def process(self, mol, port):
fragmentLabel = mol.GetTitle()+'_' +\
'_'.join(get_sd_data(mol, 'TORSION_ATOMS_ParentMol').split())
torsion_tag = 'TORSION_ATOMS_FRAGMENT'
torsion_atoms_in_fragment = get_sd_data(mol, torsion_tag).split()
dihedral_atom_indices = [int(x) - 1 for x in torsion_atoms_in_fragment]
print(fragmentLabel, torsion_atoms_in_fragment, dihedral_atom_indices)
try:
dih, _ = get_dihedral(mol, dihedral_atom_indices)
if self.args.best_conf:
torsional_conformers = get_best_conf(mol, dih,
self.args.num_points)
else:
torsional_conformers = gen_torsional_confs(
mol, dih, self.args.num_points, include_input=False)
if self.args.split_confs:
for pose in split_confs(torsional_conformers):
self.success.emit(pose)
else:
self.success.emit(torsional_conformers)
self.log.info(
'%d torsional conformers generated for fragment %s.' %
(torsional_conformers.NumConfs(), fragmentLabel))
except Exception as e:
self.log.error(
"Could not generate conformers for fragment %s: %s" %
(fragmentLabel, e))
self.failure.emit(mol)
def process(self, record, port):
if record.has_value(self.args.in_mol_field):
mol = record.get_value(self.args.in_mol_field)
else:
self.log.error("Could not find molecules in OEMolRecord")
self.failure.emit(record)
return
conf = mol.GetActive()
conf_title = get_sd_data(conf, "CONFORMER_LABEL")
tor_atoms = get_sd_data(mol, "TORSION_ATOMS_ParentMol").split()
parent_name = conf_title[:-3]
dih_label = "_".join(str(x) for x in tor_atoms)
conf_idx = int(conf_title[-2:])
if parent_name in self.fragment_library:
if dih_label in self.fragment_library[parent_name]:
self.fragment_library[parent_name][dih_label][
conf_idx
] = mol.CreateCopy()
else:
self.fragment_library[parent_name][dih_label] = [None] * 24
self.fragment_library[parent_name][dih_label][
conf_idx
] = mol.CreateCopy()
else:
self.fragment_library[parent_name] = {}
self.fragment_library[parent_name][dih_label] = [None] * 24
self.fragment_library[parent_name][dih_label][conf_idx] = mol.CreateCopy()
def gen_starting_confs(mol, torsion_library, max_one_bond_away=True,
num_conformers=MAX_CONFS, rms_cutoff=0.0, energy_window=25):
# Identify the atoms in the dihedral
TAGNAME = 'TORSION_ATOMS_FRAGMENT'
if not has_sd_data(mol, TAGNAME):
raise ValueError("Molecule does not have the SD Data Tag '{}'.".format(TAGNAME))
dihedralAtomIndices = [int(x)-1 for x in get_sd_data(mol, TAGNAME).split()]
inDih = \
oechem.OEOrAtom(oechem.OEOrAtom(oechem.OEHasAtomIdx(dihedralAtomIndices[0]),
oechem.OEHasAtomIdx(dihedralAtomIndices[1])),
oechem.OEOrAtom(oechem.OEHasAtomIdx(dihedralAtomIndices[2]),
oechem.OEHasAtomIdx(dihedralAtomIndices[3]))
)
mol1 = mol.CreateCopy()
mc_mol = oechem.OEMol(mol1)
if num_conformers > 1:
# Set criterion for rotatable bond
if False and max_one_bond_away:
# this max function makes this seem potentially broken
only_one_bond_away = distance_predicate(dihedralAtomIndices[1],
dihedralAtomIndices[2])
rotor_predicate = oechem.OEAndBond(only_one_bond_away,
oechem.PyBondPredicate(isRotatableBond))
elif False:
# this ONLY samples special bonds & neglects "regualr" torsions
rotor_predicate = oechem.PyBondPredicate(isRotatableBond)
else:
# try this more general sampling, but leave prior versions untouched
rotor_predicate = oechem.OEOrBond(oechem.OEIsRotor(),
oechem.PyBondPredicate(isRotatableBond))
#Initialize conformer generator and multi-conformer library
conf_generator = configure_omega(torsion_library, rotor_predicate,
rms_cutoff, energy_window, num_conformers)
# Generator conformers
if not conf_generator(mc_mol, inDih):
raise ValueError("Conformers cannot be generated.")
logging.debug("Generated a total of %d conformers for %s.", mc_mol.NumConfs(),
mol.GetTitle())
for conf_no, conf in enumerate(mc_mol.GetConfs()):
conformer_label = mol.GetTitle()+'_' +\
'_'.join(get_sd_data(mol, 'TORSION_ATOMS_ParentMol').split()) +\
'_{:02d}'.format(conf_no)
oechem.OESetSDData(conf, "CONFORMER_LABEL", conformer_label)
conf.SetTitle(conformer_label)
return mc_mol
def gen_torsional_confs(mol, dih, num_points, include_input=False):
"""Drives the primary torsion in the molecule and generates labeled
torsional conformers.
Inputs:
mol - OEMol
must have a 'CONFORMER_LABEL' in the sd_data
"""
angle_list = [2*i*oechem.Pi/num_points for i in range(num_points)]
dih_atoms = [x for x in dih.GetAtoms()]
# Create new output OEMol
torsion_conformers = oechem.OEMol(mol)
if not include_input:
torsion_conformers.DeleteConfs()
for conf_id, conf in enumerate(mol.GetConfs()):
conf_name = get_sd_data(conf, 'CONFORMER_LABEL')
for angle_idx, angle in enumerate(angle_list):
angle_deg = int(round(angle*oechem.Rad2Deg))
oechem.OESetTorsion(conf,
dih_atoms[0], dih_atoms[1], dih_atoms[2], dih_atoms[3],
angle)
new_conf = torsion_conformers.NewConf(conf)
new_conf.SetDimension(3)
new_conf_name = conf_name + '_{:02d}'.format(angle_idx)
oechem.OESetSDData(new_conf, 'CONFORMER_LABEL', new_conf_name)
oechem.OESetSDData(new_conf, 'TORSION_ANGLE', "{:.0f}".format(angle_deg))
new_conf.SetDoubleData('TORSION_ANGLE', angle_deg)
new_conf.SetTitle('{}: Angle {:.0f}'.format(conf_name, angle_deg))
return torsion_conformers
def process(self, record, port):
if record.has_value(self.args.in_mol_field):
mol = record.get_value(self.args.in_mol_field)
fragmentLabel = (
mol.GetTitle() + "_" +
"_".join(get_sd_data(mol, "TORSION_ATOMS_ParentMol").split()))
torsion_tag = "TORSION_ATOMS_FRAGMENT"
torsion_atoms_in_fragment = get_sd_data(mol, torsion_tag).split()
dihedral_atom_indices = [
int(x) - 1 for x in torsion_atoms_in_fragment
]
try:
dih, _ = get_dihedral(mol, dihedral_atom_indices)
if self.args.best_conf:
torsional_conformers = get_best_conf(
mol, dih, self.args.num_points)
else:
torsional_conformers = gen_torsional_confs(
mol, dih, self.args.num_points, include_input=False)
if self.args.split_confs:
for pose in split_confs(torsional_conformers):
record = OEMolRecord()
record.set_mol(pose)
self.success.emit(record)
else:
record = OEMolRecord()
record.set_mol(torsional_conformers)
self.success.emit(torsional_conformers)
self.log.info(
"%d torsional conformers generated for fragment %s." %
(torsional_conformers.NumConfs(), fragmentLabel))
except Exception as e:
self.log.error(
"Could not generate conformers for fragment %s: %s" %
(fragmentLabel, e))
self.failure.emit(record)
else:
self.log.error("Could not find molecules in OEMolRecord!")
