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merkys / Chemistry-OpenSMILES

OpenSMILES format reader and writer

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Nondeterministic tetrahedral chirality at anomeric centers in print

merkys opened this issue · comments

commented

It has been observed that tetrahedral chirality setting at anomeric centers changes randomly in print via Chemistry::OpenSMILES::Writer::write_SMILES(). Failcase: N[C@@]12NC(N[C@]2(NC(N1))N).

commented

This can be offset by removing chiral setting from tetrahedral chiral centers with less than four distinct neighbours. Added procedure Chemistry::OpenSMILES::clean_chiral_centers() to do that in v0.4.4.

commented

This can be offset by removing chiral setting from tetrahedral chiral centers with less than four distinct neighbours. Added procedure Chemistry::OpenSMILES::clean_chiral_centers() to do that in v0.4.4.

Some exotic cases, for example COD entry 2211925, suffer from this problem despite Chemistry::OpenSMILES::clean_chiral_centers(). It seems that proper ring detection has to be performed in order to deal with this issue.