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.Testing the bitslice algorithm for popcount- July 5, 2008 This is part 7 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 want to compute the popcount of molecular fingerprints containing 1024 bits. My algorithm has been to compute the popcount 8,..http://www.dalkescientific.com/writings/diary/archive/2008/07/05/bitslice_and_popcount.htm... HAKMEM 169 and other popcount implementations- July 3, 2008 This is part 6 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 HAKMEM Many other people have worked on doing high speed population counts. In 1972 the AI Laboratory at MIT published...http://www.dalkescientific.com/writings/diary/archive/2008/07/03/hakmem_and_other_popcount... Faster block Tanimoto calculations- July 1, 2008 This is part 5 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 After much analysis and digging in part 4 I managed to get my C extension to Python to compute fingerprints pretty quickly. I...http://www.dalkescientific.com/writings/diary/archive/2008/07/01/faster_tanimtocat_search_... |