def exercise_multiple_atoms(mon_lib_srv, ener_lib):
geometry, xrs = make_initial_grm(mon_lib_srv, ener_lib, raw_records1)
# output for debugging!!!
# show_sorted_geometry(geometry, xrs, 'before_exersice_multiple_atoms.geo')
xrs_add = iotbx.pdb.input(source_info=None, lines=raw_records3) \
.xray_structure_simple()
proxy1 = geometry_restraints.bond_simple_proxy(
i_seqs=(3,9),
distance_ideal=2.0,
weight=3000)
proxy2 = geometry_restraints.bond_simple_proxy(
i_seqs=(4,10),
distance_ideal=2.0,
weight=3000)
new_xrs = xrs.concatenate(xrs_add)
all_sites_cart = new_xrs.sites_cart()
number_of_new_atoms = len(xrs_add.sites_cart())
new_geometry = geometry.new_included_bonded_atoms(
proxies=[proxy1, proxy2],
sites_cart=all_sites_cart,
site_symmetry_table=xrs_add.site_symmetry_table(),
nonbonded_types=flex.std_string(["OH2"]*number_of_new_atoms),
nonbonded_charges=flex.int(number_of_new_atoms, 0),
skip_max_proxy_distance_calculation=True)
# output for debugging!!!
# show_sorted_geometry(new_geometry, new_xrs,
# 'after_exersice_multiple_atoms.geo')
assert new_geometry.pair_proxies().bond_proxies.simple.size() == 8
assert new_geometry.pair_proxies().bond_proxies.asu.size() == 2
assert new_geometry.pair_proxies().nonbonded_proxies.simple.size() == 11
assert new_geometry.pair_proxies().nonbonded_proxies.asu.size() == 4
def __init__(O,
sites_cart,
geometry_restraints_manager,
geometry_restraints_flags,
lbfgs_termination_params,
lbfgs_exception_handling_params):
O.grm = geometry_restraints_manager
cs = O.grm.crystal_symmetry
sst = O.grm.site_symmetry_table
sites_frac = cs.unit_cell().fractionalize(sites_cart)
O.x = sst.pack_coordinates(sites_frac=sites_frac)
O.proxies = geometry_restraints.shared_bond_simple_proxy()
for i_seq,pair_sym_dict in enumerate(O.grm.shell_sym_tables[0]):
for j_seq,sym_ops in pair_sym_dict.items():
assert i_seq <= j_seq
bond_params = O.grm.bond_params_table[i_seq][j_seq]
for rt_mx_ji in sym_ops:
O.proxies.append(geometry_restraints.bond_simple_proxy(
i_seqs=[i_seq, j_seq],
rt_mx_ji=rt_mx_ji,
params=bond_params))
def get_target_result():
f, _ = O.compute_functional_and_gradients()
return dev_target_result(
target=f,
n_bond_proxies=O.proxies.size(),
bond_residual_sum=f)
O.first_target_result = get_target_result()
import scitbx.lbfgs
O.minimizer = scitbx.lbfgs.run(
target_evaluator=O,
termination_params=lbfgs_termination_params,
exception_handling_params=lbfgs_exception_handling_params)
f, _ = O.compute_functional_and_gradients()
O.final_target_result = get_target_result()
def get_basepair_hbond_proxies(
pdb_hierarchy,
bp_phil_params,
hbond_distance_cutoff=3.4):
assert pdb_hierarchy is not None
bond_proxies_result = []
angle_proxies_result = []
if len(bp_phil_params) > 0:
# return bond_proxies_result, angle_proxies_result
selection_cache = pdb_hierarchy.atom_selection_cache()
pdb_atoms = pdb_hierarchy.atoms()
# dashes = open('dashes.pml', 'w')
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]]
if base_pair.saenger_class == 0:
hbonds, saenger_class = get_h_bonds_for_basepair(
a1, a2, distance_cutoff=hbond_distance_cutoff,
log=sys.stdout, verbose=-1)
base_pair.saenger_class = saenger_class
hbonds = get_h_bonds_for_particular_basepair((a1, a2), base_pair.saenger_class)
for hb in hbonds:
dist = hb[0].distance(hb[1])
if dist < hbond_distance_cutoff:
if base_pair.restrain_hbonds:
hb_target, hb_sigma = get_hb_lenght_targets(hb)
p = geometry_restraints.bond_simple_proxy(
i_seqs=[hb[0].i_seq, hb[1].i_seq],
distance_ideal=hb_target,
weight=1.0/hb_sigma**2,
slack=0,
top_out=False,
limit=1,
origin_id=1)
bond_proxies_result.append(p)
# print "bond:", hb[0].id_str(), hb[1].id_str(), "(%4.2f, %4.2f)" % (hb_target, hb_sigma)
# s1 = pdb_atoms[hb[0].i_seq].id_str()
# s2 = pdb_atoms[hb[1].i_seq].id_str()
# ps = "dist chain \"%s\" and resi %s and name %s, chain \"%s\" and resi %s and name %s\n" % (
# s1[14:15], s1[15:19], s1[5:8], s2[14:15], s2[15:19], s2[5:8])
# dashes.write(ps)
if base_pair.restrain_hb_angles:
