Regarding the use of $$$$ in the title, Chris, you might want to read http://blueobelisk.shapado.com/questions/what-is-the-minimum-needed-to-correctly-identify-records-in-an-sd-file. It seems that this is not allowed by the spec...
- Noel 2011/1/25 Chris Morley <c.mor...@gaseq.co.uk>: > Your file othermol.sdf was a proper sdf file but the molecules all had a > title "$$$$". The use of the delimiter string as a title is not good > practice and confused OpenBabel. I'll see if I can correct this, but if you > change the titles to Mol1, Mol2, etc. and name PatternMol, the command below > gives: > >>PatternMol >>Mol1 Tanimoto from PatternMol = 0.5 >>Mol2 Tanimoto from PatternMol = 0.575 >>Mol3 Tanimoto from PatternMol = 0.95 >>Mol4 Tanimoto from PatternMol = 0.825 >>Mol5 Tanimoto from PatternMol = 0.673913 > > which is I think what you want. The revised othermols.sdf is attached. > > Chris > > > On 25/01/2011 02:47, chakravar...@ncbs.res.in wrote: >> >> Dear Chris Morley, >> >> I tried your technique of holding ctrl to input more than one file. It >> helps, but, >> I did not get desired output. >> >> Here is my input and output. >> >> ======================================================== >> Input: >> [ OpenBabel12221015072D >> >> 23 22 0 0 0 0 0 0 0 0999 V2000 >> 7.7424 -9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> ................................................................. >> ................................................................. >> 2.6281 -18.1511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 1 2 1 0 0 0 0 >> ................... >> ................... >> 22 23 1 0 0 0 0 >> M END >> $$$$ >> $$$$ ] n times >> >> OpenBabel12221015072D >> >> 25 24 0 0 0 0 0 0 0 0999 V2000 >> 7.7424 -9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> ................................................................. >> ................................................................. >> 6.7196 -7.5210 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 >> 1 2 1 0 0 0 0 >> ................... >> ................... >> 24 25 1 0 0 0 0 >> M END >> $$$$ >> ===================================================== >> Output: >>> >>> Tanimoto from first mol = 0.869565 >> >> Possible superstructure of first mol >> >> ===================================================== >> The command I am using is (in linux) -> babel patternmol.sdf >> othermols.sdf -ofpt >> Both in Windows GUI and linux I receive same error message. It reads... >> >> ================================================= >> *** Open Babel Warning in ReadMolecule >> WARNING: Problems reading a MDL file >> Cannot read atom and bond count >> Expected standard 6 character atom and bond count >> ================================================== >> >> Both in linux and windows, output contains tanimoto coefficient only for >> first >> molecule in othermols.sdf. >> >> Is the problem arising because of othermols.sdf format ? Molecule >> separators "M >> END" "$$$$" ? ( Enclosed patternmol.sdf and othermols.sdf files ) >> >> It must be a trivial problem, but I could not figure it out all by myself. >> >> Any help is greatly appreciated >> >> Thankyou >> Chakravarthy >> >> From: Chris Morley<c.morley@ga...> - 2011-01-24 10:34 >> >> When there are only a small number of molecules, fpt format will give >> you what you want; you are nearly there. >> >> In the GUI, select sdf for the input format and ftp for the output. >> Open the sdf file with the pattern molecule, then open the sdf file with >> all the other molecules you want to compare to it, holding CTRL as you >> leave the open dialog (which allows more than one input file). >> Click Convert, and you will get a list of the Tanimoto coefficients >> between the first molecule and each of the rest, using the default FP2 >> fingerprint. >> >> On the command line (Windows or Linux): >> obabel patternmol.sdf othermols.sdf -ofpt >> >> Chris >> > > > ------------------------------------------------------------------------------ > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! > Finally, a world-class log management solution at an even better price-free! > Download using promo code Free_Logger_4_Dev2Dev. Offer expires > February 28th, so secure your free ArcSight Logger TODAY! > http://p.sf.net/sfu/arcsight-sfd2d > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
