbars are condensed, and only 1 widget appears at a time in this modeAll recently opened files will be located in a submenu of the File menuThe main scale starts at 75%All windows will now display properly on small resolutions including preferences and the periodic table of elementsThe 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 computerThis procedure begins by selecting the Deactivate ChemDoodle menu item in the Help menuThis option is only present for activated copies of ChemDoodle.
- New ruler shapes measure and display dimensions in various units.
- Added polyline/polygon and freeform shapesControl points are anchors for further connections and closing shapesPen shapes can now be closed as well.
- New Remove Selected Bonds and Calculate Covalent Bonds menu functions have been added to the Structure menuCalculate 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 inchesAll 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 constantYou 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 filesThis ratio controls all measurements performed in ChemDoodle.
- Atom text can now be rotated.
- Morgan indices can now be assigned to atoms as identifier objectsThis 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 toolbars zoom combobox.
- Keyboard shortcuts have been intuitively assigned to almost all menu itemsThe 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) users 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 sizeWhen 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 appearsThe first tab is not modified if it is the only one present.
- Symbol font from ChemDraw files is now converted to Unicode upon readOutput 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 werent being saved properly.
- Fixed a few issues when setting filetype associations to the Windows registryOn 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 printingNote that you cannot print outside of the intrinsic printer marginsTo 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 doesnt 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 wouldnt disappear, even if the warning was followed.
- Fixed bug where overlapping atoms werent 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 didnt 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.