angle_proxies_result += get_angle_proxies_for_bond(hb)
else:
print "NA hbond rejected:",hb[0].id_str(), hb[1].id_str(), "distance=%.2f" % dist
# dashes.close()
return geometry_restraints.shared_bond_simple_proxy(bond_proxies_result), \
angle_proxies_result
def exercise_add_new_bond_restraint_in_place(mon_lib_srv, ener_lib):
geometry, xrs = make_initial_grm(mon_lib_srv, ener_lib, raw_records4)
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(0,3),
distance_ideal=2.0,
weight=3000)
assert not geometry.is_bonded_atoms(0,3)
assert not geometry.is_bonded_atoms(3,0)
geometry.add_new_bond_restraints_in_place([proxy], xrs.sites_cart())
assert geometry.is_bonded_atoms(0,3)
assert geometry.is_bonded_atoms(3,0)
assert geometry.pair_proxies().bond_proxies.simple.size() == 8
assert geometry.pair_proxies().bond_proxies.asu.size() == 0
assert geometry.pair_proxies().nonbonded_proxies.simple.size() == 8
assert geometry.pair_proxies().nonbonded_proxies.asu.size() == 0
def _add_bond(i_seqs,
bond_params_table,
bond_asu_table,
value,
esd,
rt_mx_ji,
):
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs,
distance_ideal=value,
weight=1/esd**2)
bond_params_table.update(i_seq=i_seqs[0],
j_seq=i_seqs[1],
params=proxy)
bond_asu_table.add_pair(
i_seq=i_seqs[0],
j_seq=i_seqs[1],
rt_mx_ji=rt_mx_ji,
)
def exercise_single_atom(mon_lib_srv, ener_lib):
geometry, xrs = make_initial_grm(mon_lib_srv, ener_lib, raw_records1)
# output for debugging!!!
# show_sorted_geometry(geometry, xrs, 'before_exersice_single_atoms.geo')
xrs_add = iotbx.pdb.input(source_info=None, lines=raw_records2) \
.xray_structure_simple()
proxy1 = geometry_restraints.bond_simple_proxy(
i_seqs=(3,9),
distance_ideal=2.0,
weight=3000,
origin_id=1)
new_xrs = xrs.concatenate(xrs_add)
all_sites_cart = new_xrs.sites_cart()
number_of_new_atoms = len(xrs_add.sites_cart())
new_geometry = geometry.new_included_bonded_atoms(
proxies=[proxy1],
sites_cart=all_sites_cart,
site_symmetry_table=xrs_add.site_symmetry_table(),
nonbonded_types=flex.std_string(["OH2"]*number_of_new_atoms),
nonbonded_charges=flex.int(number_of_new_atoms, 0),
skip_max_proxy_distance_calculation=True)
# output for debugging!!!
# show_sorted_geometry(new_geometry, new_xrs,
# 'after_exersice_single_atoms.geo')
assert new_geometry.is_bonded_atoms(3,9)
assert new_geometry.pair_proxies().bond_proxies.simple.size() == 8
assert new_geometry.pair_proxies().bond_proxies.asu.size() == 1
# That's the way to get them:
simple, asu = new_geometry.get_covalent_bond_proxies()
assert simple.size() + asu.size() == 8
simple, asu = new_geometry.get_all_bond_proxies()
assert simple.size() + asu.size() == 9, "%d, %d" % (simple.size(), asu.size())
assert new_geometry.pair_proxies().nonbonded_proxies.simple.size() == 10
assert new_geometry.pair_proxies().nonbonded_proxies.asu.size() ==2
assert new_geometry.get_hbond_proxies_iseqs() == [(3, 9)]
simple, asu = new_geometry.get_covalent_bond_proxies()
assert simple.size() + asu.size() == 8, "%d" % (simple.size() + asu.size())
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 adjust_geometry_restraints_manager(hierarchy,
grm,
error_i_seqs,
log=None,
):
# obsolete
t0=time.time()
mon_lib_srv = server.server()
pdb_atoms = hierarchy.atoms()
sites_cart = pdb_atoms.extract_xyz()
resnames=[]
bond_counters = [0,0]
angle_counters = [0,0]
checked=[]
for i_seq in error_i_seqs:
atom = pdb_atoms[i_seq]
ag = atom.parent()
if ag.resname in checked: continue
rg = ag.parent()
# need to be able to check in user defined location
monomer_restraints = mon_lib_srv.get_comp_comp_id_direct(
ag.resname,
pH_range="low",
)
checked.append(ag.resname)
if monomer_restraints is None: continue
resnames.append('"%s%s %s%5s"' % (' ',
ag.resname,
rg.parent().id,
rg.resseq,
))
for bond in monomer_restraints.bond_list:
bond.show()
