def _create_hbond_angles_proxies(
N_atom,
O_atom,
prev_atoms,
angle_restraint_type=0, # 0-No restraint, 1-outside, 2-inside, 3-beta
):
result = []
if angle_restraint_type == 0:
return result
# print "Making angles for bond:", N_atom.id_str(), "---", O_atom.id_str()
# print "prev_atoms:"
# for a in prev_atoms:
# print " ", a.id_str()
C_atoms = []
CA_atoms = []
C_1_atoms = []
# print " C_atoms:",
for atom in O_atom.parent().atoms():
if atom.name == " C " and _ac_match(O_atom, atom):
C_atoms.append(atom)
# print " ",atom.id_str()
# print " CA_atoms:",
for atom in N_atom.parent().atoms():
if atom.name == " CA " and _ac_match(N_atom, atom):
CA_atoms.append(atom)
# print " ",atom.id_str()
# print " C_1_atoms:",
for atom in prev_atoms:
if atom.name == " C " and _ac_match(N_atom, atom):
C_1_atoms.append(atom)
# print " ",atom.id_str()
# building angle restraints
for C_atom in C_atoms:
p = geometry_restraints.angle_proxy(
i_seqs=[C_atom.i_seq, O_atom.i_seq, N_atom.i_seq],
angle_ideal=angle_restraints_values[angle_restraint_type -
1]["C"][0],
weight=1. /
angle_restraints_values[angle_restraint_type - 1]["C"][1]**2,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
result.append(p)
for CA_atom in CA_atoms:
p = geometry_restraints.angle_proxy(
i_seqs=[CA_atom.i_seq, N_atom.i_seq, O_atom.i_seq],
angle_ideal=angle_restraints_values[angle_restraint_type -
1]["CA"][0],
weight=1. /
angle_restraints_values[angle_restraint_type - 1]["CA"][1]**2,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
result.append(p)
for C_1_atom in C_1_atoms:
p = geometry_restraints.angle_proxy(
i_seqs=[C_1_atom.i_seq, N_atom.i_seq, O_atom.i_seq],
angle_ideal=angle_restraints_values[angle_restraint_type -
1]["C-1"][0],
weight=1. /
angle_restraints_values[angle_restraint_type - 1]["C-1"][1]**2,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
result.append(p)
return result
def _add_angle(i_seqs, geometry_proxy_registries, value, esd, origin_id):
proxy = geometry_restraints.angle_proxy(
i_seqs=i_seqs,
angle_ideal=value,
weight=1/esd**2,
origin_id=origin_id)
geometry_proxy_registries.angle.add_if_not_duplicated(proxy=proxy)
def get_angle_proxies_for_bond(coordination):
#
# works for SF4
# does not work for F3S
#
angles = []
if coordination is None: return angles
for a1, a2 in coordination:
assert a1.name.find("FE") > -1
if a1.parent().resname in ['F3S']: break
assert a1.parent().resname in ['SF4']
ii = int(a1.name.strip()[-1])
for i in range(1, 5):
if i == ii: continue
name = 'S%d' % i
a3 = a1.parent().get_atom(name)
angle_ideal = sf4_coordination[('S', 'FE', 'S')][0]
weight = sf4_coordination[('S', 'FE', 'S')][1]
p = geometry_restraints.angle_proxy(
i_seqs=[a3.i_seq, a1.i_seq, a2.i_seq],
angle_ideal=angle_ideal,
weight=1. / weight**2,
origin_id=origin_ids.get_origin_id('metal coordination'))
angles.append(p)
return angles
def get_proxies(coordination):
