def test_atom_map(self):
"""Test get atom map"""
from openeye import oechem
tagged_smiles = '[H:5][C:1]#[N+:4][C:3]([H:9])([H:10])[C:2]([H:6])([H:7])[H:8]'
mol_1 = openeye.smiles_to_oemol('CC[N+]#C')
inf = get_fn('ethylmethylidyneamonium.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
atom_map = utils.get_atom_map(tagged_smiles, mol_1)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i+1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping-1))
atom_2.SetAtomicNum(i+1)
self.assertEqual(oechem.OECreateCanSmiString(mol_1), oechem.OECreateCanSmiString(mol_2))
# Test aromatic molecule
tagged_smiles = '[H:10][c:4]1[c:3]([c:2]([c:1]([c:6]([c:5]1[H:11])[H:12])[C:7]([H:13])([H:14])[H:15])[H:8])[H:9]'
mol_1 = openeye.smiles_to_oemol('Cc1ccccc1')
inf = get_fn('toluene.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
atom_map = utils.get_atom_map(tagged_smiles, mol_1)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i+1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping-1))
atom_2.SetAtomicNum(i+1)
self.assertEqual(oechem.OECreateCanSmiString(mol_1), oechem.OECreateCanSmiString(mol_2))
def test_generat_torsions(self):
""" Tests finding torsion to drive """
from openeye import oechem
infile = get_fn('butane.pdb')
ifs = oechem.oemolistream(infile)
inp_mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, inp_mol)
outfile_path = tempfile.mkdtemp()[1]
qmscan.generate_torsions(inp_mol=inp_mol,
output_path=outfile_path,
interval=30,
tar=False)
input_files = []
pattern = '*.pdb'
for path, subdir, files in os.walk(outfile_path):
for name in files:
if fnmatch(name, pattern):
input_files.append(os.path.join(path, name))
contents = open(input_files[0]).read()
pdb = get_fn('butane_10_7_4_3_0.pdb')
compare_contents = open(pdb).read()
self.assertEqual(contents, compare_contents)
shutil.rmtree(outfile_path)
def test_extract_geom_opt():
"""Tests extraction of optimized geometry"""
structure = get_fn('MPR.psf')
scan = qmdb.parse_gauss(
[get_fn('MPR.scan1.pos.log'),
get_fn('MPR.scan1.neg.log')], structure)
scan.extract_geom_opt()
def test_update_param_struct_cont(self):
""" Tests that update parameter updates assigned parameters in the structure """
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'),
get_fn('par_all36_cgenff.prm'))
structure = get_fn('butane.psf')
logfiles = get_fn('MP2_torsion_scan/')
frag = qmdb.parse_psi4_out(logfiles, structure)
frag = frag.remove_nonoptimized()
to_optimize = [('CG331', 'CG321', 'CG321', 'CG331')]
model = TorsionFitModelOMM(param=param,
frags=frag,
param_to_opt=to_optimize,
sample_phase=True,
continuous_phase=True)
par.update_param_from_sample(model.parameters_to_optimize,
param,
model=model,
rj=model.rj,
phase=model.sample_phase,
n_5=model.sample_n5,
model_type='openmm')
torsion = frag.structure.dihedrals[0]
self.assertEqual(
torsion.type,
param.dihedral_types[(torsion.atom1.type, torsion.atom2.type,
torsion.atom3.type, torsion.atom4.type)])
def test_param_from_db(self):
""" Tests parameterizing from database """
param = CharmmParameterSet(get_fn('par_all36_cgenff.prm'),
get_fn('top_all36_cgenff.rtf'))
torsion = ('CG331', 'CG321', 'CG321', 'CG331')
db = sqlite_plus.load(get_fn('butane.db'))
par.add_missing(torsion, param, sample_n5=True)
self.assertEqual(param.dihedral_types[torsion][0].phi_k, 0.03819)
self.assertEqual(param.dihedral_types[torsion][1].phi_k, 0.03178)
self.assertEqual(param.dihedral_types[torsion][2].phi_k, 0.0)
self.assertEqual(param.dihedral_types[torsion][3].phi_k, 0.0)
self.assertEqual(param.dihedral_types[torsion][4].phi_k, 0.0)
self.assertEqual(param.dihedral_types[torsion][5].phi_k, 0.0)
par.update_param_from_sample(param_list=torsion,
param=param,
db=db,
rj=False,
model_type='openmm')
self.assertEqual(param.dihedral_types[torsion][0].phi_k, 0.086424)
