Polymer project update | (working session) PAMAM was failing to have its chemical information assigned because some step was adding Hs where they shouldn’t have been. CD should look at the workflow that amde the input PDB to see if some step was erroneously adding Hs. If the place where Hs were erroneously being added was in Molecule.from_pdb, this is a toolkit bug and needs to be fixed. SMARTS generated and added to the substructure library should have map inidces ([:1]). This may not have an effect for chemcial information assignment (like in from_pdb) but this is essential for the correct operation of perceive residues Vulcanized rubber doesn’t seem to have any repeating substructures, and it’s not clea that we’ll ever be able to process it correctly. To make a substurcture SMARTS for phosphotyrosine, we need some reference for its chemistry. All of CDs code looks good, the only problem is that the starting point for automatically generating the phosphotyrosine SMARTS is a PDB instead of an information source that contains chemical info (like SDF or SMILES)
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