def set_rota_result(self):
from mmtbx.rotamer.sidechain_angles import SidechainAngles
sidechain_angles = SidechainAngles(show_errs=True)
if self.resname == "MSE": curres = "MET"
else: curres = self.resname
all_dict = construct_complete_sidechain(self.three[self.index],
self.altloc)
#print all_dict
kwargs = self.get_start_kwargs()
try:
chis = sidechain_angles.measureChiAngles(self.three[self.index],
all_dict.get(self.altloc))
except AttributeError:
kwargs['incomplete'] = True
result = rotamer(**kwargs)
print('%s is missing some sidechain atoms' % result.id_str(),
file=sys.stderr)
self.rota_result = rotalyze.rotamer(**kwargs)
return
#print all_dict.get(self.altloc).keys()
if None in chis:
result = rotamer(**kwargs)
print('%s may be missing some sidechain atoms' %\
result.id_str(), file=sys.stderr)
self.rota_result = rotalyze.rotamer(**kwargs)
return
cur_res = self.resname.lower().strip()
if cur_res == 'mse':
cur_res = 'met'
value = self.rota_eval.evaluate(cur_res, chis)
if value == None:
self.rota_result = rotalyze.rotamer(**kwargs)
return
kwargs['score'] = value * 100
wrap_chis = self.rotamer_id.wrap_chis(self.resname.strip(),
chis,
symmetry=False)
if value >= rotalyze.ALLOWED_THRESHOLD: evaluation = "Favored"
elif value >= rotalyze.OUTLIER_THRESHOLD: evaluation = "Allowed"
else:
evaluation = "OUTLIER"
kwargs['outlier'] = True
kwargs['rotamer_name'] = evaluation
kwargs['evaluation'] = evaluation
if evaluation != "OUTLIER":
kwargs['outlier'] = False
kwargs['rotamer_name'] = self.rotamer_id.identify(
self.resname, wrap_chis)
# deal with unclassified rotamers
if kwargs['rotamer_name'] == '':
kwargs['rotamer_name'] = "UNCLASSIFIED"
# fill out wrap_chis win None til len == 4
while (len(wrap_chis) < 4):
wrap_chis.append(None)
kwargs['chi_angles'] = wrap_chis
self.rota_result = rotalyze.rotamer(**kwargs)
def set_rota_result(self) :
from mmtbx.rotamer.sidechain_angles import SidechainAngles
sidechain_angles = SidechainAngles(show_errs=True)
if self.resname == "MSE" : curres = "MET"
else : curres = self.resname
all_dict = construct_complete_sidechain(self.three[self.index],self.altloc)
#print all_dict
kwargs = self.get_start_kwargs()
try :
chis = sidechain_angles.measureChiAngles(
self.three[self.index],
all_dict.get(self.altloc))
except AttributeError :
kwargs['incomplete'] = True
result = rotamer(**kwargs)
print >> sys.stderr, '%s is missing some sidechain atoms'%result.id_str()
self.rota_result = rotalyze.rotamer(**kwargs)
return
#print all_dict.get(self.altloc).keys()
if None in chis :
result = rotamer(**kwargs)
print >> sys.stderr, '%s may be missing some sidechain atoms' %\
result.id_str()
self.rota_result = rotalyze.rotamer(**kwargs)
return
cur_res = self.resname.lower().strip()
if cur_res == 'mse':
cur_res = 'met'
value = self.rota_eval.evaluate(cur_res, chis)
if value == None :
self.rota_result = rotalyze.rotamer(**kwargs)
return
kwargs['score'] = value * 100
wrap_chis = self.rotamer_id.wrap_chis(self.resname.strip(),
chis,symmetry=False)
if value >= rotalyze.ALLOWED_THRESHOLD : evaluation = "Favored"
elif value >= rotalyze.OUTLIER_THRESHOLD : evaluation = "Allowed"
else :
evaluation = "OUTLIER"
kwargs['outlier'] = True
kwargs['rotamer_name'] = evaluation
kwargs['evaluation'] = evaluation
if evaluation != "OUTLIER" :
kwargs['outlier'] = False
kwargs['rotamer_name'] = self.rotamer_id.identify(self.resname, wrap_chis)
# deal with unclassified rotamers
if kwargs['rotamer_name'] == '' : kwargs['rotamer_name'] = "UNCLASSIFIED"
# fill out wrap_chis win None til len == 4
while (len(wrap_chis) < 4) : wrap_chis.append(None)
kwargs['chi_angles'] = wrap_chis
self.rota_result = rotalyze.rotamer(**kwargs)
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)
def __init__(self, pdb_hierarchy,
data_version="8000",
outliers_only=False,
show_errors=False,
out=sys.stdout,
quiet=False):
validation.__init__(self)
self.n_allowed = 0
self.n_favored = 0
from mmtbx.rotamer.sidechain_angles import SidechainAngles
from mmtbx.rotamer import rotamer_eval
from mmtbx.rotamer.rotamer_eval import RotamerID
from mmtbx.validation import utils
self.data_version = data_version
# if self.data_version == "500": self.outlier_threshold = 0.01
if self.data_version == "8000": self.outlier_threshold = OUTLIER_THRESHOLD
else: raise ValueError(
"data_version given to RotamerEval not recognized (%s)." % data_version)
sidechain_angles = SidechainAngles(show_errors)
rotamer_evaluator = rotamer_eval.RotamerEval(
data_version=data_version)
rotamer_id = rotamer_eval.RotamerID() # loads in the rotamer names
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
current_rotamers = {}
for model in pdb_hierarchy.models():
for chain in model.chains():
