def __init__(self, *args, **kwds):
super(restrained_crystal_structure_builder,
self).__init__(*args, **kwds)
geom = geometry_restraints
adp = adp_restraints
self._proxies = {}
self._proxies = {
'bond':
geometry_restraints.shared_bond_simple_proxy(),
'angle':
geometry_restraints.shared_angle_proxy(),
'dihedral':
geometry_restraints.shared_dihedral_proxy(),
'planarity':
geometry_restraints.shared_planarity_proxy(),
'chirality':
geometry_restraints.shared_chirality_proxy(),
'bond_similarity':
geometry_restraints.shared_bond_similarity_proxy(),
'adp_similarity':
adp_restraints.shared_adp_similarity_proxy(),
'rigid_bond':
adp_restraints.shared_rigid_bond_proxy(),
'isotropic_adp':
adp_restraints.shared_isotropic_adp_proxy(),
'fixed_u_eq_adp':
adp_restraints.shared_fixed_u_eq_adp_proxy(),
'adp_u_eq_similarity':
adp_restraints.shared_adp_u_eq_similarity_proxy(),
'adp_volume_similarity':
adp_restraints.shared_adp_volume_similarity_proxy(),
}
class dihedral_restraint_test_case(geometry_restraints_test_case):
manager = restraints.manager(
dihedral_proxies=geometry_restraints.shared_dihedral_proxy([
geom.dihedral_proxy((21, 19, 24, 26), 180, 1),
geom.dihedral_proxy((5, 26, 28, 7), 60, 1)
]))
proxies = manager.dihedral_proxies
restraint_t = geom.dihedral
def generate_torsion_restraints(
pdb_hierarchy,
sites_cart,
selection=None,
sigma=2.5,
limit=15.0,
chi_angles_only=False,
top_out_potential=False,
origin_id=2):
torsion_proxies = geometry_restraints.shared_dihedral_proxy()
if pdb_hierarchy.atoms().size() < 4:
return torsion_proxies
assert not pdb_hierarchy.atoms().extract_i_seq().all_eq(0)
bool_pdbh_selection = flex.bool(pdb_hierarchy.atoms_size(), False)
if (selection is not None):
if (isinstance(selection, flex.bool)):
bool_pdbh_selection = selection
elif (isinstance(selection, flex.size_t)):
bool_pdbh_selection.set_selected(selection, True)
if selection is None:
bool_pdbh_selection = flex.bool(pdb_hierarchy.atoms_size(), True)
actual_selection = bool_pdbh_selection.iselection()
assert len(sites_cart) == len(actual_selection)
weight = 1.0 / (sigma**2)
selection_to_sites_map = get_selection_to_sites_map(
sites_cart=sites_cart,
selection=actual_selection)
residue_torsions = collect_residue_torsion_angles(
pdb_hierarchy=pdb_hierarchy,
atom_selection=bool_pdbh_selection,
chi_angles_only=chi_angles_only)
for residue_info in residue_torsions:
for chi in residue_info.chis:
i_seqs = chi.i_seqs
sites = []
for i_seq in i_seqs:
sites.append(selection_to_sites_map[i_seq])
di = geometry_restraints.dihedral(
sites=sites, angle_ideal=0.0, weight=weight)
angle_ideal = di.angle_model
dp = geometry_restraints.dihedral_proxy(
i_seqs=i_seqs,
angle_ideal=angle_ideal,
weight=weight,
limit=limit,
top_out=top_out_potential,
origin_id=origin_id)
torsion_proxies.append(dp)
return torsion_proxies
def generate_torsion_restraints(
pdb_hierarchy,
sites_cart,
selection=None,
sigma=2.5,
limit=15.0,
chi_angles_only=False,
top_out_potential=False,
origin_id=None):
torsion_proxies = geometry_restraints.shared_dihedral_proxy()
if pdb_hierarchy.atoms_size() < 4:
return torsion_proxies
assert not pdb_hierarchy.atoms().extract_i_seq().all_eq(0)
bool_pdbh_selection = flex.bool(pdb_hierarchy.atoms_size(), False)
if (selection is not None):
if (isinstance(selection, flex.bool)):
bool_pdbh_selection = selection
elif (isinstance(selection, flex.size_t)):