self.assertEqual(param.dihedral_types[torsion][1].phi_k, 0.019074)
self.assertEqual(param.dihedral_types[torsion][2].phi_k, 0.0)
self.assertEqual(param.dihedral_types[torsion][3].phi_k, -1.834546)
self.assertEqual(param.dihedral_types[torsion][4].phi_k, -1.86807)
self.assertEqual(param.dihedral_types[torsion][5].phi_k, -2.860622)
def test_set_phase_0(self):
""" Test set phases to 0 """
param = CharmmParameterSet(get_fn('par_all36_cgenff.prm'), get_fn('top_all36_cgenff.rtf'))
torsion = ('CG331', 'CG321', 'CG321', 'CG331')
self.assertEqual(param.dihedral_types[torsion][1].phase, 180.0)
par.set_phase_0(torsion, param)
self.assertEqual(param.dihedral_types[torsion][1].phase, 0.0)
def test_remove_nonoptimized(self):
""" Test remove non_optimized structures """
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure, pattern="*.out2")
self.assertEqual(test_scan.n_frames, 14)
scan_opt = test_scan.remove_nonoptimized()
self.assertEqual(scan_opt.n_frames, 13)
def test_to_optimize(self):
"""Tests generate to_optimize list"""
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'), get_fn('par_all36_cgenff.prm'))
stream = (get_fn('PRL.str'))
to_optimize = qmdb.to_optimize(param, stream)
self.assert_(len(to_optimize) == 19)
reverse = tuple(reversed(to_optimize[0]))
self.assert_(reverse not in to_optimize)
def test_create_context(self):
""" Test create context """
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure)
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'), get_fn('par_all36_cgenff.prm'))
test_scan.integrator = mm.VerletIntegrator(0.004*u.picoseconds)
test_scan.create_context(param)
def test_copy_torsions(self):
""" Test copy torsions"""
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure)
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'), get_fn('par_all36_cgenff.prm'))
test_scan.compute_energy(param)
test_scan.copy_torsions()
def test_remove_nonoptimized(self):
""" Test remove non_optimized structures """
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure, pattern="*.out2")
self.assertEqual(test_scan.n_frames, 14)
scan_opt = test_scan.remove_nonoptimized()
self.assertEqual(scan_opt.n_frames, 13)
def test_generate_input(self):
"""Test generate psi4 input files"""
root = get_fn('torsion_scan/10_7_4_3')
qmscan.generate_scan_input(root, 'pdb', 'butane', ['MP2'], ['aug-cc-pvtz'], symmetry='C1')
contents = open(get_fn('torsion_scan/10_7_4_3/0/butane_10_7_4_3_0.dat')).read()
compare_content = open(get_fn('butane_10_7_4_3_0.dat')).read()
self.assertEqual(contents, compare_content)
def test_set_phase_0(self):
""" Test set phases to 0 """
param = CharmmParameterSet(get_fn('par_all36_cgenff.prm'),
get_fn('top_all36_cgenff.rtf'))
torsion = ('CG331', 'CG321', 'CG321', 'CG331')
self.assertEqual(param.dihedral_types[torsion][1].phase, 180.0)
par.set_phase_0(torsion, param)
self.assertEqual(param.dihedral_types[torsion][1].phase, 0.0)
def test_add_missing(self):
""" Test add missing parameters """
param = CharmmParameterSet(get_fn('par_all36_cgenff.prm'), get_fn('top_all36_cgenff.rtf'))
torsion = ('CG331', 'CG321', 'CG321', 'CG331')
self.assertEqual(len(param.dihedral_types[torsion]), 2)
par.add_missing(param=param, param_list=torsion)
self.assertEqual(len(param.dihedral_types[torsion]), 5)
par.add_missing(param=param, param_list=torsion, sample_n5=True)
self.assertEqual(len(param.dihedral_types[torsion]), 6)
def test_to_optimize(self):
"""Tests generate to_optimize list"""
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'),
get_fn('par_all36_cgenff.prm'))
stream = (get_fn('PRL.str'))
to_optimize = qmdb.to_optimize(param, stream)
self.assert_(len(to_optimize) == 19)
reverse = tuple(reversed(to_optimize[0]))
self.assert_(reverse not in to_optimize)
def test_copy_torsions(self):
""" Test copy torsions"""
