bool OEMDLStereoFromBondStereo(OEMolBase &mol, bool alterBondMarks=false)
Sets the OEChem TK stereochemistry of each atom from the
wedge and hash bonds in the connection table.
See example in Figure: Example of using default OEMDLStereoFromBondStereo
- The molecule of which stereochemistry is being set.
The given molecule has to have 2D coordinates.
- The boolean argument controls whether an attempt should be made to repair stereocenters that throw warnings
due to ambiguous bond marking patterns (disabled by default with alterBondMarks=``false``).
If this action is enabled, warnings will continue to be issued to allow user inspection and verification
of the modified bond marks. However, once the corrected structure(s) have been rewritten
with any format that captures bond stereomark information, a re-read of the structure(s)
should emit fewer stereocenter correction warnings. Enabling the bond mark alteration activity will
aggressively attempt to repair ambiguous bond marking patterns by possibly applying more than one stereo mark, or marking ring bond(s).
See example in Figure: Example of enabling alterBondMarks OEMDLStereoFromBondStereo
Example of using default OEMDLStereoFromBondStereo behavior: before (A) and after (B) calling the OEMDLStereoFromBondStereo function
Example of enabling alterBondMarks OEMDLStereoFromBondStereo behavior: before (A) and after (B) calling the OEMDLStereoFromBondStereo function