atom1 = ag.get_atom(bond.atom_id_1)
atom2 = ag.get_atom(bond.atom_id_2)
i_seqs = (atom1.i_seq, atom2.i_seq)
bond_param = grm.bond_params_table.lookup(*list(i_seqs))
if bond_param:
bond_param.distance_ideal = bond.value_dist
bond_counters[0]+=1
else:
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs,
distance_ideal=bond.value_dist,
weight=1/(bond.value_dist_esd**2),
)
grm.add_new_bond_restraints_in_place([proxy], sites_cart)
bond_counters[1]+=1
lookup={}
for angle in monomer_restraints.angle_list:
atom1 = ag.get_atom(angle.atom_id_1)
atom2 = ag.get_atom(angle.atom_id_2)
atom3 = ag.get_atom(angle.atom_id_3)
i_seqs = (atom1.i_seq, atom2.i_seq, atom3.i_seq)
lookup[i_seqs]=angle
i_seqs = (atom3.i_seq, atom2.i_seq, atom1.i_seq)
lookup[i_seqs]=angle
for angle_proxy in grm.angle_proxies:
if angle_proxy.i_seqs in lookup:
i_seqs = angle_proxy.i_seqs
angle = lookup[i_seqs]
angle_proxy.angle_ideal = angle.value_angle
angle_proxy.weight = 1/angle.value_angle_esd**2
angle_counters[0]+=1
del lookup[i_seqs]
i_seqs = list(i_seqs)
i_seqs.reverse()
del lookup[tuple(i_seqs)]
if lookup:
done = []
for i_seqs in lookup:
if i_seqs in done: continue
proxy = geometry_restraints.angle_proxy(
i_seqs=i_seqs,
angle_ideal=angle.value_angle,
weight=1/angle.value_angle_esd**2,
)
grm.add_angles_in_place([proxy])
angle_counters[1]+=1
i_seqs=list(i_seqs)
i_seqs.reverse()
done.append(tuple(i_seqs))
def adjust_geometry_proxies_registeries(hierarchy,
#bond_params_table,
#bond_asu_table,
gpr,
error_i_seqs,
log=None,
):
t0=time.time()
mon_lib_srv = server.server()
pdb_atoms = hierarchy.atoms()
sites_cart = pdb_atoms.extract_xyz()
resnames=[]
bond_counters = [0,0]
angle_counters = [0,0]
checked=[]
atoms_added={}
for i_seq in error_i_seqs:
atom = pdb_atoms[i_seq]
ag = atom.parent()
if ag.resname in checked: continue
rg = ag.parent()
# need to be able to check in user defined location
monomer_restraints = mon_lib_srv.get_comp_comp_id_direct(
ag.resname,
pH_range="low",
)
checked.append(ag.resname)
if monomer_restraints is None: continue
atom_dict = monomer_restraints.atom_dict()
resnames.append('"%s%s %s%5s"' % (' ',
ag.resname,
rg.parent().id,
rg.resseq,
))
for bond in monomer_restraints.bond_list:
atom1 = ag.get_atom(bond.atom_id_1)
if atom1 is None: continue
atom2 = ag.get_atom(bond.atom_id_2)
if atom2 is None: continue
i_seqs = [atom1.i_seq, atom2.i_seq]
i_seqs.sort()
bond_table_entry = gpr.bond_simple.table[i_seqs[0]]
if i_seqs[1] in bond_table_entry:
bond_simple = gpr.bond_simple.proxies[i_seqs[0]]
bond_simple.distance_ideal = bond.value_dist
bond_simple.weight=1/bond.value_dist_esd**2
bond_counters[0]+=1
else:
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs,
distance_ideal=bond.value_dist,
weight=1/(bond.value_dist_esd**2),
)
gpr.bond_simple.proxies.append(proxy)
atoms_added[atom1.i_seq] = atom_dict.get(atom1.name.strip(), None)
atoms_added[atom2.i_seq] = atom_dict.get(atom2.name.strip(), None)
bond_counters[1]+=1
lookup={}
for angle in monomer_restraints.angle_list:
atom1 = ag.get_atom(angle.atom_id_1)
if atom1 is None: continue
atom2 = ag.get_atom(angle.atom_id_2)
if atom2 is None: continue
atom3 = ag.get_atom(angle.atom_id_3)
if atom3 is None: continue
i_seqs = (atom1.i_seq, atom2.i_seq, atom3.i_seq)
lookup[i_seqs]=angle
i_seqs = (atom3.i_seq, atom2.i_seq, atom1.i_seq)
lookup[i_seqs]=angle
for angle_proxy in gpr.angle.proxies:
if angle_proxy.i_seqs in lookup:
i_seqs = angle_proxy.i_seqs
angle = lookup[i_seqs]
angle_proxy.angle_ideal = angle.value_angle
angle_proxy.weight = 1/angle.value_angle_esd**2
angle_counters[0]+=1
del lookup[i_seqs]
i_seqs = list(i_seqs)
i_seqs.reverse()
del lookup[tuple(i_seqs)]
if lookup:
done = []
for i_seqs in lookup:
if i_seqs in done: continue
proxy = geometry_restraints.angle_proxy(
i_seqs=i_seqs,
angle_ideal=angle.value_angle,
weight=1/angle.value_angle_esd**2,
)
gpr.angle.add_if_not_duplicated(proxy)
