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 ?
Mikhail Rybalkin [ Editor ]
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.