def update_xyz(self, sites_cart):
self.pdb_hierarchy.atoms().set_xyz(sites_cart)
pre_atoms = [
atom.pdb_label_columns()
for atom in self.pdb_hierarchy_super.atoms()
]
self.expansion = self.expansion.update_xyz(sites_cart=sites_cart)
self.pdb_hierarchy_super = self.expansion.ph_super_sphere
new_atoms = [
atom.pdb_label_columns()
for atom in self.pdb_hierarchy_super.atoms()
]
#if(self.expansion.ph_super_sphere.atoms_size()!=pre_size):
if (pre_atoms != new_atoms):
if (self.debug):
print(
"the content of the super sphere has been changed,reset up fragments"
)
#Note: the atom size of self.expansion.ph_super_sphere gets changeed,
#while the atom size in super_sphere_geometry_restraints_manager
#does not get changed. Re-generate the object of expand
if (1):
self.expansion = expand(
pdb_hierarchy=self.pdb_hierarchy,
crystal_symmetry=self.crystal_symmetry,
select_within_radius=self.select_within_radius)
self.pdb_hierarchy_super = self.expansion.ph_super_sphere
self.get_fragments()
self.get_fragment_hierarchies_and_charges()
def run(prefix):
"""
Exercise supercell.
"""
of = open("%s.pdb"%prefix,"w")
print >> of, pdb_str
of.close()
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
ph = pdb_inp.construct_hierarchy()
sites_cart_start = ph.atoms().extract_xyz()
o = super_cell.expand(
pdb_hierarchy = ph,
crystal_symmetry = pdb_inp.crystal_symmetry(),
select_within_radius = 11)
#
o.write_super_cell_selected_in_sphere(file_name="%s_super_sphere.pdb"%prefix)
sites_cart = ph.atoms().extract_xyz()
o.update(sites_cart = sites_cart)
o.write_super_cell_selected_in_sphere(file_name="%s_super_sphere.pdb"%prefix)
#
sites_cart_super_sphere_answer = iotbx.pdb.input(source_info=None,
lines=pdb_str_super_sphere_answer).atoms().extract_xyz()
super_sphere_answer = list(sites_cart_super_sphere_answer.as_double())
super_sphere = list(o.ph_super_sphere.atoms().extract_xyz().as_double())
super_sphere_answer.sort()
super_sphere.sort()
assert approx_equal(super_sphere_answer,super_sphere)
def run(file_name, pdb_code):
pdb_inp = iotbx.pdb.input(file_name=file_name)
pdb_hierarchy = pdb_inp.construct_hierarchy()
n_atoms = pdb_hierarchy.atoms().size()
if (n_atoms > 10000): return None
if (len(list(pdb_hierarchy.models())) > 1): return None
fraction_of_nonH_incomplete = complete_model(pdb_hierarchy=pdb_hierarchy)
cs = pdb_inp.crystal_symmetry()
resolution = get_resolution(pdb_inp=pdb_inp)
super_cell = expand(pdb_hierarchy=pdb_hierarchy,
crystal_symmetry=cs,
create_restraints_manager=False)
symmetry_ss_bonds = find_ss_across_symmetry(super_cell=super_cell)
result_occupancies = get_altloc_counts(pdb_hierarchy=pdb_hierarchy)
ligands = get_non_standard_items(pdb_hierarchy=pdb_hierarchy)
result = group_args(
number_of_atoms=pdb_hierarchy.atoms().size(),
number_of_atoms_super_sphere=super_cell.ph_super_sphere.atoms().size(),
occupancies=result_occupancies,
unit_cell=cs.unit_cell().parameters(),
space_group_symbol=cs.space_group().type().lookup_symbol(),
resolution=resolution,
data_type=pdb_inp.get_experiment_type(),
ligands=ligands,
symmetry_ss_bonds=symmetry_ss_bonds,
fraction_of_nonH_incomplete=fraction_of_nonH_incomplete)
easy_pickle.dump(pdb_code + ".pkl", result)
def _expand(self):
expansion = expand(
pdb_hierarchy = self.pdb_hierarchy,
crystal_symmetry = self.crystal_symmetry,
select_within_radius = self.params.cluster.select_within_radius)
pdb_hierarchy_super = expansion.ph_super_sphere
pdb_hierarchy_super.write_pdb_file(file_name="supersphere.pdb",
crystal_symmetry = expansion.cs_box)