self.failure.emit(record)
def process(self, record, port):
if record.has_value(self.args.in_mol_field):
mol = record.get_value(self.args.in_mol_field)
fragmentLabel = (
mol.GetTitle() + "_" +
"_".join(get_sd_data(mol, "TORSION_ATOMS_ParentMol").split()))
try:
starting_conformers = gen_starting_confs(
mol,
self.torsion_library,
max_one_bond_away=True,
num_conformers=self.args.max_confs,
rms_cutoff=self.args.rms_cutoff,
energy_window=self.args.energy_window,
)
if self.args.split_output:
for pose in split_confs(starting_conformers):
pose_record = OEMolRecord()
pose_record.set_mol(pose)
self.success.emit(pose_record)
else:
multi_conf_record = OEMolRecord()
multi_conf_record.set_mol(starting_conformers)
self.success.emit(multi_conf_record)
self.log.info(
"%d starting conformers generated for fragment %s." %
(starting_conformers.NumConfs(), fragmentLabel))
except Exception as e:
self.log.error(
"Could not generate conformers for fragment %s: %s" %
(fragmentLabel, e))
self.failure.emit(record)
else:
self.log.error("Could not find molecules in OEMolRecord!")
self.failure.emit(record)
def process(self, mol, port):
"""
The input to this cube will be an OEMol with one or more conformers
with "CONFORMER_LABEL" SD Data of the form 'XY-1234567_1_2_3_4_00_00'
"""
num_confs = mol.NumConfs()
last_conf = mol.GetActive()
last_conf_name = oechem.OEGetSDData(last_conf, "CONFORMER_LABEL")
self.log.info(
"Processing conformer {} on {} at {:%Y-%m-%d %H:%M:%S}".format(
last_conf_name, os.environ["HOSTNAME"],
datetime.datetime.now()))
if num_confs == self.args.num_points:
self.success.emit(mol)
self.log.info(
"Completed scan for {} on {} at {:%Y-%m-%d %H:%M:%S}".format(
mol.GetTitle(), os.environ["HOSTNAME"],
datetime.datetime.now()))
return
if num_confs == 1 and not mol.HasData(self.conf_selection_tag):
self.log.info(
"Conformer {} is a fresh starting conformer on {} at {:%Y-%m-%d %H:%M:%S}"
.format(mol.GetTitle(), os.environ["HOSTNAME"],
datetime.datetime.now()))
mol.SetIntData(self.conf_selection_tag, last_conf.GetIdx())
last_conf.SetDoubleData("TORSION_ANGLE", 0.0)
oechem.OESetSDData(last_conf, "TORSION_ANGLE", "0.0")
self.log.info(
"Sending conformer {} to energy calculation from {} at {:%Y-%m-%d %H:%M:%S}"
.format(last_conf_name, os.environ["HOSTNAME"],
datetime.datetime.now()))
self.to_energy_calc.emit(mol)
return
try:
torsion_tag = "TORSION_ATOMS_FRAGMENT"
torsion_atoms_in_fragment = get_sd_data(mol, torsion_tag).split()
dihedral_atom_indices = [
int(x) - 1 for x in torsion_atoms_in_fragment
]
dih, _ = get_dihedral(mol, dihedral_atom_indices)
dih_atoms = [x for x in dih.GetAtoms()]
# if the last energy calculation failed
if not oechem.OEHasSDData(last_conf, "PSI4_ENERGY"):
self.log.info(
"Conformer {} found to have NO ENERGY on {} at {:%Y-%m-%d %H:%M:%S}"
.format(last_conf_name, os.environ["HOSTNAME"],
datetime.datetime.now()))
mol.PopActive()
last_conf = mol.GetActive()
new_conf = mol.NewConf(last_conf)
mol.PushActive(new_conf)
conf_no = num_confs
conformer_label = last_conf_name[:-3] + "_{:02d}".format(conf_no)
oechem.OESetSDData(new_conf, "CONFORMER_LABEL", conformer_label)
angle = num_confs * 2 * oechem.Pi / self.args.num_points
angle_deg = oechem.Rad2Deg * angle
new_conf.SetDoubleData("TORSION_ANGLE", angle_deg)
oechem.OESetSDData(new_conf, "TORSION_ANGLE",
"{:.1f}".format(angle_deg))
if not oechem.OESetTorsion(new_conf, dih_atoms[0], dih_atoms[1],
