def test_run_antechamber_charges():
molecule_name = "acetate"
input_filename = utils.get_data_filename("chemicals/acetate/acetate.mol2")
with utils.enter_temp_directory(): # Prevents creating tons of GAFF files everywhere.
gaff_mol2_filename, frcmod_filename = utils.run_antechamber(
molecule_name, input_filename, charge_method=None, net_charge=-1
)
def test_parse_ligand_filename():
molecule_name = "sustiva"
input_filename = utils.get_data_filename("chemicals/sustiva/sustiva.mol2")
name, ext = utils.parse_ligand_filename(input_filename)
eq(name, "sustiva")
eq(ext, ".mol2")
def test_drugs():
database_filename = utils.get_data_filename("chemicals/drugs/Zdd.mol2.gz")
ifs = openeye.oechem.oemolistream(database_filename)
for molecule in ifs.GetOEGraphMols():
with utils.enter_temp_directory():
molecule_name, tripos_mol2_filename = utils.molecule_to_mol2(molecule)
yield lambda : utils.test_molecule(molecule_name, tripos_mol2_filename) # Cute trick to iteratively run this test over entire database.
def test_drugs():
import openeye.oechem
database_filename = utils.get_data_filename("chemicals/drugs/Zdd.mol2.gz")
ifs = openeye.oechem.oemolistream(database_filename)
for molecule in ifs.GetOEGraphMols():
with utils.enter_temp_directory():
molecule_name, tripos_mol2_filename = utils.molecule_to_mol2(molecule)
yield utils.tag_description(lambda : utils.test_molecule(molecule_name, tripos_mol2_filename), "Testing drugs %s" % molecule_name)
def test_smiles_conversion():
pdb_filename = utils.get_data_filename("chemicals/proteins/1vii.pdb")
smiles = "Cc1ccccc1" # Also known as toluene.
temperature = 300 * u.kelvin
friction = 0.3 / u.picosecond
timestep = 0.01 * u.femtosecond
protein_traj = md.load(pdb_filename)
protein_traj.center_coordinates()
protein_top = protein_traj.top.to_openmm()
protein_xyz = protein_traj.openmm_positions(0)
ligand_trajectories, ffxml = utils.smiles_to_mdtraj_ffxml([smiles])
ligand_traj = ligand_trajectories[0]
ligand_traj.center_coordinates()
eq(ligand_traj.n_atoms, 15)
eq(ligand_traj.n_frames, 1)
# Move the pre-centered ligand sufficiently far away from the protein to avoid a clash.
min_atom_pair_distance = (
((ligand_traj.xyz[0] ** 2.0).sum(1) ** 0.5).max() + ((protein_traj.xyz[0] ** 2.0).sum(1) ** 0.5).max() + 0.3
)
ligand_traj.xyz += np.array([1.0, 0.0, 0.0]) * min_atom_pair_distance
ligand_xyz = ligand_traj.openmm_positions(0)
ligand_top = ligand_traj.top.to_openmm()
forcefield = app.ForceField("amber10.xml", ffxml, "tip3p.xml")
model = app.modeller.Modeller(protein_top, protein_xyz)
model.add(ligand_top, ligand_xyz)
model.addSolvent(forcefield, padding=0.4 * u.nanometer)
system = forcefield.createSystem(
model.topology, nonbondedMethod=app.PME, nonbondedCutoff=1.0 * u.nanometers, constraints=app.HAngles
)
integrator = mm.LangevinIntegrator(temperature, friction, timestep)
simulation = app.Simulation(model.topology, system, integrator)
simulation.context.setPositions(model.positions)
print("running")
simulation.step(1)
def test_drugs():
path = tempfile.mkdtemp()
database_filename = utils.get_data_filename("chemicals/drugs/Zdd.mol2.gz")
cmd = "gunzip -c %s > %s/Zdd.mol2" % (database_filename, path)
os.system(cmd)
cmd = """awk '/MOLECULE/{close(x);x="%s/molecule_"i++".mol2"}{print > x}' %s/Zdd.mol2""" % (path, path)
os.system(cmd)
n_molecules = 3404
if os.environ.get("TRAVIS", None) == 'true':
n_molecules = 25 # If running on travis, only test the first 25 molecules due to speed.
