def set_rotamer_to_reference(self,
xray_structure,
mon_lib_srv=None,
log=None,
quiet=False):
if self.mon_lib_srv is None:
self.mon_lib_srv = mon_lib_srv
assert isinstance(self.mon_lib_srv,
mmtbx.monomer_library.server.server)
if (log is None): log = sys.stdout
make_sub_header("Correcting rotamer outliers to match reference model",
out=log)
sa = SidechainAngles(False)
r = rotalyze.rotalyze(pdb_hierarchy=self.pdb_hierarchy)
rot_list_reference = {}
coot_reference = {}
for key in self.pdb_hierarchy_ref.keys():
hierarchy = self.pdb_hierarchy_ref[key]
rot_list_reference[key] = \
rotalyze.rotalyze(pdb_hierarchy=hierarchy)
model_hash = {}
model_chis = {}
reference_hash = {}
reference_chis = {}
model_outliers = 0
for rot in r.results:
model_hash[rot.id_str()] = rot.rotamer_name
if rot.rotamer_name == "OUTLIER":
model_outliers += 1
for key in rot_list_reference.keys():
reference_hash[key] = {}
for rot in rot_list_reference[key].results:
reference_hash[key][rot.id_str()] = rot.rotamer_name
print >> log, "** evaluating rotamers for working model **"
for model in self.pdb_hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
all_dict = rotalyze.construct_complete_sidechain(
residue_group)
for atom_group in residue_group.atom_groups():
try:
atom_dict = all_dict.get(atom_group.altloc)
chis = sa.measureChiAngles(atom_group, atom_dict)
if chis is not None:
key = utils.id_str(chain_id=chain.id,
resseq=residue_group.resseq,
resname=atom_group.resname,
icode=residue_group.icode,
altloc=atom_group.altloc)
model_chis[key] = chis
except Exception:
print >> log, \
' %s%5s %s is missing some sidechain atoms, **skipping**' % (
chain.id, residue_group.resid(),
atom_group.altloc+atom_group.resname)
if model_outliers == 0:
print >> log, "No rotamer outliers detected in working model"
return
else:
print >> log, "Number of rotamer outliers: %d" % model_outliers
print >> log, "\n** evaluating rotamers for reference model **"
for file in self.pdb_hierarchy_ref.keys():
hierarchy = self.pdb_hierarchy_ref[file]
reference_chis[file] = {}
for model in hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
all_dict = rotalyze.construct_complete_sidechain(
residue_group)
for atom_group in residue_group.atom_groups():
try:
atom_dict = all_dict.get(atom_group.altloc)
chis = sa.measureChiAngles(
atom_group, atom_dict)
if chis is not None:
key = utils.id_str(
chain_id=chain.id,
resseq=residue_group.resseq,
resname=atom_group.resname,
icode=residue_group.icode,
altloc=atom_group.altloc)
reference_chis[file][key] = chis
except Exception:
print >> log, \
' %s%5s %s is missing some sidechain atoms, **skipping**' % (
chain.id, residue_group.resid(),
atom_group.altloc+atom_group.resname)
print >> log, "\n** fixing outliers **"
sites_cart_start = xray_structure.sites_cart()
for model in self.pdb_hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
if len(residue_group.conformers()) > 1:
print >> log, " %s%5s %s has multiple conformations, **skipping**" % (
chain.id, residue_group.resid(),
" " + residue_group.atom_groups()[0].resname)
continue
for conformer in residue_group.conformers():
for residue in conformer.residues():
if residue.resname == "PRO":
continue
key = utils.id_str(
chain_id=chain.id,
resseq=residue_group.resseq,
resname=residue_group.atom_groups()[0].resname,
icode=residue_group.icode,
altloc=conformer.altloc)
if len(chain.id) == 1:
chain_id = " " + chain.id
else:
chain_id = chain.id
file_key = '%s%s%s' % (residue.resname, chain_id,
residue_group.resid())
file_key = file_key.strip()
file_match = self.residue_match_hash.get(file_key)
if file_match is not None:
file = file_match[0]
else:
continue
model_rot = model_hash.get(key)
reference_rot = reference_hash[file].get(
self.one_key_to_another(file_match[1]))
m_chis = model_chis.get(key)
r_chis = reference_chis[file].get(
self.one_key_to_another(file_match[1]))
if model_rot is not None and reference_rot is not None and \
m_chis is not None and r_chis is not None:
if (model_rot == 'OUTLIER' and \
reference_rot != 'OUTLIER'): # or \
#atom_group.resname in ["LEU", "VAL", "THR"]:
self.change_residue_rotamer_in_place(
sites_cart_start, residue, m_chis,
r_chis, self.mon_lib_srv)
xray_structure.set_sites_cart(
sites_cart_start)
elif self.params.strict_rotamer_matching and \
(model_rot != 'OUTLIER' and reference_rot != 'OUTLIER'):
if model_rot != reference_rot:
self.change_residue_rotamer_in_place(
sites_cart_start, residue, m_chis,
r_chis, self.mon_lib_srv)
xray_structure.set_sites_cart(
