Convert C alpha only protein structure to all atoms structure using Modeller

Usage:

./modeller_ca_to_all_atoms.py input_structure_ca.pdb [bb]

It returns modeller_out.pdb, an all atoms structure.

The script extracts distances between C alpha atoms and read the beta factor column of the pdb to get the standard deviation from the target distance and applies a Gaussian distance restraint along with the stereochemical restraints (BOND, ANGLE, DIHEDRAL, IMPROPER).

The script can also handle backbone only protein structure and return a full atom protein. Just add the bb keyword argument.