November 1st, 2010Additions:
· 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.
November 1st, 2010Additions:
· 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.
November 1st, 2010Additions:
· 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.
November 1st, 2010Additions:
· 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.
November 1st, 2010New 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
December 20th, 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.
December 19th, 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.
November 7th, 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.
July 16th, 2009Additions:
· 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.
June 15th, 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.
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