def get_dihedrals_and_phi_psi(model):
from cctbx.geometry_restraints import dihedral_proxy_registry
dihedral_registry = dihedral_proxy_registry(strict_conflict_handling=True)
dihedral_registry.initialize_table()
from mmtbx.conformation_dependent_library import generate_protein_threes
grm = model._processed_pdb_file.geometry_restraints_manager()
dihedral_proxies = grm.get_dihedral_proxies().deep_copy()
for p in dihedral_proxies:
dihedral_registry.add_if_not_duplicated(p)
for three in generate_protein_threes(hierarchy=model.get_hierarchy(),
geometry=None):
proxies = three.get_dummy_dihedral_proxies(only_psi_phi_pairs=False)
for p in proxies:
dihedral_registry.add_if_not_duplicated(p)
return dihedral_registry.proxies
def get_complete_dihedral_proxies_2(model, log=None):
from six.moves import cStringIO as StringIO
from cctbx.geometry_restraints import dihedral_proxy_registry
from mmtbx.conformation_dependent_library import generate_protein_threes
if log is None:
log = StringIO
dihedral_registry = dihedral_proxy_registry(strict_conflict_handling=True)
dihedral_registry.initialize_table()
grm = model.get_restraints_manager().geometry
dihedral_proxies = grm.get_dihedral_proxies().deep_copy()
for p in dihedral_proxies:
dihedral_registry.add_if_not_duplicated(p)
for three in generate_protein_threes(hierarchy=model.get_hierarchy(),
geometry=None):
proxies = three.get_dummy_dihedral_proxies(only_psi_phi_pairs=False)
for p in proxies:
dihedral_registry.add_if_not_duplicated(p)
return dihedral_registry.proxies
def get_dihedrals_and_phi_psi(processed_pdb_file):
from cctbx.geometry_restraints import dihedral_proxy_registry
dihedral_registry = dihedral_proxy_registry(
strict_conflict_handling=True)
dihedral_registry.initialize_table()
from mmtbx.conformation_dependent_library import generate_protein_threes
grm = processed_pdb_file.geometry_restraints_manager()
dihedral_proxies = grm.get_dihedral_proxies().deep_copy()
for p in dihedral_proxies:
dihedral_registry.add_if_not_duplicated(p)
for three in generate_protein_threes(
hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy,
geometry=None):
proxies = three.get_dummy_dihedral_proxies(
only_psi_phi_pairs=False)
for p in proxies:
dihedral_registry.add_if_not_duplicated(p)
return dihedral_registry.proxies
def run(args):
assert len(args) == 0
#
r = geometry_restraints.angle_proxy_registry(
strict_conflict_handling=True)
r.initialize_table()
r.process(
source_info=source_info_server(),
proxy=geometry_restraints.angle_proxy(
i_seqs=(4,2,7), angle_ideal=0, weight=1))
r.process(
source_info=source_info_server(),
proxy=geometry_restraints.angle_proxy(
i_seqs=(5,2,3), angle_ideal=0, weight=1))
assert r.lookup_i_proxy((4,2,7)) == 0
assert r.lookup_i_proxy((7,2,4)) == 0
assert r.lookup_i_proxy((2,7,4)) is None
assert r.lookup_i_proxy((3,2,5)) == 1
assert r.lookup_i_proxy((5,2,3)) == 1
assert r.lookup_i_proxy((5,3,2)) is None
#
r = geometry_restraints.dihedral_proxy_registry(
strict_conflict_handling=True)
r.initialize_table()
r.process(
source_info=source_info_server(),
proxy=geometry_restraints.dihedral_proxy(
i_seqs=(4,7,2,3), angle_ideal=0, weight=1))
r.process(
source_info=source_info_server(),
proxy=geometry_restraints.dihedral_proxy(
i_seqs=(8,2,3,5), angle_ideal=0, weight=1))
r.process(
source_info=source_info_server(),
proxy=geometry_restraints.dihedral_proxy(
i_seqs=(6,3,1,9), angle_ideal=0, weight=1))
assert r.lookup_i_proxy((3,2,7,4)) == (0, 1)
assert r.lookup_i_proxy((4,2,7,3)) == (0, -1)
assert r.lookup_i_proxy((4,7,2,3)) == (0, 1)
assert r.lookup_i_proxy((3,7,2,4)) == (0, -1)
assert r.lookup_i_proxy((5,2,3,8)) == (1, 1)
assert r.lookup_i_proxy((6,3,1,9)) == (2, -1)
#
print "OK"
def run(args):
assert len(args) == 0
#
r = geometry_restraints.angle_proxy_registry(strict_conflict_handling=True)
r.initialize_table()
r.process(source_info=source_info_server(),
proxy=geometry_restraints.angle_proxy(i_seqs=(4, 2, 7),
angle_ideal=0,
weight=1))
r.process(source_info=source_info_server(),
proxy=geometry_restraints.angle_proxy(i_seqs=(5, 2, 3),
angle_ideal=0,
weight=1))
assert r.lookup_i_proxy((4, 2, 7)) == 0
assert r.lookup_i_proxy((7, 2, 4)) == 0
assert r.lookup_i_proxy((2, 7, 4)) is None
assert r.lookup_i_proxy((3, 2, 5)) == 1
assert r.lookup_i_proxy((5, 2, 3)) == 1
assert r.lookup_i_proxy((5, 3, 2)) is None
#
r = geometry_restraints.dihedral_proxy_registry(
strict_conflict_handling=True)
r.initialize_table()
r.process(source_info=source_info_server(),
proxy=geometry_restraints.dihedral_proxy(i_seqs=(4, 7, 2, 3),
angle_ideal=0,
weight=1))
r.process(source_info=source_info_server(),
proxy=geometry_restraints.dihedral_proxy(i_seqs=(8, 2, 3, 5),
angle_ideal=0,
weight=1))
r.process(source_info=source_info_server(),
proxy=geometry_restraints.dihedral_proxy(i_seqs=(6, 3, 1, 9),
angle_ideal=0,
weight=1))
assert r.lookup_i_proxy((3, 2, 7, 4)) == (0, 1)
assert r.lookup_i_proxy((4, 2, 7, 3)) == (0, -1)
assert r.lookup_i_proxy((4, 7, 2, 3)) == (0, 1)
assert r.lookup_i_proxy((3, 7, 2, 4)) == (0, -1)
assert r.lookup_i_proxy((5, 2, 3, 8)) == (1, 1)
assert r.lookup_i_proxy((6, 3, 1, 9)) == (2, -1)
#
print("OK")
