Macs in Chemistry

Insanely Great Science

Java Applet Technology: The Past and Future and The End


An interesting article from ChemAxon on the history and demise of Java Applets.


iPython Notebook to calc physicochemical properties


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.




Vortex script to classify acid, base, neutral


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 6.3 released


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 updated


Marvin has been updated to version 6.2.1


Marvin 6.2 released


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.
  • COPY – PASTE BETWEEN MARVINSKETCH AND MARVIN FOR JAVASCRIPT: Structures can be copied from and to the canvas of our Java based MarvinSketch and Marvin for JavaScript .
  • R-groups added to Marvin for JavaScript: R-group definitions can be created and edited; and attachment points can be added to a structure
  • Chinese Name to Structure: Frequent OCR errors in Chinese characters are now corrected automatically

Marvin 6.1.5 has been released

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


Marvin 6.1.3 released


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.


Marvin 6.1.2 released


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.


  • Editing
  • 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
  • Import/Export
  • MolInputStream and MolImporter could have different format options.
  • MolImporter did not close its inputstream when an exception was thrown in the constructor.
  • 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
  • Calculations
  • Topology Analysis
  • Missing method has been added: TopologyAnalyserPlugin.getFsp3(). API Documentation
  • logD
  • 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

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
Marvin for JavaScript news
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


Marvin Update

New features and improvements
Image I/O
The following file extensions were removed from the "Files of Type" list on the Import Image dialog: *.ps, *.pdf, and "All Files".
PDF files can be imported through the "File > Open" menu.
Calculation Services
SOAP version 1.2 webservices are supported.

There are a number of bug fixes.

On the Mac clipboard handling has been improved, On Mac OS X, copy-paste (from MarvinSketch to, e.g., TextEdit) did not transfer the atom colors.


Indexing the internet in a chemically intelligent manner

Some time ago I described a Safari extension that uses the to index a web page for chemical content.

For an example of a “chemicalized” page have a look at this

As you can see below all molecules mentioned in the page become links that on a mouse over reveal the structure, they also provide a handy ribbon of structures across the top of the page that is useful for quickly scanning and navigation.


A recent publication by Southan and Stracz, Extracting and connecting chemical structures from text sources using Journal of Cheminformatics 2013, 5:20 describes how this information is being used to provide better indexing of the internet in a chemically intelligent manner. They include a demonstration of a number of web pages and document sources that were indexed in this manner including PDF’s from the patent office. now has 15000 unique visitors a month – which is a huge growth compared to spring 2012. These users contribute to the database every day, making sure it’s up-to-date and contains new interests as well. The database today contains 327000 structures that were converted from 545000 names and identifiers coming from 367000 webpages.

These structures and links have now been uploaded to PubChem and if you are interested in what sort of molecules have been registered via you can browse them on the PubChem website here


Marvin Updated

Marvin 5.12.2 has been released with a couple of bug fixes

Molecule Representation

  • Conversion from explicit hydrogen to implicit one removed stereo centers not having explicit hydrogen ligand.


  • Non ring bond information were imported as query strings from SMARTS.
  • After SMARTS import, those atoms that had no explicit aromatic property but had aromatic bond got query aromaticity property.


Marvin 5.12.1 released

New features and improvements


S orbitals and oval shaped s or p orbitals are imported from CDX/CDXML.


Painting, Charge symbol on carbon atoms was missing when the atom numbers were visible and the display of carbon atom labels was turned off. When two atoms had more than one electron flow arrows between them, the electron flow arrows overlapped each other. The second electron flow arrow started from a wrong position when a single electron and an electron pair flow arrow started from an atom which had a lone pair and a radical as well.

Editing, Atom Lists and NOT Lists could not be created by typing atomic symbols separated with commas (e.g., "f,br,cl" or "!f,br,cl").

