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")
def get_dummy_dihedral_proxies(self, only_psi_phi_pairs=True):
from cctbx.geometry_restraints import dihedral_proxy
atoms = self.get_phi_psi_atoms(only_psi_phi_pairs=only_psi_phi_pairs)
proxies = []
for dihedral in atoms:
proxy = dihedral_proxy(
i_seqs=[atom.i_seq for atom in dihedral],
angle_ideal=0,
weight=1)
proxies.append(proxy)
return 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=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 get_dummy_dihedral_proxies(self, only_psi_phi_pairs=True):
#
# Needs testing. One of the candidates is 3j0d, chain I, the first
# residue is missing CA atom.
#
from cctbx.geometry_restraints import dihedral_proxy
atoms = self.get_phi_psi_atoms(only_psi_phi_pairs=only_psi_phi_pairs)
proxies = []
if atoms is None: return proxies
for dihedral in atoms:
if None not in dihedral:
proxy = dihedral_proxy(
i_seqs=[atom.i_seq for atom in dihedral],
angle_ideal=0,
weight=1)
proxies.append(proxy)
return proxies
def get_dummy_dihedral_proxies(self, only_psi_phi_pairs=True):
#
# Needs testing. One of the candidates is 3j0d, chain I, the first
# residue is missing CA atom.
#
from cctbx.geometry_restraints import dihedral_proxy
atoms = self.get_phi_psi_atoms(only_psi_phi_pairs=only_psi_phi_pairs)
proxies = []
if atoms is None: return proxies
for dihedral in atoms:
if None not in dihedral:
proxy = dihedral_proxy(
i_seqs=[atom.i_seq for atom in dihedral],
angle_ideal=0,
weight=1)
proxies.append(proxy)
return proxies
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 update_restraints(self, sites_cart, dihedral_proxies, angle_proxies):
if 1:
from libtbx.utils import null_out
log = null_out()
else:
import sys
log = sys.stdout
try:
phi = self._get_dihedral(
sites_cart=sites_cart, dihedral_proxies=self.conformation_proxies, i_proxy=self.i_phi_proxy
)
except Exception: # XXX BAD
phi = None
try:
psi = self._get_dihedral(
sites_cart=sites_cart, dihedral_proxies=self.conformation_proxies, i_proxy=self.i_psi_proxy
)
except Exception: # XXX BAD
psi = None
# Shows real dihedral value
if phi is not None:
print >> log, "phi", phi.angle_model, phi.delta
if psi is not None:
print >> log, "psi", psi.angle_model, psi.delta
if phi is not None and psi is not None:
# get restraint from our database here
geometry = pgd_lib.lookup(
residue=self.residue_name, next_residue=self.next_residue_name, phi=phi.angle_model, psi=psi.angle_model
)
# grab angles from our database
# using zip() on i_dynamic_angles and our values
# plug it into restraints in angle proxies
angles = [
self._get_angle(sites_cart=sites_cart, angle_proxies=angle_proxies, i_proxy=i_proxy)
for i_proxy in self.i_dynamic_angles
]
for angle, angle_name, i_proxy in zip(
angles, conformation_dependent_geometry.angles.angle_names, self.i_dynamic_angles
):
# i_dynamic_angles contains None for angles/atoms that don't
# exist so don't have restraints to update.
if i_proxy is not None:
new_angle_ideal, new_weight = self._get_average_and_weight(geometry, angle_name)
# Create a new angle proxy here with our restraint
new_angle_proxy = geometry_restraints.angle_proxy(
i_seqs=angle_proxies[i_proxy].i_seqs, angle_ideal=new_angle_ideal, weight=new_weight
)
# Overwrite the old proxy
angle_proxies[i_proxy] = new_angle_proxy
# Show that we actually did update the proxy
proxy = angle_proxies[i_proxy]
print >> log, self.residue_name, self.next_residue_name,
print >> log, angle_name, proxy.i_seqs, proxy.angle_ideal, proxy.weight
# grab dihedrals from our database
# using zip() on i_dynamic_dihedrals and our values
# plug it into restraints in dihedral proxies
dihedrals = [
self._get_dihedral(sites_cart=sites_cart, dihedral_proxies=dihedral_proxies, i_proxy=i_proxy)
for i_proxy in self.i_dynamic_dihedrals
]
for dihedral, dihedral_name, i_proxy in zip(
dihedrals, conformation_dependent_geometry.angles.dihedral_names, self.i_dynamic_dihedrals
):