dih_atoms[2], dih_atoms[3], angle):
self.log.error(
"Could not rotate conformer {} by {:.1f} on {} at {:%Y-%m-%d %H:%M:%S}"
.format(
last_conf_name,
angle_deg,
os.environ["HOSTNAME"],
datetime.datetime.now(),
))
mol.SetIntData(self.conf_selection_tag, new_conf.GetIdx())
self.log.info(
"Sending conformer {} to energy calculation from {} at {:%Y-%m-%d %H:%M:%S}"
.format(conformer_label, os.environ["HOSTNAME"],
datetime.datetime.now()))
self.to_energy_calc.emit(mol)
except Exception as e:
self.log.error(
"COuld not drive torsion in conformer {} on {} at {:%Y-%m-%d %H:%M:%S}: {}"
.format(last_conf_name, os.environ["HOSTNAME"],
datetime.datetime.now(), e))
self.failure.emit(mol)
def process(self, record, port):
if record.has_value(self.args.in_mol_field):
mol = record.get_value(self.args.in_mol_field)
else:
self.log.error("Could not find molecules in OEMolRecord")
self.failure.emit(record)
return
parent_torsion_tag = "TORSION_ATOMS_ParentMol"
torsion_atoms_in_parent = get_sd_data(mol, parent_torsion_tag).split()
dih_name = mol.GetTitle() + "_" + "_".join(torsion_atoms_in_parent)
torsion_tag = "TORSION_ATOMS_FRAGMENT"
torsion_atoms_in_fragment = get_sd_data(mol, torsion_tag).split()
dihedral_atom_indices = [int(x) - 1 for x in torsion_atoms_in_fragment]
if dihedral_atom_indices is None:
self.log.warn("Unable to find labelled torsion in %s" % dih_name)
self.failure.emit(record)
return
opt_basis = self.args.opt_basis
spe_basis = self.args.spe_basis
# If fragment contains S
# use 6-31+G* instead of 6-31G*
# use 6-31+G** instead of 6-31G**
need_diffuse = False
if oechem.OECount(mol, oechem.OEIsSulfur()) > 0:
need_diffuse = True
for atom in mol.GetAtoms(oechem.OEIsHeavy()):
if atom.GetFormalCharge() < 0:
need_diffuse = True
if need_diffuse:
if opt_basis == "6-31G*":
self.log.warn(
"Using 6-31+G* instead of 6-31G* as opt basis because fragment contains S."
)
opt_basis = "6-31+G*"
if spe_basis == "6-31G*":
self.log.warn(
"Using 6-31+G* instead of 6-31G* as spe basis because fragment contains S."
)
spe_basis = "6-31+G*"
if opt_basis == "6-31G**":
self.log.warn(
"Using 6-31+G** instead of 6-31G** as opt basis because fragment contains S."
)
opt_basis = "6-31+G**"
if spe_basis == "6-31G**":
self.log.warn(
"Using 6-31+G** instead of 6-31G** as spe basis because fragment contains S."
)
spe_basis = "6-31+G**"
try:
if self.args.only_selected_conformer:
conf_selection_tag = "SELECTED_CONFORMER"
key_conf_id = mol.GetIntData(conf_selection_tag)
for conf in mol.GetConfs():
if conf.GetIdx() != key_conf_id:
continue
conf_name = get_sd_data(conf, "CONFORMER_LABEL")
else:
conf_name = get_sd_data(mol, "CONFORMER_LABEL")
time_stamp = "{:%Y-%m-%d %H:%M:%S}".format(datetime.datetime.now())
hostname = socket.gethostname()
self.log.info("Starting psi4 calculation for %s on %s at %s" %
(conf_name, hostname, time_stamp))
if self.args.only_selected_conformer:
oechem.OESetSDData(conf, "%s start time" % self.name,
time_stamp)
else:
oechem.OESetSDData(mol, "%s start time" % self.name,
time_stamp)
dih, _ = get_dihedral(mol, dihedral_atom_indices)
calculate_energy(
mol,
dih,
spe_method=self.args.spe_method,
spe_basis=spe_basis,
geom_opt_technique=self.args.geom_opt_technique,
opt_method=self.args.opt_method,
opt_basis=opt_basis,
geom_maxiter=self.args.geom_maxiter,
only_selected_conf=self.args.only_selected_conformer,
molden_output=self.args.molden_output,
