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_remove_nonoptimized(self):
""" Test remove non_optimized structures """
structure = get_fun('butane.psf')
scan = get_fun('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_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_create_context(self):
""" Test create context """
structure = get_fun('butane.psf')
scan = get_fun('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure)
param = CharmmParameterSet(get_fun('top_all36_cgenff.rtf'), get_fun('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_fun('butane.psf')
scan = get_fun('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure)
param = CharmmParameterSet(get_fun('top_all36_cgenff.rtf'), get_fun('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_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_to_dataframe(self):
""" Tests to dataframe """
structure = get_fun('butane.psf')
scan = get_fun('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure)
test_scan.to_dataframe()
structure = get_fun('MPR.psf')
scan = qmdb.parse_gauss([get_fun('MPR.scan1.pos.log'), get_fun('MPR.scan1.neg.log')], structure)
scan.extract_geom_opt()
scan.to_dataframe(psi4=False)
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_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_fun('butane.psf')
scan = get_fun('MP2_torsion_scan/')
test_scan = qmdb.parse_psi4_out(scan, structure, pattern="*.out2")
param = CharmmParameterSet(get_fun('top_all36_cgenff.rtf'), get_fun('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_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_continuous(self):
""" Tests that update parameter updates the reverse dihedral too in continuous """
param = CharmmParameterSet(get_fun('top_all36_cgenff.rtf'), get_fun('par_all36_cgenff.prm'))
structure = get_fun('butane.psf')
logfiles = get_fun('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_fun('butane.psf')
scan = get_fun('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_fun('top_all36_cgenff.rtf'), get_fun('par_all36_cgenff.prm'))
structure = get_fun('butane.psf')
logfiles = get_fun('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_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_fun('top_all36_cgenff.rtf'), get_fun('par_all36_cgenff.prm'))
structure = get_fun('butane.psf')
logfiles = get_fun('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_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_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)
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)
self.assert_(isinstance(model_omm, TorsionFitModelOMM))
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_fun('top_all36_cgenff.rtf'), get_fun('par_all36_cgenff.prm'))
structure = get_fun('butane.psf')
logfiles = get_fun('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)
self.assert_(isinstance(model_omm, TorsionFitModelOMM))
self.assert_(isinstance(sampler, pymc.MCMC))
path = '../../../n5/10000/random_{}_{}/random_{}_{}.sqlite'.format(
args.iterations, args.repeats, args.iterations, args.repeats)
print(path)
db = sqlite_plus.load(path)
par.add_missing(param_list=param_to_opt, param=param, sample_n5=True)
par.set_phase_0(param_list=param_to_opt, param=param)
par.update_param_from_sample(param_list=param_to_opt,
param=param,
db=db,
i=-1,
rj=False,
n_5=True,
phase=False)
print(param.dihedral_types[param_to_opt[0]])
butane_scan = ScanSet.parse_psi4_out(scan, structure)
optimized = butane_scan.remove_nonoptimized()
model = Model.TorsionFitModel(param=param,
frags=optimized,
init_random=False,
param_to_opt=param_to_opt,
rj=True,
sample_n5=True)
sampler = MCMC(model.pymc_parameters,
db=sqlite_plus,
dbname=args.db_name,
verbose=5)
sampler.sample(args.iterations)