Added optimizeHydrogenBonds() - Githubissues

openmm / pdbfixer

PDBFixer fixes problems in PDB files

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Added optimizeHydrogenBonds() #303

Open peastman opened 1 month ago

peastman commented 1 month ago

This adds a function for optimizing the hydrogen bonding network of a protein. It does it in two ways:

Rotating the terminal groups of HIS, ASN, and GLN sidechains by 180 degrees.
Switching HIS residues between the HID and HIE forms.

It considers all possible combinations to find the one that maximizes the number of hydrogen bonds.