**self.psi4opts)
if self.args.only_selected_conformer:
conf_selection_tag = "SELECTED_CONFORMER"
key_conf_id = mol.GetIntData(conf_selection_tag)
for conf in mol.GetConfs():
if conf.GetIdx() != key_conf_id:
continue
conf_name = get_sd_data(conf, "CONFORMER_LABEL")
else:
conf_name = get_sd_data(mol, "CONFORMER_LABEL")
time_stamp = "{:%Y-%m-%d %H:%M:%S}".format(datetime.datetime.now())
hostname = socket.gethostname()
self.log.info("Completed psi4 calculation for %s on %s at %s" %
(conf_name, hostname, time_stamp))
if self.args.only_selected_conformer:
oechem.OESetSDData(conf, "%s end time" % self.name, time_stamp)
else:
oechem.OESetSDData(mol, "%s end time" % self.name, time_stamp)
optimized_mol_record = OEMolRecord()
optimized_mol_record.set_mol(mol)
self.success.emit(optimized_mol_record)
except Exception as e:
print(e)
# traceback.print_stack()
self.log.error("Error with {} {}".format(mol.GetTitle(), e))
self.failure.emit(record)
def construct_dihedral_energy_profile(torsion_conformers, num_points=24):
angle_list = np.array([360 * i / num_points for i in range(num_points)])
num_confs = 0
profile = np.full(num_points, np.nan)
for mol in torsion_conformers:
if not mol:
continue
num_confs += 1
conf = mol.GetActive()
conf_title = get_sd_data(conf, "CONFORMER_LABEL")
tor_atoms = get_sd_data(mol, "TORSION_ATOMS_ParentMol").split()
parent_name = conf_title[:-3]
dih_label = "_".join(str(x) for x in tor_atoms)
fragment_label = parent_name + "_" + dih_label
angle_idx = int(conf_title[-2:])
profile[angle_idx] = np.float(get_sd_data(conf, "PSI4_ENERGY"))
logging.debug("angle_idx: %d", angle_idx)
logging.debug("Psi4 Energy: %f",
float(get_sd_data(conf, "PSI4_ENERGY")))
# check for angles where no energies are available
for angle in angle_list[np.all(np.isnan(profile))]:
logging.warning(
"Warning: No energies found for angle {:.1f} for fragment: {}".
format(angle, fragment_label))
# calculate relative energies
min_energy = np.nanmin(profile)
profile -= min_energy
profile[np.isnan(profile)] = -1 # set nans to -1
torsional_strain = np.column_stack((angle_list, profile))
# combine conformers
output_conformers = oechem.OEMol(torsion_conformers[0])
output_conformers.DeleteConfs()
title = fragment_label
output_conformers.SetTitle(title)
# setup normalization
torsion_tag = "TORSION_ATOMS_FRAGMENT"
torsion_atoms_in_fragment = get_sd_data(mol, torsion_tag).split()
print(torsion_atoms_in_fragment)
dihedral_atom_indices = [int(x) - 1 for x in torsion_atoms_in_fragment]
dih, _ = get_dihedral(output_conformers, dihedral_atom_indices)
for old_conf in torsion_conformers:
if old_conf:
new_conf = output_conformers.NewConf(old_conf)
normalize_coordinates(new_conf, dih)
oechem.OEClearSDData(new_conf)
for dp in oechem.OEGetSDDataPairs(old_conf.GetActive()):
if dp.GetTag() not in ["OEConfTitle", "CONFORMER_LABEL"]:
oechem.OESetSDData(new_conf, dp.GetTag(), dp.GetValue())
torsion_angle = get_sd_data(old_conf, "TORSION_ANGLE")
title = fragment_label + ": Angle " + torsion_angle
new_conf.SetTitle(title)
write_energy_profile_to_sddata(output_conformers, torsional_strain.copy())
# Calculate all possible torsion inchi keys for this fragment
torsion_inchi_list = []
inchi_key = oechem.OECreateInChIKey(output_conformers)
_, b, c, _ = get_torsion_oeatom_list(output_conformers)
for a in b.GetAtoms(oechem.OEIsHeavy()):
for d in c.GetAtoms(oechem.OEIsHeavy()):
