What are the open source tools for calculate Tanimoto coefficient of compounds in smiles format ?

Asked by [ Editor ] over 1 year ago

i want to compound similarity search i.e i have 1000 compounds each compound would be search with the remaining 999 compounds and generate a matrix from that . Any tool available for such thing ?

3 answers

Mikhail Rybalkin [ Editor ] Sep 1, 2011 (Edited Sep 1, 2011)

There is Chemistry Toolkit Rosetta Wiki with different toolkits comparison. Here is a page with similarity calculation example: http://ctr.wikia.com/wiki/Report_the_similarity_between_two_structures

You can find code snippets there for Indigo, OpenBabel, RDKit and Cactvs.

NN comments

Andrew Dalke [ Editor ] Sep 2, 2011 (Edited Sep 20, 2011)

My chemfp project has Python tools for generating fingerprints from OpenBabel, OEChem, and RDKit into a common format. The documentation includes an example of generating a distance matrix.

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Vladimir Chupakhin [ Editor ] Sep 1, 2011 (Edited Jan 31, 2013)

Knime, R (with rcdk), openbabel, etc.

NN comments

Unfortunatelly, chemdiff doesn’t calculate similarity between structures yet. It just compares them and report unique and common molecules.

Sep 1, 2011

rybalkin oops! removed…

Sep 1, 2011

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What are the open source tools for calculate Tanimoto coefficient of compounds in smiles format ?

3 answers

Mikhail Rybalkin [ Editor ] Sep 1, 2011 (Edited Sep 1, 2011)

Andrew Dalke [ Editor ] Sep 2, 2011 (Edited Sep 20, 2011)

Vladimir Chupakhin [ Editor ] Sep 1, 2011 (Edited Jan 31, 2013)

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What are the open source tools for calculate Tanimoto coefficient of compounds in smiles format ?

3 answers

Mikhail Rybalkin [ Editor ] Sep 1, 2011 (Edited Sep 1, 2011)

Andrew Dalke [ Editor ] Sep 2, 2011 (Edited Sep 20, 2011)

Vladimir Chupakhin [ Editor ] Sep 1, 2011 (Edited Jan 31, 2013)

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