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 get_stacking_proxies(pdb_hierarchy, stacking_phil_params, grm, mon_lib_srv,
plane_cache):
result = []
assert pdb_hierarchy is not None
if len(stacking_phil_params) < 1:
return result
if grm is None:
return result
selection_cache = pdb_hierarchy.atom_selection_cache()
pdb_atoms = pdb_hierarchy.atoms()
for stacking_pair in stacking_phil_params:
if (stacking_pair.base1 is not None and stacking_pair.base2 is not None
and stacking_pair.enabled):
selected_atoms_1 = selection_cache.iselection(stacking_pair.base1)
selected_atoms_2 = selection_cache.iselection(stacking_pair.base2)
if len(selected_atoms_1) == 0:
raise Sorry(
"Selection %s in stacking_pair retusulted in 0 atoms." %
(stacking_pair.base1))
if len(selected_atoms_2) == 0:
raise Sorry(
"Selection %s in stacking_pair retusulted in 0 atoms." %
(stacking_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 stacking_pair.sigma < 1e-5:
raise Sorry(
"Sigma for stacking 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 / (stacking_pair.sigma**2),
target_angle_deg=0,
slack=0,
top_out=False,
limit=1,
origin_id=0
) # special case default but not "covalent geometry"
result.append(proxy)
return result
def get_stacking_proxies(pdb_hierarchy, stacking_phil_params, grm,
mon_lib_srv, plane_cache):
result = []
assert pdb_hierarchy is not None
if len(stacking_phil_params) < 1:
return result
if grm is None:
return result
selection_cache = pdb_hierarchy.atom_selection_cache()
pdb_atoms = pdb_hierarchy.atoms()
for stacking_pair in stacking_phil_params:
if (stacking_pair.base1 is not None and stacking_pair.base2 is not None
and stacking_pair.enabled):
selected_atoms_1 = selection_cache.iselection(stacking_pair.base1)
selected_atoms_2 = selection_cache.iselection(stacking_pair.base2)
if len(selected_atoms_1) == 0:
raise Sorry("Selection %s in stacking_pair retusulted in 0 atoms." % (
stacking_pair.base1))
if len(selected_atoms_2) == 0:
raise Sorry("Selection %s in stacking_pair retusulted in 0 atoms." % (
stacking_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 stacking_pair.sigma < 1e-5:
raise Sorry("Sigma for stacking 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/(stacking_pair.sigma**2),
target_angle_deg=0,
slack=0,
top_out=False,
limit=1,
origin_id=0)
result.append(proxy)
return result
