def test_xyz_format_conversion(self):
"""Test conversions from string to list xyz formats"""
xyz_str0 = """N 2.24690600 -0.00006500 0.11597700
C -1.05654800 1.29155000 -0.02642500
C -1.05661400 -1.29150400 -0.02650600
C -0.30514100 0.00000200 0.00533200
C 1.08358900 -0.00003400 0.06558000
H -0.39168300 2.15448600 -0.00132500
H -1.67242600 1.35091400 -0.93175000
H -1.74185400 1.35367700 0.82742800
H -0.39187100 -2.15447800 0.00045500
H -1.74341400 -1.35278100 0.82619100
H -1.67091600 -1.35164600 -0.93286400
"""
xyz_list, atoms, x, y, z = get_xyz_matrix(xyz_str0)
# test all forms of input for get_xyz_string():
xyz_str1 = get_xyz_string(coords=xyz_list, symbols=atoms)
xyz_str2 = get_xyz_string(coords=xyz_list, numbers=[7, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1])
mol, _ = molecules_from_xyz(xyz_str0)
xyz_str3 = get_xyz_string(coords=xyz_list, mol=mol)
self.assertEqual(xyz_str0, xyz_str1)
self.assertEqual(xyz_str1, xyz_str2)
self.assertEqual(xyz_str2, xyz_str3)
self.assertEqual(atoms, ['N', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H'])
self.assertEqual(x, [2.246906, -1.056548, -1.056614, -0.305141, 1.083589, -0.391683, -1.672426, -1.741854,
-0.391871, -1.743414, -1.670916])
self.assertEqual(y[1], 1.29155)
self.assertEqual(z[-1], -0.932864)
def show_sticks(xyz=None, species=None, project_directory=None):
"""
Draws the molecule in a "sticks" style according to the supplied xyz coordinates
Returns whether successful of not
If successful, save an image using draw_3d
"""
xyz = check_xyz_species_for_drawing(xyz, species)
coordinates, _, _, _, _ = get_xyz_matrix(xyz)
s_mol, b_mol = molecules_from_xyz(xyz)
mol = b_mol if b_mol is not None else s_mol
try:
_, rd_mol, _ = rdkit_conf_from_mol(mol, coordinates)
except ValueError:
return False
mb = Chem.MolToMolBlock(rd_mol)
p = p3d.view(width=400, height=400)
p.addModel(mb, 'sdf')
p.setStyle({'stick': {}})
# p.setBackgroundColor('0xeeeeee')
p.zoomTo()
p.show()
draw_3d(xyz=xyz,
species=species,
project_directory=project_directory,
save_only=True)
return True
def check_converge_and_geom_consist(spc,
job_types=['composite', 'freq'],
basis_job='composite'):
basis_xyz = None
done = determine_convergence(spc[basis_job], basis_job, spc['ts'])
if done:
try:
basis_xyz = parse_xyz_from_file(spc[basis_job])
except:
pass
else:
if 'species' in spc \
and not spc['species'].check_xyz_isomorphism(xyz=basis_xyz):
basis_xyz = None
if not basis_xyz:
return
spc['geom'] = basis_xyz
spc['final_xyz'] = basis_xyz
spc['checkfile'] = ''
spc['charge'], spc['multiplicity'] = parse_charge_and_mult(spc[basis_job])
try:
spc['smiles'] = xyz_to_mol(spc['geom']).to_smiles()
except:
try:
spc['smiles'] = molecules_from_xyz(spc['geom'],
spc['multiplicity'],
spc['charge'])[0].to_smiles()
except:
spc['smiles'] = ''
logging.warning(f"Cannot generate SMILES for {spc['label']}")
# Assume checkfile is located under the same dir and named check.chk
check_path = os.path.join(os.path.dirname(spc[basis_job]), 'check.chk')
if os.path.isfile(check_path):
spc['checkfile'] = check_path
for job_type in job_types:
if job_type == basis_job:
continue
xyz_to_compare = None
done = determine_convergence(spc[job_type], job_type, spc['ts'])
if done:
try:
xyz_to_compare = parse_xyz_from_file(spc[job_type])
except:
pass
if not xyz_to_compare or not compare_confs(basis_xyz, xyz_to_compare):
# It seems like only basis job is well done
spc[job_type] = ''
continue
return spc
def test_rdkit_conf_from_mol(self):
"""Test rdkit_conf_from_mol"""
_, b_mol = converter.molecules_from_xyz(self.xyz2)
xyz, _, _, _, _ = converter.get_xyz_matrix(self.xyz2)
conf, rd_mol, indx_map = converter.rdkit_conf_from_mol(mol=b_mol,
coordinates=xyz)
self.assertTrue(conf.Is3D())
self.assertEqual(rd_mol.GetNumAtoms(), 5)
self.assertEqual(indx_map, {0: 0, 1: 1, 2: 2, 3: 3, 4: 4})
def get_rmg_species_from_a_species_dict(
species_dict: dict,
raise_error: bool = False,
) -> Optional[Species]:
"""
Get an RMG Species instance that corresponds to a species specified under the rmg.species
section of the T3 input file (a species dictionary).
