class MinimizationTestCase(unittest.TestCase):
def setUp(self):
self.molecule = Molecule(pdb_file_location='tests/data/ref01.pdb')
self.parameters = Parameters()
self.molecule.set_force_field_parameters(self.parameters)
self.optimization = GradientDescent(self.atom_energy_function)
self.optimization.dimensions_number = 3
self.optimization.iterations = 40
self.optimization.precision = 0.01
self.optimization.small_step = 0.00015
self.optimization.smallest_step = self.optimization.small_step / 128
self.force_field = ForceField(self.parameters)
self.atom_index = 0
def test_gradient_descent(self):
self.atom_index = 0
for j in range(5):
self.optimization.run()
atom = self.molecule.atoms[self.atom_index]
atom.translate_starting_point(
self.optimization.best_particle.dimensions)
self.atom_index += 1
energy = self.force_field.calculate_energy(self.molecule)
# self.force_field.print_energy()
self.assertEqual(energy, 599.882043366674)
def atom_energy_function(self, particle):
a = self.molecule.atoms[self.atom_index]
a.translate_starting_point(particle.dimensions)
return self.force_field.calculate_energy(self.molecule,
atom=a,
protect_bonds=False)
def setUp(self):
self.molecule = Molecule(pdb_file_location='tests/data/ref01.pdb')
self.parameters = Parameters()
self.molecule.set_force_field_parameters(self.parameters)
self.optimization = GradientDescent(self.atom_energy_function)
self.optimization.dimensions_number = 3
self.optimization.iterations = 40
self.optimization.precision = 0.01
self.optimization.small_step = 0.00015
self.optimization.smallest_step = self.optimization.small_step / 128
self.force_field = ForceField(self.parameters)
self.atom_index = 0
def _populate_molecule(self):
pointer = np.array([0, 0, 0])
c_n_separator = np.array([1.3350, 0, 0])
i = 0
for a in self.sequence:
i += 1
abbreviation = code_map[a]
residue = Molecule(pdb_file_location='data/catalog/' +
abbreviation + '.pdb')
if i == 1:
Fasta._add_n_terminal_hydrogen(residue)
if i == len(self.sequence):
Fasta._add_c_terminal_oxygen(residue)
n_terminal = residue.amino_acids[0].atoms_map['N']
c_terminal = residue.amino_acids[0].atoms_map['C']
delta = np.array(n_terminal.point) - np.array(pointer)
residue.translate(-delta)
for a in residue.atoms:
a.res_seq = i
self.molecule.atoms.append(a.copy())
pointer = np.array(c_terminal.point) + c_n_separator
def test_rotation(self):
parameters = Parameters()
self.generated.set_force_field_parameters(parameters)
topology = self.generated.get_topology()
phi = []
psi = []
for i in range(len(input_phi_psi)):
phi.append(input_phi_psi[i][1])
psi.append(input_phi_psi[i][2])
topology.rotate_backbone('PHI', phi)
topology.rotate_backbone('PSI', psi)
expected = Molecule(pdb_file_location='tests/data/rotated.pdb')
rmsd = self.generated.rmsd(expected)
self.assertLess(rmsd, 0.05)
def __init__(self, sequence):
self.sequence = sequence
self.molecule = Molecule()
class Fasta:
def __init__(self, sequence):
self.sequence = sequence
self.molecule = Molecule()
def to_pdb(self):
self._populate_molecule()
self.molecule.add_sequential_ids()
self.molecule.update_internal_state()
parameters = Parameters()
self.molecule.set_force_field_parameters(parameters)
self._rotate_to_default_position()
return self.molecule
def _populate_molecule(self):
pointer = np.array([0, 0, 0])
c_n_separator = np.array([1.3350, 0, 0])
i = 0
for a in self.sequence:
i += 1
abbreviation = code_map[a]
residue = Molecule(pdb_file_location='data/catalog/' +
abbreviation + '.pdb')
if i == 1:
Fasta._add_n_terminal_hydrogen(residue)
if i == len(self.sequence):
Fasta._add_c_terminal_oxygen(residue)
n_terminal = residue.amino_acids[0].atoms_map['N']
c_terminal = residue.amino_acids[0].atoms_map['C']
delta = np.array(n_terminal.point) - np.array(pointer)
residue.translate(-delta)
for a in residue.atoms:
a.res_seq = i
self.molecule.atoms.append(a.copy())
pointer = np.array(c_terminal.point) + c_n_separator
def _rotate_to_default_position(self):
topology = self.molecule.get_topology()
for i in range(len(self.molecule.amino_acids)):
amino_acid = self.molecule.amino_acids[i]
backbone_torsions_map = topology.backbone_torsions_map[
amino_acid.sequence]
if not amino_acid.is_last():
topology.fix_nitrogen(amino_acid,
self.molecule.amino_acids[i + 1])
topology.fix_alpha_carbon(amino_acid,
self.molecule.amino_acids[i + 1])
if 'PSI' in backbone_torsions_map:
topology.rotate_proper_dihedral(backbone_torsions_map['PSI'],
180.0)
if 'PHI' in backbone_torsions_map:
topology.rotate_proper_dihedral(backbone_torsions_map['PHI'],
180.0)
if 'OMEGA' in backbone_torsions_map:
topology.rotate_proper_dihedral(backbone_torsions_map['OMEGA'],
180.0)
# if not amino_acid.is_first(): topology.set_side_chain_torsion(amino_acid, 0)
for i in range(len(self.molecule.amino_acids)):
amino_acid = self.molecule.amino_acids[i]
if not amino_acid.is_last():
topology.fix_oxygen(amino_acid,
self.molecule.amino_acids[i + 1])
topology.fix_amine_hydrogen_torsion(
amino_acid, self.molecule.amino_acids[i + 1])
topology.fix_amine_hydrogen(amino_acid,
self.molecule.amino_acids[i + 1])
topology.fix_amine_hydrogen_angle_to_ca(amino_acid)
@staticmethod
def _add_n_terminal_hydrogen(residue):
n = residue.amino_acids[0].atoms_map['N']
h1 = residue.amino_acids[0].atoms_map['H']
h1.name = 'H1'
# ATOM 9 H1 ASN A 1 -8.330 3.957 0.261 1.00 0.00 H
# ATOM 10 H2 ASN A 1 -8.740 5.068 -0.889 1.00 0.00 H
# ATOM 11 H3 ASN A 1 -9.877 4.041 -0.293 1.00 0.00 H
h2 = h1.copy().translate([-0.3, -0.5, -1.3])
h3 = h1.copy().translate([0, -1.1, -0.3])
h2.name = 'H2'
h3.name = 'H3'
residue.atoms.append(h2)
residue.atoms.append(h3)
residue.update_internal_state()
@staticmethod
def _add_c_terminal_oxygen(residue):
o_atom = residue.amino_acids[0].atoms_map['O']
oxt_atom = o_atom.copy().translate([-1.5, +0.0, 1.7])
oxt_atom.name = 'OXT'
residue.atoms.append(oxt_atom)
residue.update_internal_state()
def test_generate_molecule(self):
expected = Molecule(pdb_file_location='tests/data/generated.pdb')
rmsd = self.generated.rmsd(expected)
self.assertLess(rmsd, 0.0006)
def setUp(self):
self.parameters = Parameters()
self.ligand = Molecule(pdb_file_location='tests/data/ligand.pdb')
def test_read_molecule(self): molecule = Molecule(pdb_file_location='tests/data/1l2y-01.pdb') self.assertEqual(len(molecule.amino_acids), 20)