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")