def test_atomtyper_elemental(self):
"""
Test elemental atomtype sampler for hydrogen
"""
atomtype_sampler = smarty.AtomTypeSampler(
self.mols_alkethoh,
self.basetypes,
self.basetypes,
self.combine_decs,
replacements_filename=self.replacements,
reference_typed_molecules=self.mols_alkethoh_ref,
temperature=0.1,
verbose=False,
decorator_behavior='combinatorial-decorators',
element=1)
# run sampler with optional outputs
traj = 'test_smarty.csv'
plot = 'test_smarty.pdf'
atomtype_sampler.run(5, traj)
# test trajectory analysis functions on smarty output
timeseries = score_utils.load_trajectory(traj)
scores_vs_time = score_utils.scores_vs_time(timeseries)
score_utils.create_plot_file(traj, plot, True, False)
# check if score is 100% at first iteration
if scores_vs_time['all'][0] == 1.0:
raise Exception(
"Scoring problem, 100% at first iteration for total")
def test_random_sampler(self):
"""
Test FragmentSampler runs for 10 iterations with no failures
Test score_utils functions with the outputFile
"""
typetag = 'Torsion'
sampler = FragmentSampler(self.molecules,
typetag,
self.atom_OR_bases,
self.atom_OR_decors,
self.atom_AND_decors,
self.bond_OR_bases,
self.bond_AND_decors,
AtomIndexOdds=self.atom_odds,
BondIndexOdds=self.bond_odds,
replacements=self.replacements,
initialtypes=None,
SMIRFF=self.SMIRFF,
temperature=0.0,
outputFile=self.outputFile)
fracfound = sampler.run(10)
# load_trajectory converts csv file to dictionary
timeseries = score_utils.load_trajectory('%s.csv' % self.outputFile)
# scores_vs_time converts num/den entries to fractional scores
scores_vs_time = score_utils.scores_vs_time(timeseries)
# test plotting function
score_utils.create_plot_file('%s.csv' % self.outputFile,
'%s.pdf' % self.outputFile)
def test_random_sampler(self):
"""
Test FragmentSampler runs for 10 iterations with no failures
Test score_utils functions with the outputFile
"""
typetag = 'Torsion'
sampler = FragmentSampler(self.molecules, typetag, self.atom_OR_bases,
self.atom_OR_decors, self.atom_AND_decors, self.bond_OR_bases,
self.bond_AND_decors,
AtomIndexOdds = self.atom_odds, BondIndexOdds = self.bond_odds,
replacements = self.replacements, initialtypes = None,
SMIRFF = self.SMIRFF, temperature = 0.0, outputFile = self.outputFile)
fracfound = sampler.run(10)
# load_trajectory converts csv file to dictionary
timeseries = score_utils.load_trajectory('%s.csv' % self.outputFile)
# scores_vs_time converts num/den entries to fractional scores
scores_vs_time = score_utils.scores_vs_time(timeseries)
# test plotting function
score_utils.create_plot_file('%s.csv' % self.outputFile, '%s.pdf' % self.outputFile)