bool_pdbh_selection.set_selected(selection, True)
if selection is None:
bool_pdbh_selection = flex.bool(pdb_hierarchy.atoms_size(), True)
actual_selection = bool_pdbh_selection.iselection()
assert len(sites_cart) == len(actual_selection)
weight = 1.0 / (sigma**2)
selection_to_sites_map = get_selection_to_sites_map(
sites_cart=sites_cart,
selection=actual_selection)
residue_torsions = collect_residue_torsion_angles(
pdb_hierarchy=pdb_hierarchy,
atom_selection=bool_pdbh_selection,
chi_angles_only=chi_angles_only)
for residue_info in residue_torsions:
for chi in residue_info.chis:
i_seqs = chi.i_seqs
sites = []
for i_seq in i_seqs:
sites.append(selection_to_sites_map[i_seq])
di = geometry_restraints.dihedral(
sites=sites, angle_ideal=0.0, weight=weight)
angle_ideal = di.angle_model
dp = geometry_restraints.dihedral_proxy(
i_seqs=i_seqs,
angle_ideal=angle_ideal,
weight=weight,
limit=limit,
top_out=top_out_potential,
origin_id=origin_id)
torsion_proxies.append(dp)
return torsion_proxies
def __init__(self, *args, **kwds):
super(restrained_crystal_structure_builder, self).__init__(*args, **kwds)
geom = geometry_restraints
adp = adp_restraints
self._proxies = {}
self._proxies = {
'bond': geometry_restraints.shared_bond_simple_proxy(),
'angle': geometry_restraints.shared_angle_proxy(),
'dihedral': geometry_restraints.shared_dihedral_proxy(),
'planarity': geometry_restraints.shared_planarity_proxy(),
'chirality': geometry_restraints.shared_chirality_proxy(),
'bond_similarity': geometry_restraints.shared_bond_similarity_proxy(),
'adp_similarity': adp_restraints.shared_adp_similarity_proxy(),
'rigid_bond': adp_restraints.shared_rigid_bond_proxy(),
'isotropic_adp': adp_restraints.shared_isotropic_adp_proxy(),
'fixed_u_eq_adp': adp_restraints.shared_fixed_u_eq_adp_proxy(),
'adp_u_eq_similarity': adp_restraints.shared_adp_u_eq_similarity_proxy(),
'adp_volume_similarity': adp_restraints.shared_adp_volume_similarity_proxy(),
}
def read_pdb():
pdbstring = """\
ATOM 0 CA GLY A 3 5.804 -2.100 7.324 1.00 1.36 C
ATOM 1 C GLY A 3 4.651 -1.149 7.578 1.00 1.01 C
ATOM 2 O GLY A 3 3.598 -1.553 8.071 1.00 1.38 O
ATOM 3 N GLY A 3 6.706 -1.622 6.294 1.00 1.11 N
ATOM 4 CA PHE A 4 3.819 1.134 7.419 1.00 0.89 C
ATOM 5 CB PHE A 4 4.397 2.380 8.094 1.00 1.13 C
ATOM 6 C PHE A 4 3.185 1.509 6.084 1.00 0.94 C
ATOM 7 N PHE A 4 4.852 0.121 7.242 1.00 0.88 N
ATOM 8 O PHE A 4 2.361 2.421 6.010 1.00 1.47 O
ATOM 9 CA LEU A 5 3.055 1.059 3.693 1.00 0.87 C
ATOM 10 CB LEU A 5 3.965 0.435 2.634 1.00 1.13 C
ATOM 11 C LEU A 5 1.634 0.527 3.541 1.00 0.87 C
ATOM 12 N LEU A 5 3.576 0.800 5.030 1.00 0.92 N
ATOM 13 O LEU A 5 1.246 -0.440 4.196 1.00 1.23 O
"""
pdb_inp = iotbx.pdb.input(lines=flex.split_lines(pdbstring),
source_info=None)
sites_cart = pdb_inp.atoms().extract_xyz()
# TRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3
# TRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2
dihedral_proxies = geometry_restraints.shared_dihedral_proxy()
# residue 1
psi = geometry_restraints.dihedral_proxy(i_seqs=[3, 0, 1, 7],
angle_ideal=160.0,
weight=1 / 30.0**2,
periodicity=3)
dihedral_proxies.append(psi)
# residue 2
phi = geometry_restraints.dihedral_proxy(i_seqs=[1, 7, 4, 6],
angle_ideal=60.0,
weight=1 / 20.0**2,
periodicity=3)
dihedral_proxies.append(phi)
psi = geometry_restraints.dihedral_proxy(i_seqs=[7, 4, 6, 8],
angle_ideal=160.0,
weight=1 / 30.0**2,
