def exercise():
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=pdb_str,
force_symmetry=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
xray_structure = processed_pdb_file.xray_structure()
geometry_restraints = processed_pdb_file.geometry_restraints_manager(
show_energies=False)
sites_cart = xray_structure.sites_cart()
atoms = pdb_hierarchy.atoms()
riding_h_manager = riding.manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints=geometry_restraints)
h_parameterization = riding_h_manager.h_parameterization
diagnostics = parameterization.diagnostics_parameterization(
connectivity_obj=riding_h_manager.connectivity_obj,
h_parameterization=h_parameterization,
sites_cart=sites_cart,
threshold=0.05)
h_distances = diagnostics.h_distances
unk_list = diagnostics.unk_list
# There are 90 H atoms in the pdb_string, check if all of them are recognized
assert (len(
h_parameterization.keys()) == 90), 'Not all H atoms are parameterized'
# For each H atom, check if distance between computed H and that in input model is
# not too large
type_list = []
for ih in h_distances:
labels = atoms[ih].fetch_labels()
hp = h_parameterization[ih]
type_list.append(hp.htype)
assert (h_distances[ih] < 0.03), 'distance too large: %s atom: %s (%s) residue: %s ' \
% (hp.htype, atoms[ih].name, ih, labels.resseq.strip())
# Check if there are atoms with unknown parameterization
assert (len(unk_list) == 0), 'Some H atoms are not recognized'
# Check that parameterization types are correct
assert (len(h_parameterization) == 90), 'Fewer H atoms than expected'
for type1, type2 in zip(type_list, type_list_known):
assert (type1 == type2)
def exercise(pdb_str):
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=pdb_str,
restraints_loading_flags={"use_neutron_distances": True},
force_symmetry=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
xray_structure = processed_pdb_file.xray_structure()
geometry_restraints = processed_pdb_file.geometry_restraints_manager(
show_energies=False)
sites_cart = xray_structure.sites_cart()
atoms = pdb_hierarchy.atoms()
riding_h_manager = riding.manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints=geometry_restraints)
h_parameterization = riding_h_manager.h_parameterization
diagnostics = parameterization.diagnostics_parameterization(
connectivity_obj=riding_h_manager.connectivity_obj,
h_parameterization=h_parameterization,
sites_cart=sites_cart,
threshold=0.05)
h_distances = diagnostics.h_distances
unk_list = diagnostics.unk_list
number_h = diagnostics.number_h
# For each H atom, check if distance between computed H and that in input model is
# not too large
type_list = []
for ih in h_distances:
labels = atoms[ih].fetch_labels()
hp = h_parameterization[ih]
type_list.append(hp.htype)
assert (h_distances[ih] < 0.1), 'distance too large: %s atom: %s (%s) residue: %s ' \
% (hp.htype, atoms[ih].name, ih, labels.resseq.strip())
#
assert (len(unk_list) == 0), 'Some H atoms are not recognized'
if (pdb_str != pdb_str_02):
assert (number_h == len(h_parameterization.keys())), \
'Not all H atoms are parameterized'
def exercise():
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
file_name = None,
raw_records = pdb_str,
force_symmetry = True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
xray_structure = processed_pdb_file.xray_structure()
geometry_restraints = processed_pdb_file.geometry_restraints_manager(
show_energies = False)
sites_cart = xray_structure.sites_cart()
atoms = pdb_hierarchy.atoms()
riding_h_manager = riding.manager(
pdb_hierarchy = pdb_hierarchy,
geometry_restraints = geometry_restraints)
h_parameterization = riding_h_manager.h_parameterization
diagnostics = parameterization.diagnostics_parameterization(
connectivity_obj = riding_h_manager.connectivity_obj,
h_parameterization = h_parameterization,
sites_cart = sites_cart,
threshold = 0.05)
h_distances = diagnostics.h_distances
unk_list = diagnostics.unk_list
# There are 53 H atoms in the pdb_string, check if all of them are recognized
# Note: one H atom (VAL 7 HA) is bound to two CA atoms at once
assert (len(h_parameterization.keys()) == 68), \
'Not all H atoms are parameterized'
type_list = []
for ih in h_distances:
labels = atoms[ih].fetch_labels()
hp = h_parameterization[ih]
type_list.append(hp.htype)
assert (h_distances[ih] < 0.2), \
'distance too large: %s atom: %s (%s) residue: %s ' \
% (hp.htype, atoms[ih].name, ih, labels.resseq.strip())
assert(len(unk_list) == 0), 'Some H atoms are not recognized'
for type1, type2 in zip(type_list, type_list_known):
assert (type1 == type2)
