def _get_sorted(O,
unit_cell,
sites_cart,
pdb_atoms,
by_value="residual",
use_segids_in_place_of_chainids=False):
assert by_value in ["residual", "delta"]
if (O.size() == 0): return []
import cctbx.geometry_restraints
from scitbx.array_family import flex
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
deltas = flex.abs(O.deltas(sites_cart=sites_cart))
residuals = O.residuals(sites_cart=sites_cart)
if (by_value == "residual"):
data_to_sort = residuals
elif (by_value == "delta"):
data_to_sort = deltas
i_proxies_sorted = flex.sort_permutation(data=data_to_sort, reverse=True)
sorted_table = []
for i_proxy in i_proxies_sorted:
proxy = O[i_proxy]
if proxy.origin_id != origin_ids.get_origin_id('covalent geometry'):
continue
sigma = cctbx.geometry_restraints.weight_as_sigma(proxy.weight)
score = sqrt(residuals[i_proxy]) / sigma
proxy_atoms = get_atoms_info(
pdb_atoms,
iselection=proxy.i_seqs,
use_segids_in_place_of_chainids=use_segids_in_place_of_chainids)
sorted_table.append((proxy, proxy_atoms))
return sorted_table
def get_ssbond_proxies(grm):
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
specific_origin_id = origin_ids.get_origin_id('SS BOND')
pair_proxies = grm.pair_proxies()
return (pair_proxies.bond_proxies.simple.proxy_select(
origin_id=specific_origin_id))
def exercise_bond_over_symmetry(mon_lib_srv, ener_lib):
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records9)
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(),
build_grm=True)
grm = model.get_restraints_manager().geometry
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (29, 0)
h = model.get_hierarchy()
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(32, 4),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
proxy2 = geometry_restraints.bond_simple_proxy(
i_seqs=(32, 24),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
grm.add_new_bond_restraints_in_place(proxies=[proxy, proxy2],
sites_cart=h.atoms().extract_xyz())
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (30, 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)
#
# Not clear why ZN-NE2 bond adds as 2 bonds.
assert_lines_in_text(
outtxt, """\
bond pdb="ZN ZN A 8 "
pdb=" NE2 HIS B 304 "
ideal model delta sigma weight residual sym.op.
2.900 2.969 -0.069 5.00e-02 4.00e+02 1.92e+00 -x-1/2,y+1/2,-z+3/4
""")
assert_lines_in_text(
outtxt, """\
bond pdb=" NE2 HIS B 304 "
pdb="ZN ZN A 8 "
ideal model delta sigma weight residual sym.op.
2.900 2.969 -0.069 5.00e-02 4.00e+02 1.92e+00 -x-1/2,y-1/2,-z+3/4
""")
def get_ssbond_proxies_asu(grm):
#*a*s*ymmetric *u*nit bond proxies. Should find bonds between symmetry mates, etc.
#I don't have this quite working yet
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
specific_origin_id = origin_ids.get_origin_id('SS BOND')
pair_proxies = grm.pair_proxies()
return(pair_proxies.bond_proxies.asu.proxy_select(origin_id=specific_origin_id))
def exercise_bond_near_symmetry3(mon_lib_srv, ener_lib):
""" Since neighbors_fast_pair_generator for non-symmetry interactions
provides only (i,j) pair and not (j,i), and there's no sorting involved
(no way to guess what to check), there was a bug where non-symmetry interaction
was missed in add_new_bond_restraints_in_place.
Actually testing that both bonds are added without symmetry operators.
