OEAnnotateDepictionProblems

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.

disp

The OE2DMolDisplay object being annotated.

The following code snippet show how to use the OEAnnotateDepictionProblems function. 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)

Example of incorrect trans double bond depiction

Note

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. The OEPrepareDepiction function throws a warning when this problem occurs.