Import/Export, MRV and CML export wrote out characters incorrectly which are not supported by the character set. SDF files having invalid header could not been imported. Deuterium and tritium isotopes were converted to simple hydrogen atom if a molecule was exported to ChemAxon compressed MOL format (CSMOL). MolExporter.exportToObject() added an extra newline to SMILES. Nitrogens connecting two aromatic rings had radical after import if nitrogen was bracketed in the SMILES representation. Absolute stereo flag was missing during InChi export/import and InChiKey export.

Molecule Representation, Number of added implicit Hydrogen atoms were incorrect in some cases for positively charged sulfur atom.

Calculation, After canonical tautomer generation, the information of "double cis or trans" bond type might have been lost in certain cases.


Accessing the Chemical Identifier Resolver from Marvin

With the release of Marvin 5.12.0 users can now also access a custom web-service to extend name to structure conversion - for instance, with corporate IDs or common name dictionaries. I thought it might be useful to have a look at this new feature however I don’t have a corporate web service that I can use. This is where use of the Chemical Identifier Resolver (CIR) comes into play


Marvin 5.12.0 has been released

Marvin 5.12.0 has been released. This has an important updates for Mac OS X users, in that image to structure conversion using OSRA and text OCR for scanned documents is now supported on Mac OS X.


In addition Structure Checker configuration can be accessed via URL from MarvinSketch, Structure Checker application, and via Structure Checker API call. Users can now also access a custom web-service to extend name to structure conversion - for instance, with corporate IDs or common name dictionaries. Typing abbreviated group names is now case sensitive, When pasting unrecognised format onto the canvas, "Import as" dialog appears, and the user can choose the correct format. Structures can be copied as "Daylight SMARTS" and "ChemAxon SMARTS (CXSMARTS)" formats. The MMFF94 forcefield has been added to Generate3D and can also be used in the Conformer Plugin and Molecular Dynamics Plugin.

The complete release notes are available here


Marvin Update

ChemAxon have just announced an update to Marvin the latest version is 5.11.5

Structures copied from ChemDraw or Accelrys Draw could not be pasted onto MarvinSketch has been fixed.


Marvin Updated

Marvin from ChemAxon has been updated to version 5.11

New features and improvements

  • Image I/O
    • Recently added rendering options are now available to be set from MolPrinter API (Absolute label visibility, Peptide display type, R-group visibility, Any bond style, Lone pair rendering style, Charge rendering style). Documentation
  • MSketch GUI
  • MSketch applet
  • Graphical object handling
    • When an MMidPoint object was set as an end point for an MPolyLine, getting the MMidPoint location caused a StackOverFlowError.
  • Import/Export
    • Document to Structure (d2s)
      • Names broken over two lines with a hyphen (-) are now recognized.
      • Names followed by a superscript text, for instance, a reference or footnote number (e.g., "aspirin11") are now recognized.
    • Name to Structure (n2s)
      • In some cases, such as "4-methylthiophenylmethyl", there is an ambiguity whether "thiophenyl" refers to a compound derived from thiophene or thiophenol. Name to Structure now gives priority to the thiophenol related compound interpretation; though, "thiophenyl" by itself will still be supported as thiophene derivatives.
  • Painting
    • If R-group visibility was turned off and any of the bonds had label(s) to paint, an ArrayIndexOutOfBounds exception was thrown.
  • Image I/O
    • Display parameters of charge, lone pair, peptide could not be set for molexporter. The default values were charge "in a circle", lone pair "as line", peptide "three letter format". Image copy also used these values.
  • Import/Export
    • MOL, SDF, RXN, RDF
      • Aliphatic query properties of atoms with query string were not read from MDL formats.
      • After importing Extended MOL files that contain superatom S-groups the orientation of S-groups could be changed.
      • Atom containing both aliphatic and unsaturated query properties were exported incorrectly to MDL formats.
      • SDF import returned structure with incorrect S-group embedding.
      • SMILES T* option did not export all SDF fields, but only those which appeared in the first molecule.
  • Molecule Representation
    • S-groups
      • Two superatom S-groups being each others' parents caused infinite loop. In these cases, now java.lang.IllegalStateException is thrown.
    • Valence Check
  • Stereochemistry
    • Cloning of BicyclostereoDescriptor in RxnMolecules threw java.lang.ArrayIndexOutOfBoundException.
  • Clean 2D
    • Terminal methyl-group in phosphate-ester was cleaned incorrectly.
    • Clean2D could not handle condensed adamantane derivatives. Forum topic
  • Calculations
    • Other (HBDA, Huckel Analysis, ...)
      • The --pH command line option did not work in hydrogen bond acceptor-donor calculation.
  • Structure Checker
    • If fixer action was not defined, default fixer was not applied in structurechecker command line tool.


