Macs in Chemistry

Insanely Great Science

Cheminformatics on a Mac


A little while back I wrote a detailed tutorial for getting a wide variety of cheminformatics tools running on a Mac.

Someone just let me know about an issue with OSRA a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES

It turns out that OSRA requires ghostscript to process pdf images, this can be installed using brew.

brew install ghostscript

MedChem Wizard KNIME workflow


The MedChemWizard is a KNIME workflow designed to assist medicinal chemists with idea generation, ligand design and lead optimization using a number of common functional group transformations and medchem rules-of-thumb, this tutorial provided by Dr. Alastair Donald gives a detailed description of it's use.



Mobile Molecular DataSheet


The Mobile Molecular DataSheet has been updated, this is an important update and adds a number of exciting new features. There is now the ability to calculate a variety of chemical properties and add these to the data sheet. Importantly these are calculated locally on the mobile device rather than via an internet service.

The properties that are now available include:

  • Molecular formula/weight, # heavy atoms, H-acceptors/donors, # rotatable bonds.
  • Log P & molar refractivity: both calculated by an atom contribution method (S. A. Wildman and G. M. Crippen JCICS 39 868-873 1999), which requires implementation of substructure searching.
  • Bad valences: reviews the valence counts for each of the main group atoms and reports egregious mistakes (e.g. pentavalent carbon).
  • Stereochemistry: sites for R/S and E/Z stereochemistry are identified and their labels calculated, with unspecified or known ambiguous cases classified appropriately.
  • Tautomers: common H-shifts are identified and the complete list of tautomeric forms are enumerated, with duplicate equivalent molecules removed, and racemised stereocentres labelled accordingly.
  • PAINS filters: the original set of queries for identifying frequent hitters and other high throughput screening problem compounds is applied, and any matches are identified.
  • Mass distribution: the isotope distribution is calculated for integral masses, as well as the exact mass for the base peak.

The results are also displayed on the individual molecules with bad valencies highlighted, stereochemistry labeled, and PAINS substructures highlighted.

This update really demonstrates the computing power of the mobile devices (Requires iOS8).




I have three printers and have to order three different sets of printer cartridges, why?


Swift's unprecendented growth


The latest RedMonk Programming Language Rankings are now available, these rankings have been run since 2010 using essentially the same methodology so we can compare with historical data. The plot below compares popularity of Stack Overflow and GitHub.


Whilst the top ten is pretty much as expected

1 JavaScript
2 Java
4 Python
5 C#
5 C++
5 Ruby
9 C
10 Objective-C

Perhaps the most important change is just outside the top 20.

the growth that Swift experienced is essentially unprecedented in the history of these rankings. When we see dramatic growth from a language it typically has jumped somewhere between 5 and 10 spots, and the closer the language gets to the Top 20 or within it, the more difficult growth is to come by. And yet Swift has gone from our 68th ranked language during Q3 to number 22 this quarter, a jump of 46 spots.

Swift is an innovative new programming language for Cocoa and Cocoa Touch and you can find out more about Swift on the Apple Developer site,