def exercise(pdb_str, use_ideal_bonds_angles):
# --------------------------------------------------------------
# code to switch off CDL
# --------------------------------------------------------------
#params_line = grand_master_phil_str
#params = iotbx.phil.parse(
# input_string=params_line, process_includes=True).extract()
#params.pdb_interpretation.restraints_library.cdl=False
# ---------------------------------------------------------------
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=pdb_str,
force_symmetry=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
xray_structure = processed_pdb_file.xray_structure()
#
geometry_restraints = processed_pdb_file.geometry_restraints_manager(
show_energies=False)
sites_cart = xray_structure.sites_cart()
atoms = pdb_hierarchy.atoms()
# #mol = mmtbx.model.manager(
# # restraints_manager = restraints_manager,
# # xray_structure = xray_structure,
# # pdb_hierarchy = pdb_hierarchy)
# #mol.geometry_minimization(nonbonded=True)
#
grf = cctbx.geometry_restraints.flags.flags(default=True)
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart=sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=geometry_restraints,
geometry_restraints_flags=grf,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
xray_structure.set_sites_cart(sites_cart)
pdb_hierarchy.adopt_xray_structure(xray_structure)
sites_cart = xray_structure.sites_cart()
riding_h_manager = riding.manager(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints=geometry_restraints,
use_ideal_bonds_angles=use_ideal_bonds_angles)
h_parameterization = riding_h_manager.h_parameterization
diagnostics = parameterization.diagnostics_parameterization(
connectivity_obj=riding_h_manager.connectivity_obj,
h_parameterization=h_parameterization,
sites_cart=sites_cart,
threshold=0.05)
h_distances = diagnostics.h_distances
unk_list = diagnostics.unk_list
number_h = diagnostics.number_h
#type_list = []
for ih in h_distances:
labels = atoms[ih].fetch_labels()
hp = h_parameterization[ih]
#type_list.append(hp.htype)
if use_ideal_bonds_angles:
assert (h_distances[ih] < 0.03), \
'distance too large: %s atom: %s (%s) residue: %s ' \
% (hp.htype, atoms[ih].name, ih, labels.resseq.strip())
else:
assert (h_distances[ih] < 1e-8), \
'distance too large: %s atom: %s (%s) residue: %s ' \
% (hp.htype, atoms[ih].name, ih, labels.resseq.strip())
print 'type: %s distance: %s atom: %s (%s) residue: %s ' % \
(hp.htype, h_distances[ih], atoms[ih].name, ih, labels.resseq)
assert (number_h == len(h_parameterization.keys())), \
'Not all H atoms are parameterized'
assert (len(unk_list) == 0), 'Some H atoms are not recognized'
def exercise():
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=pdb_str,
force_symmetry=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
xray_structure = processed_pdb_file.xray_structure()
geometry_restraints = processed_pdb_file.geometry_restraints_manager(
show_energies=False)
sites_cart = xray_structure.sites_cart()
atoms = pdb_hierarchy.atoms()
riding_h_manager = riding.manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints=geometry_restraints)
h_parameterization = riding_h_manager.h_parameterization
h_connectivity = riding_h_manager.h_connectivity
diagnostics = parameterization.diagnostics_parameterization(
connectivity_obj=riding_h_manager.connectivity_obj,
h_parameterization=h_parameterization,
sites_cart=sites_cart,
threshold=0.05)
#number_h = diagnostics.number_h
#double_H = diagnostics.double_H
h_distances = diagnostics.h_distances
unk_list = diagnostics.unk_list
#unk_ideal_list = diagnostics.unk_ideal_list
#long_distance_list = diagnostics.long_distance_list
#n_connect = diagnostics.n_connect
#slipped = diagnostics.slipped
# There are 152 H atoms in the pdb_string, check if all of them are recognized
assert (len(
h_parameterization.keys()) == 152), 'Not all H atoms are parameterized'
# For each H atom, check if distance compared to input model is not > 0.05
# 0.0014 = uncertainty for distance if uncertainty of coordinate = 0.001
type_list = []
for ih in h_distances:
labels = atoms[ih].fetch_labels()
hp = h_parameterization[ih]
type_list.append(hp.htype)
assert (h_distances[ih] < 0.05), 'distance too large: %s atom: %s (%s) residue: %s ' \
% (hp.htype, atoms[ih].name, ih, labels.resseq.strip())
# KEEP: useful for debugging
#for ih in h_parameterization.keys():
# hp = h_parameterization[ih]
# print "'"+hp.htype+"'"+',',
#
assert (len(unk_list) == 0), 'Some H atoms are not recognized'
for type1, type2 in zip(type_list, type_list_known):
assert (type1 == type2)