def build_den_proxies(self, pdb_hierarchy):
from mmtbx.geometry_restraints.torsion_restraints import utils
self.atoms_per_chain = \
self.count_atoms_per_chain(pdb_hierarchy=pdb_hierarchy)
self.atoms_per_chain_ref = \
self.count_atoms_per_chain(pdb_hierarchy=self.pdb_hierarchy_ref)
self.resid_hash_ref = \
utils.build_resid_hash(pdb_hierarchy=self.pdb_hierarchy_ref)
self.i_seq_hash = \
utils.build_i_seq_hash(pdb_hierarchy=pdb_hierarchy)
self.i_seq_hash_ref = \
utils.build_i_seq_hash(pdb_hierarchy=self.pdb_hierarchy_ref)
self.name_hash = \
utils.build_name_hash(pdb_hierarchy=pdb_hierarchy)
self.name_hash_ref = \
utils.build_name_hash(pdb_hierarchy=self.pdb_hierarchy_ref)
self.ref_atom_pairs, self.ref_distance_hash = \
self.find_atom_pairs(pdb_hierarchy=self.pdb_hierarchy_ref,
resid_hash=self.resid_hash_ref)
self.remove_non_matching_pairs()
if self.den_network_file is not None:
self.den_atom_pairs = self.load_den_network()
else:
self.random_ref_atom_pairs = \
self.select_random_den_restraints()
self.den_atom_pairs = self.get_den_atom_pairs()
self.check_den_pair_consistency()
if self.export_den_pairs:
self.dump_den_network()
def build_den_proxies(self, pdb_hierarchy):
from mmtbx.geometry_restraints.torsion_restraints import utils
self.atoms_per_chain = \
self.count_atoms_per_chain(pdb_hierarchy=pdb_hierarchy)
self.atoms_per_chain_ref = \
self.count_atoms_per_chain(pdb_hierarchy=self.pdb_hierarchy_ref)
self.resid_hash_ref = \
utils.build_resid_hash(pdb_hierarchy=self.pdb_hierarchy_ref)
self.i_seq_hash = \
utils.build_i_seq_hash(pdb_hierarchy=pdb_hierarchy)
self.i_seq_hash_ref = \
utils.build_i_seq_hash(pdb_hierarchy=self.pdb_hierarchy_ref)
self.name_hash = \
utils.build_name_hash(pdb_hierarchy=pdb_hierarchy)
self.name_hash_ref = \
utils.build_name_hash(pdb_hierarchy=self.pdb_hierarchy_ref)
self.ref_atom_pairs, self.ref_distance_hash = \
self.find_atom_pairs(pdb_hierarchy=self.pdb_hierarchy_ref,
resid_hash=self.resid_hash_ref)
self.remove_non_matching_pairs()
if self.den_network_file is not None:
self.den_atom_pairs = self.load_den_network()
else:
self.random_ref_atom_pairs = \
self.select_random_den_restraints()
self.den_atom_pairs = self.get_den_atom_pairs()
self.check_den_pair_consistency()
if self.export_den_pairs:
self.dump_den_network()
def build_dihedral_hash(self,
dihedral_proxies=None,
sites_cart=None,
pdb_hierarchy=None,
include_hydrogens=False,
include_main_chain=True,
include_side_chain=True):
if not include_hydrogens:
i_seq_element_hash = \
utils.build_element_hash(pdb_hierarchy=pdb_hierarchy)
i_seq_name_hash = \
utils.build_name_hash(pdb_hierarchy=pdb_hierarchy)
dihedral_hash = dict()
for dp in dihedral_proxies:
try:
#check for H atoms if required
if not include_hydrogens:
for i_seq in dp.i_seqs:
if i_seq_element_hash[i_seq] == " H":
raise StopIteration()
#ignore backbone dihedrals
if not include_main_chain:
sc_atoms = False
for i_seq in dp.i_seqs:
if i_seq_name_hash[i_seq][0:4] not in [
' CA ', ' N ', ' C ', ' O '
]:
sc_atoms = True
break
if not sc_atoms:
raise StopIteration()
if not include_side_chain:
sc_atoms = False
for i_seq in dp.i_seqs:
if i_seq_name_hash[i_seq][0:4] \
not in [' CA ', ' N ', ' C ', ' O ']:
sc_atoms = True
break
if sc_atoms:
raise StopIteration()
key = ""
for i_seq in dp.i_seqs:
key = key + i_seq_name_hash[i_seq]
di = \
cctbx.geometry_restraints.dihedral(
sites_cart=sites_cart,
proxy=dp)
