bool OEAnnotateDepictionProblems(OE2DMolDisplay &disp)
Annotates various depiction problems on the molecule. Currently it can mark double bonds which are not depicted correctly according to their cis/trans stereo specifications.
OE2DMolDisplayobject being annotated.
The following code snippet show how to use the
See the generated image in Figure: Example of incorrect
trans double bond depiction.
The highlighting indicates that the double bond specified in the
input SMILES string as trans is depicted as cis.
mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C1CCC2C/C=C/CCCC2C1") oedepict.OEPrepareDepiction(mol) width, height = 200, 200 opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OEAnnotateDepictionProblems(disp) oedepict.OERenderMolecule("OEAnnotateDepictionProblems.png", disp)
OEDepict TK uses built-in ring system templates when
generating 2D coordinates.
Generating 2D coordinates which are inconsistent with
cis/trans stereo bond specification can occur due to
a missing ring template.
OEPrepareDepiction function throws
a warning when this problem occurs.