def __call__(self, receptor, receptor_coordinates, ligand,
ligand_coordinates):
energy, interface_receptor, interface_ligand = calculate_dfire(
receptor, ligand, self.potential.dfire_energy,
receptor_coordinates, ligand_coordinates,
DEFAULT_CONTACT_RESTRAINTS_CUTOFF)
interface_receptor = set(interface_receptor)
interface_ligand = set(interface_ligand)
# Code to consider contacts in the interface
perc_receptor_restraints = ScoringFunction.restraints_satisfied(
receptor.restraints, interface_receptor)
perc_ligand_restraints = ScoringFunction.restraints_satisfied(
ligand.restraints, interface_ligand)
# Calculate membrane interaction
# TODO: refactor restraints_satisfied
membrane_intersection = ScoringFunction.restraints_satisfied(
receptor.membrane, interface_receptor)
membrane_penalty = 0.
if membrane_intersection > 0.:
membrane_penalty = 999.0 * membrane_intersection
return (energy + perc_receptor_restraints * energy +
perc_ligand_restraints * energy -
membrane_penalty) * self.weight
def __call__(self, receptor, receptor_coordinates, ligand,
ligand_coordinates):
"""Calculates the MJ3h potential taking into account the contacts between receptor
and ligand. Receptor and ligand are DockingModel objects.
"""
energy = 0.0
interface_receptor = []
interface_ligand = []
for index_rec, res1 in enumerate(receptor.objects):
for index_lig, res2 in enumerate(ligand.objects):
[x1, y1, z1] = receptor_coordinates[index_rec]
[x2, y2, z2] = ligand_coordinates[index_lig]
distance = (x1 - x2)**2 + (y1 - y2)**2 + (z1 - z2)**2
if distance < MJ3h.max_distance_cutoff:
if distance < MJ3h.min_distance_cutoff:
energy += self.penalization
else:
try:
i_rec = MJ3h.potentials_dict[res1.name]
i_lig = MJ3h.potentials_dict[res2.name]
energy += self.potentials[i_rec][i_lig]
except:
pass
if distance <= self.cutoff:
interface_receptor.append(index_rec)
interface_ligand.append(index_lig)
interface_receptor = set(interface_receptor)
interface_ligand = set(interface_ligand)
energy *= -1.
perc_receptor_restraints = ScoringFunction.restraints_satisfied(
receptor.restraints, interface_receptor)
perc_ligand_restraints = ScoringFunction.restraints_satisfied(
ligand.restraints, interface_ligand)
return energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy
def __call__(self, receptor, receptor_coordinates, ligand, ligand_coordinates):
energy, interface_receptor, interface_ligand = calculate_dfire(receptor, ligand,
self.potential.dfire_energy,
receptor_coordinates, ligand_coordinates)
# Code to consider contacts in the interface
perc_receptor_restraints = ScoringFunction.restraints_satisfied(receptor.restraints, set(interface_receptor))
perc_ligand_restraints = ScoringFunction.restraints_satisfied(ligand.restraints, set(interface_ligand))
return energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy
def __call__(self, receptor, receptor_coordinates, ligand, ligand_coordinates):
energy, interface_receptor, interface_ligand = calculate_dfire(receptor, receptor_coordinates,
ligand, ligand_coordinates,
self.potential.dfire_dist_to_bins,
self.potential.dfire_energy,
interface_cutoff=self.cutoff)
perc_receptor_restraints = ScoringFunction.restraints_satisfied(receptor.restraints, interface_receptor)
perc_ligand_restraints = ScoringFunction.restraints_satisfied(ligand.restraints, interface_ligand)
return (energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy) * self.weight
def __call__(self, receptor, receptor_coordinates, ligand,
ligand_coordinates):
energy, interface_receptor, interface_ligand = calculate_pisa(
receptor, receptor_coordinates, ligand, ligand_coordinates,
self.potential.pisa_energy, DEFAULT_CONTACT_RESTRAINTS_CUTOFF)
perc_receptor_restraints = ScoringFunction.restraints_satisfied(
receptor.restraints, interface_receptor)
perc_ligand_restraints = ScoringFunction.restraints_satisfied(
ligand.restraints, interface_ligand)
return energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy
def __call__(self, receptor, receptor_coordinates, ligand, ligand_coordinates):
energy, interface_receptor, interface_ligand = calculate_dfire(receptor, receptor_coordinates,
ligand, ligand_coordinates,
self.potential.dfire_dist_to_bins,
self.potential.dfire_energy,
interface_cutoff=self.cutoff)
perc_receptor_restraints = ScoringFunction.restraints_satisfied(receptor.restraints, interface_receptor)
perc_ligand_restraints = ScoringFunction.restraints_satisfied(ligand.restraints, interface_ligand)
return energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy
def __call__(self, receptor, receptor_coordinates, ligand, ligand_coordinates):
"""Computes the pyDockDNA scoring energy using receptor and ligand which are
instances of DockingModel.