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure)
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'),
get_fn('par_all36_cgenff.prm'))
test_scan.compute_energy(param)
test_scan.copy_torsions()
def test_create_context(self):
""" Test create context """
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure)
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'),
get_fn('par_all36_cgenff.prm'))
test_scan.integrator = mm.VerletIntegrator(0.004 * u.picoseconds)
test_scan.create_context(param)
def test_add_missing(self):
""" Test add missing parameters """
param = CharmmParameterSet(get_fn('par_all36_cgenff.prm'),
get_fn('top_all36_cgenff.rtf'))
torsion = ('CG331', 'CG321', 'CG321', 'CG331')
self.assertEqual(len(param.dihedral_types[torsion]), 2)
par.add_missing(param=param, param_list=torsion)
self.assertEqual(len(param.dihedral_types[torsion]), 5)
par.add_missing(param=param, param_list=torsion, sample_n5=True)
self.assertEqual(len(param.dihedral_types[torsion]), 6)
def test_to_dataframe(self):
""" Tests to dataframe """
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure)
test_scan.to_dataframe()
structure = get_fn('MPR.psf')
scan = qmdb.parse_gauss([get_fn('MPR.scan1.pos.log'), get_fn('MPR.scan1.neg.log')], structure)
scan.extract_geom_opt()
scan.to_dataframe(psi4=False)
def test_converged_structures():
"""Tests that non converged coordinates in Gaussian log files are discarded"""
structure = get_fn('MPR.psf')
scan = qmdb.parse_gauss(get_fn('MPR.scan1.pos.log'), structure)
log = Gaussian(get_fn('MPR.scan1.pos.log'))
data = log.parse()
assert_array_equal(data.atomcoords.shape, scan.xyz.shape)
converted = convertor(data.scfenergies, "eV", "kJmol-1") - \
min(convertor(data.scfenergies[:len(data.atomcoords)], "eV", "kJmol-1"))
assert_array_equal(converted[:47], scan.qm_energy)
def test_converged_structures():
"""Tests that non converged coordinates in Gaussian log files are discarded"""
structure = get_fn('MPR.psf')
scan = qmdb.parse_gauss(get_fn('MPR.scan1.pos.log'), structure)
log = Gaussian(get_fn('MPR.scan1.pos.log'))
data = log.parse()
assert_array_equal(data.atomcoords.shape, scan.xyz.shape)
converted = convertor(data.scfenergies, "eV", "kJmol-1") - \
min(convertor(data.scfenergies[:len(data.atomcoords)], "eV", "kJmol-1"))
assert_array_equal(converted[:47], scan.qm_energy)
def test_read_logfile():
"""Tests the logfile parser"""
structure = get_fn('PRL.psf')
logfiles = [get_fn('PRL.scan2.neg.log'), get_fn('PRL.scan2.pos.log')]
scan = qmdb.parse_gauss(logfiles, structure)
scan1 = Gaussian(logfiles[0])
scan2 = Gaussian(logfiles[1])
data1 = scan1.parse()
data2 = scan2.parse()
assert_almost_equal(scan.xyz[:40]*10, data1.atomcoords, decimal=6)
assert_almost_equal(scan.xyz[40:]*10, data2.atomcoords, decimal=6)
def test_read_logfile():
"""Tests the logfile parser"""
structure = get_fn('PRL.psf')
logfiles = [get_fn('PRL.scan2.neg.log'), get_fn('PRL.scan2.pos.log')]
scan = qmdb.parse_gauss(logfiles, structure)
scan1 = Gaussian(logfiles[0])
scan2 = Gaussian(logfiles[1])
data1 = scan1.parse()
data2 = scan2.parse()
assert_almost_equal(scan.xyz[:40] * 10, data1.atomcoords, decimal=6)
assert_almost_equal(scan.xyz[40:] * 10, data2.atomcoords, decimal=6)
def test_to_dataframe(self):
""" Tests to dataframe """
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure)
test_scan.to_dataframe()
structure = get_fn('MPR.psf')
scan = qmdb.parse_gauss(
[get_fn('MPR.scan1.pos.log'),
get_fn('MPR.scan1.neg.log')], structure)
scan.extract_geom_opt()
scan.to_dataframe(psi4=False)
def test_generate_input(self):
"""Test generate psi4 input files"""
root = get_fn('torsion_scan/10_7_4_3')
qmscan.generate_scan_input(root,
'pdb',
'butane', ['MP2'], ['aug-cc-pvtz'],
symmetry='C1')
contents = open(
