Just a quick question. I start from correct geometries (generated with
ligprep) and I superpose many molecules on a reference ligand. The overlap
is very good but sometimes the aromatic rings are not planar due to the
restraints. How can I check automatically in batch mode that the atoms in
the aligned molecules written in the sdf file have the same valence as in
the original sdf file (e.g. the atoms in the non-planar rings are still
aromatic)? Can I do that by comparing the canonical SMILES of the original
molecule with the canonical SMILES of the aligned?




Thomas Evangelidis

Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic

email: tev...@pharm.uoa.gr


website: https://sites.google.com/site/thomasevangelidishomepage/
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