Args:
species_dict (dict): The species dictionary to process.
raise_error (bool, optional): Whether to raise an error if a Species instance cannot be generated.
Default: ``False``.
Raises:
ValueError: If the species dictionary does not have a specified structure (if ``raise_error`` is ``True``).
Returns:
Species: The corresponding RMG species instance.
"""
species = None
errored = False
if species_dict['adjlist'] is not None:
species = Species(label=species_dict['label']).from_adjacency_list(
species_dict['adjlist'])
elif species_dict['smiles'] is not None:
species = Species(label=species_dict['label'],
smiles=species_dict['smiles'])
elif species_dict['inchi'] is not None:
species = Species(label=species_dict['label'],
inchi=species_dict['inchi'])
elif species_dict['xyz'] is not None:
for xyz in species_dict['xyz']:
mol_bo = molecules_from_xyz(xyz=xyz)[1]
if mol_bo is not None:
species = Species(
label=species_dict['label']).from_adjacency_list(
mol_bo.to_adjacency_list())
break
else:
errored = True
else:
errored = True
if errored and raise_error:
raise ValueError(
f"The species corresponding to {species_dict['label']} does not have a specified structure."
)
return species
def rotate_molecule_to_lowest_conformer(
arkane_log,
local_path,
input_filename,
multiplicity=1,
charge=0,
):
"""
Given the input file, rotate the molecule to lowest conformer
args:
arkane_log: the gaussian file read by Arkane
local_path (str): local path to the job
input_filename (str): the name of the input file
multiplicity (int)
charge (int)
return:
xyz (str): the xyz string used in arc geometry or gaussian geometry input
"""
# Find the degree to rotate
v_list, angle = arkane_log.loadScanEnergies()
v_list = np.array(v_list, np.float64)
point = np.argmin(v_list)
res = 360.0 / (len(v_list) - 1)
deg_increment = point * res
# Find the xyz geometry
coords, numbers, _ = arkane_log.loadGeometry()
coords = coords.tolist()
xyz = get_xyz_string(coords=coords, numbers=numbers)
# Find the pivot and scan
pivot, scan, _, _ = find_scan_info_from_input_file(local_path,
input_filename)
# Change the structure
mol = molecules_from_xyz(xyz, multiplicity=multiplicity, charge=charge)[1]
conf, rd_mol, indx_map = rdkit_conf_from_mol(mol, coords)
rd_scan = [indx_map[i - 1] for i in scan]
new_xyz = set_rdkit_dihedrals(conf,
rd_mol,
indx_map,
rd_scan,
deg_increment=deg_increment)
return get_xyz_string(coords=new_xyz, numbers=numbers)
def test_xyz_to_smiles(self):
"""Test xyz to SMILES conversion and inferring correct bond orders"""
xyz1 = """S -0.06618943 -0.12360663 -0.07631983
O -0.79539707 0.86755487 1.02675668
O -0.68919931 0.25421823 -1.34830853
N 0.01546439 -1.54297548 0.44580391
C 1.59721519 0.47861334 0.00711000
