[Open Babel] computation of L5 not working via command line
Hi All, this is how I use openbabel to compute descriptors, L5 is not working, though (openbabel version is 2.3.1). $obabel -:CCC -otxt --append MW -osmi CCC 44.0956 1 molecule converted $obabel -:CCC -otxt --append L5 -osmi CCC nan 1 molecule converted Thanks for your help, with best regards, Martin -- Dipl-Inf. Martin Gütlein Phone: +49 (0)761 203 7633 (office) +49 (0)177 623 9499 (mobile) Email: guetl...@informatik.uni-freiburg.de -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] computation of L5 not working via command line
On 06/06/2012 13:39, Martin Guetlein wrote: > Hi All, > > this is how I use openbabel to compute descriptors, L5 is not working, > though (openbabel version is 2.3.1). > > $obabel -:CCC -otxt --append MW -osmi > CCC 44.0956 > 1 molecule converted > $obabel -:CCC -otxt --append L5 -osmi > CCC nan > 1 molecule converted The descriptor L5 returns a boolean HBD<5 && HBA1<10 && MW<500 && logP<5 and so should be used like: obabel 40mols.smi -osmi --filter L5 Nc1nc2[nH]nnc2c(=O)[nH]11 ... Nc1ccc(cc1)S(=O)(=O)c1ccc(N)cc1 38 CCc1nc(N)nc(N)c1c1ccc(Cl)cc140 34 molecules converted I'll add a usage note to the description of L5. But using it in the way you are attempting is clearly a good idea. I'll look into it. Thanks. Chris -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