angle_counters[1]+=1
i_seqs=list(i_seqs)
i_seqs.reverse()
done.append(tuple(i_seqs))
if resnames:
print >> log, "\n Adjusted restraints in %d residue(s) for low pH in %0.1fs" % (
len(resnames),
time.time()-t0,
)
print >> log, " Residues changed"
for resname in resnames:
print >> log, " %s" % resname
print >> log, " Changed %d bond restraint(s), added %d bond restraint(s)" % (
bond_counters[0],
bond_counters[1],
)
print >> log, " Changed %d angle restraint(s), added %d angle restraint(s)\n" % (
angle_counters[0],
angle_counters[1],
)
#else:
# print >> log, " Time to perform restraint checks: %0.1f" % (time.time()-t0)
return atoms_added
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 exercise(verbose=0):
distance_ideal = 1.8
default_vdw_distance = 3.6
vdw_1_4_factor = 3.5/3.6
sites_cart_manual = flex.vec3_double([
(1,3,0), (2,3,0), (3,2,0), (3,1,0), (4,1,0), (3,4,0), (4,3,0), (5,3,0),
(6,2,0), (7,2,0), (8,3,0), (7,4,0), (6,4,0), (7,5,0), (6,6,0), (8,6,0)])
bond_proxies = geometry_restraints.bond_sorted_asu_proxies(asu_mappings=None)
for i_seqs in [(0,1),(1,2),(2,3),(3,4),(1,5),(2,6),(5,6),
(6,7),(7,8),(8,9),(9,10),(10,11),(11,12),
(12,7),(11,13),(13,14),(14,15),(15,13)]:
bond_proxies.process(geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs, distance_ideal=distance_ideal, weight=100))
angle_proxies = geometry_restraints.shared_angle_proxy()
for i_seqs,angle_ideal in [[(0,1,2),135],
[(0,1,5),135],
[(1,2,3),135],
[(3,2,6),135],
[(2,3,4),120],
[(1,2,6),90],
[(2,6,5),90],
[(6,5,1),90],
[(5,1,2),90],
[(2,6,7),135],
[(5,6,7),135],
[(6,7,8),120],
[(6,7,12),120],
[(7,8,9),120],
[(8,9,10),120],
[(9,10,11),120],
[(10,11,12),120],
[(11,12,7),120],
[(12,7,8),120],
[(10,11,13),120],
[(12,11,13),120],
[(11,13,15),150],
[(11,13,14),150],
[(13,15,14),60],
[(15,14,13),60],
[(14,13,15),60]]:
angle_proxies.append(geometry_restraints.angle_proxy(
i_seqs=i_seqs, angle_ideal=angle_ideal, weight=1))
if (0 or verbose):
dump_pdb(file_name="manual.pdb", sites_cart=sites_cart_manual)
for traditional_convergence_test in [True,False]:
for sites_cart_selection in [True, False]:
sites_cart = sites_cart_manual.deep_copy()
if sites_cart_selection:
sites_cart_selection = flex.bool(sites_cart.size(), True)
sites_cart_selection[1] = False
assert bond_proxies.asu.size() == 0
bond_params_table = geometry_restraints.extract_bond_params(
n_seq=sites_cart.size(),
bond_simple_proxies=bond_proxies.simple)
manager = geometry_restraints.manager.manager(
bond_params_table=bond_params_table,
angle_proxies=angle_proxies)
minimized = geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=manager,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
traditional_convergence_test=traditional_convergence_test,
drop_convergence_test_max_drop_eps=1.e-20,
drop_convergence_test_iteration_coefficient=1,
max_iterations=1000),
sites_cart_selection=sites_cart_selection,
)
assert minimized.minimizer.iter() > 100
sites_cart_minimized_1 = sites_cart.deep_copy()
if (0 or verbose):
dump_pdb(
file_name="minimized_1.pdb", sites_cart=sites_cart_minimized_1)
bond_deltas = geometry_restraints.bond_deltas(
sites_cart=sites_cart_minimized_1,
proxies=bond_proxies.simple)
angle_deltas = geometry_restraints.angle_deltas(
sites_cart=sites_cart_minimized_1,
proxies=angle_proxies)
if (0 or verbose):
for proxy,delta in zip(bond_proxies.simple, bond_deltas):
print "bond:", proxy.i_seqs, delta
for proxy,delta in zip(angle_proxies, angle_deltas):
print "angle:", proxy.i_seqs, delta
assert is_below_limit(
value=flex.max(flex.abs(bond_deltas)), limit=0, eps=1.e-6)
assert is_below_limit(
value=flex.max(flex.abs(angle_deltas)), limit=0, eps=2.e-6)
sites_cart += matrix.col((1,1,0)) - matrix.col(sites_cart.min())
unit_cell_lengths = list( matrix.col(sites_cart.max())
+ matrix.col((1,-1.2,4)))
unit_cell_lengths[1] *= 2
unit_cell_lengths[2] *= 2
xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=unit_cell_lengths,
