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chemdoodle

htmlwidgets for chemdoodle web components

 

Just came across this site https://github.com/zachcp/chemdoodle

This repo is for the creation of an HTMLWidget for visualizing moleules based on the ChemDoodle WebComponent library, the HTMLWidgets package, and the Chemistry Development Kit via rCDK.

Looks to be under active development.


Comments

Flot plots updated

 

I have updated the page showing the interactive plots using Flot and ChemDoodle Web Components

I have a regular need to share results from my work and historically this has been via a paper reports that have more recently been replaced by electronic versions. Whilst useful, these reports lack the interactivity, in particular it is extremely useful to be able to easily link data points on a scatter plot with the corresponding chemical structure. So I’ve started using web-based reports to add extra functionality. Unfortunately it has often required the addition of applets or plugins that I can’t be sure the viewer will have available so with the advent of HTML5 I’ve been exploring writing the reports using just HTML and javascript. One of the major challenges is to produce interactive plots instead of using static images, and I’ve been exploring the use of Flot to produce a plot with chemical structures produced using either a web-service like ChemSpider or a javascript library of web components developed by ChemDoodle.

flot


Comments

ChemDoodle Web Components updated

 

iChemLabs announced the release of version 8 of the ChemDoodle Web Components, the largest update of the library to date. The ChemDoodle Web Components is an industry leading HTML5 toolkit for building scientific applications for web and mobile platforms. The ChemDoodle Web Components are licensed under the open source GPLv3 license or under a commercial license.

cwc8-1024x931

Executive Summary: Version 8 is the largest update to the ChemDoodle Web Components library to date. The sketcher has seen significant work, with new drawing tools (rings, chains, templates, atom label tool, more). Condensed labels with abbreviations are now supported, for advanced chemistry. New 2D shapes include dynamic brackets, atom mappings and variable attachment points, while molecular surfaces (vdW, SAS, Connolly) can now be generated and rendered in 3D components. The shader system used by the 3D components has been dramatically improved for much faster performance (and new improvements added like gamma correction) and a deferred shader has been implemented to provide advanced graphics techniques like outlining, software antialiasing and screen space ambient occlusion. Shadows can now be rendered in 3D scenes. The entire website has also been improved, with new advanced tutorials for working with the sketcher to listen to user changes, or show off an advanced in browser sketcher interface that mimics the desktop software, for instance. SVG can now be exported from the ChemDoodle Web Components in addition to PNG. A new iChemLabs Cloud service allows developers to match entire mechanisms for educational eBooks and advanced reaction databases. There is a lot in this update, please see the links below for more information.

New Features:

  1. The sketcher has been significantly developed. A new requireStartingAtom option allows you to disable to starting atom requirement while sketching. A new resizable option enables the user to resize the sketcher canvas. A new floatDrawTools option uses a floating toolbar for the drawing tools, just like the desktop software. Several new tools have been added, including an arbitrary ring size and arbitrary chain size tool. An atom label tool has been added with a text input field (like in the desktop software) to enter custom atom labels, including advanced condensed labels; space will open the text field by keyboard while the return or enter key will close it or repeat the last typed label for a hovered atom. Templates can now be added in the same manner as the desktop software using the new Templates widget; you can modify and add to the template library. The MolGrabber widget now allows the loading of any content (multiple molecules and shapes) and will insert the content in its entirety to the canvas. The MolGrabber widget will now also alert you if you press the Load button before the Show button. New buttons are available for centering the content in the sketcher as well as for horizontal and vertical flipping. The Open dialog now slides down from the toolbar as a Popover. The lasso tool and selections now use a dashed line just like in the desktop software. When using the labels tools in the sketcher, the periodic table canvas now selects oxygen by default and will revert back to label mode of the currently selected element if chosen from the toolbar. Silicon has been added to the default labels group. Placing unsaturated rings (like benzene) now better lay out double bonds to avoid overvalencing atoms. Hovering bonds are now more responsive, especially for elongated bonds. Pushers now can be set by clicking and then clicking again, no drag necessary.
  2. A new UIs component has been added, called Popover. A Popover is modal and can slide in from other components or appear in its own component for user input.
  3. Added mobile support for the UIs interface elements. For example, previously dialogs couldnt be moved on mobile devices, now they can.
  4. Complex labels can now be handled, with the required additional tools for parsing, formatting and rendering. With this feature, your chemical structures can contain advanced chemical labels consisting of element symbols, abbreviations (a dictionary controlled by you) and numbers and parenthesis for multiplicities. The labels are automatically formatted chemically and oriented based on least interference with surrounding bonds. Some examples include COOH, CO2Me, N3, CH2(CH2)4OH, C3H7O, Tosyl, myAbbreviation, and more. Use this to create concise publication quality figures directly in your websites.
  5. Added a wavy bond type.
  6. New shapes have been included. New 2D shapes include dynamic brackets for repeating groups, atom mappings for reactions and variable attachment points (VAPs). New 3D shapes include molecular surfaces. The ChemDoodle JSON specification has been updated to support these shapes.
  7. Molecular surfaces can now be generated and rendered for sets of atoms in 3D. Supported types include van der Waals, solvent accessible and solvent excluded (also known as a Connolly surface). You can control resolutions for all and the probe radius for solvent based surfaces. Rendering styles include Dots, Mesh and Solid and all colors, transparency, etc. can be controlled through visual specifications.
  8. The shader system for the 3D components has been redone. Several improvements in the Phong shader allow us to render higher quality graphics with lower quality meshes, leading to significant performance improvements across the entire 3D ChemDoodle Web Components.
  9. A deferred shader system has been developed allowing the implementation of advanced shader procedures for generating graphics. Currently implemented are outlining, screen space ambient occlusion (SSAO) and software antialiasing (FXAA). SSAO in particular is very powerful as it allows us to simulate how much ambient light is accessible to objects in crowded spaces, allowing us to shade the scene in a more accurate manner. This works on all geometries, but the feature can really be shown off in space filling all-atom models of large macromolecules.
  10. Shadows can now be rendered in 3D scenes. You can control the intensity of the shadows with the shadowintensity3D visual specification.
  11. Gamma correction has been implemented for brighter, more color accurate rendering controlled by the gammaCorrection_3D visual specification.
  12. The VisualSpecifications class now provides a copy() function for creating style sheet copies.
  13. Added a new bond visual specification for absolute saturation widths: bondsuseAbsoluteSaturationWidths2D.
  14. Bonds now split colors based on their substituent atom colors, with the bondssplitColor visual specification. The bondsuseJMOLColors and bonds_usePYMOLColors specifications have been removed. Use the corresponding atom specifications instead.
  15. Made wedge width an absolute value in line with desktop software with a default value of 6.
  16. Components now center 2D content much more pleasantly by calculating bounds of atom labels in addition to coordinates and using a constant internal padding.
  17. The preview, hover, select and error colors are now controlled by visual specifications.
  18. A new iChemLabs Cloud call, mechanismMatch(), is now provided to match mechanisms. You can see it in action here.
  19. Updated van der Waals radii data.
  20. Added the rest of the new elements as defined by IUPAC.
  21. Updated the library to use some newer standardized HTML5 functions, removing the polyfills from the ChemDoodle.extensions package.
  22. The PNG package has been refactored to provide both an open() function for loading the PNG into a new window and a string() method for creating a string object of the PNG content.
  23. A new SVG package has been added to create Scalable Vector Graphics data from the ChemDoodle Web Components, similar to the PNG package for bitmap graphics.
  24. Minor graphical improvements for the UIs decorations.
  25. Updated jQuery to version 2.2.4. Updated jQuery mousewheel to version 3.1.13.
  26. Updated the entire website. Added more advanced tutorials: Image Export, Initializing Components after Closing the DOM, Sketcher: Application Window, Sketcher: Listening to User Changes.

Full details of the update https://web.chemdoodle.com/installation/changelog/.


Comments

ChemDoodle 8.1 available

 

A new update for the very popular chemical drawing application ChemDoodle has been released. Version 8.1 looks to be a significant update with several useful new features and a few bug fixes.