if a.GetIdx() == c.GetIdx() or d.GetIdx() == b.GetIdx():
continue
torsion_inchi = inchi_key + get_modified_inchi_key(
output_conformers, [a, b, c, d])
torsion_inchi_list.append(torsion_inchi)
return output_conformers, torsional_strain, torsion_inchi_list
def gen_starting_confs(
mol,
torsion_library,
max_one_bond_away=True,
num_conformers=MAX_CONFS,
rms_cutoff=0.0,
energy_window=25,
):
# Identify the atoms in the dihedral
TAGNAME = "TORSION_ATOMS_FRAGMENT"
if not has_sd_data(mol, TAGNAME):
raise ValueError(
"Molecule does not have the SD Data Tag '{}'.".format(TAGNAME))
dihedralAtomIndices = [
int(x) - 1 for x in get_sd_data(mol, TAGNAME).split()
]
inDih = oechem.OEOrAtom(
oechem.OEOrAtom(
oechem.OEHasAtomIdx(dihedralAtomIndices[0]),
oechem.OEHasAtomIdx(dihedralAtomIndices[1]),
),
oechem.OEOrAtom(
oechem.OEHasAtomIdx(dihedralAtomIndices[2]),
oechem.OEHasAtomIdx(dihedralAtomIndices[3]),
),
)
mol1 = mol.CreateCopy()
mc_mol = oechem.OEMol(mol1)
# Tag torsion atoms with their dihedral index
for atom in mc_mol.GetAtoms():
if atom.GetIdx() == dihedralAtomIndices[0]:
atom.SetData("dihidx", 0)
if atom.GetIdx() == dihedralAtomIndices[1]:
atom.SetData("dihidx", 1)
if atom.GetIdx() == dihedralAtomIndices[2]:
atom.SetData("dihidx", 2)
if atom.GetIdx() == dihedralAtomIndices[3]:
atom.SetData("dihidx", 3)
if num_conformers > 1:
# Set criterion for rotatable bond
if False and max_one_bond_away:
# this max function makes this seem potentially broken
only_one_bond_away = distance_predicate(dihedralAtomIndices[1],
dihedralAtomIndices[2])
rotor_predicate = oechem.OEAndBond(
only_one_bond_away, oechem.PyBondPredicate(isRotatableBond))
elif False:
# this ONLY samples special bonds & neglects "regualr" torsions
rotor_predicate = oechem.PyBondPredicate(isRotatableBond)
else:
# try this more general sampling, but leave prior versions untouched
rotor_predicate = oechem.OEOrBond(
oechem.OEIsRotor(), oechem.PyBondPredicate(isRotatableBond))
# Initialize conformer generator and multi-conformer library
conf_generator = configure_omega(torsion_library, rotor_predicate,
rms_cutoff, energy_window,
num_conformers)
# Generator conformers
if not conf_generator(mc_mol, inDih):
raise ValueError("Conformers cannot be generated.")
logging.debug(
"Generated a total of %d conformers for %s.",
mc_mol.NumConfs(),
mol.GetTitle(),
)
# Reassign
new_didx = [-1, -1, -1, -1]
for atom in mc_mol.GetAtoms():
if atom.HasData("dihidx"):
new_didx[atom.GetData("dihidx")] = atom.GetIdx()
oechem.OEClearSDData(mc_mol)
oechem.OESetSDData(mc_mol, TAGNAME,
" ".join(str(x + 1) for x in new_didx))
oechem.OESetSDData(
mc_mol,
"TORSION_ATOMS_ParentMol",
get_sd_data(mol, "TORSION_ATOMS_ParentMol"),
)
oechem.OESetSDData(
mc_mol,
"TORSION_ATOMPROP",
f"cs1:0:1;1%{new_didx[0]+1}:1%{new_didx[1]+1}:1%{new_didx[2]+1}:1%{new_didx[3]+1}",
)
for conf_no, conf in enumerate(mc_mol.GetConfs()):
conformer_label = (
mol.GetTitle() + "_" +
"_".join(get_sd_data(mol, "TORSION_ATOMS_ParentMol").split()) +
"_{:02d}".format(conf_no))
oechem.OESetSDData(conf, "CONFORMER_LABEL", conformer_label)
conf.SetTitle(conformer_label)
return mc_mol
def calculate_energy(mol,
dih,
spe_method="SCF",
spe_basis="6-31G",
geom_opt_technique="None",
opt_method="SCF",
opt_basis="6-31G",
geom_maxiter=100,
only_selected_conf=False,
molden_output=False,
**psi4opts):
"""Calculates the energy for a single conformer at a single dihedral angle.
