def test_update_existing_conf(self):
rism_toluene = RISM_3D_calculation('test/toluene')
rism_toluene_copy = RISM_3D_calculation('test/toluene_copy')
can = 'Cc1ccccc1'
wr = Writer(self.ses)
wr.write_rism(rism_toluene)
dbi = DBInterface(self.ses)
db_mol = dbi.get_molecule(can)
db_conf = db_mol.find_0rmsd_conformation()
assert str(db_conf.Source) == 'None'
wr.write_rism(rism_toluene_copy, {'Source': 'David'})
dbi = DBInterface(self.ses)
db_mol = dbi.get_molecule(can)
db_conf = db_mol.find_0rmsd_conformation()
assert str(db_conf.Source) == 'David'
self.ses.rollback()
def test_parse_rism_folder_files(self):
folder = 'test/toluene'
calculation = RISM_3D_calculation(folder)
results = """dGhyd(KH)= 2.09294808E+001 kcal/mol
dGhyd(GF)= 1.34305025E+001 kcal/mol
PMV= 1.51209629E+002 AA^3
dGhyd(UC)= -2.21336115625 kcal/mol
"""
assert calculation.file_dic['results'] == results
def test_write_new_mol_and_new_conf_and_conf_props(self):
rism_toluene = RISM_3D_calculation('test/toluene')
can = 'Cc1ccccc1'
wr = Writer(self.ses)
wr.write_rism(rism_toluene, {'Source': 'David'})
dbi = DBInterface(self.ses)
db_mol = dbi.get_molecule(can)
db_conf = db_mol.find_0rmsd_conformation()
assert str(db_conf.Source) == 'David'
self.ses.rollback()
def test_write_rism_calculation(self):
rism_toluene = RISM_3D_calculation('test/toluene')
can = 'Cc1ccccc1'
wr = Writer(self.ses)
wr.write_rism(rism_toluene, {'Source': 'David'})
dbi = DBInterface(self.ses)
db_mol = dbi.get_molecule(can)
db_conf = db_mol.find_0rmsd_conformation()
db_calc = db_conf.get_rism_calculations()[0]
assert db_calc.SolvE == 1.34305025E+001
assert db_calc.Temperature == '298'
self.ses.rollback()
def test_write_new_mol_and_new_0_conf(self):
rism_toluene = RISM_3D_calculation('test/toluene')
can = 'Cc1ccccc1'
wr = Writer(self.ses)
wr.write_rism(rism_toluene)
dbi = DBInterface(self.ses)
db_mol = dbi.get_molecule(can)
db_can = str(db_mol.SMILES)
db_conf = db_mol.find_0rmsd_conformation()
pymol = pybel.readstring('mol', str(db_conf.Mol))
assert can == db_can
# assert xyz == db_xyz
self.ses.rollback()
def parse_rism_folders(folders):
"""Accepts list (or tuple) of folders and writes
3DRISM_calculation data to db.
"""
ses = create_session()
wr = Writer(ses)
for folder in folders:
try:
rism = RISM_3D_calculation(folder)
wr.write_rism(rism, conf_attributes, rism_attributes)
ses.commit()
print folder + ' written'
except OSError, e:
warnings.warn(str(e), UserWarning)
except TypeError, e:
warnings.warn(str(e), UserWarning)
def test_parse_rism_folder_rism_paths(self):
folder = 'test/toluene'
calculation = RISM_3D_calculation(folder)
assert calculation.rism3d_folder == "test/toluene"
assert calculation.file_path_dic['topology'] == 'test/toluene/toluene.prmtop'
assert calculation.file_path_dic['input'] == \
'test/toluene/toluene.pdb'
assert calculation.file_path_dic['parameters'] == \
'test/toluene/run3drismgaff.sh'
assert calculation.file_path_dic['results'] == \
'test/toluene/results.txt'
assert calculation.file_path_dic['output'] == \
'test/toluene/out.425966'
assert calculation.file_path_dic['solvent'] == \
'test/toluene/solvent_gen_file.sh'
assert calculation.runtime == 2790
def test_parse_rism_folder_mol_conversion(self):
folder = 'test/toluene'
calculation = RISM_3D_calculation(folder)
smi = 'Cc1ccccc1'
assert calculation.pymol.write('can').strip() == smi
def test_parse_rism_folder_energy(self):
folder = 'test/toluene'
calculation = RISM_3D_calculation(folder)
energy = 1.34305025E+001
assert calculation.solvation_energy == energy
def test_parse_rism_folder_input(self):
folder = 'test/toluene'
calculation = RISM_3D_calculation(folder)
assert calculation.file_dic['input'] == \
"""ATOM 1 C1 MOL 1 3.537 1.423 0.000 1.00 0.00
def test_parse_rism_folder_unambigious(self):
folder = 'test/scary'
with pytest.raises(TypeError) as excinfo:
RISM_3D_calculation(folder)
info = """Found multiple files of type *.prmtop in folder {}.""".format(folder)
assert excinfo.value.message == info
def test_parse_rism_folder_empty_folder(self):
folder = 'test/stupid_empty_folder'
with pytest.raises(TypeError) as excinfo:
RISM_3D_calculation(folder)
info = """Couldn't find *.prmtop file in folder {}.""".format(folder)
assert excinfo.value.message == info
def test_initialization(self):
with pytest.raises(OSError) as excinfo:
RISM_3D_calculation('not_a_folder')
assert excinfo.value.message == 'not_a_folder is not a folder.'