get_fn('torsion_scan/10_7_4_3/0/butane_10_7_4_3_0.dat')).read()
compare_content = open(get_fn('butane_10_7_4_3_0.dat')).read()
self.assertEqual(contents, compare_content)
def test_sort_nrotors(self):
"""Tests sorting fragments by nrotors"""
ifs = get_fn('frags.smi')
out_dir = self.get_writes_dir()
fragment._sort_by_rotbond(ifs, outdir=out_dir)
mol = oechem.OEGraphMol()
for n in range(1, 6):
db = get_fn('nrotor_{}.smi'.format(n), written=True)
moldb = oechem.OEMolDatabase(db)
for idx in range(moldb.GetMaxMolIdx()):
if moldb.GetMolecule(mol, idx):
nrotor = sum([bond.IsRotor() for bond in mol.GetBonds()])
self.assertEquals(n, nrotor)
def test_turn_off_param(self):
""" Test turning off parameters """
structure = CharmmPsfFile(get_fn('butane_charge_off.psf'))
param = CharmmParameterSet(get_fn('par_all36_cgenff.prm'), get_fn('top_all36_cgenff.rtf'))
par.turn_off_params(structure, param, bonds=True, angles=True, dihedral=True, urey_bradley=True, lj=True,
copy=False)
scan = get_fn('MP2_torsion_scan/')
butane_scan = qmdb.parse_psi4_out(scan, get_fn('butane_charge_off.psf'))
butane_scan.compute_energy(param)
self.assertTrue((butane_scan.mm_energy.value_in_unit(unit.kilojoule_per_mole) == 0).all())
def test_compute_energy(self):
""" Tests compute mm energy"""
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure, pattern="*.out2")
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'), get_fn('par_all36_cgenff.prm'))
self.assertFalse(test_scan._have_mm_energy)
scan_opt = test_scan.remove_nonoptimized()
scan_opt.compute_energy(param)
self.assertTrue(scan_opt._have_mm_energy)
mm_energy = np.array([22.66381775, 13.11040092, 3.04552792, 7.83767718,
15.21426107, 7.0116804 , 0. , 7.00802623,
15.21461956, 7.83696204, 3.04525798, 13.10813678, 22.66375837])
np.testing.assert_almost_equal(scan_opt.mm_energy._value, mm_energy, 4)
def test_sort_nrotors(self):
"""Tests sorting fragments by nrotors"""
ifs = get_fn('frags.smi')
out_dir = self.get_writes_dir()
fragment._sort_by_rotbond(ifs, outdir=out_dir)
mol = oechem.OEGraphMol()
for n in range(1, 6):
db = get_fn('nrotor_{}.smi'.format(n), written=True)
moldb = oechem.OEMolDatabase(db)
for idx in range(moldb.GetMaxMolIdx()):
if moldb.GetMolecule(mol, idx):
nrotor = sum([bond.IsRotor() for bond in mol.GetBonds()])
self.assertEquals(n, nrotor)
def test_update_param_continuous(self):
""" Tests that update parameter updates the reverse dihedral too in continuous """
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'), get_fn('par_all36_cgenff.prm'))
structure = get_fn('butane.psf')
logfiles = get_fn('MP2_torsion_scan/')
frag = qmdb.parse_psi4_out(logfiles, structure)
frag = frag.remove_nonoptimized()
to_optimize = [('CG331', 'CG321', 'CG321', 'CG331')]
model = TorsionFitModelOMM(param=param, frags=frag, param_to_opt=to_optimize, sample_phase=True,
continuous_phase=True)
torsion = model.parameters_to_optimize[0]
torsion_reverse = tuple(reversed(torsion))
self.assertEqual(param.dihedral_types[torsion], param.dihedral_types[torsion_reverse])
def test_parse_psi4_out(self):
""" Tests psi4 outfile parser"""
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
butane_scan = qmdb.parse_psi4_out(scan, structure, pattern="*.out2")
butane_scan = butane_scan.remove_nonoptimized()
self.assertEqual(butane_scan.n_atoms, 14)
self.assertEqual(butane_scan.n_chains, 1)
self.assertEqual(butane_scan.n_residues, 1)
self.assertEqual(butane_scan.n_frames, 13)
self.assertEqual(butane_scan.qm_energy.shape, (13, ))
angles = np.arange(0, 370, 30)
np.testing.assert_equal(butane_scan.angles, angles)
torsion = np.array([3, 6, 9, 13])
np.testing.assert_equal(butane_scan.torsion_index[0], torsion)
def test_parse_psi4_out(self):
""" Tests psi4 outfile parser"""
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
butane_scan = qmdb.parse_psi4_out(scan, structure, pattern="*.out2")
