def get_bp_plan_proxies(a1, a2, base_pair, grm, mon_lib_srv, plane_cache):
result_plan_p = []
result_parr_p = []
seqs = get_plane_i_seqs_from_residues(a1.parent(), a2.parent(), grm,
mon_lib_srv, plane_cache)
for i_seqs, j_seqs in seqs:
if len(i_seqs) > 2 and len(j_seqs) > 2:
if base_pair.restrain_parallelity:
if base_pair.parallelity_sigma < 1e-5:
raise Sorry(
"Sigma for parallelity basepair restraints should be > 1e-5"
)
proxy = geometry_restraints.parallelity_proxy(
i_seqs=flex.size_t(i_seqs),
j_seqs=flex.size_t(j_seqs),
weight=1 / (base_pair.parallelity_sigma**2),
target_angle_deg=0,
slack=0,
top_out=False,
limit=1,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
result_parr_p.append(proxy)
if base_pair.restrain_planarity:
if base_pair.planarity_sigma < 1e-5:
raise Sorry(
"Sigma for planarity basepair restraints should be > 1e-5"
)
w = 1. / (base_pair.planarity_sigma**2)
proxy = geometry_restraints.planarity_proxy(
i_seqs=flex.size_t(i_seqs + j_seqs),
weights=[w] * len(i_seqs + j_seqs),
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
result_plan_p.append(proxy)
return result_plan_p, result_parr_p
def get_basepair_plane_proxies(pdb_hierarchy, bp_phil_params, grm, mon_lib_srv,
plane_cache):
assert pdb_hierarchy is not None
result_planarities = []
result_parallelities = []
if len(bp_phil_params) < 1:
return result_planarities, result_parallelities
if grm is None:
return result_planarities, result_parallelities
selection_cache = pdb_hierarchy.atom_selection_cache()
pdb_atoms = pdb_hierarchy.atoms()
for base_pair in bp_phil_params:
if (base_pair.base1 is not None and base_pair.base2 is not None
and base_pair.enabled):
selected_atoms_1 = selection_cache.iselection(base_pair.base1)
selected_atoms_2 = selection_cache.iselection(base_pair.base2)
if len(selected_atoms_1) == 0:
raise Sorry(
"Selection %s in base_pair retusulted in 0 atoms." %
(base_pair.base1))
if len(selected_atoms_2) == 0:
raise Sorry(
"Selection %s in base_pair retusulted in 0 atoms." %
(base_pair.base2))
a1 = pdb_atoms[selected_atoms_1[0]]
a2 = pdb_atoms[selected_atoms_2[0]]
r1 = a1.parent()
r2 = a2.parent()
seqs = get_plane_i_seqs_from_residues(r1, r2, grm, mon_lib_srv,
plane_cache)
for i_seqs, j_seqs in seqs:
if len(i_seqs) > 2 and len(j_seqs) > 2:
if base_pair.restrain_parallelity:
if base_pair.parallelity_sigma < 1e-5:
raise Sorry(
"Sigma for parallelity basepair restraints should be > 1e-5"
)
proxy = geometry_restraints.parallelity_proxy(
i_seqs=flex.size_t(i_seqs),
j_seqs=flex.size_t(j_seqs),
weight=1 / (base_pair.parallelity_sigma**2),
target_angle_deg=0,
slack=0,
top_out=False,
limit=1,
origin_id=1)
result_parallelities.append(proxy)
if base_pair.restrain_planarity:
if base_pair.planarity_sigma < 1e-5:
raise Sorry(
"Sigma for planarity basepair restraints should be > 1e-5"
)
w = 1. / (base_pair.planarity_sigma**2)
proxy = geometry_restraints.planarity_proxy(
i_seqs=flex.size_t(i_seqs + j_seqs),
weights=[w] * len(i_seqs + j_seqs),
origin_id=1)
result_planarities.append(proxy)
return result_planarities, result_parallelities
def get_basepair_plane_proxies(
pdb_hierarchy,
bp_phil_params,
grm,
mon_lib_srv,
plane_cache):
assert pdb_hierarchy is not None
result_planarities = []
result_parallelities = []
if len(bp_phil_params) < 1:
return result_planarities, result_parallelities
if grm is None:
return result_planarities, result_parallelities
selection_cache = pdb_hierarchy.atom_selection_cache()
pdb_atoms = pdb_hierarchy.atoms()
for base_pair in bp_phil_params:
if (base_pair.base1 is not None and base_pair.base2 is not None
and base_pair.enabled):
selected_atoms_1 = selection_cache.iselection(base_pair.base1)
selected_atoms_2 = selection_cache.iselection(base_pair.base2)
if len(selected_atoms_1) == 0:
raise Sorry("Selection %s in base_pair retusulted in 0 atoms." % (
base_pair.base1))
if len(selected_atoms_2) == 0:
raise Sorry("Selection %s in base_pair retusulted in 0 atoms." % (
base_pair.base2))
a1 = pdb_atoms[selected_atoms_1[0]]
a2 = pdb_atoms[selected_atoms_2[0]]
r1 = a1.parent()
r2 = a2.parent()
seqs = get_plane_i_seqs_from_residues(r1, r2, grm,mon_lib_srv, plane_cache)
for i_seqs, j_seqs in seqs:
if len(i_seqs) > 2 and len(j_seqs) > 2:
if base_pair.restrain_parallelity:
if base_pair.parallelity_sigma < 1e-5:
raise Sorry("Sigma for parallelity basepair restraints should be > 1e-5")
proxy=geometry_restraints.parallelity_proxy(
i_seqs=flex.size_t(i_seqs),
j_seqs=flex.size_t(j_seqs),
weight=1/(base_pair.parallelity_sigma**2),
target_angle_deg=0,
slack=0,
top_out=False,
limit=1,
origin_id=1)
result_parallelities.append(proxy)
if base_pair.restrain_planarity:
if base_pair.planarity_sigma < 1e-5:
raise Sorry("Sigma for planarity basepair restraints should be > 1e-5")
w = 1./(base_pair.planarity_sigma**2)
proxy=geometry_restraints.planarity_proxy(
i_seqs=flex.size_t(i_seqs+j_seqs),
weights=[w]*len(i_seqs+j_seqs),
origin_id=1)
result_planarities.append(proxy)
return result_planarities, result_parallelities
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 _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