# i_dynamic_dihedrals contains None for dihedrals/atoms that don't
# exist so don't have restraints to update.
if i_proxy is not None:
new_angle_ideal, new_weight = self._get_average_and_weight(geometry, dihedral_name)
new_angle_ideal = dihedral_proxies[i_proxy].angle_ideal
new_weight = dihedral_proxies[i_proxy].weight
# Create a new dihedral proxy here with our restraint
new_dihedral_proxy = geometry_restraints.dihedral_proxy(
i_seqs=dihedral_proxies[i_proxy].i_seqs, angle_ideal=new_angle_ideal, weight=new_weight
)
# Overwrite the old proxy
dihedral_proxies[i_proxy] = new_dihedral_proxy
# Show that we actually did update the proxy
proxy = dihedral_proxies[i_proxy]
print >> log, self.residue_name, self.next_residue_name,
print >> log, dihedral_name, proxy.i_seqs, proxy.angle_ideal, proxy.weight
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 update_restraints(self, sites_cart, dihedral_proxies, angle_proxies):
if (1):
from libtbx.utils import null_out
log = null_out()
else:
import sys
log = sys.stdout
try:
phi = self._get_dihedral(
sites_cart=sites_cart,
dihedral_proxies=self.conformation_proxies,
i_proxy=self.i_phi_proxy)
except Exception: # XXX BAD
phi = None
try:
psi = self._get_dihedral(
sites_cart=sites_cart,
dihedral_proxies=self.conformation_proxies,
i_proxy=self.i_psi_proxy)
except Exception: # XXX BAD
psi = None
# Shows real dihedral value
if phi is not None:
print('phi', phi.angle_model, phi.delta, file=log)
if psi is not None:
print('psi', psi.angle_model, psi.delta, file=log)
if phi is not None and psi is not None:
# get restraint from our database here
geometry = pgd_lib.lookup(residue=self.residue_name,
next_residue=self.next_residue_name,
phi=phi.angle_model,
psi=psi.angle_model)
# grab angles from our database
# using zip() on i_dynamic_angles and our values
# plug it into restraints in angle proxies
angles = [
self._get_angle(sites_cart=sites_cart,
angle_proxies=angle_proxies,
i_proxy=i_proxy)
for i_proxy in self.i_dynamic_angles
]
for angle, angle_name, i_proxy in zip(
angles, conformation_dependent_geometry.angles.angle_names,
self.i_dynamic_angles):
# i_dynamic_angles contains None for angles/atoms that don't
# exist so don't have restraints to update.
if i_proxy is not None:
new_angle_ideal, new_weight = \
self._get_average_and_weight(geometry, angle_name)
# Create a new angle proxy here with our restraint
new_angle_proxy = geometry_restraints.angle_proxy(
i_seqs=angle_proxies[i_proxy].i_seqs,
angle_ideal=new_angle_ideal,
weight=new_weight)
# Overwrite the old proxy
angle_proxies[i_proxy] = new_angle_proxy
# Show that we actually did update the proxy
proxy = angle_proxies[i_proxy]
print(self.residue_name,
self.next_residue_name,
end=' ',
file=log)
print(angle_name,
proxy.i_seqs,
proxy.angle_ideal,
proxy.weight,
file=log)
# grab dihedrals from our database
# using zip() on i_dynamic_dihedrals and our values
# plug it into restraints in dihedral proxies
dihedrals = [
self._get_dihedral(sites_cart=sites_cart,
dihedral_proxies=dihedral_proxies,
i_proxy=i_proxy)
for i_proxy in self.i_dynamic_dihedrals
]
for dihedral, dihedral_name, i_proxy in zip(
dihedrals,
conformation_dependent_geometry.angles.dihedral_names,
self.i_dynamic_dihedrals):