"""
elec, vdw, interface_receptor, interface_ligand = cdna.calculate_energy(receptor_coordinates, ligand_coordinates,
receptor.charges, ligand.charges,
receptor.vdw_energy, ligand.vdw_energy,
receptor.vdw_radii, ligand.vdw_radii,
DEFAULT_CONTACT_RESTRAINTS_CUTOFF)
energy = (elec + parameters.scoring_vdw_weight * vdw)*-1.
perc_receptor_restraints = ScoringFunction.restraints_satisfied(receptor.restraints, set(interface_receptor))
perc_ligand_restraints = ScoringFunction.restraints_satisfied(ligand.restraints, set(interface_ligand))
return (energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy) * self.weight
def __call__(self, receptor, receptor_coordinates, ligand,
ligand_coordinates):
"""Computes the truncated VdW energy using receptor and ligand which are
instances of the DockingModel class"""
vdw_energy, interface_receptor, interface_ligand = cvdw.calculate_vdw(
receptor_coordinates, ligand_coordinates, receptor.vdw_energy,
ligand.vdw_energy, receptor.vdw_radii, ligand.vdw_radii,
DEFAULT_CONTACT_RESTRAINTS_CUTOFF)
energy = vdw_energy * -1.0 * self.weight
perc_receptor_restraints = ScoringFunction.restraints_satisfied(
receptor.restraints, set(interface_receptor))
perc_ligand_restraints = ScoringFunction.restraints_satisfied(
ligand.restraints, set(interface_ligand))
return energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy
def evaluate_energy(self, receptor, receptor_coordinates, ligand,
ligand_coordinates):
coordinates = np.append(receptor_coordinates.coordinates,
ligand_coordinates.coordinates).reshape(
(-1, 3))
energy, interface_receptor, interface_ligand = calculate_dfire2(
self.res_index, self.atom_index, coordinates,
self.potential.energy, self.molecule_length,
DEFAULT_CONTACT_RESTRAINTS_CUTOFF)
# Code to consider contacts in the interface
perc_receptor_restraints = ScoringFunction.restraints_satisfied(
receptor.restraints, set(interface_receptor))
perc_ligand_restraints = ScoringFunction.restraints_satisfied(
ligand.restraints, set(interface_ligand))
return energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy
def __call__(self, receptor, receptor_coordinates, ligand,
ligand_coordinates):
"""Computes the pyDock scoring energy using receptor and ligand which are
instances of DockingModel
"""
energy, interface_receptor, interface_ligand = csipper.calculate_sipper(
receptor_coordinates, ligand_coordinates, self.energy,
receptor.indexes, ligand.indexes, receptor.atoms_per_residue,
ligand.atoms_per_residue, len(receptor.atoms_per_residue),
len(ligand.atoms_per_residue), receptor.oda, ligand.oda)
perc_receptor_restraints = ScoringFunction.restraints_satisfied(
receptor.restraints, interface_receptor)
perc_ligand_restraints = ScoringFunction.restraints_satisfied(
ligand.restraints, interface_ligand)
return (energy + perc_receptor_restraints * energy +
perc_ligand_restraints * energy) * self.weight
def __call__(self, receptor, receptor_coordinates, ligand,
ligand_coordinates):
"""Computes the SD scoring energy using receptor and ligand which are
instances of DockingModel
"""
energy, interface_receptor, interface_ligand = sd.calculate_energy(
receptor_coordinates, ligand_coordinates, receptor.charges,
ligand.charges, receptor.vdw_energy, ligand.vdw_energy,
receptor.vdw_radii, ligand.vdw_radii,
DEFAULT_CONTACT_RESTRAINTS_CUTOFF)
perc_receptor_restraints = ScoringFunction.restraints_satisfied(
receptor.restraints, set(interface_receptor))
perc_ligand_restraints = ScoringFunction.restraints_satisfied(
ligand.restraints, set(interface_ligand))
return energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy
def __call__(self, receptor, receptor_coordinates, ligand, ligand_coordinates):
"""Computes the pyDock scoring energy using receptor and ligand which are
instances of DockingModel.