"""
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records8)
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
h = model.get_hierarchy()
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(64, 37),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
proxy2 = geometry_restraints.bond_simple_proxy(
i_seqs=(72, 37),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
grm.add_new_hbond_restraints_in_place(
proxies=[proxy, proxy2],
sites_cart=h.atoms().extract_xyz(),
max_distance_between_connecting_atoms=10)
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="",
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
outtxt = out.getvalue()
assert not show_diff(
outtxt, """\
Bond restraints: 2
Sorted by residual:
bond pdb=" O ARG A 25 "
pdb=" N AASN A 29 "
ideal model delta sigma weight residual
2.900 2.934 -0.034 5.00e-02 4.00e+02 4.53e-01
bond pdb=" O ARG A 25 "
pdb=" N BASN A 29 "
ideal model delta sigma weight residual
2.900 2.888 0.012 5.00e-02 4.00e+02 5.59e-02
""")
def get_ssbond_proxies(grm):
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
specific_origin_id = origin_ids.get_origin_id('SS BOND')
#origin id selects for a particular kind of bond in this case ssbond
#see modules/cctbx_project/cctbx/geometry_restraints/auto_linking_types.py for supported interaction types
#see modules/cctbx_project/cctbx/geometry_restraints/manager.py for additional sample code
pair_proxies = grm.pair_proxies()
return(pair_proxies.bond_proxies.simple.proxy_select(origin_id=specific_origin_id))
def get_outliers(self,
proxies,
unit_cell,
sites_cart,
pdb_atoms,
sigma_cutoff,
outliers_only=True,
use_segids_in_place_of_chainids=False):
from scitbx.array_family import flex
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
site_labels = flex.bool(sites_cart.size(), True).iselection()
sorted_table, not_shown = proxies.get_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
origin_id=origin_ids.get_origin_id('covalent geometry'))
# this can happen for C-alpha-only models, etc.
if (sorted_table is None):
return []
outliers = []
for restraint_info in sorted_table:
(i_seq, j_seq, i_seqs, ideal, model, slack, delta, sigma, weight,
residual, sym_op_j, rt_mx) = restraint_info
bond_atoms = get_atoms_info(
pdb_atoms,
iselection=i_seqs,
use_segids_in_place_of_chainids=use_segids_in_place_of_chainids
)
if sym_op_j:
import scitbx
m3 = rt_mx.r().as_double()
m3 = scitbx.matrix.sqr(m3)
t = rt_mx.t().as_double()
t = scitbx.matrix.col((t[0], t[1], t[2]))
xyz = unit_cell.fractionalize(
flex.vec3_double([bond_atoms[1].xyz]))
new_xyz = unit_cell.orthogonalize(m3.elems * xyz + t)
bond_atoms[1].xyz = new_xyz[0]
outlier = bond(atoms_info=bond_atoms,
target=ideal,
model=model,
sigma=sigma,
slack=slack,
delta=delta,
residual=residual,
symop=sym_op_j,
outlier=True,
xyz=get_mean_xyz(bond_atoms))
if (outlier.score > sigma_cutoff):
outliers.append(outlier)
elif (not outliers_only):
outlier.outlier = False
outliers.append(outlier)
return outliers
def exclude_H_on_links(self):
origin_ids = linking_class()
rm = self.model.get_restraints_manager()
bond_proxies_simple, asu = rm.geometry.get_all_bond_proxies(
sites_cart=self.model.get_sites_cart())
elements = self.model.get_hierarchy().atoms().extract_element()
exclusion_iseqs = list()
exclusion_dict = dict()
all_proxies = [p for p in bond_proxies_simple]
for proxy in asu:
all_proxies.append(proxy)
# Loop through bond proxies to find links (origin_id != 0)
for proxy in all_proxies:
if (isinstance(proxy, ext.bond_simple_proxy)): i, j = proxy.i_seqs
elif (isinstance(proxy, ext.bond_asu_proxy)):
i, j = proxy.i_seq, proxy.j_seq
else:
assert 0 # never goes here
if proxy.origin_id != 0:
exclusion_iseqs.extend([i, j])
exclusion_dict[i] = proxy.origin_id
exclusion_dict[j] = proxy.origin_id
sel_remove = flex.size_t()
# Now find H atoms bound to linked atoms
removed_dict = dict()
for proxy in all_proxies:
