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substructure search SMARTS query - structure not redrawn #4

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nwoetzel opened this issue Jul 28, 2016 · 1 comment
Open

substructure search SMARTS query - structure not redrawn #4

nwoetzel opened this issue Jul 28, 2016 · 1 comment

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@nwoetzel
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When using wildcards in a SMARTS substructure search, the JSME editor cannot draw the structure.
JSME uses Openchemlib.js to convert SMILES/SMARTS to structures. This does not always work for wildcards as it seems, e.g.:

  • *C -> AC
  • AC causes error when pasting
    A structure with an 'any atom' can be drawn that gives that smile: *1cncnc1
    but this cannot be converted by jsem/openchemlib back to the structure
@nwoetzel
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Also CDK cannot help, since the SMARTSParser.parse returns an IAtomQueryContainer which cannot be used in MoleculeWriter; and there is no way yet to convert IAtomQueryContainer to an IAtomContainer (that I know of)

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