space_group_symbol="P112"))
for serial,site in zip(count(1), sites_cart):
xray_structure.add_scatterer(xray.scatterer(
label="C%02d"%serial,
site=xray_structure.unit_cell().fractionalize(site)))
if (0 or verbose):
xray_structure.show_summary().show_scatterers()
p1_structure = (xray_structure
.apply_shift((-.5,-.5,0))
.expand_to_p1()
.apply_shift((.5,.5,0)))
for shift in [(1,0,0), (0,1,0), (0,0,1)]:
p1_structure.add_scatterers(p1_structure.apply_shift(shift).scatterers())
if (0 or verbose):
open("p1_structure.pdb", "w").write(p1_structure.as_pdb_file())
nonbonded_cutoff = 6.5
asu_mappings = xray_structure.asu_mappings(
buffer_thickness=nonbonded_cutoff)
bond_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
geometry_restraints.add_pairs(bond_asu_table, bond_proxies.simple)
shell_asu_tables = crystal.coordination_sequences.shell_asu_tables(
pair_asu_table=bond_asu_table,
max_shell=3)
shell_sym_tables = [shell_asu_table.extract_pair_sym_table()
for shell_asu_table in shell_asu_tables]
bond_params_table = geometry_restraints.extract_bond_params(
n_seq=sites_cart.size(),
bond_simple_proxies=bond_proxies.simple)
atom_energy_types = flex.std_string(sites_cart.size(), "Default")
nonbonded_params = geometry_restraints.nonbonded_params(
factor_1_4_interactions=vdw_1_4_factor,
const_shrink_1_4_interactions=0,
default_distance=default_vdw_distance)
nonbonded_params.distance_table.setdefault(
"Default")["Default"] = default_vdw_distance
pair_proxies = geometry_restraints.pair_proxies(
bond_params_table=bond_params_table,
shell_asu_tables=shell_asu_tables,
model_indices=None,
conformer_indices=None,
nonbonded_params=nonbonded_params,
nonbonded_types=atom_energy_types,
nonbonded_distance_cutoff_plus_buffer=nonbonded_cutoff)
if (0 or verbose):
print "pair_proxies.bond_proxies.n_total():", \
pair_proxies.bond_proxies.n_total(),
print "simple:", pair_proxies.bond_proxies.simple.size(),
print "sym:", pair_proxies.bond_proxies.asu.size()
print "pair_proxies.nonbonded_proxies.n_total():", \
pair_proxies.nonbonded_proxies.n_total(),
print "simple:", pair_proxies.nonbonded_proxies.simple.size(),
print "sym:", pair_proxies.nonbonded_proxies.asu.size()
print "min_distance_nonbonded: %.2f" % flex.min(
geometry_restraints.nonbonded_deltas(
sites_cart=sites_cart,
sorted_asu_proxies=pair_proxies.nonbonded_proxies))
s = StringIO()
pair_proxies.bond_proxies.show_histogram_of_model_distances(
sites_cart=sites_cart,
f=s,
prefix="[]")
assert s.getvalue().splitlines()[0] == "[]Histogram of bond lengths:"
assert s.getvalue().splitlines()[5].startswith("[] 1.80 - 1.80:")
s = StringIO()
pair_proxies.bond_proxies.show_histogram_of_deltas(
sites_cart=sites_cart,
f=s,
prefix="][")
assert s.getvalue().splitlines()[0] == "][Histogram of bond deltas:"
assert s.getvalue().splitlines()[5].startswith("][ 0.000 - 0.000:")
s = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
max_items=3,
f=s,
prefix=":;")
l = s.getvalue().splitlines()
assert l[0] == ":;Bond restraints: 18"
assert l[1] == ":;Sorted by residual:"
assert l[2].startswith(":;bond ")
assert l[3].startswith(":; ")
assert l[4] == ":; ideal model delta sigma weight residual"
for i in [5,-2]:
assert l[i].startswith(":; 1.800 1.800 ")
assert l[-1] == ":;... (remaining 15 not shown)"
s = StringIO()
pair_proxies.nonbonded_proxies.show_histogram_of_model_distances(
sites_cart=sites_cart,
f=s,
prefix="]^")
assert not show_diff(s.getvalue(), """\
]^Histogram of nonbonded interaction distances:
]^ 2.16 - 3.03: 3
]^ 3.03 - 3.89: 12
]^ 3.89 - 4.75: 28
]^ 4.75 - 5.61: 44
]^ 5.61 - 6.48: 54
""")
s = StringIO()
pair_proxies.nonbonded_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
max_items=7,
f=s,
prefix=">,")
assert not show_diff(s.getvalue(), """\
>,Nonbonded interactions: 141
>,Sorted by model distance:
>,nonbonded 15
>, 15
>, model vdw sym.op.
>, 2.164 3.600 -x+2,-y+1,z
...