Scripting Vortex 3

ChemAxon's Calculator (cxcalc) is a really useful command line program in Marvin Beans and JChem that performs chemical calculations using calculator plugins. There are a lot of calculations provided by ChemAxon (e.g. charge, pKa, logP, logD), and others can be added by writing custom plugins, perhaps one of the most useful is the ability to calculate the acidic and basic pKa. Calculation of pKa is essential to get a reasonable hold on the LogD of a molecule. LogD is probably the most critical physicochemical property in drug discovery, it has a major influence on absorption, cell penetration, metabolism, CYP450 inhibition and induction, PGP transporter activity and activity at the HERG channel, and is often a critical component of any structure activity relationship.

These scripts make use of cxcalc to generate data columns in Vortex


ChemAxon US UGM

ChemAxon have announced the program and are calling for participants for ChemAxon's 4th US User Group Meeting (US-UGM) which will take place in San Diego, CA on September 27-28. Read More...

Plotting in Instant JChem

Plotting in Instant JChem

ChemAxon UGM

ChemAxon's US UGM, Sept 27-28, San Diego, CA 

Marvin Updated

Marvin Updated

Rule of 7 Applescript

An applescript to generate and plot physiochemical properties It uses cxcalc from ChemAxon to generate the data and Aabel from Gigawiz to plot the results. Read More...

Marvin Update

ChemAxon continue to update their applications and I just thought I'd mention this new Marvin feature. If you select a structure you get a menu option to search either PubChem or ChemSpider. Read More...

ChemAxon User Group Meeting

ChemAxon User Group Meeting: May 19-20th Training day: May 18th Read More...

ChemAxon Updates

Updates to Marvin and JChem.

Applescript Chemistry Workflow

A chemistry workflow created using Applescript, Chemaxon tools and Aabel. Read More...

LibraryMCS Review

Added LibraryMCS review.

ChemAxon User Group Meeting

ChemAxon EU and US user group meetings.

Marvin and JChem updates

ChemAxon have announced a couple of updates.

ChemAxon UGM

ChemAxon's 2009 European User Group Meeting

News Updates

A collection of software updates

Updates roundup

Rapidweaver update

News Snippets

Just back from vacation, here are few snippets of news. Read More...

ChemAxon User Group Meeting in Boston

I see ChemAxon have announced details of their first US User group meeting Read More...


A few updates and news snippets

ChemAxon's 2008 European User Group Meeting

The program is now available for ChemAxon's 2008 European User Group Meeting being held on Wednesday and Thursday, May 7-8th at the Thermal Hotel Spa in Visegrad, Hungary. Read More...

Marvin and JChem

Marvin and JChem have been updated

Marvin Update

Marvin 5.0.1 has been released.

ChemAxon's 2008 European User Group Meeting

ChemAxon's 2008 European User Group Meeting will be held on Wednesday and Thursday, May 7-8 at the Thermal Hotel, in Visegrad, Hungary Read More...

Instant JChem Review

A review of Instant JChem an easy to use chemical structure database. Read More...

Mavin Review

I've written a review of Marvin from Chemaxon.