Andrew Dalke's writingsWritings from the software side of bioinformatics and chemical informatics, with a heaping of Python thrown in for good measure. Code to taste. Best served at room temperature.Block Tanimoto calculations- June 28, 2008 This is part 4 of an on-going series dealing with molecular fingerprints: Molecular fingerprints, background Generating molecular fingerprints with OpenBabel Computing Tanimoto scores, quickly Block Tanimoto calculations Faster block Tanimoto calculations HAKMEM 169 and other popcount implementations Testing the bitslice algorithm for popcount Comments One query, many targets In part 3 I wrote a C function to compute the Tanimoto similarity score between two fingerprints. The..http://www.dalkescientific.com/writings/diary/archive/2008/06/28/block_tanimoto_calculatio... Generating molecular fingerprints with OpenBabel- June 27, 2008 This is part 2 of an on-going series dealing with molecular fingerprints: Molecular fingerprints, background Generating molecular fingerprints with OpenBabel Computing Tanimoto scores, quickly Block Tanimoto calculations Faster block Tanimoto calculations HAKMEM 169 and other popcount implementations Testing the bitslice algorithm for popcount Comments I am not yet going to discuss implementation details of how to generate molecular fingerprints. I'll assume you have access to...http://www.dalkescientific.com/writings/diary/archive/2008/06/27/generating_fingerprints_w... Computing Tanimoto scores, quickly- June 27, 2008 This is part 3 of an on-going series dealing with molecular fingerprints: Molecular fingerprints, background Generating molecular fingerprints with OpenBabel Computing Tanimoto scores, quickly Block Tanimoto calculations Faster block Tanimoto calculations HAKMEM 169 and other popcount implementations Testing the bitslice algorithm for popcount Comments For now my driving example will be to print the Tanimoto values for each compound in a data set, in order. I get to control...http://www.dalkescientific.com/writings/diary/archive/2008/06/27/computing_tanimoto_scores... Molecular fingerprints, background- June 26, 2008 This is part 1 of an on-going series dealing with molecular fingerprints: Molecular fingerprints, background Generating molecular fingerprints with OpenBabel Computing Tanimoto scores, quickly Block Tanimoto calculations Faster block Tanimoto calculations HAKMEM 169 and other popcount implementations Testing the bitslice algorithm for popcount Comments A molecular "fingerprint" is a widely used concept in chemical informatics. Comparing molecules is hard. Comparing bitstrings.http://www.dalkescientific.com/writings/diary/archive/2008/06/26/fingerprint_background.ht... |