def test_systematic_search_multiplicity(self):
self.conformer_3rad.ase_molecule.set_calculator(ase.calculators.emt.EMT())
self.conformer_4rad.ase_molecule.set_calculator(ase.calculators.emt.EMT())
confs_3rad = systematic_search(self.conformer_3rad, delta=180.0, energy_cutoff = "default",
rmsd_cutoff = "default", multiplicity = True)
confs_4rad = systematic_search(self.conformer_4rad, delta=180.0, energy_cutoff = "high",
rmsd_cutoff = "loose", multiplicity = True)
self.assertTrue(confs_3rad[0].rmg_molecule.multiplicity == 2)
self.assertTrue(confs_3rad[1].rmg_molecule.multiplicity == 4)
self.assertTrue(confs_4rad[0].rmg_molecule.multiplicity == 1)
self.assertTrue(confs_4rad[1].rmg_molecule.multiplicity == 3)
self.assertTrue(confs_4rad[2].rmg_molecule.multiplicity == 5)
def generate_conformers(self, ase_calculator=None):
"""
A method to generate an ensemble of low energy conformers.
Currently only supports a systematic search with the goal of adding evolutionary searches
Variables:
- method (str): the method of the conformer search. Currently only systematic is supported
- calculator (ASECalculator): the calculator you want to evaluate your conformers with.
Returns:
- ts (dict): a dictionary containing an ensemble of low energy transition state geometries in
the forward and reverse direction
"""
assert ase_calculator, "Please provide an ASE calculator object"
from autotst.conformer.systematic import systematic_search
for direction, conformers in self.ts.items():
conformer = conformers[0]
conformer.ase_molecule.set_calculator(ase_calculator)
conformers = systematic_search(conformer, delta=120)
for conformer in conformers:
conformer.direction = direction
self.ts[direction] = conformers
return self.ts
def generate_conformers(self, ase_calculator):
from autotst.conformer.systematic import systematic_search, find_all_combos
for smiles, conformers in self.conformers.items():
conformer = conformers[0]
conformer.ase_molecule.set_calculator(ase_calculator)
conformers = systematic_search(conformer)
self.conformers[smiles] = conformers
return self.conformers
def generate_conformers(self, method="systematic", calculator=None):
possible_methods = [
"systematic",
# "ga",
# "es"
]
assert calculator, "Please provide an ASE calculator object"
assert method in possible_methods, "Please provide a valid conformer search method."
from autotst.conformer.systematic import systematic_search, find_all_combos
for smiles, conformers in self.conformers.items():
conformer = conformers[0]
conformer.ase_molecule.set_calculator(calculator)
conformers = systematic_search(conformer)
self.conformers[smiles] = conformers
return self.conformers
def generate_conformers(self, method="systematic", calculator=None):
"""
This isn't working right now...
"""
possible_methods = [
"systematic",
# "ga",
# "es"
]
assert calculator, "Please provide an ASE calculator object"
assert method in possible_methods, "Please provide a valid conformer search method."
from autotst.conformer.systematic import systematic_search, find_all_combos
for direction, conformers in self.ts.iteritems():
conformer = conformers[0]
conformer.ase_molecule.set_calculator(calculator)
#print conformer.ase_molecule.get_calculator()
_, conformers = systematic_search(conformer)
self.ts[direction] = conformers
return self.ts
def test_systematic_search(self):
self.conformer.ase_molecule.set_calculator(EMT())
confs = systematic_search(self.conformer, delta=180)
self.assertTrue(0 < len(confs) <= 3)
def test_systematic_search(self):
"Test that the systematic search can find more than 1 conformer"
self.conformer.ase_molecule.set_calculator(ase.calculators.emt.EMT())
confs = systematic_search(self.conformer, delta=180.0)
self.assertTrue(1 < len(confs) <= 3)