dihedral_hash[key] = di.angle_model
except StopIteration:
pass
return dihedral_hash
def build_dihedral_hash(self,
dihedral_proxies=None,
sites_cart=None,
pdb_hierarchy=None,
include_hydrogens=False,
include_main_chain=True,
include_side_chain=True):
if not include_hydrogens:
i_seq_element_hash = \
utils.build_element_hash(pdb_hierarchy=pdb_hierarchy)
i_seq_name_hash = \
utils.build_name_hash(pdb_hierarchy=pdb_hierarchy)
dihedral_hash = dict()
for dp in dihedral_proxies:
try:
#check for H atoms if required
if not include_hydrogens:
for i_seq in dp.i_seqs:
if i_seq_element_hash[i_seq] == " H":
raise StopIteration()
#ignore backbone dihedrals
if not include_main_chain:
sc_atoms = False
for i_seq in dp.i_seqs:
if i_seq_name_hash[i_seq][0:4] not in [' CA ',' N ',' C ',' O ']:
sc_atoms = True
break
if not sc_atoms:
raise StopIteration()
if not include_side_chain:
sc_atoms = False
for i_seq in dp.i_seqs:
if i_seq_name_hash[i_seq][0:4] \
not in [' CA ', ' N ', ' C ', ' O ']:
sc_atoms = True
break
if sc_atoms:
raise StopIteration()
key = ""
for i_seq in dp.i_seqs:
key = key+i_seq_name_hash[i_seq]
di = \
cctbx.geometry_restraints.dihedral(
sites_cart=sites_cart,
proxy=dp)
dihedral_hash[key] = di.angle_model
except StopIteration:
pass
return dihedral_hash
def __init__(self,
processed_pdb_file,
reference_hierarchy_list=None,
reference_file_list=None,
mon_lib_srv=None,
ener_lib=None,
has_hd=False,
params=None,
selection=None,
log=None):
assert [reference_hierarchy_list, reference_file_list].count(None) == 1
if (log is None):
log = sys.stdout
self.params = params
self.selection = selection
self.mon_lib_srv = mon_lib_srv
self.ener_lib = ener_lib
self.pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
self.pdb_hierarchy.reset_i_seq_if_necessary()
sites_cart = self.pdb_hierarchy.atoms().extract_xyz()
if self.selection is None:
self.selection = flex.bool(len(sites_cart), True)
if reference_hierarchy_list is None:
reference_hierarchy_list = \
utils.process_reference_files(
reference_file_list=reference_file_list,
log=log)
if reference_file_list is None:
reference_file_list = \
["ref%d" % x for x in range(len(reference_hierarchy_list))]
#
# this takes 20% of constructor time.
self.dihedral_proxies_ref = utils.get_reference_dihedral_proxies(
reference_hierarchy_list=reference_hierarchy_list,
reference_file_list=reference_file_list,
mon_lib_srv=self.mon_lib_srv,
ener_lib=self.ener_lib,
log=log)
self.i_seq_name_hash = utils.build_name_hash(
pdb_hierarchy=self.pdb_hierarchy)
#reference model components
self.sites_cart_ref = {}
self.pdb_hierarchy_ref = {}
self.i_seq_name_hash_ref = {}
self.reference_dihedral_hash = {}
self.reference_file_list = reference_file_list
#triage reference model files
for file, hierarchy in zip(reference_file_list,
reference_hierarchy_list):
self.sites_cart_ref[file] = hierarchy.atoms().extract_xyz()
self.pdb_hierarchy_ref[file] = hierarchy
self.i_seq_name_hash_ref[file] = \
utils.build_name_hash(
pdb_hierarchy=hierarchy)
self.reference_dihedral_hash[file] = \
self.build_dihedral_hash(
dihedral_proxies=self.dihedral_proxies_ref[file],
sites_cart=self.sites_cart_ref[file],
pdb_hierarchy=hierarchy,
include_hydrogens=self.params.hydrogens,
include_main_chain=self.params.main_chain,
include_side_chain=self.params.side_chain)
self.match_map = None
self.proxy_map = None
self.build_reference_dihedral_proxy_hash()
