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The attached file crashes during read in the trunk code.
My debugger reports duplicatedSymClass not initialized at line 781 in perception.cpp.
2009-11-14 17:23:22 UTC in Open Babel
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With the trunk code (under Windows), the molecules below cause the external InChI code to give a warning like:
Wrong 0D stereo descriptor(s): #3
S(N1[CH](c2ccccc2C=C1)C#N)(c1ccc(cc1)C)(=O)=O
c12c(O[CH](C1=O)C(C)C)cc1c(c2)ccc(=O)o1
c12[C]3([C@H]4([N@@](CCc1c1ccccc1[nH]2)C[C@H](C=C4CC)C3))C(=O)OC.
2009-11-13 16:02:47 UTC in Open Babel
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chrismorl committed revision 3451 to the Open Babel SVN repository, changing 2 files.
2009-10-25 11:39:00 UTC in Open Babel
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chrismorl committed revision 3450 to the Open Babel SVN repository, changing 6 files.
2009-10-24 22:09:39 UTC in Open Babel
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I've re-opened this because I have done some work to see how feasible it would be to make fastsearch find structures irrespective of whether certain atoms are aromatic or not.
The -s option can now accept atoms like [#7], meaning aromatic or non-aromatic N. This is used as a SMARTS string in the second stage; for the fastsearch matching these atoms are converted to the non-aromatic form ...
2009-10-19 18:23:39 UTC in Open Babel
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Fixed as suggested in r3447 in dev code.
Actually, the whole function needs some work.
2009-10-19 09:50:51 UTC in Open Babel
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chrismorl committed revision 3447 to the Open Babel SVN repository, changing 2 files.
2009-10-19 09:45:18 UTC in Open Babel
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see 2828279 (assuming the problem is the same).
2009-10-13 15:29:37 UTC in Open Babel
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This was corrected in the trunk code but unfortunately did not get incorporated in v2.2.3
CML1 is of course obsolete, so I hope that you are not writing in this format out of choice.
Chris.
2009-10-13 15:26:46 UTC in Open Babel
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Sorry to be slow commenting on this.
The same results are obtained using an ordinary SMARTS query so the problem is not really to do with fast search. As fredrikw has said, the problem is that SMART regards aliphatic and aromatic atoms as different.
In example-3.sdf, the search is for a ring with 4 aromatic carbons and two aromatic nitrogens with an attached carboxylic acid or ester. It...
2009-10-13 15:15:11 UTC in Open Babel