"""
elec, vdw, solv_rec, solv_lig, interface_receptor, interface_ligand = cpydock.calculate_energy(receptor_coordinates, ligand_coordinates,
receptor.charges, ligand.charges,
receptor.vdw_energy, ligand.vdw_energy,
receptor.vdw_radii, ligand.vdw_radii,
receptor.hydrogens, ligand.hydrogens,
receptor.sasa, ligand.sasa,
receptor.des_energy, ligand.des_energy,
3.9)
solv = -1*(solv_rec + solv_lig)
energy = (elec + parameters.scoring_vdw_weight * vdw + solv)*-1.
perc_receptor_restraints = ScoringFunction.restraints_satisfied(receptor.restraints, set(interface_receptor))
perc_ligand_restraints = ScoringFunction.restraints_satisfied(ligand.restraints, set(interface_ligand))
return energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy
def _default(self, receptor, receptor_coordinates, ligand, ligand_coordinates):
energy = 0.0
dist_matrix = scipy.spatial.distance.cdist(receptor_coordinates, ligand_coordinates)
interface_receptor = []
interface_ligand = []
for rec_index, rec_tobi in enumerate(receptor.objects):
for lig_index, lig_tobi in enumerate(ligand.objects):
d = dist_matrix[rec_index][lig_index]
if d <= 8.0:
if rec_tobi >= 20 and lig_tobi >= 20:
# Small distance, backbone-backbone
if d <= 4.5:
energy += self.potential.tobi_sc_1[rec_tobi][lig_tobi]
else:
if d <= 6.0:
energy += self.potential.tobi_sc_2[rec_tobi][lig_tobi]
else:
# Medium distance, backbone-sidechain
if rec_tobi >= 20 or lig_tobi >= 20:
if d <= 5.5:
energy += self.potential.tobi_sc_1[rec_tobi][lig_tobi]
else:
if d <= 7.0:
energy += self.potential.tobi_sc_2[rec_tobi][lig_tobi]
else:
# Large distance, sidechain-sidechain
if d <= 6.5:
energy += self.potential.tobi_sc_1[rec_tobi][lig_tobi]
else:
if d <= 8.0:
energy += self.potential.tobi_sc_2[rec_tobi][lig_tobi]
if d <= self.cutoff:
interface_receptor.append(rec_index)
interface_ligand.append(lig_index)
interface_receptor = set(interface_receptor)
interface_ligand = set(interface_ligand)
energy *= -1.
perc_receptor_restraints = ScoringFunction.restraints_satisfied(receptor.restraints, interface_receptor)
perc_ligand_restraints = ScoringFunction.restraints_satisfied(ligand.restraints, interface_ligand)
return (energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy) * self.weight
def test_call_scoring_function_interface(self):
sf = ScoringFunction()
sf(None, None, None, None)
assert False