I am calculating the van der Waal interactions between atoms in the PDB file python. As this interaction does not involve bonded atoms and the atoms which are two bonds away (1-3 atoms) along the chain. However, removing bonded atoms and the atoms which are just two bonds away (1 - 3) makes the codes slower in python as it involves nested for loops. Is there any module in python (like biopython) that just computes the van der Waal interactions between (1 - 4) atoms in the given PDB file?
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