#
# This takes 80% of constructor time!!!
self.residue_match_hash = {} # {key_model: ('file_name', key_ref)}
self.match_map = {} # {'file_name':{i_seq_model:i_seq_ref}}
if params.use_starting_model_as_reference:
self.get_matching_from_self()
else:
self.get_matching_from_ncs(log=log)
if self.match_map == {}:
# making empty container
new_ref_dih_proxies = self.reference_dihedral_proxies = \
cctbx.geometry_restraints.shared_dihedral_proxy()
else:
new_ref_dih_proxies = self.get_reference_dihedral_proxies(
processed_pdb_file=processed_pdb_file)
def __init__(self,
processed_pdb_file,
reference_hierarchy_list=None,
reference_file_list=None,
mon_lib_srv=None,
ener_lib=None,
has_hd=False,
params=None,
selection=None,
log=None):
assert [reference_hierarchy_list,
reference_file_list].count(None) == 1
if(log is None):
log = sys.stdout
self.params = params
self.selection = selection
self.mon_lib_srv = mon_lib_srv
self.ener_lib = ener_lib
self.pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
self.pdb_hierarchy.reset_i_seq_if_necessary()
sites_cart = self.pdb_hierarchy.atoms().extract_xyz()
if self.selection is None:
self.selection = flex.bool(len(sites_cart), True)
if reference_hierarchy_list is None:
reference_hierarchy_list = \
utils.process_reference_files(
reference_file_list=reference_file_list,
log=log)
if reference_file_list is None:
reference_file_list = \
["ref%d" % x for x in range(len(reference_hierarchy_list))]
#
# this takes 20% of constructor time.
self.dihedral_proxies_ref = utils.get_reference_dihedral_proxies(
reference_hierarchy_list=reference_hierarchy_list,
reference_file_list=reference_file_list,
mon_lib_srv=self.mon_lib_srv,
ener_lib=self.ener_lib,
log=log)
self.i_seq_name_hash = utils.build_name_hash(
pdb_hierarchy=self.pdb_hierarchy)
#reference model components
self.sites_cart_ref = {}
self.pdb_hierarchy_ref = {}
self.i_seq_name_hash_ref = {}
self.reference_dihedral_hash = {}
self.reference_file_list = reference_file_list
#triage reference model files
for file, hierarchy in zip(reference_file_list,
reference_hierarchy_list):
self.sites_cart_ref[file] = hierarchy.atoms().extract_xyz()
self.pdb_hierarchy_ref[file] = hierarchy
self.i_seq_name_hash_ref[file] = \
utils.build_name_hash(
pdb_hierarchy=hierarchy)
self.reference_dihedral_hash[file] = \
self.build_dihedral_hash(
dihedral_proxies=self.dihedral_proxies_ref[file],
sites_cart=self.sites_cart_ref[file],
pdb_hierarchy=hierarchy,
include_hydrogens=self.params.hydrogens,
include_main_chain=self.params.main_chain,
include_side_chain=self.params.side_chain)
self.match_map = None
self.proxy_map = None
self.build_reference_dihedral_proxy_hash()
#
# This takes 80% of constructor time!!!
self.residue_match_hash = {} # {key_model: ('file_name', key_ref)}
self.match_map = {} # {'file_name':{i_seq_model:i_seq_ref}}
if params.use_starting_model_as_reference:
self.get_matching_from_self()
else:
self.get_matching_from_ncs(log=log)
if self.match_map == {}:
# making empty container
new_ref_dih_proxies = self.reference_dihedral_proxies = \
cctbx.geometry_restraints.shared_dihedral_proxy()
else:
new_ref_dih_proxies = self.get_reference_dihedral_proxies(
processed_pdb_file=processed_pdb_file)