"""
# Argument validation
if geom_opt_technique not in ["None", "QM", "MM"]:
geom_opt_technique = "None"
parent_torsion_tag = "TORSION_ATOMS_ParentMol"
torsion_atoms_in_parent = get_sd_data(mol, parent_torsion_tag).split()
dih_name = mol.GetTitle() + "_" + "_".join(torsion_atoms_in_parent)
if only_selected_conf:
conf_selection_tag = "SELECTED_CONFORMER"
if not mol.HasData(conf_selection_tag):
raise ValueError("Could not find 'SELECTED_CONFORMER' Tag in %s.",
dih_name)
key_conf_id = mol.GetIntData(conf_selection_tag)
for conf in mol.GetConfs():
if only_selected_conf:
if conf.GetIdx() != key_conf_id:
continue
conf_name = get_sd_data(conf, "CONFORMER_LABEL")
if only_selected_conf:
logging.debug("Only running psi4 calculation for %s" % conf_name)
else:
logging.debug("Running psi4 calculation for %s" % conf_name)
angle_deg = conf.GetDoubleData("TORSION_ANGLE")
normalize_coordinates(conf, dih)
try:
energy, psi_mol, wavefcn = psi4_calculation(
conf, dih, conf_name, angle_deg, spe_method, spe_basis,
geom_opt_technique, opt_method, opt_basis, geom_maxiter,
**psi4opts)
except ValueError as e:
logging.error(e)
raise ValueError(
"Failed to run calculation for conformer %s angle %d.",
conf_name,
angle_deg,
)
PSI4_OPT_METHOD_KEY = "PSI4_OPT_METHOD"
PSI4_OPT_BASIS_KEY = "PSI4_OPT_BASIS"
prev_opt_method = oechem.OEGetSDData(conf, PSI4_OPT_METHOD_KEY)
if len(prev_opt_method) > 0:
prev_opt_method += "_"
prev_opt_basis = oechem.OEGetSDData(conf, PSI4_OPT_BASIS_KEY)
if len(prev_opt_basis) > 0:
prev_opt_basis += "_"
complete_opt_method = prev_opt_method + str(opt_method)
complete_opt_basis = prev_opt_basis + str(opt_basis)
get_conf_from_psi4_mol(mol, psi_mol, conf)
logging.debug("Completed psi4 calculation for %s with energy %f" %
(conf_name, energy))
conf.SetEnergy(energy)
oechem.OESetSDData(conf, "PSI4_ENERGY", str(energy))
conf.SetDoubleData("PSI4_ENERGY", energy)
if geom_opt_technique == "QM":
oechem.OESetSDData(conf, PSI4_OPT_METHOD_KEY, complete_opt_method)
oechem.OESetSDData(conf, PSI4_OPT_BASIS_KEY, complete_opt_basis)
oechem.OESetSDData(conf, "PSI4_SPE_METHOD", str(spe_method))
oechem.OESetSDData(conf, "PSI4_SPE_BASIS", str(spe_basis))
# write wavefuction
if molden_output:
wf_filename = "{}_{}.molden".format("wavefcn", conf_name)
psi4.molden(wavefcn, wf_filename)
try:
with open(wf_filename, "r") as fptr:
molden_data = fptr.read()
conf.SetData("MOLDEN_DATA", molden_data)
except IOError as e:
print(
"Unable to save wave function data ",
wf_filename,
" because of error: ",
e,
)
if psi4opts:
save_sddata(mol, psi4opts)