def _get_docking_model(self, molecule, restraints):
atoms = molecule.atoms
# Assign properties to atoms
for atom in atoms:
res_name = atom.residue_name
if res_name == "HIS":
res_name = 'HID'
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, restraints, elec_charges, vdw_energies, vdw_radii,
reference_points=reference_points, n_modes=molecule.n_modes.copy())
except AttributeError:
return SDModel(atoms, coordinates, restraints, elec_charges, vdw_energies, vdw_radii,
reference_points=reference_points)
def _get_docking_model(self, molecule, restraints):
atoms = molecule.atoms
parsed_restraints = {}
# Assign properties to atoms
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]
res_name = atom.residue_name
atom_name = atom.name
if res_name in DNAAdapter.to_translate:
res_name = DNAAdapter.to_translate[res_name]
if atom_name in amber.translate:
atom_name = amber.translate[atom.name]
atom_id = "%s-%s" % (res_name, atom_name)
try:
atom.amber_type = amber.amber_types[atom_id]
except Exception as e:
# Maybe H N-terminal?
if atom_name in ['H1', 'H2', 'H3']:
atom_name = 'H'
atom_id = "%s-%s" % (res_name, atom_name)
atom.amber_type = amber.amber_types[atom_id]
else:
raise e
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)
def _get_docking_model(self, molecule, restraints):
atoms = molecule.atoms
parsed_restraints = {}
# Assign properties to atoms
for atom_index, atom in enumerate(atoms):
res_name = atom.residue_name
atom_name = atom.name
if res_name == "HIS":
res_name = 'HID'
if atom_name in amber.translate:
atom_name = amber.translate[atom.name]
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]
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)
def _get_docking_model(self, molecule, restraints):
atoms = molecule.atoms
energy = sipper_energy
parsed_restraints = {}
indexes = np.array(
[res_to_index[residue.name] for residue in molecule.residues])
coordinates = molecule.copy_coordinates()
atoms_per_residue = np.array(
[len(residue.atoms) for residue in molecule.residues])
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)
def _get_docking_model(self, molecule, restraints):
atoms = molecule.atoms
energy = sipper_energy
indexes = np.array([res_to_index[residue.name] for residue in molecule.residues])
coordinates = molecule.copy_coordinates()
atoms_per_residue = np.array([len(residue.atoms) for residue in molecule.residues])
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, restraints, energy, indexes, atoms_per_residue, oda_values,
reference_points=reference_points, n_modes=molecule.n_modes.copy())
except AttributeError:
return SIPPERModel(atoms, coordinates, restraints, energy, indexes, atoms_per_residue, oda_values,
reference_points=reference_points)
def _get_docking_model(self, molecule, restraints):
atoms = molecule.atoms
parsed_restraints = {}
# Assign properties to atoms
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]
res_name = atom.residue_name
atom_name = atom.name
if res_name == "HIS":
res_name = 'HID'
if atom_name in amber.translate:
atom_name = amber.translate[atom.name]
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
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()
des_energy, des_radii = solvation.get_solvation(molecule)
# Calculate desolvation reference energy
log.info('Calculating reference SASA...')
structure = Structure()
des_radii_no_H = []
for i, atom in enumerate(atoms):
if not atom.is_hydrogen():
structure.addAtom(atom.name, atom.residue_name,
atom.residue_number, atom.chain_id, atom.x,
atom.y, atom.z)
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)
def test_create_model_adapter_interface(self):
adapter = ModelAdapter(None, None)
assert not adapter
def _get_docking_model(self, molecule, restraints):
atoms = molecule.atoms
parsed_restraints = {}
# Assign properties to atoms
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]
res_name = atom.residue_name
atom_name = atom.name
if res_name == "HIS":
res_name = 'HID'
if atom_name in amber.translate:
atom_name = amber.translate[atom.name]
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
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()
des_energy, des_radii = solvation.get_solvation(molecule)
# Calculate desolvation reference energy
log.info('Calculating reference SASA...')
structure = Structure()
des_radii_no_H = []
for i, atom in enumerate(atoms):
if not atom.is_hydrogen():
structure.addAtom(atom.name, atom.residue_name, atom.residue_number, atom.chain_id,
atom.x, atom.y, atom.z)
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)