butane_scan = butane_scan.remove_nonoptimized()
self.assertEqual(butane_scan.n_atoms, 14)
self.assertEqual(butane_scan.n_chains, 1)
self.assertEqual(butane_scan.n_residues, 1)
self.assertEqual(butane_scan.n_frames, 13)
self.assertEqual(butane_scan.qm_energy.shape, (13,))
angles = np.arange(0, 370, 30)
np.testing.assert_equal(butane_scan.angles, angles)
torsion = np.array([3, 6, 9, 13])
np.testing.assert_equal(butane_scan.torsion_index[0], torsion)
def test_update_param_struct_cont(self):
""" Tests that update parameter updates assigned parameters in the structure """
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'), get_fn('par_all36_cgenff.prm'))
structure = get_fn('butane.psf')
logfiles = get_fn('MP2_torsion_scan/')
frag = qmdb.parse_psi4_out(logfiles, structure)
frag = frag.remove_nonoptimized()
to_optimize = [('CG331', 'CG321', 'CG321', 'CG331')]
model = TorsionFitModelOMM(param=param, frags=frag, param_to_opt=to_optimize, sample_phase=True,
continuous_phase=True)
par.update_param_from_sample(model.parameters_to_optimize, param, model=model, rj=model.rj,
phase=model.sample_phase, n_5=model.sample_n5, model_type='openmm')
torsion = frag.structure.dihedrals[0]
self.assertEqual(torsion.type, param.dihedral_types[(torsion.atom1.type, torsion.atom2.type,
torsion.atom3.type, torsion.atom4.type)])
def test_get_multiplicity_traces(self):
"""Tests turing multiplicity bitstring into multiplicity traces"""
db = sqlite_plus.load(get_fn('butane.db'))
param_list = db.get_sampled_torsions()
mult = db.get_multiplicity_trace(param_list[0], n5=True)
keys = ['1', '2', '3', '4', '5', '6']
self.assertEqual(set(mult.keys()), set(keys))
def test_compute_energy(self):
""" Tests compute mm energy"""
structure = get_fn('butane.psf')
scan = get_fn('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure, pattern="*.out2")
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'),
get_fn('par_all36_cgenff.prm'))
self.assertFalse(test_scan._have_mm_energy)
scan_opt = test_scan.remove_nonoptimized()
scan_opt.compute_energy(param)
self.assertTrue(scan_opt._have_mm_energy)
mm_energy = np.array([
22.66381775, 13.11040092, 3.04552792, 7.83767718, 15.21426107,
7.0116804, 0., 7.00802623, 15.21461956, 7.83696204, 3.04525798,
13.10813678, 22.66375837
])
np.testing.assert_almost_equal(scan_opt.mm_energy._value, mm_energy, 4)
def test_add_missing_cond(self):
""" Tests that add_missing adds missing terms to parameters_to_optimize """
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'), get_fn('par_all36_cgenff.prm'))
structure = get_fn('butane.psf')
logfiles = get_fn('MP2_torsion_scan/')
frag = qmdb.parse_psi4_out(logfiles, structure)
frag = frag.remove_nonoptimized()
to_optimize = [('CG331', 'CG321', 'CG321', 'HGA2')]
model = TorsionFitModelOMM(param=param, frags=frag, param_to_opt=to_optimize, sample_phase=True,
continuous_phase=True)
par.add_missing(param_list=to_optimize, param=param)
for i in model.frags[0].structure.dihedrals:
key = (i.atom1.type, i.atom2.type, i.atom3.type, i.atom4.type)
key_reverse = tuple(reversed(key))
if key in model.parameters_to_optimize or key_reverse in model.parameters_to_optimize:
self.assert_(len(i.type) == 5)
def test_update_param_continuous(self):
""" Tests that update parameter updates the reverse dihedral too in continuous """
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'),
get_fn('par_all36_cgenff.prm'))
structure = get_fn('butane.psf')
logfiles = get_fn('MP2_torsion_scan/')
frag = qmdb.parse_psi4_out(logfiles, structure)
frag = frag.remove_nonoptimized()
to_optimize = [('CG331', 'CG321', 'CG321', 'CG331')]
model = TorsionFitModelOMM(param=param,
frags=frag,
param_to_opt=to_optimize,
sample_phase=True,
continuous_phase=True)
torsion = model.parameters_to_optimize[0]
