def __init__(self,
pdb_hierarchy,
geometry_restraints,
use_ideal_bonds_angles=True):
self.cs = geometry_restraints.crystal_symmetry
self.pdb_hierarchy = pdb_hierarchy
self.connectivity_manager = connectivity.determine_connectivity(
pdb_hierarchy=self.pdb_hierarchy,
geometry_restraints=geometry_restraints)
self.h_connectivity = self.connectivity_manager.h_connectivity
self.double_H = self.connectivity_manager.double_H
self.connectivity_slipped = self.connectivity_manager.connectivity_slipped
self.parameterization_manager = parameterization.manager(
h_connectivity=self.h_connectivity,
sites_cart=self.pdb_hierarchy.atoms().extract_xyz(),
use_ideal_bonds_angles=use_ideal_bonds_angles)
self.h_parameterization = \
self.parameterization_manager.determine_parameterization()
self.parameterization_cpp = []
for hp in self.h_parameterization:
if (hp is not None):
self.parameterization_cpp.append(hp)
self.hd_selection = self.pdb_hierarchy.atom_selection_cache().\
selection("element H or element D")
self.not_hd_selection = ~self.hd_selection
def __init__(self,
pdb_hierarchy,
geometry_restraints,
use_ideal_bonds_angles=True,
process_manager=True):
self.pdb_hierarchy = pdb_hierarchy
self.geometry_restraints = geometry_restraints
self.use_ideal_bonds_angles = use_ideal_bonds_angles
#
self.hd_selection = self.pdb_hierarchy.atom_selection_cache().\
selection("element H or element D")
self.not_hd_selection = ~self.hd_selection
self.h_parameterization = []
self.parameterization_cpp = []
if process_manager is True:
connectivity_manager = connectivity.determine_connectivity(
pdb_hierarchy=self.pdb_hierarchy,
geometry_restraints=geometry_restraints)
h_connectivity = connectivity_manager.h_connectivity
diagnostics_connectivity = connectivity_manager.get_diagnostics()
parameterization_manager = parameterization.manager(
h_connectivity=h_connectivity,
sites_cart=self.pdb_hierarchy.atoms().extract_xyz(),
use_ideal_bonds_angles=use_ideal_bonds_angles)
self.h_parameterization = parameterization_manager.h_parameterization
self.parameterization_cpp = self.get_parameterization_cpp(
h_parameterization=self.h_parameterization)
def __init__(self,
pdb_hierarchy,
geometry_restraints,
use_ideal_bonds_angles=True,
process_manager=True,
use_ideal_dihedral=False,
ignore_h_with_dof=False):
self.pdb_hierarchy = pdb_hierarchy
self.geometry_restraints = geometry_restraints
self.use_ideal_bonds_angles = use_ideal_bonds_angles
self.ignore_h_with_dof = ignore_h_with_dof
#
self.hd_selection = self.pdb_hierarchy.atom_selection_cache().\
selection("element H or element D")
self.not_hd_selection = ~self.hd_selection
self.h_parameterization = []
self.parameterization_cpp = []
if process_manager is True:
connectivity_manager = connectivity.determine_connectivity(
pdb_hierarchy=self.pdb_hierarchy,
geometry_restraints=geometry_restraints)
h_connectivity = connectivity_manager.h_connectivity
diagnostics_connectivity = connectivity_manager.get_diagnostics()
parameterization_manager = parameterization.manager(
h_connectivity=h_connectivity,
sites_cart=self.pdb_hierarchy.atoms().extract_xyz(),
use_ideal_bonds_angles=use_ideal_bonds_angles,
site_labels=[
atom.id_str().replace('pdb=', '').replace('"', '')
for atom in pdb_hierarchy.atoms()
],
use_ideal_dihedral=use_ideal_dihedral,
ignore_h_with_dof=self.ignore_h_with_dof)
self.h_parameterization = parameterization_manager.h_parameterization
self.parameterization_cpp = self.get_parameterization_cpp(
h_parameterization=self.h_parameterization)