def test_two_molecules(individual, protein, ligand):
individual.genes['Ligand'] = Molecule(parent=individual, path=datapath(ligand))
individual.genes['Protein'] = Molecule(parent=individual, path=datapath(protein))
individual.__ready__()
individual.__expression_hooks__()
with expressed(individual):
assert individual.expressed is True
def test_vina(individual, protein, ligand, affinity):
individual.genes['Protein'] = Molecule(parent=individual, path=datapath(protein))
individual.genes['Ligand'] = Molecule(parent=individual, path=datapath(ligand))
individual.__ready__()
individual.__expression_hooks__()
objective = Vina(weight=-1.0)
with expressed(individual):
assert affinity == objective.evaluate(individual)
def do(self, proteinpath, ligandpath, objective, obj_kwargs):
from gaudi.base import MolecularIndividual, expressed
from gaudi.genes.molecule import Molecule
individual = MolecularIndividual(dummy=True)
individual.genes['Protein'] = protein = Molecule(path=proteinpath)
individual.genes['Ligand'] = ligand = Molecule(path=ligandpath)
individual.__ready__()
individual.__expression_hooks__()
obj = objective(**obj_kwargs)
with expressed(individual):
score = obj.evaluate(individual)
individual.genes['Protein'].compound.destroy()
individual.genes['Ligand'].compound.destroy()
del individual
return score
def test_nwchem(individual, ligand, energy):
individual.genes['Ligand'] = Molecule(parent=individual,
path=datapath(ligand))
individual.__ready__()
individual.__expression_hooks__()
objective = NWChem(targets=['Ligand'], title='test', weight=-1.0)
with expressed(individual):
assert abs(energy - objective.evaluate(individual)) < 0.0001
def search_gene(individual, path, **kwargs):
individual.genes['Molecule'] = Molecule(parent=individual,
path=datapath(path))
individual.genes['Search'] = search = Search.with_validation(
parent=individual, precision=3, **kwargs)
individual.__ready__()
individual.__expression_hooks__()
return search
def rotamers(individual, path, position, seed):
individual.genes['Molecule'] = Molecule(parent=individual, path=datapath(path))
individual.genes['Rotamers'] = rotamers = Rotamers(parent=individual, with_original=True,
residues=[('Molecule', position)])
individual.__ready__()
individual.__expression_hooks__()
rotamers.allele = [seed]
return rotamers
def energy(individual, path):
individual.genes['Molecule'] = Molecule(parent=individual,
path=datapath(path))
individual.__ready__()
individual.__expression_hooks__()
objective = Energy()
with expressed(individual):
return objective.evaluate(individual)
def nma_gene(individual, path, **kwargs):
individual.genes['Molecule'] = Molecule(parent=individual,
path=datapath(path))
individual.genes['NMA'] = nma = NormalModes.with_validation(
parent=individual, precision=3, **kwargs)
individual.__ready__()
individual.__expression_hooks__()
return nma
def dsx(individual, protein, ligand, **kwargs):
individual.genes['Protein'] = Molecule(parent=individual,
path=datapath(protein))
individual.genes['Ligand'] = Molecule(parent=individual,
path=datapath(ligand))
individual.__ready__()
individual.__expression_hooks__()
options = dict(weight=-1.0,
terms=[True, False, False, True, False],
proteins=['Protein'],
ligands=['Ligand'],
sorting=1,
cofactor_mode=0,
with_metals=False)
options.update(kwargs)
objective = DSX(**options)
with expressed(individual):
return objective.evaluate(individual)
def test_molecule(individual, path, atoms):
absolute_path = os.path.abspath(datapath(path))
individual.genes['Molecule'] = Molecule(parent=individual, path=absolute_path)
individual.__ready__()
individual.__expression_hooks__()
assert individual.genes['Molecule'].compound.mol.numAtoms == atoms
assert individual.genes['Molecule'].compound.mol.openedAs[0] == absolute_path
with expressed(individual):
assert individual.expressed is True
def test_molecule(individual, individual2, path1, path2, threshold):
absolute_path1 = os.path.abspath(datapath(path1))
absolute_path2 = os.path.abspath(datapath(path2))
individual.genes['Molecule'] = Molecule(parent=individual,
path=absolute_path1)
individual.__ready__()
individual.__expression_hooks__()
individual2.genes['Molecule'] = Molecule(parent=individual2,
path=absolute_path2)
individual2.__ready__()
individual2.__expression_hooks__()
with expressed(individual, individual2):
sqrmsd = _rmsd_squared(
individual.genes['Molecule']._expressed_coordinates,
individual2.genes['Molecule']._expressed_coordinates)
assert abs(sqrmsd - threshold * threshold) < 0.01
assert rmsd(individual, individual2, ['Molecule'], threshold)
def interactions(individual, path, which):
individual.genes['Molecule'] = Molecule(parent=individual,
path=datapath(path))
individual.__ready__()
individual.__expression_hooks__()
kwargs = dict(probes=['Molecule'], radius=10 * random(), which=which)
objective = Contacts(**kwargs)
with expressed(individual):
return objective.evaluate(individual)
def torsions(individual, path, angle, **kwargs):
individual.genes['Molecule'] = Molecule(parent=individual,
path=datapath(path))
individual.genes['Torsion'] = torsion = Torsion(parent=individual,
target='Molecule',
**kwargs)
individual.__ready__()
individual.__expression_hooks__()
torsion.allele = [angle] * torsion.max_bonds
return torsion
def trajectory_setup(individual, molecule, traj, frame, max_frame):
individual.genes['Molecule'] = Molecule(parent=individual,
path=datapath(molecule))
gene = Trajectory(parent=individual,
path=datapath(traj),
max_frame=max_frame,
target='Molecule')
individual.genes['Trajectory'] = gene
individual.__ready__()
individual.__expression_hooks__()
gene.allele = frame
return gene
def test_coordination_uncorrected(individual, path, metal, ligands, geometry, score):
individual.genes['Molecule'] = Molecule(parent=individual, path=datapath(path))
individual.__ready__()
individual.__expression_hooks__()
objective = Coordination(probe=('Molecule', metal), residues=[('Molecule', '*')],
atom_elements=('C N O S'.split()), geometry=geometry,
weight=-1.0)
with expressed(individual):
sphere = objective.coordination_sphere(individual)[:objective.n_vertices]
assert len(sphere) == len(ligands)
assert sorted(ligands) == sorted([a.serialNumber for (d, a) in sphere])
fitness = objective.evaluate(individual)
assert abs(fitness - score) < 0.0001
def test_topology(individual, path, atoms, bonds, residues):
individual.genes['Molecule'] = Molecule(parent=individual,
path=datapath(path))
individual.__ready__()
individual.__expression_hooks__()
objective = Energy()
with expressed(individual):
molecules = objective.molecules(individual)
topology = objective.chimera_molecule_to_openmm_topology(*molecules)
assert topology.getNumAtoms() == sum(m.numAtoms for m in molecules)
assert len(list(topology.bonds())) == sum(m.numBonds
for m in molecules)
assert topology.getNumResidues() == sum(m.numResidues
for m in molecules)