def __init__(self,
pdb_hierarchy,
geometry_restraints,
use_ideal_bonds_angles=True,
process_manager=True):
self.pdb_hierarchy = pdb_hierarchy
self.geometry_restraints = geometry_restraints
self.use_ideal_bonds_angles = use_ideal_bonds_angles
#
self.hd_selection = self.pdb_hierarchy.atom_selection_cache().\
selection("element H or element D")
self.not_hd_selection = ~self.hd_selection
self.h_parameterization = []
self.parameterization_cpp = []
if process_manager is True:
connectivity_manager = connectivity.determine_connectivity(
pdb_hierarchy=self.pdb_hierarchy,
geometry_restraints=geometry_restraints)
h_connectivity = connectivity_manager.h_connectivity
diagnostics_connectivity = connectivity_manager.get_diagnostics()
parameterization_manager = parameterization.manager(
h_connectivity=h_connectivity,
sites_cart=self.pdb_hierarchy.atoms().extract_xyz(),
use_ideal_bonds_angles=use_ideal_bonds_angles)
self.h_parameterization = parameterization_manager.h_parameterization
self.parameterization_cpp = self.get_parameterization_cpp(
h_parameterization=self.h_parameterization)
def __init__(self,
pdb_hierarchy,
geometry_restraints,
use_ideal_bonds_angles=True):
self.cs = geometry_restraints.crystal_symmetry
self.pdb_hierarchy = pdb_hierarchy
self.connectivity_manager = connectivity.determine_connectivity(
pdb_hierarchy=self.pdb_hierarchy,
geometry_restraints=geometry_restraints)
self.h_connectivity = self.connectivity_manager.h_connectivity
self.double_H = self.connectivity_manager.double_H
self.connectivity_slipped = self.connectivity_manager.connectivity_slipped
self.parameterization_manager = parameterization.manager(
h_connectivity=self.h_connectivity,
sites_cart=self.pdb_hierarchy.atoms().extract_xyz(),
use_ideal_bonds_angles=use_ideal_bonds_angles)
self.h_parameterization = \
self.parameterization_manager.determine_parameterization()
self.parameterization_cpp = []
for hp in self.h_parameterization:
if (hp is not None):
self.parameterization_cpp.append(hp)
self.hd_selection = self.pdb_hierarchy.atom_selection_cache().\
selection("element H or element D")
self.not_hd_selection = ~self.hd_selection
def __init__(self,
pdb_hierarchy,
geometry_restraints,
use_ideal_bonds_angles=True,
process_manager=True,
use_ideal_dihedral=False,
ignore_h_with_dof=False):
self.pdb_hierarchy = pdb_hierarchy
self.geometry_restraints = geometry_restraints
self.use_ideal_bonds_angles = use_ideal_bonds_angles
self.ignore_h_with_dof = ignore_h_with_dof
#
self.hd_selection = self.pdb_hierarchy.atom_selection_cache().\
selection("element H or element D")
self.not_hd_selection = ~self.hd_selection
self.h_parameterization = []
self.parameterization_cpp = []
if process_manager is True:
connectivity_manager = connectivity.determine_connectivity(
pdb_hierarchy=self.pdb_hierarchy,
geometry_restraints=geometry_restraints)
h_connectivity = connectivity_manager.h_connectivity
diagnostics_connectivity = connectivity_manager.get_diagnostics()
parameterization_manager = parameterization.manager(
h_connectivity=h_connectivity,
sites_cart=self.pdb_hierarchy.atoms().extract_xyz(),
use_ideal_bonds_angles=use_ideal_bonds_angles,
site_labels=[
atom.id_str().replace('pdb=', '').replace('"', '')
for atom in pdb_hierarchy.atoms()
],
use_ideal_dihedral=use_ideal_dihedral,
ignore_h_with_dof=self.ignore_h_with_dof)
self.h_parameterization = parameterization_manager.h_parameterization
self.parameterization_cpp = self.get_parameterization_cpp(
h_parameterization=self.h_parameterization)
def exercise2():
pdb_str = """
CRYST1 16.660 12.742 18.240 90.00 90.00 90.00 P 1
SCALE1 0.060024 0.000000 0.000000 0.00000
SCALE2 0.000000 0.078481 0.000000 0.00000
SCALE3 0.000000 0.000000 0.054825 0.00000
ATOM 1 N TYR A 7 9.837 5.000 6.625 1.00 15.00 N
ATOM 2 CA TYR A 7 10.084 6.426 6.798 1.00 15.00 C
ATOM 3 C TYR A 7 11.431 6.813 6.197 1.00 15.00 C
ATOM 4 O TYR A 7 11.660 6.642 5.000 1.00 15.00 O
ATOM 5 CB TYR A 7 10.042 6.803 8.281 1.00 15.00 C
ATOM 6 CG TYR A 7 8.697 6.593 8.948 1.00 15.00 C
ATOM 7 CD1 TYR A 7 7.540 6.413 8.198 1.00 15.00 C
ATOM 8 CD2 TYR A 7 8.586 6.575 10.332 1.00 15.00 C
ATOM 9 CE1 TYR A 7 6.315 6.222 8.807 1.00 15.00 C
ATOM 10 CE2 TYR A 7 7.364 6.384 10.950 1.00 15.00 C
ATOM 11 CZ TYR A 7 6.233 6.208 10.183 1.00 15.00 C
ATOM 12 OH TYR A 7 5.015 6.018 10.794 1.00 15.00 O
ATOM 13 HA TYR A 7 9.398 6.930 6.331 1.00 15.00 H
ATOM 14 HB2 TYR A 7 10.693 6.264 8.757 1.00 15.00 H