self.crystal_symmetry_ss = expansion.cs_box
# Use same route for CCTBX and QM !
# if(self.restraints_source.source_of_restraints_qm()):
if 1:
self.pdb_hierarchy_super_completed = model_completion.run(
#pdb_hierarchy = pdb_hierarchy_super,
crystal_symmetry = expansion.cs_box,
model_completion = False,
pdb_filename = "supersphere.pdb",
original_pdb_filename = None)
else:
self.pdb_hierarchy_super_completed = pdb_hierarchy_super
selection = flex.bool(
self.pdb_hierarchy_super_completed.atoms().size(), False)
self.selection = selection.set_selected(
flex.size_t(range(self.pdb_hierarchy.atoms().size())), True)
self.restraints_manager = self.restraints_source.update(
pdb_hierarchy = self.pdb_hierarchy_super_completed,
crystal_symmetry = expansion.cs_box)
def __init__(self,
working_folder="ase",
clustering_method=None,
altloc_method=None,
maxnum_residues_in_cluster=20,
charge_embedding=False,
two_buffers=False,
pdb_hierarchy=None,
qm_engine_name=None,
crystal_symmetry=None,
clustering=True,
qm_run=True,
cif_objects=None,
debug=False,
charge_cutoff=8.0,
save_clusters=False):
self.charge_embedding = charge_embedding
self.two_buffers = two_buffers
self.crystal_symmetry = crystal_symmetry
self.working_folder = os.path.abspath(working_folder)
self.pdb_hierarchy = pdb_hierarchy
self.charge_cutoff = charge_cutoff
self.system_size = pdb_hierarchy.atoms_size()
self.qm_engine_name = qm_engine_name
self.clustering_method = clustering_method
self.altloc_method = altloc_method
self.debug = debug
self.maxnum_residues_in_cluster = maxnum_residues_in_cluster
self.save_clusters = save_clusters
raw_records = pdb_hierarchy.as_pdb_string(
crystal_symmetry=crystal_symmetry)
self.charge_service = charges_class(raw_records=raw_records,
ligand_cif_file_names=cif_objects)
if (os.path.exists(self.working_folder) is not True):
os.mkdir(self.working_folder)
self.backbone_connections = fragment_utils.get_backbone_connections(
self.pdb_hierarchy)
self.get_altloc_molecular_indices()
if (1):
self.altloc_atoms = [
atom for atom in list(pdb_hierarchy.atoms())
if atom.pdb_label_columns()[4] != " "
]
self.expansion = expand(pdb_hierarchy=self.pdb_hierarchy,
crystal_symmetry=self.crystal_symmetry,
select_within_radius=10.0)
self.pdb_hierarchy_super = self.expansion.ph_super_sphere
## write expansion.pdb as the reference for capping
self.expansion_file = "expansion.pdb"
self.expansion.write_super_cell_selected_in_sphere(
file_name=self.expansion_file)
if (clustering):
self.yoink_dat_path = os.path.join(qrefine, "plugin", "yoink",
"dat")
self.pyoink = PYoink(
os.path.join(qrefine, "plugin", "yoink", "Yoink-0.0.1.jar"))
self.qm_run = qm_run
#t0 = time.time()
self.set_up_cluster_qm()
def run(prefix):
"""
Make sure expand works for this particular file.
"""
pdb_name = os.path.join(
qr_unit_tests_data,
"1bdw_ala_refine_001_complete_minimized.pdb_modified.pdb")
pdb_inp = iotbx.pdb.input(pdb_name)
ph = pdb_inp.construct_hierarchy()
cs = pdb_inp.crystal_symmetry()
super_cell = expand(pdb_hierarchy=ph, crystal_symmetry=cs)
return interacting_pairs
if __name__ == "__main__":
f = qr_unit_tests_data + "/1yjp.pdb"
print("1. clustering")
pdb_inp = iotbx.pdb.input(f)
ph = pdb_inp.construct_hierarchy()
run(ph)
print("2. fragment for residues 1 and 2")
pdb_inp = iotbx.pdb.input(f)
ph = pdb_inp.construct_hierarchy()
run(ph, core=[1, 2])
print("3. clustering within expanded ph")
pdb_inp = iotbx.pdb.input(f)
cs = pdb_inp.crystal_symmetry()
ph = pdb_inp.construct_hierarchy()
expansion = expand(pdb_hierarchy=ph,
crystal_symmetry=cs,
select_within_radius=10.0).ph_super_sphere
run(expansion)
print("4. fragment for residues 1 and 2 within expanded ph")
pdb_inp = iotbx.pdb.input(f)
ph = pdb_inp.construct_hierarchy()
cs = pdb_inp.crystal_symmetry()
expansion = expand(pdb_hierarchy=ph,
crystal_symmetry=cs,
select_within_radius=10.0).ph_super_sphere
run(expansion, core=[1, 2])