I am trying to read a small molecule from PDB file and match its atom numbers to the same molecule in a SDF file. I have tried both matching SMART patterns and using OBIsomorphismMapper, both work for 70% of cases. However there are cases for which OpenBabel can not simply get the right SMILES from just the PDB file (e.g. adds extra double bonds or miss ones). For example in PDB ID 1KF6 and ligand name IPE, if you generate SMILES from PDB you will get OCCO/C=C/OCCO/C=C/O/C=C/O while the correct one should be OCCOCCOCCOCCOCCO. I would appreciate if someone can give me some advise on this.
Thanks, Sam
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