Dear all, I would like to find similar molecules within library and compute Tanimoto coefficient.
I'm right by assuming that, using -at0.0, I should retrieve all molecules? obabel library.fs -Smol.smi -ofpt -at0.0 (version 2.3.2) But I get only 1098 compounds out of a total of 1579, along with 262 warning messages like: Open Babel Warning in ParseSmiles Invalid SMILES string: 1 unmatched ring bonds. or: Open Babel Warning in ParseRingBond Number not parsed correctly as a ring bond If I use the library.smi file instead of .fs, I get only 19 molecules (-at0.0), and no error message. If I convert the library smiles file into sdf, and depending on the compound in -Smol.smi, sometimes all molecules are converted, as I expect with -at0.0, sometimes only a few are converted, sometimes only one with e.g. this output: ZINC00089110 183 bits set 00410030 01248d00 a0084102 40100e04 40050001 00200809 10000480 102c1402 03484900 821a4081 40350020 40011a80 540a8518 202d0000 00000420 00000104 24484000 02000b00 400920c0 02000101 000a0500 38040694 40808c00 0448829e 00200010 20203620 44404010 88040150 008000e2 c11e0003 ac824010 c3010680 1 molecule converted I'm trying to get a sample smi file to send as example, but until now I'm not able to reproduce every case I have written above. Did you already encounter such behavior, or is there a known bug I'm not aware of? Regards, Pascal ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
