Hi everyone, I've just released version 1.0 of my fingerprint generation and Tanimoto similarity search package. It includes support for RDKit and two other chemistry toolkits.
You can download it from http://code.google.com/p/chem-fingerprints/ Here's an example from the documentation of how to generate the RDKit path fingerprints from ChEBI, which doesn't store the record id in the title line but only in the "ChEBI ID" tag. rdkit2fps --id-tag "ChEBI ID" ChEBI_lite.sdf.gz -o rdkit_chebi.fps Once you have fingerprints for the queries and the targets then you can do a Tanimoto similarity search (in this case for the k=5 nearest neighbors) like this: simsearch -k 5 -q pubchem_queries.fps pubchem_targets.fps Parts of the underlying Python library are available for others to use. There's even documentation, including examples of use, at: http://readthedocs.org/docs/chemfp/en/latest/ Let me know what you think and if there are any problems. Andrew Dalke [email protected] ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