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
for rg in chain.residue_groups():
all_dict = construct_complete_sidechain(rg)
for atom_group in rg.atom_groups():
coords = get_center(atom_group)
resname = atom_group.resname
occupancy = get_occupancy(atom_group)
kwargs = {
"chain_id" : chain_id,
"resseq" : rg.resseq,
"icode" : rg.icode,
"altloc" : atom_group.altloc,
"resname" : resname,
"xyz" : coords,
"occupancy" : occupancy,
}
atom_dict = all_dict.get(atom_group.altloc)
res_key = get_residue_key(atom_group=atom_group)
try:
chis = sidechain_angles.measureChiAngles(
atom_group,
atom_dict)#.get(conformer.altloc))
except AttributeError:
if show_errors:
kwargs['incomplete'] = True
result = rotamer(**kwargs)
print >> out, '%s is missing some sidechain atoms' % \
result.id_str()
self.results.append(result)
continue
if (chis is not None):
if None in chis:
continue
cur_res = resname.lower().strip()
if cur_res == 'mse':
cur_res = 'met'
value = rotamer_evaluator.evaluate(cur_res, chis)
if value is not None:
self.n_total += 1
kwargs['score'] = value * 100
wrap_chis = rotamer_id.wrap_chis(resname.strip(), chis,
symmetry=False)
sym_chis = wrap_chis[:]
sym_chis = rotamer_id.wrap_sym(resname.strip(), sym_chis)
evaluation = self.evaluateScore(value)
kwargs['evaluation'] = evaluation
if evaluation == "OUTLIER":
kwargs['outlier'] = True
kwargs['rotamer_name'] = evaluation
else:
kwargs['outlier'] = False
kwargs['rotamer_name'] = rotamer_id.identify(resname,
wrap_chis)
#deal with unclassified rotamers
if kwargs['rotamer_name'] == '':
kwargs['rotamer_name'] = "UNCLASSIFIED"
while (len(wrap_chis) < 4):
wrap_chis.append(None)
kwargs['chi_angles'] = wrap_chis
result = rotamer(**kwargs)
if (result.is_outlier()) or (not outliers_only):
self.results.append(result)
out_count, out_percent = self.get_outliers_count_and_fraction()
self.out_percent = out_percent * 100.0
def __init__(
self, pdb_hierarchy, data_version="8000", outliers_only=False, show_errors=False, out=sys.stdout, quiet=False
):
validation.__init__(self)
self.n_allowed = 0
self.n_favored = 0
from mmtbx.rotamer.sidechain_angles import SidechainAngles
from mmtbx.rotamer import rotamer_eval
from mmtbx.rotamer.rotamer_eval import RotamerID
from mmtbx.validation import utils
self.data_version = data_version
# if self.data_version == "500": self.outlier_threshold = 0.01
if self.data_version == "8000":
self.outlier_threshold = 0.003
else:
raise ValueError("data_version given to RotamerEval not recognized (%s)." % data_version)
sidechain_angles = SidechainAngles(show_errors)
rotamer_evaluator = rotamer_eval.RotamerEval(data_version=data_version)
rotamer_id = rotamer_eval.RotamerID() # loads in the rotamer names
use_segids = utils.use_segids_in_place_of_chainids(hierarchy=pdb_hierarchy)
current_rotamers = {}
for model in pdb_hierarchy.models():
for chain in model.chains():
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
for rg in chain.residue_groups():
all_dict = construct_complete_sidechain(rg)
for atom_group in rg.atom_groups():
coords = get_center(atom_group)
resname = atom_group.resname
occupancy = get_occupancy(atom_group)
kwargs = {
"chain_id": chain_id,
"resseq": rg.resseq,
"icode": rg.icode,
"altloc": atom_group.altloc,
"resname": resname,
"xyz": coords,
"occupancy": occupancy,
}
atom_dict = all_dict.get(atom_group.altloc)
res_key = get_residue_key(atom_group=atom_group)
try:
chis = sidechain_angles.measureChiAngles(atom_group, atom_dict) # .get(conformer.altloc))
except AttributeError:
if show_errors:
kwargs["incomplete"] = True
result = rotamer(**kwargs)
print >> out, "%s is missing some sidechain atoms" % result.id_str()
self.results.append(result)
continue
if chis is not None:
if None in chis:
continue
cur_res = resname.lower().strip()
if cur_res == "mse":
cur_res = "met"
value = rotamer_evaluator.evaluate(cur_res, chis)
if value is not None:
self.n_total += 1
kwargs["score"] = value * 100
wrap_chis = rotamer_id.wrap_chis(resname.strip(), chis, symmetry=False)
sym_chis = wrap_chis[:]
sym_chis = rotamer_id.wrap_sym(resname.strip(), sym_chis)
evaluation = self.evaluateScore(value)
kwargs["evaluation"] = evaluation
if evaluation == "OUTLIER":
kwargs["outlier"] = True
kwargs["rotamer_name"] = evaluation
else:
kwargs["outlier"] = False
kwargs["rotamer_name"] = rotamer_id.identify(resname, wrap_chis)
# deal with unclassified rotamers
if kwargs["rotamer_name"] == "":
kwargs["rotamer_name"] = "UNCLASSIFIED"
while len(wrap_chis) < 4:
wrap_chis.append(None)
kwargs["chi_angles"] = wrap_chis
result = rotamer(**kwargs)
if (result.is_outlier()) or (not outliers_only):
self.results.append(result)
out_count, out_percent = self.get_outliers_count_and_fraction()
self.out_percent = out_percent * 100.0