#
# TODO
# - check that only one link is made to each resiude
# e.g. 1a6y "2080 ZN ZN B 451 .*." "1874 CB CYS B 153 .*."
#
def _bond_generator(atoms):
for atom in atoms['others']:
yield atoms['metal'], atom
def _angle_generator(atoms):
for i, a1 in enumerate(atoms['others']):
for j, a2 in enumerate(atoms['others']):
if i == j: break
yield a1, atoms['metal'], a2
bonds = []
angles = []
if coordination is None: return bonds, angles
atoms = None
for metal_i_seq, atoms in coordination.items():
if len(atoms['others']) < 4: continue
cyss = []
hiss = []
for atom in atoms['others']:
if atom.parent().resname == 'CYS':
cyss.append(atom)
elif atom.parent().resname == 'HIS':
hiss.append(atom)
key = (len(cyss), len(hiss))
metal_name = atoms['metal'].name.strip()
ideals = database[metal_name][key]
if not atoms: continue #return None, None
for a1, a2 in _bond_generator(atoms):
key = (a1.name.strip(), a2.name.strip())
if key not in ideals: continue
t = ideals[key]
p = geometry_restraints.bond_simple_proxy(
i_seqs=[a1.i_seq, a2.i_seq],
distance_ideal=t[0],
weight=1.0 / t[1]**2,
slack=0,
top_out=False,
limit=1,
origin_id=origin_ids.get_origin_id('metal coordination'))
bonds.append(p)
for a1, a2, a3 in _angle_generator(atoms):
key = (a1.name.strip(), a2.name.strip(), a3.name.strip())
if key not in ideals: continue
t = ideals[key]
p = geometry_restraints.angle_proxy(
i_seqs=[a1.i_seq, a2.i_seq, a3.i_seq],
angle_ideal=t[0],
weight=1.0 / t[1]**2,
origin_id=origin_ids.get_origin_id('metal coordination'))
angles.append(p)
return bonds, angles
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_angle_proxies_for_bond(atoms):
angle_values = {
'O6 N4': [(122.8, 3.00), (117.3, 2.86)],
'N4 O6': [(117.3, 2.86), (122.8, 3.00)],
'N2 O2': [(122.2, 2.88), (120.7, 2.20)],
'O2 N2': [(120.7, 2.20), (122.2, 2.88)],
'N6 O4': [(115.6, 8.34), (121.2, 4.22)],
'O4 N6': [(121.2, 4.22), (115.6, 8.34)]
}
proxies = []
anames = [atoms[0].name.strip(), atoms[1].name.strip()]
rnames = [atoms[0].id_str().split()[1], atoms[1].id_str().split()[1]]
if sorted(anames) == ['N1', 'N3']:
if get_one_letter_rna_dna_name(rnames[0]) in ['G', 'C']:
if anames[0] == 'N1':
vals = [(119.1, 2.59), (116.3, 2.66)]
else:
vals = [(116.3, 2.66), (119.1, 2.59)]
else:
if anames[0] == 'N1':
vals = [(116.2, 3.46), (115.8, 2.88)]
else:
vals = [(115.8, 2.88), (116.2, 3.46)]
else:
key = "%s %s" % (anames[0], anames[1])
vals = angle_values.get(key, None)
if vals is not None:
for i in range(2):
atoms_for_angle = [None, None, None]
aname = anames[i]
if (aname == 'N1' or aname == 'N2' or aname == 'N3'
or aname == 'O2'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C2')
elif (aname == 'N4' or aname == 'O4'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C4')
elif (aname == 'N6' or aname == 'O6'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C6')
if atoms_for_angle[0] is not None:
atoms_for_angle[1] = atoms[i]
atoms_for_angle[2] = atoms[1 - i]
if atoms_for_angle.count(None) == 0:
i_seqs_for_angle = [x.i_seq for x in atoms_for_angle]
p = geometry_restraints.angle_proxy(
i_seqs=i_seqs_for_angle,
angle_ideal=vals[i][0],
weight=1. / vals[i][1]**2,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
proxies.append(p)
return proxies
def get_angle_proxies_for_bond(atoms):
angle_values = {'O6 N4': [(122.8, 3.00), (117.3, 2.86)],
'N4 O6': [(117.3, 2.86), (122.8, 3.00)],
'N2 O2': [(122.2, 2.88), (120.7, 2.20)],
'O2 N2': [(120.7, 2.20), (122.2, 2.88)],
'N6 O4': [(115.6, 8.34), (121.2, 4.22)],
'O4 N6': [(121.2, 4.22), (115.6, 8.34)]}
proxies = []
anames = [atoms[0].name.strip(),
atoms[1].name.strip()]
rnames = [atoms[0].id_str().split()[1],
atoms[1].id_str().split()[1]]
if sorted(anames) == ['N1', 'N3']:
if get_one_letter_rna_dna_name(rnames[0]) in ['G', 'C']:
if anames[0] == 'N1':
vals = [(119.1, 2.59), (116.3, 2.66)]
else:
vals = [(116.3, 2.66), (119.1, 2.59)]
else:
if anames[0] == 'N1':
vals = [(116.2, 3.46), (115.8, 2.88)]
else:
vals = [(115.8, 2.88), (116.2, 3.46)]
else:
key = "%s %s" % (anames[0], anames[1])
vals = angle_values.get(key, None)
if vals is not None:
for i in range(2):
atoms_for_angle = [None, None, None]
aname = anames[i]
if (aname == 'N1' or aname == 'N2' or aname == 'N3' or aname == 'O2'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C2')