# i_dynamic_dihedrals contains None for dihedrals/atoms that don't
# exist so don't have restraints to update.
if i_proxy is not None:
new_angle_ideal, new_weight = \
self._get_average_and_weight(geometry, dihedral_name)
new_angle_ideal = dihedral_proxies[i_proxy].angle_ideal
new_weight = dihedral_proxies[i_proxy].weight
# Create a new dihedral proxy here with our restraint
new_dihedral_proxy = geometry_restraints.dihedral_proxy(
i_seqs=dihedral_proxies[i_proxy].i_seqs,
angle_ideal=new_angle_ideal,
weight=new_weight)
# Overwrite the old proxy
dihedral_proxies[i_proxy] = new_dihedral_proxy
# Show that we actually did update the proxy
proxy = dihedral_proxies[i_proxy]
print(self.residue_name,
self.next_residue_name,
end=' ',
file=log)
print(dihedral_name,
proxy.i_seqs,
proxy.angle_ideal,
proxy.weight,
file=log)
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
""")
def _apply_link_using_proxies(link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
# distance,
rt_mx_ji,
):
######################################
def _get_restraint_i_seqs(atom_group1,
atom_group2,
restraint,
):
i_seqs = []
keys = restraint.cif_keywords()
if "value_dist" in keys:
attrs = [
"atom_1_comp_id",
"atom_id_1",
"atom_2_comp_id",
"atom_id_2",
]
elif "period" in keys:
attrs = [
"atom_1_comp_id",
"atom_id_1",
"atom_2_comp_id",
"atom_id_2",
"atom_3_comp_id",
"atom_id_3",
"atom_4_comp_id",
"atom_id_4",
]
elif "value_angle" in keys:
attrs = [
"atom_1_comp_id",
"atom_id_1",
"atom_2_comp_id",
"atom_id_2",
"atom_3_comp_id",
"atom_id_3",
]
elif "volume_sign" in keys:
attrs = [
"atom_centre_comp_id",
"atom_id_centre",
"atom_1_comp_id",
"atom_id_1",
"atom_2_comp_id",
"atom_id_2",
"atom_3_comp_id",
"atom_id_3",
]
elif "plane_id" in keys:
attrs = [
"atom_comp_id",
"atom_id",
]
else:
assert 0
for i, attr in enumerate(attrs):
if i%2:
# name
name = getattr(restraint, attr)
for atom in atoms:
# uses names to confirm link
if atom.name.strip()==name.strip():
i_seqs.append(atom.i_seq)
break
else:
# name not found, could be hydrogen or ...
return None
else:
# atoms
if getattr(restraint, attr)==1:
atoms = atom_group1.atoms()
else:
atoms = atom_group2.atoms()
return i_seqs
###############
def _check_i_seqs(atom_group1, atom_group2, i_seqs):
atoms = []
for i_seq in i_seqs:
for atom in list(atom_group1.atoms())+list(atom_group2.atoms()):
if atom.i_seq==i_seq:
atoms.append(atom)
break
d2 = linking_utils.get_distance2(*atoms) # XXXX needs to be sym aware
if d2>9: return False
return True
#############
assert link
count = 0
#
bond_i_seqs = []
for bond in link.bond_list:
i_seqs = _get_restraint_i_seqs(atom_group1,
atom_group2,
bond,
)
if i_seqs is None: continue
if not _check_i_seqs(atom_group1, atom_group2, i_seqs): # check distances
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
i_seqs = _get_restraint_i_seqs(atom_group1,
atom_group2,
bond,
)
if i_seqs is None: continue
value = "value_dist"
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs,
distance_ideal=getattr(bond, value),
weight=1/bond.value_dist_esd**2)