Additions

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

Fixes

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

Comments

ChemDoodle 8.0.1 is now available.

 

Just noticed this message.

ChemDoodle 8.0.1 is now available. However, automatic update is not allowed for Mac OS X. You must manually update ChemDoodle by downloading the latest version of ChemDoodle from www.chemdoodle.com, and re-installing it. NOTE: You must close ChemDoodle before re-installing the new version.
Changes in ChemDoodle 8.0.1
Executive Summary
This is a minor update fixing issues brought to our attention since the ChemDoodle 8 launch. For changes to version 8, scroll down.
Fixes

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

ChemDoodle 8 is a massive update to ChemDoodle. Included are hundreds of new features and improvements, recommended to us by users like you. Enjoy and please spread the word!
New Features

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



Comments

ChemBioDraw and Word 15

 

A reader flagged this issue for me.

Word 2016 for Mac: I can't cut-and-paste an image from a vector drawing program I am a scientist and I routinely create images in a vector drawing program called ChemBioDraw. In past versions of Word, I was always able to copy these images to the clipboard and paste directly into the text of a document. With Word 2016 for Mac, all I get is many lines of gibberish code and no image. Am I missing something, or has the ability to handle vector graphics been eliminated from the program? FYI- a friend of mine who does design is having the same problem with a CAD program.

A quick search of the ChemBioDraw support forum highlights several threads that appear to be about the same issue.

I'm a new user of ChemDraw, and I have tried to copy/paste my structure into word and just end up with heaps of text like this:

0 0 0 0 0 0 0 0 0 0 0E 3.9121 2.7155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0E 3.9385 1.8909 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 2 4 0  1 3 4 0  3 4 4 0  4 5 4 0  6 7 1 0  7 8 2 0  8 9 1 0  9 10 2 0  10 11 1 0  6 11 2 0  12 13 1 0  13 14 2 0  14 15 1 0  15 16 2 0  16 17 1 0  12 17 2 0  2 18 1 0  18 5 1 1  19 20 4 0  19

With the rather unhelpful response

Currently our products are not supported with MS Office 2016. We plan to support MS Office 2016 for the future release/update.

The only thing I can suggest in the meantime is use the "Paste as PDF" functionality, this should allow display and round-trip editing.

I did a quick test with ChemDoodle and there don't seem to be any issues with this chemical drawing programme.


Comments

ChemDoodle 3D updated

 

ChemDoodle 3D has been updated and in addition for a limited period any customer that upgrades to or purchases ChemDoodle 8 will receive a free license for ChemDoodle 3D v2.

chemdoodle3D

New features in ChemDoodle 3D v2:

  • Full Retina display support on Mac OS X.
  • Support for high DPI Windows hardware.
  • The visual specifications of the scene can now be applied to selected content, or individual objects, as opposed to the entire scene. Right-click on objects and select the Format… menu item to show visual options for that object. New representation quick buttons are now available for modifying residue atoms and bonds, ribbon models and nucleic acid models in addition to non-residue atoms and bonds.
  • Protein and nucleic acid information can now be loaded from PDB files. Ribbon, trace and tube models can be generated for proteins. Ladder models can be generated for nucleic acids. The models are fully customizable. Control dimensions, alpha helix widths, coloring and more. Both B-spline and Catmull-Rom splines can be used to generate models. Water can be displayed as stars. Residue atoms can be controlled separately from hetatoms. Load PDB files by PDB id.
  • Periodic data can now be loaded from CIF files. Unit cells of any geometry are resolved. Functions for periodic systems will be provided in the Periodic menu. Build supercells.
  • An advanced selection system has been implemented. Select, deselect and reselect content. Select all, next molecule, inverse and by SMARTS. Use the new selection mode to select content or use the selection window to list the contents of the scene and select the content you wish to work with. The selection window is very advanced and will show you what you are currently hovering.
  • Fogging can now be defined in scenes using linear, exp1 or exp2 algorithms. Fog color can be defined as well as fog ranges.
  • A compass can be added on the bottom left of the scene or through the camera’s origin.
  • 3D scenes can now be printed.
  • Added quick quality options in the View menu to quickly switch between a range of higher and lower quality rendering settings to allow you to improve graphics or performance.
  • Image export now allows for transparent backgrounds in capable image types. This allows you to easily use ChemDoodle 3D generated graphics in various media with custom backgrounds.
  • Many new smaller features: added an option to remove shadows from text, added projection menu items, certified the correct 3D stereochemistry is generated from 2D drawings, picking can now handle any number of objects, and more.
  • Updated to support ChemDoodle Web Components v7. Shapes can now be read/written using ChemDoodle JSON.
  • Your iChemLabs account can now be accessed from ChemDoodle 3D. ChemDoodle 3D customers receive a free account for accessing ChemDoodle Mobile. If you also have ChemDoodle desktop, this is the same account.
  • Dozens more improvements and additions.
Comments