periodicity=3)
dihedral_proxies.append(psi)
# residue 3
phi = geometry_restraints.dihedral_proxy(i_seqs=[6, 12, 9, 11],
angle_ideal=60.0,
weight=1 / 20.0**2,
periodicity=3)
dihedral_proxies.append(phi)
angle_proxies = geometry_restraints.shared_angle_proxy()
## Residue 1
# a3
a = geometry_restraints.angle_proxy(i_seqs=[3, 0, 1],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
# a7
a = geometry_restraints.angle_proxy(i_seqs=[2, 1, 7],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
## Residue 2
# a1
a = geometry_restraints.angle_proxy(i_seqs=[1, 7, 4],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
# a3
a = geometry_restraints.angle_proxy(i_seqs=[7, 4, 6],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
# a7
a = geometry_restraints.angle_proxy(i_seqs=[8, 6, 12],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
## Residue 3
# a1
a = geometry_restraints.angle_proxy(i_seqs=[6, 12, 9],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
# a3
a = geometry_restraints.angle_proxy(i_seqs=[12, 9, 11],
angle_ideal=0,
weight=1)
angle_proxies.append(a)
# compute dihedral
#dihedral = geometry_restraints.dihedral(
# sites_cart=sites_cart,
# proxy=dihedral_proxies[0])
# Shows real dihedral value
#print dihedral.angle_model, dihedral.delta
cfd_list = []
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='GLY',
next_residue_name='PHE',
conformation_proxies=None,
i_phi_proxy=None, # index into dihedral_proxies
i_psi_proxy=0,
i_dynamic_angles=[None, None, 0, None, None, None,
1], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None)
cfd_list.append(cfd)
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='PHE',
next_residue_name='LEU',
conformation_proxies=None,
i_phi_proxy=1, # index into dihedral_proxies
i_psi_proxy=2,
i_dynamic_angles=[2, None, 3, None, None, None,
4], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None)
cfd_list.append(cfd)
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='LEU',
next_residue_name=None,
conformation_proxies=None,
i_phi_proxy=3, # index into dihedral_proxies
i_psi_proxy=None,
i_dynamic_angles=[5, None, 6, None, None, None,
None], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None)
cfd_list.append(cfd)
for x in range(1, 4):
print
print 'Starting cycle', x
print
for cfd in cfd_list:
cfd.update_restraints(sites_cart, dihedral_proxies, angle_proxies)
def exercise_geometry_restraints_as_cif():
quartz = xray.structure(crystal_symmetry=crystal.symmetry(
(5.01, 5.01, 5.47, 90, 90, 120), "P6222"),
scatterers=flex.xray_scatterer([
xray.scatterer("Si", (1 / 2., 1 / 2., 1 / 3.)),
xray.scatterer("O", (0.197, -0.197, 0.83333))
]))
bond_proxies = geometry_restraints.shared_bond_simple_proxy((
geometry_restraints.bond_simple_proxy(
i_seqs=[0, 1],
rt_mx_ji=sgtbx.rt_mx("x-y,x,z-2/3"),
distance_ideal=1.6,
weight=3.2),
geometry_restraints.bond_simple_proxy(i_seqs=[0, 1],
distance_ideal=1.7,
weight=1.8),
))
dihedral_proxies = geometry_restraints.shared_dihedral_proxy((
geometry_restraints.dihedral_proxy(
i_seqs=[1, 0, 1, 0],
sym_ops=(sgtbx.rt_mx("1+y,1-x+y, z-1/3"), sgtbx.rt_mx(),
sgtbx.rt_mx("x-y,x,z-2/3"), sgtbx.rt_mx("1-x,y-x,1/3-z")),
angle_ideal=-30,
weight=2),
geometry_restraints.dihedral_proxy(
i_seqs=[1, 0, 1, 0],
sym_ops=(sgtbx.rt_mx("1+y,1-x+y, z-1/3"), sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3"), sgtbx.rt_mx("x-y,x,1/3+z")),
angle_ideal=90,
