def _drug_tester(n_molecules=3404, charge_method="bcc"):
"""Helper function for running various versions of the drug parameterization benchmark."""
assert n_molecules <= 3404, "The maximum number of molecules is 3404."
assert charge_method in ["bcc", None
], "Charge method must be either None or 'bcc'"
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)
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 _tester_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb(
charge_method="bcc"):
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()
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_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.GetOEMols():
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_common_molecules():
import openeye.oechem
for molecule_name in molecules:
molecule = openmoltools.openeye.iupac_to_oemol(molecule_name)
molecule = openmoltools.openeye.get_charges(molecule)
with utils.enter_temp_directory():
tripos_mol2_filename = 'molecule.mol2'
molecule_name, tripos_mol2_filename = utils.molecule_to_mol2(molecule, tripos_mol2_filename=tripos_mol2_filename)
yield utils.tag_description(lambda : utils.test_molecule('molecule', tripos_mol2_filename), "Testing molecule %s" % molecule_name)
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.GetOEMols():
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 _drug_tester(n_molecules=3404, charge_method="bcc"):
"""Helper function for running various versions of the drug parameterization benchmark."""
assert n_molecules <= 3404, "The maximum number of molecules is 3404."
assert charge_method in ["bcc", None], "Charge method must be either None or 'bcc'"
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)
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 _tester_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb(charge_method="bcc"):
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()
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_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)