sites_cart_start)
def set_rotamer_to_reference(self,
xray_structure,
mon_lib_srv=None,
log=None,
quiet=False):
if self.mon_lib_srv is None:
self.mon_lib_srv = mon_lib_srv
assert isinstance(self.mon_lib_srv, mmtbx.monomer_library.server.server)
if(log is None): log = sys.stdout
make_sub_header(
"Correcting rotamer outliers to match reference model",
out=log)
sa = SidechainAngles(False)
r = rotalyze.rotalyze(pdb_hierarchy=self.pdb_hierarchy)
rot_list_reference = {}
coot_reference = {}
for key in self.pdb_hierarchy_ref.keys():
hierarchy = self.pdb_hierarchy_ref[key]
rot_list_reference[key] = \
rotalyze.rotalyze(pdb_hierarchy=hierarchy)
model_hash = {}
model_chis = {}
reference_hash = {}
reference_chis = {}
model_outliers = 0
for rot in r.results:
model_hash[rot.id_str()] = rot.rotamer_name
if rot.rotamer_name == "OUTLIER":
model_outliers += 1
for key in rot_list_reference.keys():
reference_hash[key] = {}
for rot in rot_list_reference[key].results:
reference_hash[key][rot.id_str()] = rot.rotamer_name
print >> log, "** evaluating rotamers for working model **"
for model in self.pdb_hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
all_dict = rotalyze.construct_complete_sidechain(residue_group)
for atom_group in residue_group.atom_groups():
try:
atom_dict = all_dict.get(atom_group.altloc)
chis = sa.measureChiAngles(atom_group, atom_dict)
if chis is not None:
key = utils.id_str(
chain_id=chain.id,
resseq=residue_group.resseq,
resname=atom_group.resname,
icode=residue_group.icode,
altloc=atom_group.altloc)
model_chis[key] = chis
except Exception:
print >> log, \
' %s%5s %s is missing some sidechain atoms, **skipping**' % (
chain.id, residue_group.resid(),
atom_group.altloc+atom_group.resname)
if model_outliers == 0:
print >> log, "No rotamer outliers detected in working model"
return
else:
print >> log, "Number of rotamer outliers: %d" % model_outliers
print >> log, "\n** evaluating rotamers for reference model **"
for file in self.pdb_hierarchy_ref.keys():
hierarchy = self.pdb_hierarchy_ref[file]
reference_chis[file] = {}
for model in hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
all_dict = rotalyze.construct_complete_sidechain(residue_group)
for atom_group in residue_group.atom_groups():
try:
atom_dict = all_dict.get(atom_group.altloc)
chis = sa.measureChiAngles(atom_group, atom_dict)
if chis is not None:
key = utils.id_str(
chain_id=chain.id,
resseq=residue_group.resseq,
resname=atom_group.resname,
icode=residue_group.icode,
altloc=atom_group.altloc)
reference_chis[file][key] = chis
except Exception:
print >> log, \
' %s%5s %s is missing some sidechain atoms, **skipping**' % (
chain.id, residue_group.resid(),
atom_group.altloc+atom_group.resname)
print >> log, "\n** fixing outliers **"
sites_cart_start = xray_structure.sites_cart()
for model in self.pdb_hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
if len(residue_group.conformers()) > 1:
print >> log, " %s%5s %s has multiple conformations, **skipping**" % (
chain.id, residue_group.resid(),
" "+residue_group.atom_groups()[0].resname)
continue
for conformer in residue_group.conformers():
for residue in conformer.residues():
if residue.resname == "PRO":
continue
key = utils.id_str(
chain_id=chain.id,
resseq=residue_group.resseq,
resname=residue_group.atom_groups()[0].resname,
icode=residue_group.icode,
altloc=conformer.altloc)
if len(chain.id) == 1:
chain_id = " "+chain.id
else:
chain_id = chain.id
file_key = '%s%s%s' %(residue.resname,
chain_id,
residue_group.resid())
file_key = file_key.strip()
file_match = self.residue_match_hash.get(file_key)
if file_match is not None:
file = file_match[0]
else:
continue
model_rot = model_hash.get(key)
reference_rot = reference_hash[file].get(self.one_key_to_another(file_match[1]))
m_chis = model_chis.get(key)
r_chis = reference_chis[file].get(self.one_key_to_another(file_match[1]))
if model_rot is not None and reference_rot is not None and \
m_chis is not None and r_chis is not None:
if (model_rot == 'OUTLIER' and \
reference_rot != 'OUTLIER'): # or \
#atom_group.resname in ["LEU", "VAL", "THR"]:
self.change_residue_rotamer_in_place(
sites_cart_start,residue, m_chis,r_chis,self.mon_lib_srv)
xray_structure.set_sites_cart(sites_cart_start)
elif self.params.strict_rotamer_matching and \
(model_rot != 'OUTLIER' and reference_rot != 'OUTLIER'):
if model_rot != reference_rot:
self.change_residue_rotamer_in_place(
sites_cart_start,residue, m_chis,r_chis,self.mon_lib_srv)
xray_structure.set_sites_cart(sites_cart_start)