weight=3),
))
angle_proxies = geometry_restraints.shared_angle_proxy((
geometry_restraints.angle_proxy(i_seqs=[1, 0, 1],
sym_ops=(sgtbx.rt_mx("x-y,x,z-2/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3")),
angle_ideal=103,
weight=2),
geometry_restraints.angle_proxy(
i_seqs=[1, 0, 1],
sym_ops=(sgtbx.rt_mx("y+1,-x+y+1,z-1/3"), sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3")),
angle_ideal=110,
weight=5),
geometry_restraints.angle_proxy(i_seqs=[0, 1, 0],
sym_ops=(sgtbx.rt_mx("y,-x+y,z+2/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-x+y,-x,z+1/3")),
angle_ideal=150,
weight=5),
))
bond_similarity_proxies = geometry_restraints.shared_bond_similarity_proxy(
(geometry_restraints.bond_similarity_proxy(
i_seqs=[(0, 1), (0, 1), (0, 1)],
sym_ops=(sgtbx.rt_mx("x-y,x,z-2/3"), sgtbx.rt_mx("-y,x-y,z-1/3"),
sgtbx.rt_mx("y+1,-x+y+1,z-1/3")),
weights=(1, 1, 1)), ))
cif_block = iotbx.cif.model.block()
iotbx.cif.restraints.add_to_cif_block(
cif_block,
quartz,
bond_proxies=bond_proxies,
angle_proxies=angle_proxies,
dihedral_proxies=dihedral_proxies,
bond_similarity_proxies=bond_similarity_proxies)
s = StringIO()
cif_block.show(out=s)
assert not show_diff(
s.getvalue(), """\
loop_
_restr_distance_atom_site_label_1
_restr_distance_atom_site_label_2
_restr_distance_site_symmetry_2
_restr_distance_target
_restr_distance_target_weight_param
_restr_distance_diff
Si O 2_554 1.6000 0.5590 -0.0160
Si O 1 1.7000 0.7454 -2.3838
loop_
_restr_angle_atom_site_label_1
_restr_angle_atom_site_label_2
_restr_angle_atom_site_label_3
_restr_angle_site_symmetry_1
_restr_angle_site_symmetry_2
_restr_angle_site_symmetry_3
_restr_angle_target
_restr_angle_target_weight_param
_restr_angle_diff
O Si O 2_554 1 4_554 103.0000 0.7071 1.6926
O Si O 3_664 1 4_554 110.0000 0.4472 -1.3127
Si O Si 3 1 5 150.0000 0.4472 3.0700
loop_
_restr_torsion_atom_site_label_1
_restr_torsion_atom_site_label_2
_restr_torsion_atom_site_label_3
_restr_torsion_atom_site_label_4
_restr_torsion_site_symmetry_1
_restr_torsion_site_symmetry_2
_restr_torsion_site_symmetry_3
_restr_torsion_site_symmetry_4
_restr_torsion_angle_target
_restr_torsion_weight_param
_restr_torsion_diff
O Si O Si 3_664 1 2_554 7_655 -30.0000 0.7071 6.9078
O Si O Si 3_664 1 4_554 2 90.0000 0.5774 11.7036
loop_
_restr_equal_distance_class_class_id
_restr_equal_distance_class_target_weight_param
_restr_equal_distance_class_average
_restr_equal_distance_class_esd
_restr_equal_distance_class_diff_max
1 1.0000 1.6160 0.0000 0.0000
loop_
_restr_equal_distance_atom_site_label_1
_restr_equal_distance_atom_site_label_2
_restr_equal_distance_site_symmetry_2
_restr_equal_distance_class_id
Si O 2_554 1
Si O 4_554 1
Si O 3_664 1
""")
def read_pdb():
pdbstring = """\
ATOM 0 CA GLY A 3 5.804 -2.100 7.324 1.00 1.36 C
ATOM 1 C GLY A 3 4.651 -1.149 7.578 1.00 1.01 C
ATOM 2 O GLY A 3 3.598 -1.553 8.071 1.00 1.38 O
ATOM 3 N GLY A 3 6.706 -1.622 6.294 1.00 1.11 N
ATOM 4 CA PHE A 4 3.819 1.134 7.419 1.00 0.89 C
ATOM 5 CB PHE A 4 4.397 2.380 8.094 1.00 1.13 C
ATOM 6 C PHE A 4 3.185 1.509 6.084 1.00 0.94 C
ATOM 7 N PHE A 4 4.852 0.121 7.242 1.00 0.88 N
ATOM 8 O PHE A 4 2.361 2.421 6.010 1.00 1.47 O
ATOM 9 CA LEU A 5 3.055 1.059 3.693 1.00 0.87 C
ATOM 10 CB LEU A 5 3.965 0.435 2.634 1.00 1.13 C
ATOM 11 C LEU A 5 1.634 0.527 3.541 1.00 0.87 C
ATOM 12 N LEU A 5 3.576 0.800 5.030 1.00 0.92 N
ATOM 13 O LEU A 5 1.246 -0.440 4.196 1.00 1.23 O
