Improve atom mapping between chiral centers #1111
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bonded atoms and 2 are known; use the sign of the improper torsion instead of a delta. Should be more robust to any distortions in structures.
chiralimpcut keyword to atommap
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Version 6.29.5.
Previously when mapping atoms bonded to chiral centers,
atommapwould use a simple cutoff scheme comparing the improper dihedral angle formed by (M-C-M-U), where M is a mapped atom, C is the chiral center, and U is an unmapped atom. This cutoff had been intentionally chosen to be tight (10 degrees) to prevent bad mapping, but if one structure was distorted with respect to the other this could cause the mapping to fail. Now in the most common chiral case (chiral center, 2 mapped atoms, 2 unmapped atoms) the sign of each angle is used instead of a delta, i.e. the negative angle in reference is mapped to the negative angle in target and vice versa. There is still a warning printed if the delta between the angles is outside the cutoff indicating the structures may be distorted.Also added a keyword to
atommap,chiralimpcut <cut>that can be used to increase the default cutoff to beyond 10 degrees. Update the manual.