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