"""
pdb_inp = iotbx.pdb.input(
lines=flex.split_lines(pdbstring), source_info=None)
sites_cart = pdb_inp.atoms().extract_xyz()
# TRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3
# TRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2
dihedral_proxies = geometry_restraints.shared_dihedral_proxy()
# residue 1
psi = geometry_restraints.dihedral_proxy(
i_seqs=[3, 0, 1, 7],
angle_ideal=160.0,
weight=1/30.0**2,
periodicity=3
)
dihedral_proxies.append(psi)
# residue 2
phi = geometry_restraints.dihedral_proxy(
i_seqs=[1, 7, 4, 6],
angle_ideal=60.0,
weight=1/20.0**2,
periodicity=3
)
dihedral_proxies.append(phi)
psi = geometry_restraints.dihedral_proxy(
i_seqs=[7, 4, 6, 8],
angle_ideal=160.0,
weight=1/30.0**2,
periodicity=3
)
dihedral_proxies.append(psi)
# residue 3
phi = geometry_restraints.dihedral_proxy(
i_seqs=[6, 12, 9, 11],
angle_ideal=60.0,
weight=1/20.0**2,
periodicity=3
)
dihedral_proxies.append(phi)
angle_proxies = geometry_restraints.shared_angle_proxy()
## Residue 1
# a3
a = geometry_restraints.angle_proxy(
i_seqs=[3, 0, 1],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
# a7
a = geometry_restraints.angle_proxy(
i_seqs=[2, 1, 7],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
## Residue 2
# a1
a = geometry_restraints.angle_proxy(
i_seqs=[1, 7, 4],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
# a3
a = geometry_restraints.angle_proxy(
i_seqs=[7, 4, 6],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
# a7
a = geometry_restraints.angle_proxy(
i_seqs=[8, 6, 12],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
## Residue 3
# a1
a = geometry_restraints.angle_proxy(
i_seqs=[6, 12, 9],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
# a3
a = geometry_restraints.angle_proxy(
i_seqs=[12, 9, 11],
angle_ideal=0,
weight=1
)
angle_proxies.append(a)
# compute dihedral
#dihedral = geometry_restraints.dihedral(
# sites_cart=sites_cart,
# proxy=dihedral_proxies[0])
# Shows real dihedral value
#print dihedral.angle_model, dihedral.delta
cfd_list = []
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='GLY',
next_residue_name='PHE',
conformation_proxies=None,
i_phi_proxy=None, # index into dihedral_proxies
i_psi_proxy=0,
i_dynamic_angles=[None, None, 0, None, None, None, 1], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None
)
cfd_list.append(cfd)
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='PHE',
next_residue_name='LEU',
conformation_proxies=None,
i_phi_proxy=1, # index into dihedral_proxies
i_psi_proxy=2,
i_dynamic_angles=[2, None, 3, None, None, None, 4], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None
)
cfd_list.append(cfd)
cfd = conformation_dependent_restraints.conformation_dependent_restraints(
residue_name='LEU',
next_residue_name=None,
conformation_proxies=None,
i_phi_proxy=3, # index into dihedral_proxies
i_psi_proxy=None,
i_dynamic_angles=[5, None, 6, None, None, None, None], # indexes into angles in angle_proxies
i_dynamic_dihedrals=None
)
cfd_list.append(cfd)
for x in range(1, 4):
print
print 'Starting cycle', x
print
for cfd in cfd_list:
cfd.update_restraints(sites_cart, dihedral_proxies, angle_proxies)
def build_conformation_dependent_angle_proxies(
angle_proxy_registry, dihedral_proxy_registry, monomer_mappings, connectivity_i_j, connectivity_j_k, sites_cart
):
"""
Sets up conformation_dependent_restraints object.
