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[Cdk-devel] [ cdk-Bugs-848887 ] SMILES depends on order in MDL
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From: SourceForge.net <no...@so...> - 2004-04-15 21:07:43
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Bugs item #848887, was opened at 2003-11-25 13:14 Message generated for change (Settings changed) made by shk3 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=848887&group_id=20024 Category: org.openscience.cdk.smiles Group: None Status: Open Resolution: None Priority: 9 Submitted By: Stefan Kuhn (shk3) >Assigned to: Stefan Kuhn (shk3) Summary: SMILES depends on order in MDL Initial Comment: Consider the following mdl: CDK 10 10 0 0 0 0 0 0 0 0999 V2000 0.7366 -0.8176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0221 -1.2301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0221 -2.0551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7366 -2.4749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4584 -2.0551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4584 -1.2301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7366 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7366 -3.1747 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.5798 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3258 -3.6829 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 1 6 1 0 0 0 0 1 7 1 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 8 1 0 0 0 0 5 6 2 0 0 0 0 8 9 1 0 0 0 0 8 10 2 0 0 0 0 M CHG 1 8 1 M CHG 1 9 -1 M END The smiles from this looks like: [O-][N+](=O)c1ccc(cc1)C If you change the the order of the two Os, ie. M CHG 1 9 -1 => M CHG 1 10 -1 and 8 9 1 0 0 0 0 => 8 9 2 0 0 0 0 and 8 10 2 0 0 0 0 => 8 10 1 0 0 0 0 the smiles is: O=[N+]([O-])c1ccc(cc1)C According to my understanding of canonical smiles, the smiles should be the same. ---------------------------------------------------------------------- Comment By: Stefan Kuhn (shk3) Date: 2004-04-08 10:55 Message: Logged In: YES user_id=452972 The bug still exists. You can get the mdl from nmrshiftdb by looking for structure www.nmrshiftdb.org_mainz_2003-06-28_10:03:15_0033. ---------------------------------------------------------------------- Comment By: Christoph Steinbeck (steinbeck) Date: 2004-02-09 13:41 Message: Logged In: YES user_id=54358 Will be looked at today or tomorrow. ---------------------------------------------------------------------- Comment By: Stefan Kuhn (shk3) Date: 2003-11-26 08:47 Message: Logged In: YES user_id=452972 The SMILES is supposed to be canonical (as defined by daylight), so this is a bug. ---------------------------------------------------------------------- Comment By: Peter Murray-Rust (petermr) Date: 2003-11-25 20:46 Message: Logged In: YES user_id=125666 Does CDK canonicalise SMILES? If not it and such is requested I would recommend using the IChI approach when it is available. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=120024&aid=848887&group_id=20024 |