H 1.94428095 0.40772394 1.03719428
H 2.20318015 -0.14715186 -0.64755729
H 1.59252246 1.51178950 -0.33908352
H -0.87856890 -2.02453514 0.38494433
H -1.34135876 1.49608206 0.53295071"""
xyz2 = """O 2.64631000 -0.59546000 0.29327900
O 2.64275300 2.05718500 -0.72942300
C 1.71639100 1.97990400 0.33793200
C -3.48200000 1.50082200 0.03091100
C -3.85550400 -1.05695100 -0.03598300
C 3.23017500 -1.88003900 0.34527100
C -2.91846400 0.11144600 0.02829400
C 0.76935400 0.80820200 0.23396500
C -1.51123800 -0.09830700 0.09199100
C 1.28495500 -0.50051800 0.22531700
C -0.59550400 0.98573400 0.16444900
C -0.94480400 -1.39242500 0.08331900
C 0.42608700 -1.59172200 0.14650400
H 2.24536500 1.93452800 1.29979800
H 1.14735500 2.91082400 0.31665700
H -3.24115200 2.03800800 0.95768700
H -3.08546100 2.10616100 -0.79369800
H -4.56858900 1.48636200 -0.06630800
H -4.89652000 -0.73067200 -0.04282300
H -3.69325500 -1.65970000 -0.93924100
H -3.72742500 -1.73294900 0.81894100
H 3.02442400 -2.44854700 -0.56812500
H 4.30341500 -1.72127600 0.43646000
H 2.87318600 -2.44236600 1.21464900
H -0.97434200 2.00182800 0.16800300
H -1.58581300 -2.26344700 0.02264400
H 0.81122400 -2.60336100 0.13267800
H 3.16280800 1.25020800 -0.70346900"""
xyz3 = """N 2.24690600 -0.00006500 0.11597700
C -1.05654800 1.29155000 -0.02642500
C -1.05661400 -1.29150400 -0.02650600
C -0.30514100 0.00000200 0.00533200
C 1.08358900 -0.00003400 0.06558000
H -0.39168300 2.15448600 -0.00132500
H -1.67242600 1.35091400 -0.93175000
H -1.74185400 1.35367700 0.82742800
H -0.39187100 -2.15447800 0.00045500
H -1.74341400 -1.35278100 0.82619100
H -1.67091600 -1.35164600 -0.93286400"""
xyz4 = """C -0.86594600 0.19886100 2.37159000
C 0.48486900 -0.16232000 1.75422500
C 1.58322700 0.83707500 2.14923200
C 0.88213600 -1.51753600 2.17861400
N 1.17852900 -2.57013900 2.53313600
N 0.51051200 -0.21074800 0.26080100
N -0.51042000 0.21074000 -0.26079600
C -0.48479200 0.16232300 -1.75422300
C 0.86590400 -0.19926100 -2.37161200
C -1.58344900 -0.83674100 -2.14921800
C -0.88166600 1.51765700 -2.17859800
N -1.17777100 2.57034900 -2.53309500
H -1.16019200 1.20098300 2.05838400
H -1.64220300 -0.50052400 2.05954500
H -0.78054100 0.17214100 3.45935000
H 1.70120000 0.85267300 3.23368300
H 2.53492600 0.56708700 1.69019900
H 1.29214500 1.83331400 1.80886700
H 1.15987300 -1.20145600 -2.05838100
H 0.78046800 -0.17257000 -3.45937100
H 1.64236100 0.49992400 -2.05962300
H -2.53504500 -0.56650600 -1.69011500
H -1.70149200 -0.85224500 -3.23366300
H -1.29263300 -1.83308300 -1.80892900"""
xyz5 = """O 0.90973400 -0.03064000 -0.09605500
O 0.31656600 -0.00477100 -1.21127600
O 2.17315400 -0.03069900 -0.09349100"""