Finds atom indexes from registries
Looks for C_prev in m_i, most atoms in m_j, N_next in m_k.
"""
assert len(monomer_mappings) == 3
if monomer_mappings[1] is None:
residue_name = None
else:
residue_name = monomer_mappings[1].residue_name
if monomer_mappings[2] is None:
next_residue_name = None
else:
next_residue_name = monomer_mappings[2].residue_name
dihedral_i_proxies = []
conformation_proxies = geometry_restraints.shared_dihedral_proxy()
for dihedral_number, dihedral_definition in enumerate(conformation_dependent_geometry.angles.dihedral_atoms):
i_seqs = []
for residue_index, atom_name in dihedral_definition:
mm = monomer_mappings[residue_index]
if mm is not None:
i_seqs.append(getattr(mm.expected_atoms.get(atom_name), "i_seq", None))
# account for missing atoms
if len(i_seqs) == 4 and i_seqs.count(None) == 0:
if dihedral_number == 0:
# phi/psi: Restraints don't matter, we throw them away. This is just
# so we can get eventually get the current value.
phi = geometry_restraints.dihedral_proxy(
i_seqs=i_seqs, angle_ideal=60.0, weight=1 / 20.0 ** 2, periodicity=3
)
conformation_proxies.append(phi)
dihedral_i_proxies.append(None)
i_phi_proxy = 0
elif dihedral_number == 1:
psi = geometry_restraints.dihedral_proxy(
i_seqs=i_seqs, angle_ideal=160.0, weight=1 / 30.0 ** 2, periodicity=3
)
conformation_proxies.append(psi)
dihedral_i_proxies.append(None)
i_psi_proxy = 1
elif dihedral_number == 2:
# omega
dihedral_i_proxy, dihedral_sign = dihedral_proxy_registry.lookup_i_proxy(i_seqs)
dihedral_i_proxies.append(dihedral_i_proxy)
else:
pass
# we're on a dihedral with missing length or atoms that are None
else:
if dihedral_number == 0:
i_phi_proxy = None
elif dihedral_number == 1:
i_psi_proxy = None
elif dihedral_number == 2:
dihedral_i_proxies.append(None)
else:
pass
angle_i_proxies = []
for angle_definition in conformation_dependent_geometry.angles.angle_atoms:
i_seqs = []
for residue_index, atom_name in angle_definition:
mm = monomer_mappings[residue_index]
if mm is not None:
i_seqs.append(getattr(mm.expected_atoms.get(atom_name), "i_seq", None))
# account for missing atoms
if len(i_seqs) == 3 and i_seqs.count(None) == 0:
# go into angle_proxy_registry
angle_i_proxy = angle_proxy_registry.lookup_i_proxy(i_seqs)
angle_i_proxies.append(angle_i_proxy)
else:
# By filling in None for blanks, we can assume the lengths are equal
# here and other places angle_atoms/angle_names are used
angle_i_proxies.append(None)
cfd = conformation_dependent_restraints(
residue_name=residue_name,
next_residue_name=next_residue_name,
conformation_proxies=conformation_proxies,
i_phi_proxy=i_phi_proxy,
i_psi_proxy=i_psi_proxy,
i_dynamic_angles=angle_i_proxies,
i_dynamic_dihedrals=dihedral_i_proxies,
)
return cfd
def build_conformation_dependent_angle_proxies(angle_proxy_registry,
dihedral_proxy_registry,
monomer_mappings,
connectivity_i_j,
connectivity_j_k, sites_cart):
"""
Sets up conformation_dependent_restraints object.
Finds atom indexes from registries
Looks for C_prev in m_i, most atoms in m_j, N_next in m_k.