if (isinstance(proxy, ext.bond_simple_proxy)): i, j = proxy.i_seqs
elif (isinstance(proxy, ext.bond_asu_proxy)):
i, j = proxy.i_seq, proxy.j_seq
else:
assert 0 # never goes here
if (elements[i] in ["H", "D"] and j in exclusion_iseqs):
sel_remove.append(i)
removed_dict[i] = exclusion_dict[j]
if (elements[j] in ["H", "D"] and i in exclusion_iseqs):
sel_remove.append(j)
removed_dict[j] = exclusion_dict[i]
#
sl_removed = [
(atom.id_str().replace('pdb=', '').replace('"', ''),
origin_ids.get_origin_key(removed_dict[atom.i_seq]))
for atom in self.model.get_hierarchy().atoms().select(sel_remove)
]
# self.site_labels_removed = list(OrderedDict.fromkeys(sl_removed))
self.sl_removed = sl_removed
#
self.model = self.model.select(
~flex.bool(self.model.size(), sel_remove))
from __future__ import division
import copy
from scitbx.math import dihedral_angle
from libtbx.utils import Sorry
from mmtbx.conformation_dependent_library.multi_residue_class import \
ThreeProteinResidues
from mmtbx.conformation_dependent_library.cdl_utils import \
get_c_ca_n, round_to_ten, get_omega_value
from mmtbx.conformation_dependent_library.cdl_setup import columns
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
class ThreeProteinResiduesWithCDL(ThreeProteinResidues):
#
# CDL specific methods
#
def get_i_seqs(self):
atoms = {}
# i-1
if self[0]:
for name in [" C ", " CA "]: # need CA_minus_1 for omega-CDL
atom = self[0].find_atom_by(name=name)
if atom: atoms["%s_minus_1" % name.strip()] = atom
# i
for name in [" N ", " CA ", " CB ", " C ", " O ", ' H ']:
atom = self[1].find_atom_by(name=name)
if atom: atoms["%s_i" % name.strip()] = atom
# i+1
def exclude_H_on_links(self):
"""Remove H atoms bound to heavy atoms that form a link
An exception are HD1 and HE2 of HIS. The mover functionality in reduce will
take care of those.
"""
origin_ids = linking_class()
grm = self.model.get_restraints_manager()
bond_proxies_simple, asu = grm.geometry.get_all_bond_proxies(
sites_cart=self.model.get_sites_cart())
elements = self.model.get_hierarchy().atoms().extract_element()
exclusion_iseqs = list()
exclusion_dict = dict()
all_proxies = [p for p in bond_proxies_simple]
for proxy in asu:
all_proxies.append(proxy)
# Loop through bond proxies to find links (i.e. proxies with origin_id != 0)
for proxy in all_proxies:
if (isinstance(proxy, ext.bond_simple_proxy)): i, j = proxy.i_seqs
elif (isinstance(proxy, ext.bond_asu_proxy)):
i, j = proxy.i_seq, proxy.j_seq
else:
assert 0 # never goes here
if proxy.origin_id != 0:
exclusion_iseqs.extend([i, j])
exclusion_dict[i] = proxy.origin_id
exclusion_dict[j] = proxy.origin_id
sel_remove = flex.size_t()
atoms = self.model.get_atoms()
# Find H atoms bound to linked atoms
removed_dict = dict()
for proxy in all_proxies:
if (isinstance(proxy, ext.bond_simple_proxy)): i, j = proxy.i_seqs
elif (isinstance(proxy, ext.bond_asu_proxy)):
i, j = proxy.i_seq, proxy.j_seq
else:
assert 0 # never goes here
# Exception for HIS HD1 and HE2
if (atoms[i].parent().resname == 'HIS'
and atoms[i].name.strip() in ['HD1', 'DD1', 'HE2', 'DE2']):
continue
if (atoms[j].parent().resname == 'HIS'
and atoms[j].name.strip() in ['HD1', 'DD1', 'HE2', 'DE2']):
continue
if (elements[i] in ["H", "D"] and j in exclusion_iseqs):
sel_remove.append(i)
removed_dict[i] = exclusion_dict[j]
if (elements[j] in ["H", "D"] and i in exclusion_iseqs):
sel_remove.append(j)
removed_dict[j] = exclusion_dict[i]
#
sl_removed = [
(atom.id_str().replace('pdb=', '').replace('"', ''),
origin_ids.get_origin_key(removed_dict[atom.i_seq]))
for atom in self.model.get_hierarchy().atoms().select(sel_remove)
]
#
self.model = self.model.select(
~flex.bool(self.model.size(), sel_remove))
self.sl_removed = sl_removed
self.exclusion_iseqs = exclusion_iseqs
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(),
build_grm=True)
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)])