# xyz6 = """S 0.38431300 0.05370100 0.00000000
# N -1.13260000 0.07859900 0.00000000
# H 0.85151800 -1.28998600 0.00000000"""
#
# xyz7 = """N 0.00000000 0.00000000 0.44654700
# N 0.00000000 0.00000000 -0.77510900
# H 0.86709400 0.00000000 1.02859700
# H -0.86709400 0.00000000 1.02859700"""
xyz8 = """N 0.00000000 0.00000000 0.65631400
C 0.00000000 0.00000000 -0.50136500
H 0.00000000 0.00000000 -1.57173600"""
# xyz9 = """S -0.00866000 -0.60254900 0.00000000
# N -0.96878800 0.63275900 0.00000000
# N 1.01229100 0.58298500 0.00000000"""
#
# xyz10 = """O -0.79494500 -0.93969200 0.00000000
# O -0.32753500 1.24003800 0.00000000
# O 1.28811400 -0.24729000 0.00000000
# N 0.14143500 0.11571500 0.00000000
# H -1.65602000 -0.48026800 0.00000000"""
#
# xyz11 = """O 1.64973000 -0.57433600 0.02610800
# O 0.49836300 1.28744800 -0.18806200
# N -0.57621600 -0.65116600 0.24595200
# N -1.78357200 -0.10211200 -0.14953800
# N 0.61460400 0.08152700 -0.00952700
# H -0.42001200 -1.61494900 -0.03311600
# H -1.72480300 0.33507600 -1.06884500
# H -2.07362100 0.59363400 0.53038600"""
xyz12 = """O 1.10621000 0.00000000 -0.13455300
O -1.10621000 0.00000000 -0.13455300
N 0.00000000 0.00000000 0.33490500"""
# xyz13 = """O -0.37723000 -1.27051900 0.00000000
# N -0.12115000 -0.04252600 0.00000000
# N -0.95339100 0.91468300 0.00000000
# C 1.31648000 0.33217600 0.00000000
# H 1.76422500 -0.11051900 -0.89038300
# H 1.76422500 -0.11051900 0.89038300
# H 1.40045900 1.41618100 0.00000000
# H -1.88127600 0.47189500 0.00000000"""
xyz14 = """S -0.12942800 0.11104800 0.22427200
O 0.98591500 -1.00752300 -0.31179100
O -1.43956200 -0.44459900 -0.15048900
O 0.32982400 1.44755400 -0.21682700
H 1.85512700 -0.56879900 -0.36563700"""
xyz15 = """N 1.11543700 0.11100500 0.00000000
N -0.11982300 -0.03150800 0.00000000
N -1.25716400 0.01530300 0.00000000
H 1.57747800 -0.80026300 0.00000000"""
xyz16 = """O 1.21678000 -0.01490600 0.00000000
N 0.04560300 0.35628400 0.00000000
C -1.08941100 -0.23907800 0.00000000
H -1.97763400 0.37807800 0.00000000
H -1.14592100 -1.32640500 0.00000000"""
xyz17 = """S 0.00000000 0.00000000 0.18275300
O -0.94981300 -0.83167500 -0.84628900
O 0.94981300 0.83167500 -0.84628900
O 0.80426500 -0.99804200 0.85548500
O -0.80426500 0.99804200 0.85548500
H -1.67833300 -0.25442300 -1.13658700
H 1.67833300 0.25442300 -1.13658700"""
xyz18 = """S 0.00000000 0.00000000 0.12264300
O 1.45413200 0.00000000 0.12264300
O -0.72706600 1.25931500 0.12264300
O -0.72706600 -1.25931500 0.12264300"""
xyz19 = """N 1.16672400 0.35870400 -0.00000400
N -1.16670800 0.35879500 -0.00000400
C -0.73775600 -0.89086600 -0.00000100
C 0.73767000 -0.89093000 -0.00000100
C 0.00005200 1.08477000 -0.00000500
H -1.40657400 -1.74401100 0.00000000
H 1.40645000 -1.74411900 0.00000000
H 0.00009400 2.16788100 -0.00000700"""
xyz20 = """C 3.09980400 -0.16068000 0.00000600