ATOM 15 HB3 TYR A 7 10.270 7.742 8.369 1.00 15.00 H
ATOM 16 HD1 TYR A 7 7.589 6.422 7.269 1.00 15.00 H
ATOM 17 HD2 TYR A 7 9.347 6.694 10.853 1.00 15.00 H
ATOM 18 HE1 TYR A 7 5.550 6.103 8.292 1.00 15.00 H
ATOM 19 HE2 TYR A 7 7.306 6.375 11.878 1.00 15.00 H
ATOM 20 HH TYR A 7 5.000 6.415 11.534 1.00 15.00 H
TER
HETATM 21 O HOH B 1 5.307 7.545 13.240 1.00 30.00 O
TER
END
"""
edits = """
geometry_restraints.edits {
bond {
atom_selection_1 = chain A and resseq 7 and name HH
atom_selection_2 = chain B and resseq 1 and name O
distance_ideal = 1.81
sigma = 0.05
}
}
"""
type_list_known = [
'3neigbs', '2tetra', '2tetra', 'flat_2neigbs', 'flat_2neigbs',
'flat_2neigbs', 'flat_2neigbs', 'alg1b'
]
gm_phil = iotbx.phil.parse(input_string=grand_master_phil_str,
process_includes=True)
edits_phil = iotbx.phil.parse(edits)
working_phil = gm_phil.fetch(edits_phil)
params = working_phil.extract()
# Make sure the angle edit is present
assert (params.geometry_restraints.edits.bond[0].atom_selection_1 == \
"chain A and resseq 7 and name HH")
pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp,
build_grm=True,
pdb_interpretation_params=params)
pdb_hierarchy = model.get_hierarchy()
sites_cart = model.get_sites_cart()
atoms = pdb_hierarchy.atoms()
model.setup_riding_h_manager()
riding_h_manager = model.get_riding_h_manager()
h_para = riding_h_manager.h_parameterization
diagnostics = riding_h_manager.diagnostics(sites_cart=sites_cart,
threshold=0.05)
h_distances = diagnostics.h_distances
type_list = diagnostics.type_list
number_h = model.get_hd_selection().count(True)
number_h_para = len(h_para) - h_para.count(None)
connectivity_manager = connectivity.determine_connectivity(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints=model.get_restraints_manager().geometry)
double_H = connectivity_manager.double_H
# Test if number of paramterized H atoms is correct
assert (number_h == number_h_para), 'Not all H atoms are parameterized'
assert (double_H[19] == [11,
20]), 'H bound to two atoms wrongly recognized'
assert (number_h_para == 8), 'Not all H atoms are parameterized'
for ih in h_distances:
labels = atoms[ih].fetch_labels()
if (h_distances[ih] > 0.1):
assert (h_distances[ih] < 0.1), \
'distance too large: %s atom: %s (%s) residue: %s ' \
% (h_para[ih].htype, atoms[ih].name, ih, labels.resseq.strip())
for type1, type2 in zip(type_list, type_list_known):
assert (type1 == type2)
def exercise():
pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=True)
restraints_manager = model.get_restraints_manager()
angle_proxies = restraints_manager.geometry.get_all_angle_proxies()
connectivity_manager = connectivity.determine_connectivity(
pdb_hierarchy=model.get_hierarchy(),
geometry_restraints=restraints_manager.geometry)
h_connectivity = connectivity_manager.h_connectivity
# get bonds stored in connectivity
bond_list = {}
angle_list = {}
for neighbors in h_connectivity:
if (neighbors is None): continue
ih = neighbors.ih
a0 = neighbors.a0
i_a0 = a0['iseq']
a1 = neighbors.a1
i_a1 = a1['iseq']
bond_list[ih] = [i_a0, a0['dist_ideal']]
selected_atoms = tuple(sorted([ih, i_a0, i_a1]))
angle_list[selected_atoms] = a1['angle_ideal']
if neighbors.a2:
a2 = neighbors.a2
selected_atoms2 = tuple(sorted([ih, i_a0, a2['iseq']]))
angle_list[selected_atoms2] = a2['angle_ideal']
if neighbors.a3:
a3 = neighbors.a3
selected_atoms3 = tuple(sorted([ih, i_a0, a3['iseq']]))
angle_list[selected_atoms3] = a3['angle_ideal']
if neighbors.h1:
h1 = neighbors.h1
selected_atoms4 = tuple(sorted([ih, i_a0, h1['iseq']]))
angle_list[selected_atoms4] = h1['angle_ideal']
if neighbors.b1:
i_b1 = neighbors.b1['iseq']
third_nb_dict = {ih: i_b1}
bond_ctrl = {}
for i in model.xh_connectivity_table():
bond_ctrl[i[1]] = [i[0], i[3]]
# List of angle restraints
angles = [(4, 1, 12), (0, 1, 12), (2, 1, 12), (13, 4, 14), (5, 4, 14),
(5, 4, 13), (1, 4, 13), (1, 4, 14), (8, 6, 15), (5, 6, 15),
(9, 7, 16), (5, 7, 16), (10, 8, 17), (6, 8, 17), (10, 11, 19),
(7, 9, 18), (10, 9, 18)]
angle_ctrl = {}
for ap in angle_proxies:
if (ap.i_seqs in angles):
angle_ctrl[tuple(sorted(list(ap.i_seqs)))] = ap.angle_ideal
# HH needs also third neighbors:
third_nb_ctrl = {19: 8}
assert (
bond_list == bond_ctrl), '1-2 neighbors and distance_ideal are wrong'
assert (
angle_list == angle_ctrl), '1-3 neighbors and angle_ideal are wrong'
assert (third_nb_dict == third_nb_ctrl), '1-4 neighbors are wrong'