"""
assert len(monomer_mappings) == 3
if monomer_mappings[1] is None:
residue_name = None
else:
residue_name = monomer_mappings[1].residue_name
if monomer_mappings[2] is None:
next_residue_name = None
else:
next_residue_name = monomer_mappings[2].residue_name
dihedral_i_proxies = []
conformation_proxies = geometry_restraints.shared_dihedral_proxy()
for dihedral_number, dihedral_definition in enumerate(
conformation_dependent_geometry.angles.dihedral_atoms):
i_seqs = []
for residue_index, atom_name in dihedral_definition:
mm = monomer_mappings[residue_index]
if mm is not None:
i_seqs.append(
getattr(mm.expected_atoms.get(atom_name), "i_seq", None))
# account for missing atoms
if len(i_seqs) == 4 and i_seqs.count(None) == 0:
if dihedral_number == 0:
# phi/psi: Restraints don't matter, we throw them away. This is just
# so we can get eventually get the current value.
phi = geometry_restraints.dihedral_proxy(i_seqs=i_seqs,
angle_ideal=60.0,
weight=1 / 20.0**2,
periodicity=3)
conformation_proxies.append(phi)
dihedral_i_proxies.append(None)
i_phi_proxy = 0
elif dihedral_number == 1:
psi = geometry_restraints.dihedral_proxy(i_seqs=i_seqs,
angle_ideal=160.0,
weight=1 / 30.0**2,
periodicity=3)
conformation_proxies.append(psi)
dihedral_i_proxies.append(None)
i_psi_proxy = 1
elif dihedral_number == 2:
# omega
dihedral_i_proxy, dihedral_sign = dihedral_proxy_registry.lookup_i_proxy(
i_seqs)
dihedral_i_proxies.append(dihedral_i_proxy)
else:
pass
# we're on a dihedral with missing length or atoms that are None
else:
if dihedral_number == 0:
i_phi_proxy = None
elif dihedral_number == 1:
i_psi_proxy = None
elif dihedral_number == 2:
dihedral_i_proxies.append(None)
else:
pass
angle_i_proxies = []
for angle_definition in conformation_dependent_geometry.angles.angle_atoms:
i_seqs = []
for residue_index, atom_name in angle_definition:
mm = monomer_mappings[residue_index]
if mm is not None:
i_seqs.append(
getattr(mm.expected_atoms.get(atom_name), "i_seq", None))
# account for missing atoms
if len(i_seqs) == 3 and i_seqs.count(None) == 0:
# go into angle_proxy_registry
angle_i_proxy = angle_proxy_registry.lookup_i_proxy(i_seqs)
angle_i_proxies.append(angle_i_proxy)
else:
# By filling in None for blanks, we can assume the lengths are equal
# here and other places angle_atoms/angle_names are used
angle_i_proxies.append(None)
cfd = conformation_dependent_restraints(
residue_name=residue_name,
next_residue_name=next_residue_name,
conformation_proxies=conformation_proxies,
i_phi_proxy=i_phi_proxy,
i_psi_proxy=i_psi_proxy,
i_dynamic_angles=angle_i_proxies,
i_dynamic_dihedrals=dihedral_i_proxies)
return cfd
def exercise_geometry_restraints_as_cif():
quartz = xray.structure(
crystal_symmetry=crystal.symmetry(
(5.01,5.01,5.47,90,90,120), "P6222"),
scatterers=flex.xray_scatterer([
xray.scatterer("Si", (1/2.,1/2.,1/3.)),
xray.scatterer("O", (0.197,-0.197,0.83333))]))
bond_proxies = geometry_restraints.shared_bond_simple_proxy((
geometry_restraints.bond_simple_proxy(
i_seqs=[0,1],
rt_mx_ji=sgtbx.rt_mx("x-y,x,z-2/3"),
distance_ideal=1.6,
weight=3.2),
geometry_restraints.bond_simple_proxy(
i_seqs=[0,1],
distance_ideal=1.7,
weight=1.8),
))
