"the best choice of high-level programming language for computational chemistry is Python" [A. Dalke]
Many cheminformatic/modeling toolkits provide Python interfaces, as shown in the summary below. This is a good reason to consult Andrew for a training sessions, or checking Andrew's or Noel's blogs from time to time. The various open source projects, from which a few are stalled, support Python, as well as the academic/commercial OEChem toolkit. Two very important modeling programs supporting Python are Schrödinger's modeling suite and PyMol. For a training on the last two programs, you best contact the software support teams directly.
Please let me know, if other molecular modeling/ cheminformatics/ statistical modeling programs should be mentioned here !
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4 comments:
+1 for Python! Do you do any programming yourself in your current position?
Other notable programs using Python include:
- pDynamo (QM/MM simulation software) http://pdynamo.org
- AutoDock (Protein-ligand docking software) http://autodock.scripps.edu/
- MODELLER (Protein structure modeling) http://salilab.org/modeller/modeller.html
...and many others. :)
Mainly script-hacking, no time-consuming in-depth programming, I leave this to academic and commercial experts, which can focus on that. Anyway, in short, yes, and thanks to all the genius and fast commercial software support teams out there !;-)
The last things I did in Python were tweaking Modeller, and wrapping CHARMM.
Beside that, I use whatever is needed, means several (program specific) scripting dialects or in very rare cases, some object-oriented stuff, if I run into performance issues.
For our recent phenotype prediction patent (WO=2008065180) I used many different tools and languages.
Adam, thanks for the links !
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