|
From: David G. A. <ari...@cb...> - 2012-10-31 13:15:45
|
Thank you very much... maybe the documentation could warn about this here: http://openbabel.org/docs/2.3.1/Fingerprints/fingerprints.html [...] Large datasets First of all, you need to create a fastsearch index (see above). The index is created with the following command: babel mymols.sdf -ofs Substructure searching is as for small datasets, except that the fastsearch index is used instead of the original file. This command will find all molecules containing 1,2-dicyanobenzene and return the results as SMILES strings: babel mymols.fs -ifs -sN#Cc1ccccc1C#N results.smi [...] > This feature is not supported. If you think about it how the > fastsearch works, you will realise why. The FastSearch uses a > fingerprint index to quickly filter results before doing a > substructure match; SMILES strings represent molecules and have > fingerprints, but SMARTS strings are not molecules and so we cannot > generate fingerprints. > > - Noel > > On 31 October 2012 12:17, David García Aristegui <ari...@cb...> > wrote: >> Hello, i'm trying to do searches with the SMARTS patterns from >> SMARTS_InteLigand.txt: >> >> obabel FP4.fs -s '[CX4H3][#6]' -O FP4.smi >> ============================== >> *** Open Babel Error in ObtainTarget >> Cannot read the SMILES string >> 0 molecules converted >> >> obabel FP4.fs -s '[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]' -O FP4.smi >> ============================== >> *** Open Babel Error in ReadMolecule >> [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])] contained a character '!' which >> is >> invalid in SMILES >> ============================== >> *** Open Babel Error in ObtainTarget >> Cannot read the SMILES string >> 0 molecules converted >> >> I have no problems using the FP4.sdf file... or using SMILES strings for >> the searches (i.e. -s 'CCC'). >> >> Please, could you tell me what i'm doing wrong using the .fs files to do >> the SMARTS searches? >> >> Best regards. >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_sfd2d_oct >> _______________________________________________ >> OpenBabel-discuss mailing list >> Ope...@li... >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > |