def get_n_protein_residues_from_restart(in_md): n = 0 soup = simulate.soup_from_restart_files(in_md) for res in soup.residues(): if res not in data.solvent_res_types: n += 1 return n
def make_protein_restraint_pdb(in_basename, pdb): soup = simulate.soup_from_restart_files(in_basename) for a in soup.atoms(): a.bfactor = 0.0 if a.res_type not in data.solvent_res_types: a.bfactor = 1.0 soup.write_pdb(pdb)
def make_restraint_pdb(in_md, residue_indices, out_pdb, is_backbone_only=True): soup = simulate.soup_from_restart_files(in_md) for i_res in residue_indices: for a in soup.residue(i_res).atoms(): if is_backbone_only and a.type not in data.backbone_atoms: continue a.bfactor = 1.0 soup.write_pdb(out_pdb)