elif (aname == 'N4' or aname == 'O4'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C4')
elif (aname == 'N6' or aname == 'O6'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C6')
if atoms_for_angle[0] is not None:
atoms_for_angle[1] = atoms[i]
atoms_for_angle[2] = atoms[1-i]
if atoms_for_angle.count(None) == 0:
i_seqs_for_angle = [x.i_seq for x in atoms_for_angle]
p = geometry_restraints.angle_proxy(
i_seqs=i_seqs_for_angle,
angle_ideal=vals[i][0],
weight=1./vals[i][1]**2,
origin_id=1)
proxies.append(p)
return proxies
def get_angle_proxies_for_bond(coordination):
#
def _get_angle_atoms(a1, a2, resname, second_residues):
atoms = []
ii = int(a1.name.strip()[-1])
if resname == 'F3S':
for i in range(1, 5):
if i == f3s_naming.get(ii, -1): continue
name = 'S%d' % i
a3 = a1.parent().get_atom(name)
if a3: atoms.append(a3)
else:
# SF4 has a special naming scheme
for i in range(1, 5):
if i == ii: continue
name = 'S%d' % i
a3 = a1.parent().get_atom(name)
if a3: atoms.append(a3)
if resname in ['FES']:
for ag in second_residues:
if ag.id_str() == a2.parent().id_str(): continue
for name in ['SG']:
sg = ag.get_atom(name)
if sg and sg.distance(a1) < 3.5:
atoms.append(sg)
return atoms
#
angles = []
if coordination is None: return angles
second_residues = []
for a1, a2 in coordination:
second_residues.append(a2.parent())
for a1, a2 in coordination:
assert a1.name.find("FE") > -1
resname = get_cluster_name(a1, a2)
if resname in sf_clusters:
atoms = _get_angle_atoms(a1, a2, resname, second_residues)
for a3 in atoms:
angle_ideal, weight = get_angle_ideal_and_weight(a3, a1, a2)
if angle_ideal is None: continue
p = geometry_restraints.angle_proxy(
i_seqs=[a3.i_seq, a1.i_seq, a2.i_seq],
angle_ideal=angle_ideal,
weight=weight,
origin_id=origin_ids.get_origin_id('metal coordination'))
angles.append(p)
return angles
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 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 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 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 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 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 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, name1, neutron1 = _get_atom_neutron(
ag, bond.atom_id_1, bondlength=bond.value_dist)
if atom1 is None: continue
atom2, name2, neutron2 = _get_atom_neutron(
ag, bond.atom_id_2, bondlength=bond.value_dist)
if atom2 is None: continue
i_seqs = [atom1.i_seq, atom2.i_seq]
k = 0
l = 1
bond_table_entry = gpr.bond_simple.table[i_seqs[k]]
if (not bond_table_entry
or i_seqs[l] not in gpr.bond_simple.table[i_seqs[k]]):
k = 1
l = 0
bond_table_entry = gpr.bond_simple.table[i_seqs[k]]
if i_seqs[l] in bond_table_entry:
bond_simple = gpr.bond_simple.proxies[i_seqs[k]]
bond_simple.distance_ideal = bond.value_dist
bond_simple.weight = 1 / bond.value_dist_esd**2
bond_counters[0] += 1 # changed
else:
if neutron1 or neutron2:
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs,
distance_ideal=bond.value_dist_neutron,
weight=1 / (bond.value_dist_esd**2),
)
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(name1.strip(), None)
atoms_added[atom2.i_seq] = atom_dict.get(name2.strip(), None)
bond_counters[1] += 1
lookup = {}
for angle in monomer_restraints.angle_list:
atom1, name1, neutron1 = _get_atom_neutron(
ag,
angle.atom_id_1,
)
if atom1 is None: continue
atom2, name2, neutron2 = _get_atom_neutron(
ag,
angle.atom_id_2,
)
if atom2 is None: continue
atom3, name3, neutron3 = _get_atom_neutron(
ag,
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
angle = lookup[i_seqs]
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 _add_angle(i_seqs, geometry_proxy_registries, value, esd):
proxy = geometry_restraints.angle_proxy(
i_seqs=i_seqs,
angle_ideal=value,
weight=1/esd**2)
geometry_proxy_registries.angle.add_if_not_duplicated(proxy=proxy)
def adjust_geometry_restraints_manager(
hierarchy,
grm,
error_i_seqs,
log=None,
):
# obsolete
assert 0
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 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 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 _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 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"