ChemDoodle 8 released

 

The increasingly popular chemical drawing package ChemDoodle has been updated, this is a major update to an already excellent application. There also looks to be offers at the moment so this is a great time to purchase.

What is new in ChemDoodle 8

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

Browser plugin-free CIF visualization

 

A nice comparison of the options for displaying crystal structures within a browser without the need for plugins/applets.

Full blog post is here

Here we compare four open-source browser engines for plugin-free rendering of the crystalline structures in CIF format.

Comments

ChemDoodle Web Components

 

There is a very nice review of ChemDoodle Web Components in the latest issue of Journal of Cheminformatics 2015, 7:35 DOI

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses canvas and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.

Comments

ChemDoodle Web Components JCAMP Interpreter

 

Displaying spectra on the web is usually a pretty minimal experience, often simply an image file. Whilst there a number of desktop applications for viewing spectra, web-based tools were often limited to Java plugins which have now almost completely fallen out of favour.

The JCAMP data format (1) for spectra is pretty widely used and we are starting to see javascript implementations of viewers. This very nice example uses the ChemDoodle web components to display the spectra and provide interaction. Hovering close to a nucleus that has a peak correlation defined will highlight that nucleus and any other nuclei in its group along with highlighting the corresponding peak. Conversely hovering close to a peak that has correlated nuclei associated with it will highlight the set.

(1) JCAMP-DX: A Standard Form for the Exchange of Infrared Spectra in Computer Readable Form ROBERT S. McDONALD and PAUL A. WILKS, JR. Appl. Spectrosc. 42(1), pp151-162, 1988

Comments

Round trip editing

 

Office for Mac Preview is the open beta version of the upcoming version of Office 2016. One of the issues that crops up everytime there is an update is round-trip editing, i.e. the ability to copy and paste from a chemical drawing package into Word for example and then be able to copy and paste the structure back from Word into the chemical drawing application.

I've not tested it myself but I am assured that ChemDoodle behaves as expected.

If anyone has tested any other chemical drawing packages please let me know.

Comments

ChemDoodleMobile

 

ChemDoodle Mobile has been updated.

What's New in Version 1.5.0

  • Added full 3D graphics support for 3D molecules!
  • Full support for iOS8 and the new iPhone sizes
  • Buttons are now larger on larger screens
  • Various improvements to the sketcher
  • Fixed clear button where it sometimes would not work
  • Corrected bug where stereochemistry was inverted in 3D coordinate generation
  • Resolved rare issue where the app would fail to load properly
  • Significantly increased responsiveness
  • Minor changes and fixes

ChemDoodle Mobile is the most highly rated App on the Mobile Science website and is accessed with your ChemDoodle account that is provided to you for free when you purchase ChemDoodle desktop.

Comments

ChemDoodle Web Components 7 is Available

 

iChemLabs have just announced an update to ChemDoodle Web Components. This is a major update to the ChemDoodle Web Components with new additions to the 3D features, most notably Pipe and Plank models for proteins and support for high DPI displays, such as the Apple Retina display.

The following pages show off some of the new features:

Comments

ChemDoodle 7 Review

 

ChemDoodle is now firmly established as one of the key chemical drawing packages that offers an inexpensive alternative to some of the increasingly expensive drawing packages. It also has the advantage in that it supports Mac, Linux and Windows and offers access to ChemDoodle Web Components. I’ve written a review of the latest update.

