Terminal conjugated bonds in distance geometry checks #63

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maabuu merged 2 commits into maabuu:main from chmnk:dg-conjugated-bonds

Apr 16, 2025

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chmnk commented Apr 14, 2025 •

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A follow-up of #62, inspired by what we have in https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/MolAlign/AlignMolecules.cpp#L27

Changes the distance geometry check for some terminal conjugated bonds:

gets the bonds from a SMARTS match to a conjugated bond template
since to my understanding, the conjugated bonds are usually between a single/double, it groups all those bonds by atom types
for each set of atom types (C--O, N--O), the lower/higher bound will be the minimum/maximum of the lower/higher bounds with this atom type.

Maria Kadukova added 2 commits

April 7, 2025 18:07


          terminal bonds

3051f75


          symmetrize_conjugated_terminal_groups option

8a8cb0c

maabuu merged commit 96cb955 into maabuu:main

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