Hello, Thank you RDKIT. I found this is a very helpful instruction about how to get all the dihedral restraints of a molecule ( https://sourceforge.net/p/rdkit/mailman/message/34554502/ ). From the code provided, I have some questions:
Since the output is the id of the atom which is different from the id of the atom in PDB file generated by MolToPDBFile(), how can I determine which ID number corresponding to which atom exactly? Is it the id number generated by enumerateTorsions() 1 unit less than the actual id number in pdb file of same molecule? As a follow up, is there any possible ways to detect torsion restraints only on bonds that have Trans geometry when Trans geometry is possible for that bond ? For example: if I input a random chemical with SMILES string as c2ccc(CCc1ccccc1)cc2 (2 rings connected by CCCC), how should I manipulate the code so that it only output the ID of the middle parts of the molecule which is the CCCC (which has possible TRANS conformation)? Thank you so much for your help. Phuong Chau Smith College '20 Engineering and Data Science Major
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