Hi all, I am try to change my SMILES of a bunch of small molecules that I have downloaded from pubchem. The problem is that the charge in the physiological state of the molecule differs from string from pubchem e.g.
ATP charge 0: SMILES = ''C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N' ATP charge -3: 'Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])O)[C@ @H](O)[C@H]1O' My question is normally I would convert this manually but this is prone to error and for many compounds it is not very optimal. Any suggestions or work arounds highly appreciated thanks! Best
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