Пример #1
0
 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()
Пример #2
0
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)
Пример #3
0
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)
Пример #4
0
 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)
Пример #5
0
 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()
Пример #6
0
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)
Пример #7
0
    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])