>,nonbonded 4
>, 8
>, model vdw
>, 3.414 3.600
>,... (remaining 134 not shown)
""",
selections=[range(6), range(-5,0)])
vdw_1_sticks = []
vdw_2_sticks = []
for proxy in pair_proxies.nonbonded_proxies.simple:
if (proxy.vdw_distance == default_vdw_distance):
vdw_1_sticks.append(pml_stick(
begin=sites_cart[proxy.i_seqs[0]],
end=sites_cart[proxy.i_seqs[1]]))
else:
vdw_2_sticks.append(pml_stick(
begin=sites_cart[proxy.i_seqs[0]],
end=sites_cart[proxy.i_seqs[1]]))
mps = asu_mappings.mappings()
for proxy in pair_proxies.nonbonded_proxies.asu:
if (proxy.vdw_distance == default_vdw_distance):
vdw_1_sticks.append(pml_stick(
begin=mps[proxy.i_seq][0].mapped_site(),
end=mps[proxy.j_seq][proxy.j_sym].mapped_site()))
else:
vdw_2_sticks.append(pml_stick(
begin=mps[proxy.i_seq][0].mapped_site(),
end=mps[proxy.j_seq][proxy.j_sym].mapped_site()))
if (0 or verbose):
pml_write(f=open("vdw_1.pml", "w"), label="vdw_1", sticks=vdw_1_sticks)
pml_write(f=open("vdw_2.pml", "w"), label="vdw_2", sticks=vdw_2_sticks)
#
i_pdb = count(2)
for use_crystal_symmetry in [False, True]:
if (not use_crystal_symmetry):
crystal_symmetry = None
site_symmetry_table = None
else:
crystal_symmetry = xray_structure
site_symmetry_table = xray_structure.site_symmetry_table()
for sites_cart in [sites_cart_manual.deep_copy(),
sites_cart_minimized_1.deep_copy()]:
manager = geometry_restraints.manager.manager(
crystal_symmetry=crystal_symmetry,
site_symmetry_table=site_symmetry_table,
nonbonded_params=nonbonded_params,
nonbonded_types=atom_energy_types,
nonbonded_function=geometry_restraints.prolsq_repulsion_function(),
bond_params_table=bond_params_table,
shell_sym_tables=shell_sym_tables,
nonbonded_distance_cutoff=nonbonded_cutoff,
nonbonded_buffer=1,
angle_proxies=angle_proxies,
plain_pairs_radius=5)
manager = manager.select(selection=flex.bool(sites_cart.size(), True))
manager = manager.select(
iselection=flex.size_t_range(stop=sites_cart.size()))
pair_proxies = manager.pair_proxies(sites_cart=sites_cart)
minimized = geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=manager,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=1000))
if (0 or verbose):
minimized.final_target_result.show()
print "number of function evaluations:", minimized.minimizer.nfun()
print "n_updates_pair_proxies:", manager.n_updates_pair_proxies
if (not use_crystal_symmetry):
assert minimized.final_target_result.bond_residual_sum < 1.e-3
assert minimized.final_target_result.nonbonded_residual_sum < 0.1
else:
assert minimized.final_target_result.bond_residual_sum < 1.e-2
assert minimized.final_target_result.nonbonded_residual_sum < 0.1
assert minimized.final_target_result.angle_residual_sum < 1.e-3
if (0 or verbose):
pdb_file_name = "minimized_%d.pdb" % i_pdb.next()
print "Writing file:", pdb_file_name
dump_pdb(file_name=pdb_file_name, sites_cart=sites_cart)
if (manager.site_symmetry_table is None):
additional_site_symmetry_table = None
else:
additional_site_symmetry_table = sgtbx.site_symmetry_table()
assert manager.new_including_isolated_sites(
n_additional_sites=0,
site_symmetry_table=additional_site_symmetry_table,
nonbonded_types=flex.std_string()).plain_pairs_radius \
== manager.plain_pairs_radius
if (crystal_symmetry is not None):
assert len(manager.plain_pair_sym_table) == 16
if (0 or verbose):
manager.plain_pair_sym_table.show()
#
xray_structure.set_u_iso(values=flex.double([
0.77599982480241358, 0.38745781137212021, 0.20667558236418682,
0.99759840171302094, 0.8917287406687805, 0.64780251325379845,
0.24878590382983534, 0.59480621182194615, 0.58695637792905142,
0.33997130213653637, 0.51258699130743735, 0.79760289141276675,
0.39996577657875021, 0.4329328819341467, 0.70422156561726479,
0.87260110626999332]))
class parameters: pass
parameters.sphere_radius = 5
parameters.distance_power = 0.7
parameters.average_power = 0.9
parameters.wilson_b_weight = 1.3952
parameters.wilson_b_weight_auto = False
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=None,
use_hd=False,
use_u_local_only = False,
compute_gradients=False,
gradients=None,
normalization=False,
collect=True)
assert adp_energies.number_of_restraints == 69
assert approx_equal(adp_energies.residual_sum, 6.24865382467)
assert adp_energies.gradients is None
assert adp_energies.u_i.size() == adp_energies.number_of_restraints
assert adp_energies.u_j.size() == adp_energies.number_of_restraints
assert adp_energies.r_ij.size() == adp_energies.number_of_restraints
for wilson_b in [None, 10, 100]:
finite_difference_gradients = flex.double()
eps = 1.e-6
for i_scatterer in xrange(xray_structure.scatterers().size()):
rs = []
for signed_eps in [eps, -eps]:
xray_structure_eps = xray_structure.deep_copy_scatterers()
xray_structure_eps.scatterers()[i_scatterer].u_iso += signed_eps
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure_eps,
parameters=parameters,
wilson_b=wilson_b,
use_u_local_only = False,
use_hd=False,
compute_gradients=True,
gradients=None,
normalization=False,
collect=False)
rs.append(adp_energies.residual_sum)
assert adp_energies.gradients.size() \
== xray_structure.scatterers().size()
assert adp_energies.u_i == None
assert adp_energies.u_j == None
assert adp_energies.r_ij == None
finite_difference_gradients.append((rs[0]-rs[1])/(2*eps))
sel = flex.bool(xray_structure.scatterers().size(), True)
xray_structure.scatterers().flags_set_grad_u_iso(sel.iselection())
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=wilson_b,
use_u_local_only = False,
use_hd=False,
compute_gradients=True,
gradients=None,
normalization=False,
collect=False)
assert approx_equal(adp_energies.gradients, finite_difference_gradients)
print "OK"
def _create_hbond_proxy (
acceptor_atoms,
donor_atoms,
hbond_counts,
distance_ideal,
distance_cut,
remove_outliers,
weight=1.0,
sigma=None,
slack=None,
top_out=False,
log=sys.stdout) :
assert sigma is not None
assert slack is not None
donors = []
acceptors = []
for atom in acceptor_atoms :
if (atom.name == ' O ') :
acceptors.append(atom)
for atom in donor_atoms :
if (atom.name == ' N ') :
donors.append(atom)
if len(donors) > 0 and len(acceptors) > 0:
# make pairs of connecting atoms
donor_acceptor_pairs = []
if len(donors) == 1:
for acc in acceptors:
donor_acceptor_pairs.append((donors[0], acc))
elif len(donors) == 2 and len(acceptors) == 2:
donor_acceptor_pairs.append((donors[0], acceptors[0]))
donor_acceptor_pairs.append((donors[1], acceptors[1]))
elif len(donors) == 2 and len(acceptors) == 1:
for donor in donors:
donor_acceptor_pairs.append((donor, acceptors[0]))
result = []
for donor, acceptor in donor_acceptor_pairs:
# print " linking:", donor.id_str(), acceptor.id_str()
if (hbond_counts[donor.i_seq] > 0) :
print >> log, " WARNING: donor atom is already bonded, skipping"
print >> log, " %s" % donor_labels.id_str()
return None
elif (hbond_counts[acceptor.i_seq] > 0) :
print >> log, " WARNING: acceptor atom is already bonded, skipping"
print >> log, " %s" % acceptor_labels.id_str()
return None
if (remove_outliers) and (distance_cut > 0) :
dist = donor.distance(acceptor)
if (dist > distance_cut) :
print >> log, " removed outlier: %.3fA %s --> %s (cutoff:%.3fA)"%(
dist, donor.id_str(), acceptor.id_str(), distance_cut)
return None
limit = -1
if (top_out) :
limit = (distance_cut - distance_ideal)**2 * weight/(sigma**2)
print "limit: %.2f" % limit
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(donor.i_seq, acceptor.i_seq),
distance_ideal=distance_ideal,
weight=weight/(sigma ** 2),
slack=slack,
top_out=top_out,
limit=limit,
origin_id=1)
result.append(proxy)
return result
else :
print >> log, "WARNING: missing atoms!"
return None
def get_basepair_hbond_proxies(pdb_hierarchy,
bp_phil_params,
hbond_distance_cutoff=3.4):
assert pdb_hierarchy is not None
bond_proxies_result = []
angle_proxies_result = []
if len(bp_phil_params) > 0:
# return bond_proxies_result, angle_proxies_result
selection_cache = pdb_hierarchy.atom_selection_cache()
pdb_atoms = pdb_hierarchy.atoms()
# dashes = open('dashes.pml', 'w')
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]]
if base_pair.saenger_class == 0:
hbonds, saenger_class = get_h_bonds_for_basepair(
a1,
a2,
distance_cutoff=hbond_distance_cutoff,
log=sys.stdout,
verbose=-1)
base_pair.saenger_class = saenger_class
hbonds = get_h_bonds_for_particular_basepair(
(a1, a2), base_pair.saenger_class)
for hb in hbonds:
if hb[0] is None or hb[1] is None:
print "NA hbond rejected because one of the atoms is absent"
continue
dist = hb[0].distance(hb[1])
if dist < hbond_distance_cutoff:
if base_pair.restrain_hbonds:
hb_target, hb_sigma = get_hb_lenght_targets(hb)
p = geometry_restraints.bond_simple_proxy(
i_seqs=[hb[0].i_seq, hb[1].i_seq],
distance_ideal=hb_target,
weight=1.0 / hb_sigma**2,
slack=0,
top_out=False,
limit=1,
origin_id=1)
bond_proxies_result.append(p)
# print "bond:", hb[0].id_str(), hb[1].id_str(), "(%4.2f, %4.2f)" % (hb_target, hb_sigma)
# s1 = pdb_atoms[hb[0].i_seq].id_str()
# s2 = pdb_atoms[hb[1].i_seq].id_str()
# ps = "dist chain \"%s\" and resi %s and name %s, chain \"%s\" and resi %s and name %s\n" % (
# s1[14:15], s1[15:19], s1[5:8], s2[14:15], s2[15:19], s2[5:8])
# dashes.write(ps)
if base_pair.restrain_hb_angles:
angle_proxies_result += get_angle_proxies_for_bond(
hb)
else:
print "NA hbond rejected:", hb[0].id_str(
), hb[1].id_str(), "distance=%.2f" % dist
# dashes.close()
return geometry_restraints.shared_bond_simple_proxy(bond_proxies_result), \
angle_proxies_result
def _create_hbond_proxy(acceptor_atoms,
donor_atoms,
hbond_counts,
distance_ideal,
distance_cut,
remove_outliers,
weight=1.0,
sigma=None,
slack=None,
top_out=False,
log=sys.stdout):
assert sigma is not None
assert slack is not None
donors = []
acceptors = []
for atom in acceptor_atoms:
if (atom.name == ' O '):
acceptors.append(atom)
for atom in donor_atoms:
if (atom.name == ' N '):
donors.append(atom)
if len(donors) > 0 and len(acceptors) > 0:
# make pairs of connecting atoms
donor_acceptor_pairs = []
if len(donors) == 1:
for acc in acceptors:
donor_acceptor_pairs.append((donors[0], acc))
elif len(donors) == 2 and len(acceptors) == 2:
donor_acceptor_pairs.append((donors[0], acceptors[0]))
donor_acceptor_pairs.append((donors[1], acceptors[1]))
elif len(donors) == 2 and len(acceptors) == 1:
for donor in donors:
donor_acceptor_pairs.append((donor, acceptors[0]))
result = []
for donor, acceptor in donor_acceptor_pairs:
# print " linking:", donor.id_str(), acceptor.id_str()
if (hbond_counts[donor.i_seq] > 0):
print >> log, " WARNING: donor atom is already bonded, skipping"
print >> log, " %s" % donor_labels.id_str()
return None
elif (hbond_counts[acceptor.i_seq] > 0):
print >> log, " WARNING: acceptor atom is already bonded, skipping"
print >> log, " %s" % acceptor_labels.id_str()
return None
if (remove_outliers) and (distance_cut > 0):
dist = donor.distance(acceptor)
if (dist > distance_cut):
print >> log, " removed outlier: %.3fA %s --> %s (cutoff:%.3fA)" % (
dist, donor.id_str(), acceptor.id_str(), distance_cut)
return None
limit = -1
if (top_out):
limit = (distance_cut - distance_ideal)**2 * weight / (sigma**
2)
print "limit: %.2f" % limit
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(donor.i_seq, acceptor.i_seq),
distance_ideal=distance_ideal,
weight=weight / (sigma**2),
slack=slack,
top_out=top_out,
limit=limit,
origin_id=1)
result.append(proxy)
return result
else:
print >> log, "WARNING: missing atoms!"
return None
def exercise_bond_over_symmetry_2(mon_lib_srv, ener_lib):
""" This test is to illustrate that bond over symmetry actually
adds 2 proxies.
"""
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records10)
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.restraints_library.mcl=False
model = mmtbx.model.manager(
model_input = pdb_inp,
pdb_interpretation_params=params,
log=null_out())
grm = model.get_restraints_manager().geometry
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (0, 0)
h = model.get_hierarchy()
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="")
outtxt = out.getvalue()
# print(outtxt)
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(0,1),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
grm.add_new_bond_restraints_in_place(
proxies=[proxy],
sites_cart=h.atoms().extract_xyz())
simple, asu = grm.get_all_bond_proxies()
# print(simple.size(), asu.size())
assert (simple.size(), asu.size()) == (0,2)
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="")
outtxt = out.getvalue()
# print(outtxt)
assert_lines_in_text(outtxt, """\
bond pdb=" CA HIS A 2 "
pdb=" N MET A 1 "
ideal model delta sigma weight residual sym.op.
2.900 1.998 0.902 5.00e-02 4.00e+02 3.25e+02 x,y+1,z
bond pdb=" N MET A 1 "
pdb=" CA HIS A 2 "
ideal model delta sigma weight residual sym.op.
2.900 1.998 0.902 5.00e-02 4.00e+02 3.25e+02 x,y-1,z
""")
es = grm.energies_sites(sites_cart=sites_cart, compute_gradients=True)
out = StringIO()
es.show(f=out)
outtxt = out.getvalue()
# print(outtxt)
# do for x coordinate
# ATOM 1 N MET A 1 9.821 1.568 5.000 1.00 66.07 N
# ATOM 2 CA HIS A 2 9.946 12.171 5.357 1.00 66.55 C
# calculation is from geometry_restraints/bond.h: gradient_0()
# weight * 2 * delta_slack * d_distance_d_site_0(epsilon);
# print("X gradient:", 400*2*0.902*(9.946-9.821)) # 90
# Note that n=2 but residual sum is 325.349. 349 is chopped off in rounding in
# cctbx/geometry_restraints/__init__py, def _bond_show_sorted_impl(...)
# where %6.2e is used. in cctbx/geometry_restraints/energies.py: def show()
# %.6g is used which is showing more numbers.
assert_lines_in_text(outtxt, """\
bond_residual_sum (n=2): 325.349""")
# print("Gradients:", list(es.gradients))
# Seems that gradients were splitted in half (note the X gradient is 90 8 lines above)
assert approx_equal(list(es.gradients),
[(45.135801792665134, -708.451544937652, 128.90784991984805), (-45.13580179266516, 708.4515449376522, -128.90784991984813)])
