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.
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.
OEGraphMol mol = new OEGraphMol(); oechem.OESmilesToMol(mol, "C1CCC2C/C=C/CCCC2C1"); oedepict.OEPrepareDepiction(mol); int width = 200; int height = 200; double scale = OEScale.AutoScale; OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale); OE2DMolDisplay disp = new 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. The OEPrepareDepiction function throws a warning when this problem occurs.