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This issue derives from the fact the UIT considers cyclopropane and isobutane isomorphic (this is noted in theUIT Javadocs). As a result, C1C(C)CC1, contains an isobutane substructure, which thus matches the query - explaining why you see the match.
2009-11-10 20:02:21 UTC by rajarshi
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SMARTSQueryTool says that C1CC1 matches C1C(C)CC1 and C1C(C)CN1. I see this with 1.2.2, 1.2.3 and 1.3.0.
SMARTSQueryTool correctly says that C1CC1 does NOT match C1CCC1.
I have only seen the problem with cyclopropane. For example, SMARTSQueryTool correctly says that cyclobutane is not a match to cyclopentane, and it also correctly says that cyclobutane does not match C1C(C)CCC1.
It...
2009-11-10 19:10:21 UTC by volkmuth
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For single atom molecules, the main isomoprhism mehtods of the UIT should not be invoked. Rather simply loop over the target molecule atoms seeing if we can match any atom to the query atom. (This is what the SMARTS query tool does)
2009-11-10 03:28:59 UTC by rajarshi
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egonw committed revision 15058 to the The Chemistry Development Kit SVN repository, changing 1 files.
2009-11-08 21:30:50 UTC by egonw
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Since benzene ring template on the panel has only one variant of double bonds' placement, it's difficult to draw some aromatic compounds with condensed cycles. For example, try draw phenanthrene with angle ring on the right side. In such situation, double bonds must be rearranged. Simplest solution is to add another benzene template, but it will look strange.
2009-11-08 15:19:37 UTC by annulen
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egonw committed revision 15057 to the The Chemistry Development Kit SVN repository, changing 1 files.
2009-11-08 14:19:16 UTC by egonw
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egonw committed revision 15056 to the The Chemistry Development Kit SVN repository, changing 1 files.
2009-11-07 23:19:50 UTC by egonw
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egonw committed revision 15055 to the The Chemistry Development Kit SVN repository, changing 1 files.
2009-11-07 23:18:32 UTC by egonw
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egonw committed revision 15054 to the The Chemistry Development Kit SVN repository, changing 1 files.
2009-11-07 23:08:26 UTC by egonw
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egonw committed revision 15053 to the The Chemistry Development Kit SVN repository, changing 2 files.
2009-11-07 23:00:11 UTC by egonw
