OEMDLStereoFromBondStereoΒΆ

bool OEMDLStereoFromBondStereo(OEMolBase &mol, bool alterBondMarks=false)

Sets the OEChem stereochemistry of each atom from the wedge and hash bonds in the connection table. See example in Figure: Example of using default OEMDLStereoFromBondStereo

mol
The molecule of which stereochemistry is being set. The given molecule has to have 2D coordinates.
alterBondMarks
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
../../_images/OEMDLStereoFromBondStereo.png

Example of using default OEMDLStereoFromBondStereo behavior: before (A) and after (B) calling the OEMDLStereoFromBondStereo function

../../_images/OEMDLStereoFromBondStereoFixMarks.png

Example of enabling alterBondMarks OEMDLStereoFromBondStereo behavior: before (A) and after (B) calling the OEMDLStereoFromBondStereo function

Note

This function is the opposite of the OEMDLPerceiveBondStereo function.

See also