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#327 Canonical SMILES marks Se as aromatic

open
Craig
File Translation (240)
2
2012-10-23
2008-01-10
Anonymous
No

OB version: 2.1.1

Converting the attached SDF file to SMILES produces the following output:

$ babel -isdf DB03043.sdf -osmi

NC(Cc1c[nH]c2[se]ccc12)C(O)=O SDF file of DB03043
1 molecule converted
13 audit log messages

Which in a strict sense is wrong according to the openSMILES specification as non-aromatic atoms start with uppercase characters.

Discussion

  • Nobody/Anonymous

    Nobody/Anonymous - 2008-01-10

    SDF file used to generate the output.

     
    DB03043.sdf

  • Chris Morley

    Chris Morley - 2008-01-25

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    The sdf file has the selenium as part of an aromatic structure (its bonds are aromatic). There is no ambiguity in the SMILES structure; it is understood by Daylight's Depict, MarvinView and OpenBabel, although not Chem Sketch. OpenSMILES is not yet finallized and this issue is contentious. I think it is not appropriate to make changes to OpenBabel's output at the moment but just to note it as a possible bug for the future. I have reduced the priority.
    Chris