Comments

Status of WebGL

Here is an interesting article highlighting the current status of WebGL. WebGL is finally available by default in all browsers on all platforms and on both desktop and mobile devices.

Scientific applications now have the ability to creatively communicate information in both 2D and 3D through HTML5 across all platforms and can be distributed freely over the internet. We have been making sure that WebGL support in the ChemDoodle Web Components remain compliant and thorough throughout its development. So no worries if you have not yet learned WebGL, as you can take advantage of this powerful 3D graphics technology for free under the GPL license through the ChemDoodle Web Components, joining hundreds of other projects that currently use our library to create the most stunning scientific web and mobile apps.

There is a demo of what can be done with ChemDoodle Web components in the hints and tutorials.

Comments

ChemDoodle 7 released

 

The latest update to the hugely popular chemical drawing package ChemDoodle has just been announced.

Some of the new features in ChemDoodle 7:

  • 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.

If you want to find out more about ChemDoodle 7 there are a series of Webinars that describe it in detail

I hope to write a review later this week.



Comments

ChemDoodle Web Components Updated

 

The excellent ChemDoodle Web Components have been updated.

This is a bugfix update to the ChemDoodle Web Components, fixing all the issues brought to our attention. Fixes

  • WebGL based components now work in IE11.
  • iChemLabs Cloud services now work based on a queue, so all requests will proceed in the order requested, and you will no longer see a message to wait for the previous request to finish.
  • Added a iChemLabs.useHTTPS() function for websites that want only to use HTTPS.
  • Optimize zone now provides better placement when drawing triple bonds or higher.
  • Optimize zone now avoids placing substituents inside of rings.
  • Removed code calling jQuery.browser which was removed in jQuery 1.9. This code is only helpful for detecting when to use Google Chrome Frame. Note that Google Chrome Frame support (and therefore support in IE6-8) will be removed soon.
  • Fixed issue where clicking on the help button in some browsers would lock the component into a drag gesture.
  • Fixed bug where rendering atoms in 2D surrounded with a circle would error out.
  • Improved and simplified shaders.
  • Picking in 3D is now object aware, and will exclude objects if not selectable. So picking atoms for measurements is now much more responsive.
  • Fixed issue where measurements were not working in the Editor3D canvas on Android.
  • Help button now works in the Editor3DCanvas on Android.
  • Measurement values now render with a forward z-index of 1 â„«ngstrom to be placed on top of any objects in the immediate vacinity.
  • Minor syntax and lexical fixes.

There is a quick tutorial here, and many more on the ChemDoodle Web Components website

Comments

ChemDoodle Update

 

ChemDoodle has been updated to version 6.0.1, this is a free update to fix a couple of bugs.

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


Comments

ChemDoodle Web Components 6 released

iChemLabs have just announced the release of ChemDoodle Web Components 6, this is a major update to their javascript based chemical structure drawing and rendering package.

One of the most important changes from a developers point of view is the external libs (jQuery, jQuey UI, jQuery plugins, glMatrix) are now included into the ChemDoodle scope. This offers several advantages, including eliminating all library conflicts, reducing the number of files required to be installed, and controls the versions used by ChemDoodle. You can now include these libraries yourself at any version and not worry about conflicts. To use the libraries inside of ChemDoodle, call them from the ChemDoodle.lib closure. When I created the interactive graph using FLOT this was one of the issues.

There is also a new EditorCanvas3D canvas which is the 3D component allowing you to interact with and alter chemical data as the 2D Sketcher does in 2D. The 3D editor supports many new WebGL features including picking, highlighting and measurements (distances, angles and torsions).

Lewis Dot Structure style bonds can now be rendered.

As well as editing and drawing structures ChemDoodle web components provides an means to simulate NMR and mass spectra in a web browser

There are also a number of bug fixes and other improvements.

Please Note

This update includes some major refactors, such as the renaming of the sketcher files and packages and inclusion of the external libraries internal to the ChemDoodle scope, so pay careful attention when upgrading.

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