torsion_reverse = tuple(reversed(torsion))
self.assertEqual(param.dihedral_types[torsion],
param.dihedral_types[torsion_reverse])
def test_param_from_db(self):
""" Tests parameterizing from database """
param = CharmmParameterSet(get_fn('par_all36_cgenff.prm'), get_fn('top_all36_cgenff.rtf'))
torsion = ('CG331', 'CG321', 'CG321', 'CG331')
db = sqlite_plus.load(get_fn('butane.db'))
par.add_missing(torsion, param, sample_n5=True)
self.assertEqual(param.dihedral_types[torsion][0].phi_k, 0.03819)
self.assertEqual(param.dihedral_types[torsion][1].phi_k, 0.03178)
self.assertEqual(param.dihedral_types[torsion][2].phi_k, 0.0)
self.assertEqual(param.dihedral_types[torsion][3].phi_k, 0.0)
self.assertEqual(param.dihedral_types[torsion][4].phi_k, 0.0)
self.assertEqual(param.dihedral_types[torsion][5].phi_k, 0.0)
par.update_param_from_sample(param_list=torsion, param=param, db=db, rj=False, model_type='openmm')
self.assertEqual(param.dihedral_types[torsion][0].phi_k, 0.086424)
self.assertEqual(param.dihedral_types[torsion][1].phi_k, 0.019074)
self.assertEqual(param.dihedral_types[torsion][2].phi_k, 0.0)
self.assertEqual(param.dihedral_types[torsion][3].phi_k, -1.834546)
self.assertEqual(param.dihedral_types[torsion][4].phi_k, -1.86807)
self.assertEqual(param.dihedral_types[torsion][5].phi_k, -2.860622)
def test_get_sampled_torsions(self):
""" Tests get torsions sampled from db """
param_to_opt=[('CG331', 'CG321', 'CG321', 'CG331'),
('HGA3', 'CG331', 'CG321', 'HGA2'),
('HGA3', 'CG331', 'CG321', 'CG321'),
('HGA2', 'CG321', 'CG321', 'HGA2'),
('CG331', 'CG321', 'CG321', 'HGA2')]
db = sqlite_plus.load(get_fn('butane.db'))
param_list = db.get_sampled_torsions()
self.assertEqual(set(param_list), set(param_to_opt))
def test_tagged_smiles(self):
"""Test index-tagges smiles"""
from openeye import oechem
inf = get_fn('ethylmethylidyneamonium.mol2')
ifs = oechem.oemolistream(inf)
inp_mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, inp_mol)
tagged_smiles = utils.create_mapped_smiles(inp_mol)
# Tags should always be the same as mol2 molecule ordering
self.assertEqual(tagged_smiles, '[H:5][C:1]#[N+:4][C:3]([H:9])([H:10])[C:2]([H:6])([H:7])[H:8]')
def test_generat_torsions(self):
""" Tests finding torsion to drive """
from openeye import oechem
infile = get_fn('butane.pdb')
ifs = oechem.oemolistream(infile)
inp_mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, inp_mol)
outfile_path = tempfile.mkdtemp()[1]
qmscan.generate_torsions(inp_mol=inp_mol, output_path=outfile_path, interval=30, tar=False)
input_files = []
pattern = '*.pdb'
for path, subdir, files in os.walk(outfile_path):
for name in files:
if fnmatch(name, pattern):
input_files.append(os.path.join(path, name))
contents = open(input_files[0]).read()
pdb = get_fn('butane_10_7_4_3_0.pdb')
compare_contents = open(pdb).read()
self.assertEqual(contents, compare_contents )
shutil.rmtree(outfile_path)
def test_add_missing_cond(self):
""" Tests that add_missing adds missing terms to parameters_to_optimize """
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'),
get_fn('par_all36_cgenff.prm'))
structure = get_fn('butane.psf')
logfiles = get_fn('MP2_torsion_scan/')
frag = qmdb.parse_psi4_out(logfiles, structure)
frag = frag.remove_nonoptimized()
to_optimize = [('CG331', 'CG321', 'CG321', 'HGA2')]
model = TorsionFitModelOMM(param=param,
frags=frag,
param_to_opt=to_optimize,
sample_phase=True,
continuous_phase=True)
par.add_missing(param_list=to_optimize, param=param)
for i in model.frags[0].structure.dihedrals:
key = (i.atom1.type, i.atom2.type, i.atom3.type, i.atom4.type)
key_reverse = tuple(reversed(key))
if key in model.parameters_to_optimize or key_reverse in model.parameters_to_optimize:
self.assert_(len(i.type) == 5)
def test_turn_off_param(self):
""" Test turning off parameters """
