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for atom_index, atom in enumerate(atoms):
res_id = "%s.%s.%s" % (atom.chain_id, atom.residue_name, str(atom.residue_number))
if restraints and res_id in restraints:
try:
parsed_restraints[res_id].append(atom_index)
except:
parsed_restraints[res_id] = [atom_index]
oda_values = SIPPERAdapter._read_oda_values(molecule)
if oda_values:
oda_values = np.array(oda_values)
else:
# Dummy value, for performance
oda_values = np.array([0.0 for _ in range(len(molecule.residues))])
reference_points = ModelAdapter.load_reference_points(molecule)
try:
return SIPPERModel(atoms, coordinates, parsed_restraints, energy, indexes, atoms_per_residue, oda_values,
reference_points=reference_points, n_modes=molecule.n_modes.copy())
except AttributeError:
return SIPPERModel(atoms, coordinates, parsed_restraints, energy, indexes, atoms_per_residue, oda_values,
reference_points=reference_points)
parsed_restraints[res_id].append(atom_index)
except:
parsed_restraints[res_id] = [atom_index]
atom_id = "%s-%s" % (res_name, atom.name)
atom.amber_type = amber_types[atom_id]
atom.charge = charges[atom_id]
atom.mass = masses[atom.amber_type]
atom.vdw_energy = vdw.vdw_energy[atom.amber_type]
atom.vdw_radius = vdw.vdw_radii[atom.amber_type]
# Prepare common model information
elec_charges = np.array([atom.charge for atom in atoms])
vdw_energies = np.array([atom.vdw_energy for atom in atoms])
vdw_radii = np.array([atom.vdw_radius for atom in atoms])
coordinates = molecule.copy_coordinates()
reference_points = ModelAdapter.load_reference_points(molecule)
try:
return SDModel(atoms, coordinates, parsed_restraints, elec_charges, vdw_energies, vdw_radii,
reference_points=reference_points, n_modes=molecule.n_modes.copy())
except AttributeError:
return SDModel(atoms, coordinates, parsed_restraints, elec_charges, vdw_energies, vdw_radii,
reference_points=reference_points)
des_radii_no_H.append(des_radii[i])
structure.setRadii(list(des_radii_no_H))
sasa_result = freesasa.calc(structure)
sasa = []
j = 0
for i, atom in enumerate(atoms):
if not atom.is_hydrogen():
sasa.append(sasa_result.atomArea(j))
j += 1
else:
sasa.append(-1.0)
sasa = np.array(sasa)
hydrogens = np.array([0 if atom.is_hydrogen() else 1 for atom in atoms])
log.info('Done.')
reference_points = ModelAdapter.load_reference_points(molecule)
try:
return CPyDockModel(atoms, coordinates, parsed_restraints, elec_charges, vdw_energies, vdw_radii, des_energy, des_radii,
sasa, hydrogens, reference_points=reference_points, n_modes=molecule.n_modes.copy())
except AttributeError:
return CPyDockModel(atoms, coordinates, parsed_restraints, elec_charges, vdw_energies, vdw_radii, des_energy, des_radii,
sasa, hydrogens, reference_points=reference_points)
parsed_restraints[res_id].append(atom_index)
except:
parsed_restraints[res_id] = [atom_index]
atom_id = "%s-%s" % (res_name, atom_name)
atom.amber_type = amber.amber_types[atom_id]
atom.charge = amber.charges[atom_id]
atom.mass = amber.masses[atom.amber_type]
atom.vdw_energy = vdw.vdw_energy[atom.amber_type]
atom.vdw_radius = vdw.vdw_radii[atom.amber_type]
# Prepare common model information
vdw_energies = np.array([atom.vdw_energy for atom in atoms])
vdw_radii = np.array([atom.vdw_radius for atom in atoms])
coordinates = molecule.copy_coordinates()
reference_points = ModelAdapter.load_reference_points(molecule)
try:
return VdWModel(atoms, coordinates, parsed_restraints, vdw_energies, vdw_radii,
reference_points=reference_points, n_modes=molecule.n_modes.copy())
except AttributeError:
return VdWModel(atoms, coordinates, parsed_restraints, vdw_energies, vdw_radii,
reference_points=reference_points)
try:
atom.charge = amber.charges[atom_id]
except:
# Go for N-terminal
atom.charge = amber.nt_charges[atom_id]
atom.mass = amber.masses[atom.amber_type]
atom.vdw_energy = vdw.vdw_energy[atom.amber_type]
atom.vdw_radius = vdw.vdw_radii[atom.amber_type]
# Prepare common model information
elec_charges = np.array([atom.charge for atom in atoms])
vdw_energies = np.array([atom.vdw_energy for atom in atoms])
vdw_radii = np.array([atom.vdw_radius for atom in atoms])
coordinates = molecule.copy_coordinates()
reference_points = ModelAdapter.load_reference_points(molecule)
try:
return DNAModel(atoms, coordinates, parsed_restraints, elec_charges, vdw_energies, vdw_radii,
reference_points=reference_points, n_modes=molecule.n_modes.copy())
except AttributeError:
return DNAModel(atoms, coordinates, parsed_restraints, elec_charges, vdw_energies, vdw_radii,
reference_points=reference_points)