bond_params_table.update(i_seq=i_seqs[0],
j_seq=i_seqs[1],
params=proxy)
#if rt_mx_ji is None: continue
bond_asu_table.add_pair(
i_seq=i_seqs[0],
j_seq=i_seqs[1],
rt_mx_ji=rt_mx_ji,
)
count+=1
bond_i_seqs.append(i_seqs)
#
for angle in link.angle_list:
i_seqs = _get_restraint_i_seqs(atom_group1,
atom_group2,
angle,
)
if i_seqs is None: continue
proxy = geometry_restraints.angle_proxy(
i_seqs=i_seqs,
angle_ideal=angle.value_angle,
weight=1/angle.value_angle_esd**2)
geometry_proxy_registries.angle.add_if_not_duplicated(proxy=proxy)
#
for tor in link.tor_list:
i_seqs = _get_restraint_i_seqs(atom_group1,
atom_group2,
tor,
)
if i_seqs is None: continue
proxy = geometry_restraints.dihedral_proxy(
i_seqs=i_seqs,
angle_ideal=tor.value_angle,
weight=1/tor.value_angle_esd**2,
periodicity=tor.period,
)
geometry_proxy_registries.dihedral.add_if_not_duplicated(proxy=proxy)
#
for chir in link.chir_list:
i_seqs = _get_restraint_i_seqs(atom_group1,
atom_group2,
chir,
)
if i_seqs is None: continue
volume_ideal = 2.4
if chir.volume_sign[:4].lower()=="nega":
volume_ideal = -2.4
elif chir.volume_sign[:4].lower()=="zero":
volume_ideal = 0.
proxy = geometry_restraints.chirality_proxy(
i_seqs=i_seqs,
volume_ideal=volume_ideal,
both_signs=False,
weight=25.,
)
geometry_proxy_registries.chirality.add_if_not_duplicated(proxy=proxy)
#
planes = {}
weights = {}
for plane in link.plane_list:
i_seqs = _get_restraint_i_seqs(atom_group1,
atom_group2,
plane,
)
if i_seqs is None: continue
planes.setdefault(plane.plane_id, [])
planes[plane.plane_id]+=i_seqs
weights.setdefault(plane.plane_id, [])
weights[plane.plane_id].append(1/plane.dist_esd**2)
if planes:
for plane_id in planes:
if len(planes[plane_id])<4: continue
proxy = geometry_restraints.planarity_proxy(
i_seqs=planes[plane_id],
weights=weights[plane_id],
)
geometry_proxy_registries.planarity.add_if_not_duplicated(proxy=proxy)
return count, bond_i_seqs
def _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
# distance,
rt_mx_ji,
origin_id=None,
):
assert origin_id
######################################
def _get_restraint_i_seqs(
atom_group1,
atom_group2,
restraint,
):
i_seqs = []
keys = restraint.cif_keywords()
if "value_dist" in keys:
attrs = [
"atom_1_comp_id",
"atom_id_1",
"atom_2_comp_id",
"atom_id_2",
]
elif "period" in keys:
attrs = [
"atom_1_comp_id",
"atom_id_1",
"atom_2_comp_id",
"atom_id_2",
"atom_3_comp_id",
"atom_id_3",
"atom_4_comp_id",
"atom_id_4",
]
elif "value_angle" in keys:
attrs = [
"atom_1_comp_id",
"atom_id_1",
"atom_2_comp_id",
"atom_id_2",
"atom_3_comp_id",
"atom_id_3",
]
elif "volume_sign" in keys:
attrs = [
"atom_centre_comp_id",
"atom_id_centre",
"atom_1_comp_id",
"atom_id_1",
"atom_2_comp_id",
"atom_id_2",
"atom_3_comp_id",
"atom_id_3",
]
elif "plane_id" in keys:
attrs = [
"atom_comp_id",
"atom_id",
]
else:
assert 0
for i, attr in enumerate(attrs):
if i % 2:
# name
name = getattr(restraint, attr)
for atom in atoms:
# uses names to confirm link
if atom.name.strip() == name.strip():
i_seqs.append(atom.i_seq)
break
else:
# name not found, could be hydrogen or ...
return None
else:
# atoms
if getattr(restraint, attr) == 1:
atoms = atom_group1.atoms()
else:
atoms = atom_group2.atoms()
return i_seqs
###############
def _check_i_seqs(atom_group1, atom_group2, i_seqs):
atoms = []
for i_seq in i_seqs:
for atom in list(atom_group1.atoms()) + list(atom_group2.atoms()):
if atom.i_seq == i_seq:
atoms.append(atom)
break
d2 = linking_utils.get_distance2(*atoms) # XXXX needs to be sym aware
if d2 > 9: return False
return True
#############
assert link
count = 0
#
bond_i_seqs = []
for bond in link.bond_list:
i_seqs = _get_restraint_i_seqs(
atom_group1,
atom_group2,
bond,
)
if i_seqs is None: continue
if not _check_i_seqs(atom_group1, atom_group2,
i_seqs): # check distances
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
i_seqs = _get_restraint_i_seqs(
atom_group1,
atom_group2,
bond,
)
if i_seqs is None: continue
value = "value_dist"
assert origin_id
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs,
distance_ideal=getattr(bond, value),
weight=1 / bond.value_dist_esd**2,
origin_id=origin_id,
)
bond_params_table.update(i_seq=i_seqs[0],
j_seq=i_seqs[1],
params=proxy)
#if rt_mx_ji is None: continue
bond_asu_table.add_pair(
i_seq=i_seqs[0],
j_seq=i_seqs[1],
rt_mx_ji=rt_mx_ji,
)
count += 1
bond_i_seqs.append(i_seqs)
#
for angle in link.angle_list:
i_seqs = _get_restraint_i_seqs(
atom_group1,
atom_group2,
angle,
)
if i_seqs is None: continue
proxy = geometry_restraints.angle_proxy(
i_seqs=i_seqs,
angle_ideal=angle.value_angle,
weight=1 / angle.value_angle_esd**2,
origin_id=origin_id,
)
geometry_proxy_registries.angle.add_if_not_duplicated(proxy=proxy)
#
for tor in link.tor_list:
i_seqs = _get_restraint_i_seqs(
atom_group1,
atom_group2,
tor,
)
if i_seqs is None: continue
proxy = geometry_restraints.dihedral_proxy(
i_seqs=i_seqs,
angle_ideal=tor.value_angle,
weight=1 / tor.value_angle_esd**2,
periodicity=tor.period,
origin_id=origin_id,
)
geometry_proxy_registries.dihedral.add_if_not_duplicated(proxy=proxy)
#
for chir in link.chir_list:
i_seqs = _get_restraint_i_seqs(
atom_group1,
atom_group2,
chir,
)
if i_seqs is None: continue
volume_ideal = 2.4
if chir.volume_sign[:4].lower() == "nega":
volume_ideal = -2.4
elif chir.volume_sign[:4].lower() == "zero":
volume_ideal = 0.
both_signs = False
if chir.volume_sign == 'both': both_signs = True
proxy = geometry_restraints.chirality_proxy(
i_seqs=i_seqs,
volume_ideal=volume_ideal,
both_signs=both_signs,
weight=25.,
origin_id=origin_id,
)
geometry_proxy_registries.chirality.add_if_not_duplicated(proxy=proxy)
#
planes = {}
weights = {}
for plane in link.plane_list:
i_seqs = _get_restraint_i_seqs(
atom_group1,
atom_group2,
plane,
)
if i_seqs is None: continue
planes.setdefault(plane.plane_id, [])
planes[plane.plane_id] += i_seqs
weights.setdefault(plane.plane_id, [])
weights[plane.plane_id].append(1 / plane.dist_esd**2)
if planes:
for plane_id in planes:
if len(planes[plane_id]) < 4: continue
proxy = geometry_restraints.planarity_proxy(
i_seqs=planes[plane_id],
weights=weights[plane_id],
origin_id=origin_id,
)
geometry_proxy_registries.planarity.add_if_not_duplicated(
proxy=proxy)
return count, bond_i_seqs
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)