structure = CharmmPsfFile(get_fn('butane_charge_off.psf'))
param = CharmmParameterSet(get_fn('par_all36_cgenff.prm'),
get_fn('top_all36_cgenff.rtf'))
par.turn_off_params(structure,
param,
bonds=True,
angles=True,
dihedral=True,
urey_bradley=True,
lj=True,
copy=False)
scan = get_fn('MP2_torsion_scan/')
butane_scan = qmdb.parse_psi4_out(scan,
get_fn('butane_charge_off.psf'))
butane_scan.compute_energy(param)
self.assertTrue((butane_scan.mm_energy.value_in_unit(
unit.kilojoule_per_mole) == 0).all())
def test_tagged_smiles(self):
"""Test index-tagges smiles"""
from openeye import oechem
inf = get_fn('ethylmethylidyneamonium.mol2')
ifs = oechem.oemolistream(inf)
inp_mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, inp_mol)
tagged_smiles = utils.create_mapped_smiles(inp_mol)
# Tags should always be the same as mol2 molecule ordering
self.assertEqual(
tagged_smiles,
'[H:5][C:1]#[N+:4][C:3]([H:9])([H:10])[C:2]([H:6])([H:7])[H:8]')
def test_atom_map(self):
"""Test get atom map"""
from openeye import oechem
tagged_smiles = '[H:5][C:1]#[N+:4][C:3]([H:9])([H:10])[C:2]([H:6])([H:7])[H:8]'
mol_1 = openeye.smiles_to_oemol('CC[N+]#C')
inf = get_fn('ethylmethylidyneamonium.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
atom_map = utils.get_atom_map(tagged_smiles, mol_1)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i + 1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping - 1))
atom_2.SetAtomicNum(i + 1)
self.assertEqual(oechem.OECreateCanSmiString(mol_1),
oechem.OECreateCanSmiString(mol_2))
# Test aromatic molecule
tagged_smiles = '[H:10][c:4]1[c:3]([c:2]([c:1]([c:6]([c:5]1[H:11])[H:12])[C:7]([H:13])([H:14])[H:15])[H:8])[H:9]'
mol_1 = openeye.smiles_to_oemol('Cc1ccccc1')
inf = get_fn('toluene.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
atom_map = utils.get_atom_map(tagged_smiles, mol_1)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i + 1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping - 1))
atom_2.SetAtomicNum(i + 1)
self.assertEqual(oechem.OECreateCanSmiString(mol_1),
oechem.OECreateCanSmiString(mol_2))
def test_residual_energy(self):
""" Tests that total energy is resonable.
"""
db = sqlite_plus.load(get_fn('butane_np.sqlite'))
dih_list = [('CG331', 'CG321', 'CG321', 'CG331'),
('HGA2', 'CG321', 'CG321', 'HGA2'),
('CG331', 'CG321', 'CG321', 'HGA2')]
par.add_missing(param_list=dih_list, param=param, sample_n5=True)
par.update_param_from_sample(param_list=dih_list, param=param, db=db, n_5=True, rj=False, model_type='numpy')
frag.compute_energy(param=param)
self.assertTrue((frag.delta_energy._value > -0.5).all() and (frag.delta_energy._value < 0.5).all())
def test_residual_energy(self):
""" Tests that total energy is resonable.
"""
db = sqlite_plus.load(get_fn('butane_np.sqlite'))
dih_list = [('CG331', 'CG321', 'CG321', 'CG331'),
('HGA2', 'CG321', 'CG321', 'HGA2'),
('CG331', 'CG321', 'CG321', 'HGA2')]
par.add_missing(param_list=dih_list, param=param, sample_n5=True)
par.update_param_from_sample(param_list=dih_list,
param=param,
db=db,
n_5=True,
rj=False,
model_type='numpy')
frag.compute_energy(param=param)
self.assertTrue((frag.delta_energy._value > -0.5).all()
and (frag.delta_energy._value < 0.5).all())
def test_mapped_xyz(self):
"""Test writing out mapped xyz"""
from openeye import oechem, oeomega
tagged_smiles = '[H:10][c:4]1[c:3]([c:2]([c:1]([c:6]([c:5]1[H:11])[H:12])[C:7]([H:13])([H:14])[H:15])[H:8])[H:9]'
mol_1 = openeye.smiles_to_oemol('Cc1ccccc1')
inf = get_fn('toluene.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
atom_map = utils.get_atom_map(tagged_smiles, mol_1)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i + 1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping - 1))
atom_2.SetAtomicNum(i + 1)
xyz_1 = utils.to_mapped_xyz(mol_1, atom_map)
