I've been making increasing use of iPython notebooks, both as a way to perform calculations but also as a way of cataloging the work that I've been doing. One thing I seem to be doing quite regularly is calculating physicochemical properties for libraries of compounds and then creating a trellis of plots to show each of the calculated properties. In the past I've done this with a series of applescripts using several applications. This seemed an ideal task to try out using an iPython notebook.
I’ve written several Vortex scripts that use external tools to calculate physicochemical properties including the use of ChemAxon (e.g. charge, pKa, logP, logD). However I often need to simply classify molecules as acid, base, neutral or zwitterion, so I’ve updated the script to create another column containing a text annotation.
ChemAxon have just announced the release of version 6.3.
This release includes several new features including the ability to draw and analyze complex patent Markush structures, display Markush hierarchy, work with R-Groups and enumerate Markush structures.
A new Solubility Predictor, the aqueous solubility predictor is based on the topology of the input molecules, but also calculates the pH dependence and the solubility at a desired pH level.
IUPAC name conversion supports now Japanese names as well as the existing English and Chinese names even if mixed in the same document so you can extract all the chemistry from documents in these languages.
There are also updates for Marvin JS 6.3, Standardizer & Structure Checker 6.3, Instant JChem 6.3, and Compound Registration 6.3.
Marvin 6.2 from chemAxon has been released.
This is a major update and the release notes can be found here, of particular note are
- TIFF AND EPS FORMAT SUPPORT: Chemical structures can be exported to TIFF or EPS image formats in MarvinSketch and MarvinView
- R-GROUP DISPLAY AND EDITING: In MarvinSketch editing and displaying R-groups were modified and improved in several cases.
- Chinese Name to Structure: Frequent OCR errors in Chinese characters are now corrected automatically
Marvin has been updated
Bugfixes, Java Webstart did not run on Macintosh computers.
It can be downloaded from here
Note, many of you have bumped into the problem when the Gatekeeper Security of OS X blocks launching applications downloaded not from the Apple store. The solution is to modify the default settings of the Gatekeeper:
- 'Apple > System Preferences > Security & Privacy '
- In the 'General' section the setting of ' Allow applications downloaded from :' should be set to ' Anywhere'
After this you would not get the "damaged dmg" popup and you can install the downloaded dmg. After install it is probably a good idea to reset the Security settings.
If you are using Java applets it is probably worth reading this article
Apple just have introduced some new security settings in Safari for Java. In an average browser to make a Java Applet to be able to touch your file system that Applet must be signed. In the new security update of Safari this Applet must be trusted as well. This means that you have to allow for the Applet to read and write you file system. Marvin starts with accessing some files on your computer, which means that it might not start without this permission or might not behave correctly
ChemAxon have released a new update to Marvin.
Bugfixes MarvinSketch GUI MSketchPane setPiece(Molecule) method did not work, it set the molecule on the canvas instead of putting it on the cursor. Import/Export CXSMILES/CXSMARTS CXSMARTS containing valence property information was recognized and read as SMARTS. SKC Some reaction was read as R-definition from SKC format.
New features and improvements
- MarvinSketch Dialog
- 'Zoom to scaffold' checkbox option has been added to the "Preferences>Save/Load" tab. Documentation
- Structure Checker
- External structure checker configuration file URL can be set via Java System Property.
- Electron-flow arrow could not be drawn from the A-B bond to the incipient A-C bond of an A-B-C structure. Forum
- MolInputStream and MolImporter could have different format options.
- MolImporter did not close its inputstream when an exception was thrown in the constructor.
- MOL, SDF, RXN, RDF
- Molecule type property was allowed in SDF, CSSDF export.
- The coordinates of the sequence residue imported from SCSR MOL files were wrong if the residue had three attachment point.
- Color and text format of atom label is exported to CDX and imported from CDX and CDXML. Forum
- Graphical brackets were not imported from CDX files.
- Gaussian Z-matrix input format
- Command line, title line, and extra input properties were not exported to Gaussian Z-matrix input format. Forum
- Clean 2D
- Cleaning of position variation bonds could create overlapping bonds.
- Cleaning of bridged systems could result in overlapping atoms. Forum
- Topology Analysis
- Missing method has been added: TopologyAnalyserPlugin.getFsp3(). API Documentation
- New logD training documentation has been added. Documentation
- Structure Checker
- Fixer options in MarvinSketch are updated with newly defined settings.
- External checkers can be loaded from JAR file in case the JAR file contains a space.
Marvin 6.1 has been released:
New drawing and displaying features in MarvinSketch and MarvinView
Among others drawing peptid cycles and bridges is available now, and IUPAC numbers can be displayed in MarvinSketch and MarvinView
Better images to structures conversion in Document to Structure
Optical Structure Recognition tools CLiDE and Imago can be used, in addition to OSRA
New Chinese Document to Structure feature
Chemical names in the flow of Chinese sentences are detected, without the spaces that separate words in English
Homology groups has been added Structure Checker got an integral part of Marvin Beans
Installing Marvin Beans will install the fully functional Structure Checker application
- Structure Checker: Checker names and error messages can be localized or customized
- Elemental Analysis: Charge is taken into account in atomic mass calculation
- Structure Checker: “Copy as action string” option is available