dihedral_proxies = geometry_restraints.shared_dihedral_proxy((
geometry_restraints.dihedral_proxy(
i_seqs = [1,0,1,0],
sym_ops = (sgtbx.rt_mx("1+y,1-x+y, z-1/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("x-y,x,z-2/3"),
sgtbx.rt_mx("1-x,y-x,1/3-z")),
angle_ideal=-30,
weight=2),
geometry_restraints.dihedral_proxy(
i_seqs = [1,0,1,0],
sym_ops = (sgtbx.rt_mx("1+y,1-x+y, z-1/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3"),
sgtbx.rt_mx("x-y,x,1/3+z")),
angle_ideal=90,
weight=3),
))
angle_proxies = geometry_restraints.shared_angle_proxy((
geometry_restraints.angle_proxy(
i_seqs = [1,0,1],
sym_ops = (sgtbx.rt_mx("x-y,x,z-2/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3")),
angle_ideal=103,
weight=2),
geometry_restraints.angle_proxy(
i_seqs = [1,0,1],
sym_ops = (sgtbx.rt_mx("y+1,-x+y+1,z-1/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-y,x-y,z-1/3")),
angle_ideal=110,
weight=5),
geometry_restraints.angle_proxy(
i_seqs = [0,1,0],
sym_ops = (sgtbx.rt_mx("y,-x+y,z+2/3"),
sgtbx.rt_mx(),
sgtbx.rt_mx("-x+y,-x,z+1/3")),
angle_ideal=150,
weight=5),
))
bond_similarity_proxies = geometry_restraints.shared_bond_similarity_proxy((
geometry_restraints.bond_similarity_proxy(
i_seqs=[(0,1),(0,1),(0,1)],
sym_ops=(sgtbx.rt_mx("x-y,x,z-2/3"),
sgtbx.rt_mx("-y,x-y,z-1/3"),
sgtbx.rt_mx("y+1,-x+y+1,z-1/3")),
weights=(1,1,1)),
))
cif_block = iotbx.cif.model.block()
iotbx.cif.restraints.add_to_cif_block(
cif_block, quartz,
bond_proxies=bond_proxies,
angle_proxies=angle_proxies,
dihedral_proxies=dihedral_proxies,
bond_similarity_proxies=bond_similarity_proxies)
s = StringIO()
cif_block.show(out=s)
assert not show_diff(s.getvalue(), """\
loop_
_restr_distance_atom_site_label_1
_restr_distance_atom_site_label_2
_restr_distance_site_symmetry_2
_restr_distance_target
_restr_distance_target_weight_param
_restr_distance_diff
Si O 2_554 1.6000 0.5590 -0.0160
Si O 1 1.7000 0.7454 -2.3838
loop_
_restr_angle_atom_site_label_1
_restr_angle_atom_site_label_2
_restr_angle_atom_site_label_3
_restr_angle_site_symmetry_1
_restr_angle_site_symmetry_2
_restr_angle_site_symmetry_3
_restr_angle_target
_restr_angle_target_weight_param
_restr_angle_diff
O Si O 2_554 1 4_554 103.0000 0.7071 1.6926
O Si O 3_664 1 4_554 110.0000 0.4472 -1.3127
Si O Si 3 1 5 150.0000 0.4472 3.0700
loop_
_restr_torsion_atom_site_label_1
_restr_torsion_atom_site_label_2
_restr_torsion_atom_site_label_3
_restr_torsion_atom_site_label_4
_restr_torsion_site_symmetry_1
_restr_torsion_site_symmetry_2
_restr_torsion_site_symmetry_3
_restr_torsion_site_symmetry_4
_restr_torsion_angle_target
_restr_torsion_weight_param
_restr_torsion_diff
O Si O Si 3_664 1 2_554 7_655 -30.0000 0.7071 6.9078
O Si O Si 3_664 1 4_554 2 90.0000 0.5774 11.7036
loop_
_restr_equal_distance_class_class_id
_restr_equal_distance_class_target_weight_param
_restr_equal_distance_class_average
_restr_equal_distance_class_esd
_restr_equal_distance_class_diff_max
1 1.0000 1.6160 0.0000 0.0000
loop_
_restr_equal_distance_atom_site_label_1
_restr_equal_distance_atom_site_label_2
_restr_equal_distance_site_symmetry_2
_restr_equal_distance_class_id
Si O 2_554 1
Si O 4_554 1
Si O 3_664 1
""")
