[Cdk-devel] [ cdk-Feature Requests-985969 ] SMILES generator should handle cis/trans ring configurations

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Feature Requests item #985969, was opened at 2004-07-06 14:23
Message generated for change (Comment added) made by petermr
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Category: None
Group: None
Status: Open
Priority: 5
Submitted By: Stefan Kuhn (shk3)
Assigned to: Stefan Kuhn (shk3)
Summary: SMILES generator should handle cis/trans ring configurations

Initial Comment:
Currently the smiles generator does not handle e. g.
trans/cis decaline. This should be done as in
http://www.sinica.edu.tw/~scimath/msi/catalyst45/help/SMILES.doc.html.
Daylight says nonsense about this.

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Comment By: Peter Murray-Rust (petermr)
Date: 2004-07-06 15:19

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If I read this correctly this suggests that ring fusion
junctions be described by the cis/trans symbols for double
bonds (/ and \). This looks a poor method that doesn't scale
to more complex rings and anyway is a proprietary variant of
SMILES.

Daylight says nonsense about this.

Daylight states that[]C1C[C@H]2CCCC[C@H]2CC1 cis-decalin
"Cis/Trans" ring fusions are really tetrahedral chiralities

and I would agree completely with this. It is also the
approach taken by INChI.



Peter MR

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