# molecule generated from mol2 should be in the right order.
atom_map_mol2 = {
1: 0,
2: 1,
3: 2,
4: 3,
5: 4,
6: 5,
7: 6,
8: 7,
9: 8,
10: 9,
11: 10,
12: 11,
13: 12,
14: 13,
15: 14
}
xyz_2 = utils.to_mapped_xyz(mol_2, atom_map_mol2)
for ele1, ele2 in zip(xyz_1.split('\n')[:-1], xyz_2.split('\n')[:-1]):
self.assertEqual(ele1.split(' ')[2], ele2.split(' ')[2])
def test_mapped_xyz(self):
"""Test writing out mapped xyz"""
from openeye import oechem, oeomega
tagged_smiles = '[H:10][c:4]1[c:3]([c:2]([c:1]([c:6]([c:5]1[H:11])[H:12])[C:7]([H:13])([H:14])[H:15])[H:8])[H:9]'
mol_1 = openeye.smiles_to_oemol('Cc1ccccc1')
inf = get_fn('toluene.mol2')
ifs = oechem.oemolistream(inf)
mol_2 = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol_2)
atom_map = utils.get_atom_map(tagged_smiles, mol_1)
for i, mapping in enumerate(atom_map):
atom_1 = mol_1.GetAtom(oechem.OEHasAtomIdx(atom_map[mapping]))
atom_1.SetAtomicNum(i+1)
atom_2 = mol_2.GetAtom(oechem.OEHasAtomIdx(mapping-1))
atom_2.SetAtomicNum(i+1)
xyz_1 = utils.to_mapped_xyz(mol_1, atom_map)
# molecule generated from mol2 should be in the right order.
atom_map_mol2 = {1:0, 2:1, 3:2, 4:3, 5:4, 6:5, 7:6, 8:7, 9:8, 10:9, 11:10, 12:11, 13:12, 14:13, 15:14}
xyz_2 = utils.to_mapped_xyz(mol_2, atom_map_mol2)
for ele1, ele2 in zip(xyz_1.split('\n')[:-1], xyz_2.split('\n')[:-1]):
self.assertEqual(ele1.split(' ')[2], ele2.split(' ')[2])
from torsionfit.backends import sqlite_plus
import torsionfit.parameters as par
from pymc import MCMC
import pymc
from parmed.charmm import CharmmParameterSet
import unittest
try:
from simtk.openmm import app
import simtk.openmm as mm
HAVE_OPENMM = True
except ImportError:
HAVE_OPENMM = False
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'), get_fn('par_all36_cgenff.prm'))
structure = get_fn('butane.psf')
logfiles = get_fn('MP2_torsion_scan/')
frag = qmdb.parse_psi4_out(logfiles, structure)
frag = frag.remove_nonoptimized()
to_optimize = [('CG331', 'CG321', 'CG321', 'CG331')]
model_omm = TorsionFitModelOMM(param=param, frags=frag, param_to_opt=to_optimize, init_random=False)
class TestFitModel(unittest.TestCase):
""" Tests pymc model"""
def test_pymc_model(self):
""" Tests sampler """
sampler = MCMC(model_omm.pymc_parameters)
def test_generate_fragments(self):
"""Test wrapper generate fragment function"""
out_dir = self.get_writes_dir()
fragment.generate_fragments(inputf=get_fn('kinase_inhibitors.smi'),
output_dir=out_dir)
def test_generate_fragments(self):
"""Test wrapper generate fragment function"""
out_dir = self.get_writes_dir()
fragment.generate_fragments(inputf=get_fn('kinase_inhibitors.smi'), output_dir=out_dir)
from torsionfit.backends import sqlite_plus
import torsionfit.parameters as par
from pymc import MCMC
import pymc
from parmed.charmm import CharmmParameterSet
import unittest
try:
from simtk.openmm import app
import simtk.openmm as mm
HAVE_OPENMM = True
except ImportError:
HAVE_OPENMM = False
param = CharmmParameterSet(get_fn('top_all36_cgenff.rtf'),
get_fn('par_all36_cgenff.prm'))
structure = get_fn('butane.psf')
logfiles = get_fn('MP2_torsion_scan/')
frag = qmdb.parse_psi4_out(logfiles, structure)
frag = frag.remove_nonoptimized()
to_optimize = [('CG331', 'CG321', 'CG321', 'CG331')]
model_omm = TorsionFitModelOMM(param=param,
frags=frag,
param_to_opt=to_optimize,
init_random=False)
class TestFitModel(unittest.TestCase):
""" Tests pymc model"""
def test_pymc_model(self):
def test_extract_geom_opt():
"""Tests extraction of optimized geometry"""
structure = get_fn('MPR.psf')
scan = qmdb.parse_gauss([get_fn('MPR.scan1.pos.log'), get_fn('MPR.scan1.neg.log')], structure)
scan.extract_geom_opt()
