On 12/11/2010 17:57, JP wrote: > > Hi there @OpenBabel, > > A Friday evening tedious problem. > > Can anyone tell me why the following mol file > > LACMAD > ChemPy 3D 0 > > 31 32 0 0 1 0 0 0 0 0999 V2000 > 0.5638 11.8582 6.3019 N 0 0 0 0 0 0 0 0 0 0 0 0 > 1.4523 10.9079 6.2742 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.6393 8.6490 6.0005 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.6157 9.5336 6.1990 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.8701 11.5600 6.0553 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.5976 11.2436 7.3580 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.9538 13.2682 6.4783 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.0954 13.6836 7.9125 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.0709 9.2990 6.3918 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.7068 8.1628 5.7098 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.3942 6.5562 4.9445 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.2378 6.4077 4.2764 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.2488 7.3334 4.6938 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.7027 10.0757 7.0933 O 0 0 0 0 0 0 0 0 0 0 0 0 > 3.1336 11.1912 6.5004 S 0 0 0 0 0 0 0 0 0 0 0 0 > 1.0084 9.2415 5.9760 S 0 0 0 0 0 0 0 0 0 0 0 0 > 7.3632 7.8323 6.0953 S 0 0 0 0 0 0 0 0 0 0 0 0 > 2.7779 7.4849 6.3379 H 0 0 0 0 0 0 0 0 0 0 0 0 > -1.2737 12.2580 5.5375 H 0 0 0 0 0 0 0 0 0 0 0 0 > -0.9305 10.8631 5.0883 H 0 0 0 0 0 0 0 0 0 0 0 0 > 1.8847 13.3015 6.0357 H 0 0 0 0 0 0 0 0 0 0 0 0 > 0.3371 13.9095 6.2317 H 0 0 0 0 0 0 0 0 0 0 0 0 > 8.0340 6.0205 4.7697 H 0 0 0 0 0 0 0 0 0 0 0 0 > 5.9807 5.9511 3.1934 H 0 0 0 0 0 0 0 0 0 0 0 0 > 4.3071 7.5363 4.0020 H 0 0 0 0 0 0 0 0 0 0 0 0 > -1.0459 10.4681 7.9060 H 0 0 0 0 0 0 0 0 0 0 0 0 > -2.5958 10.8817 7.1791 H 0 0 0 0 0 0 0 0 0 0 0 0 > -1.6488 12.1229 7.9958 H 0 0 0 0 0 0 0 0 0 0 0 0 > 0.4883 13.3910 8.3634 H 0 0 0 0 0 0 0 0 0 0 0 0 > 1.3053 14.6861 7.8243 H 0 0 0 0 0 0 0 0 0 0 0 0 > 1.8010 12.8139 8.2817 H 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 0 0 0 0 0 > 2 16 1 0 0 0 0 > 3 4 2 0 0 0 0 > 4 15 1 0 0 0 0 > 5 1 1 0 0 0 0 > 6 5 1 0 0 0 0 > 7 1 1 0 0 0 0 > 8 7 1 0 0 0 0 > 9 4 1 0 0 0 0 > 10 9 1 0 0 0 0 > 11 17 1 0 0 0 0 > 12 11 2 0 0 0 0 > 12 13 1 0 0 0 0 > 13 10 2 0 0 0 0 > 14 9 2 0 0 0 0 > 15 2 0 0 0 0 0 > 16 3 1 0 0 0 0 > 17 10 1 0 0 0 0 > 18 3 1 0 0 0 0 > 19 5 1 0 0 0 0 > 20 5 1 0 0 0 0 > 21 7 1 0 0 0 0 > 22 7 1 0 0 0 0 > 23 11 1 0 0 0 0 > 24 12 1 0 0 0 0 > 25 13 1 0 0 0 0 > 26 6 1 0 0 0 0 > 27 6 1 0 0 0 0 > 28 6 1 0 0 0 0 > 29 8 1 0 0 0 0 > 30 8 1 0 0 0 0 > 31 8 1 0 0 0 0 > M END > > Fails when trying to babel ligand.mol ligand.smi: > > x...@yyy$ babel ligand_LACMAD.mol ligand_LACMAD.smi > ============================== > *** Open Babel Warning in ReadMolecule > WARNING: Problems reading a MDL file > Invalid bond specification, atom numbers or bond order are wrong. > > 0 molecules converted > 1 warnings 2 audit log messages > > I can see no problems with it... (atom numbers and bonds look OK too)
The first bond, and some of the others, have zero order. OpenBabel considers this an error, but do say if you would consider this to be valid. Chris ------------------------------------------------------------------------------ Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
