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_multiplicity_traces(self):
"""Tests turing multiplicity bitstring into multiplicity traces"""
db = sqlite_plus.load(get_fun('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_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 get_models(directory, pattern):
models = []
for path, subdir, files in os.walk(directory):
for name in files:
if fnmatch(name, pattern):
file = os.path.join(os.getcwd(), path, name)
model = sqlite_plus.load(file)
models.append(model)
return models
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_fun('butane.db'))
param_list = db.get_sampled_torsions()
self.assertEqual(set(param_list), set(param_to_opt))
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_residual_energy(self):
""" Tests that total energy is resonable.
"""
db = sqlite_plus.load(get_fun('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_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_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())
args = parser.parse_args()
print(args)
param_to_opt = [('CG331', 'CG321', 'CG321', 'CG331')]
param = CharmmParameterSet(
'../../../../../../data/charmm_ff/top_all36_cgenff.rtf',
'../../../../../../data/charmm_ff/par_all36_cgenff.prm')
structure = '../../../../../structure/butane.psf'
scan = '../../../../../torsion_scans/MP2_torsion_scan/'
# paramterize using end of non reversible jump
# Start sampler with values from end of non-rj chain.
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,
from pymbar.timeseries import detectEquilibration
import tqdm
import numpy as np
from torsionfit.backends import sqlite_plus
from collections import OrderedDict
# load database
dbs = OrderedDict()
for i in range(1, 24):
dbs['db_{}'.format(i)] = sqlite_plus.load(
'random_100000_{}/random_100000_{}.sqlite'.format(i, i))
t_sigma = np.zeros((23, 3))
for i, db in tqdm.tqdm(enumerate(dbs)):
[t, g, Neff] = detectEquilibration(dbs[db].sigma[:])
t_sigma[i, 0] = t
t_sigma[i, 1] = g
t_sigma[i, 2] = Neff
np.save('t_sigma', t_sigma)
t_dev = np.zeros((23, 3))
for i, db in tqdm.tqdm(enumerate(dbs)):
[t, g, Neff] = detectEquilibration(dbs[db].deviance[:])
t_dev[i, 0] = t
t_dev[i, 1] = g
t_dev[i, 2] = Neff
np.save('t_dev', t_dev)
from torsionfit.backends import sqlite_plus
from pymc import MCMC
from parmed.charmm import CharmmParameterSet
from torsionfit import parameters as par
param_to_opt = [('CG331', 'CG321', 'CG321', 'CG331')]
param = CharmmParameterSet('../../../../data/charmm_ff/top_all36_cgenff.rtf',
'../../../../data/charmm_ff/par_all36_cgenff.prm')
structure = '../../../structure/butane.psf'
scan = '../../../torsion_scans/MP2_torsion_scan/'
butane_scan = ScanSet.parse_psi4_out(scan, structure)
optimized = butane_scan.remove_nonoptimized()
# Start sampler with values from end of non-rj chain.
db = sqlite_plus.load('../n5/butane_n5_decouple_n.db')
par.add_missing(param_list=param_to_opt, param=param, sample_n5=True)
par.update_param_from_sample(param_list=param_to_opt,
param=param,
db=db,
i=-1,
rj=False,
n_5=True,
phase=False)
platform = mm.Platform.getPlatformByName('Reference')
model = Model.TorsionFitModel(param=param,
frags=optimized,
platform=platform,
param_to_opt=param_to_opt,
rj=True,
def load(self):
return sqlite_plus.load(os.path.join(testdir, 'Disaster.sqlite'))
def load(self):
return sqlite_plus.load(os.path.join(testdir, 'Disaster.sqlite'))