for k in range(n_molecules):
molecule_name = "molecule_%d" % k
mol2_filename = "%s/%s.mol2" % (path, molecule_name)
cmd = """sed -i "s/<0>/LIG/" %s""" % mol2_filename
os.system(cmd) # Have to remove the <0> because it leads to invalid XML in the forcefield files.
with utils.enter_temp_directory():
yield lambda : utils.test_molecule("LIG", mol2_filename)
def test_drugs():
path = tempfile.mkdtemp()
database_filename = utils.get_data_filename("chemicals/drugs/Zdd.mol2.gz")
cmd = "gunzip -c %s > %s/Zdd.mol2" % (database_filename, path)
os.system(cmd)
cmd = """awk '/MOLECULE/{close(x);x="%s/molecule_"i++".mol2"}{print > x}' %s/Zdd.mol2""" % (path, path)
os.system(cmd)
n_molecules = 3404
CHARGE_METHOD = "bcc"
if os.environ.get("TRAVIS", None) == 'true':
n_molecules = 25 # If running on travis, only test the first 25 molecules due to speed.
CHARGE_METHOD = None # Travis is actually too slow to do a single bcc calculation!
for k in range(n_molecules):
molecule_name = "molecule_%d" % k
mol2_filename = "%s/%s.mol2" % (path, molecule_name)
cmd = """sed -i "s/<0>/LIG/" %s""" % mol2_filename
os.system(cmd) # Have to remove the <0> because it leads to invalid XML in the forcefield files.
with utils.enter_temp_directory():
yield utils.tag_description(lambda : utils.test_molecule("LIG", mol2_filename, charge_method=CHARGE_METHOD), "Testing drugs %s with charge method %s" % (molecule_name, CHARGE_METHOD))
def test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb():
with utils.enter_temp_directory():
tar_filename = utils.get_data_filename("chemicals/freesolv/freesolve_v0.3.tar.bz2")
tar = tarfile.open(tar_filename, mode="r:bz2")
tar.extractall()
tar.close()
CHARGE_METHOD = "bcc"
if os.environ.get("TRAVIS", None) == 'true':
CHARGE_METHOD = None # Travis is actually too slow to do a single bcc calculation!
database = pickle.load(open("./v0.3/database.pickle"))
for key in database:
for directory in ["mol2files_gaff", "mol2files_sybyl"]:
gaff_filename = os.path.abspath("./v0.3/%s/%s.mol2" % (directory, key))
cmd = """sed -i "s/<0>/LIG/" %s""" % gaff_filename
os.system(cmd) # Have to remove the <0> because it leads to invalid XML in the forcefield files.
t_gaff = md.load(gaff_filename)
with utils.enter_temp_directory():
yield utils.tag_description(lambda : utils.test_molecule("LIG", gaff_filename, charge_method=CHARGE_METHOD), "Testing freesolv %s %s with charge model %s" % (directory, key, CHARGE_METHOD))
def test_run_test_molecule():
molecule_name = "sustiva"
input_filename = utils.get_data_filename("chemicals/sustiva/sustiva.mol2")
with utils.enter_temp_directory(): # Prevents creating tons of GAFF files everywhere.
utils.test_molecule(molecule_name, input_filename)
def test_run_tleap():
molecule_name = "sustiva"
input_filename = utils.get_data_filename("chemicals/sustiva/sustiva.mol2")
with utils.enter_temp_directory(): # Prevents creating tons of GAFF files everywhere.
gaff_mol2_filename, frcmod_filename = utils.run_antechamber(molecule_name, input_filename, charge_method=None)
prmtop, inpcrd = utils.run_tleap(molecule_name, gaff_mol2_filename, frcmod_filename)