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 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)
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)
