Egon is right! It is great that more and more open source tools are entering the drug design arena. On the other hand, we really need some benchmarking and feature comparisons for allowing to learn which tools should be used for which tasks.
Noel dashed off an email to Greg Landrum, the main developer (who it turns out is also the developer of YAeHMOP (Yet Another extended Huckel Molecular Orbital Package) ), and he asked him what the story was. Two days ago, he returned from holidays and pointed Noel to the correct website and the documentation, and Noel couldn't believe what he was seeing...
Some features that are cool:
(1) Molecules based on the Boost Graph Library
(2) All the Python stuff works for me on Windows!
(3) 2D depiction!!!
(4) 2D depiction that mimics 3D conformations!!!
(5) 2D --> 3D conversion in a similar method to Rajarshi's smi23D! (doesn't use stochastic promixity embedding though)
Here's a summary of some of the rest: SMILES, substructure searching, sophisticated fingerprints, machine learning stuff, a GUI, clustering, MACCS keys, descriptors (84 or so), chemical reaction transformations, implementation of Recap (not sure what this is, but there's a ref in the docs), basic pharmacophore stuff, and two types of SSSR (there's some text about this in the docs).
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