C 1.73521600 0.45534600 -0.00002200
C 0.55924400 -0.24765400 -0.00000300
C -0.73300200 0.32890400 -0.00001600
C -1.93406200 -0.42115800 0.00001300
C -3.19432700 0.11090700 0.00000900
H 3.67991400 0.15199400 -0.87914100
H 3.67984100 0.15191400 0.87923000
H 3.04908000 -1.25419800 -0.00004300
H 1.68713300 1.54476700 -0.00005100
H -0.81003200 1.41627100 -0.00004600
H -1.83479400 -1.50747300 0.00004100
H 0.61489300 -1.33808300 0.00002500
H -3.35410300 1.18597200 -0.00001700
H -4.07566100 -0.52115800 0.00003300"""
_, mol1 = converter.molecules_from_xyz(xyz1)
_, mol2 = converter.molecules_from_xyz(xyz2)
_, mol3 = converter.molecules_from_xyz(xyz3)
_, mol4 = converter.molecules_from_xyz(xyz4)
_, mol5 = converter.molecules_from_xyz(xyz5)
# _, mol6 = converter.molecules_from_xyz(xyz6)
# _, mol7 = converter.molecules_from_xyz(xyz7)
_, mol8 = converter.molecules_from_xyz(xyz8)
# _, mol9 = converter.molecules_from_xyz(xyz9)
# _, mol10 = converter.molecules_from_xyz(xyz10)
# _, mol11 = converter.molecules_from_xyz(xyz11)
_, mol12 = converter.molecules_from_xyz(xyz12)
# _, mol13 = converter.molecules_from_xyz(xyz13)
_, mol14 = converter.molecules_from_xyz(xyz14)
_, mol15 = converter.molecules_from_xyz(xyz15)
_, mol16 = converter.molecules_from_xyz(xyz16)
_, mol17 = converter.molecules_from_xyz(xyz17)
_, mol18 = converter.molecules_from_xyz(xyz18)
_, mol19 = converter.molecules_from_xyz(xyz19)
_, mol20 = converter.molecules_from_xyz(xyz20)
self.assertEqual(mol1.toSMILES(), '[NH-][S+](=O)(O)C')
self.assertEqual(mol2.toSMILES(), 'COC1C=CC(=CC=1CO)[C](C)C')
self.assertEqual(mol3.toSMILES(), '[N]=C=C(C)C')
self.assertEqual(mol4.toSMILES(), 'N#CC(N=NC(C#N)(C)C)(C)C')
self.assertEqual(mol5.toSMILES(), '[O-][O+]=O')
# self.assertEqual(mol6.toSMILES(), 'N#S') # gives '[N]S', multiplicity 3
# self.assertEqual(mol7.toSMILES(), '[NH2+]=[N-]') # gives '[N]N', multiplicity 3
self.assertEqual(mol8.toSMILES(), 'C#N')
# self.assertEqual(mol9.toSMILES(), '[N-]=[S+]#N') # gives [N]S#N, multiplicity 3
# self.assertEqual(mol10.toSMILES(), '[N+](=O)(O)[O-]') # gives None
# self.assertEqual(mol11.toSMILES(), 'N(N)[N+](=O)[O-]') # gives None
self.assertEqual(mol12.toSMILES(), '[O]N=O')
# self.assertEqual(mol13.toSMILES(), 'C[N+]([NH-])=O') # gives None
self.assertEqual(mol14.toSMILES(), 'OS(=O)[O]')
self.assertEqual(mol15.toSMILES(), '[N-]=[N+]=N')
self.assertEqual(mol16.toSMILES(), '[O]N=C')
self.assertEqual(mol17.toSMILES(), 'OS(=O)(=O)O')
self.assertEqual(mol18.toSMILES(), 'O=S(=O)=O')
self.assertEqual(mol19.toAdjacencyList(), """multiplicity 2
1 N u1 p1 c0 {4,S} {5,S}
2 N u0 p1 c0 {3,S} {5,D}
3 C u0 p0 c0 {2,S} {4,D} {6,S}
4 C u0 p0 c0 {1,S} {3,D} {7,S}
5 C u0 p0 c0 {1,S} {2,D} {8,S}
6 H u0 p0 c0 {3,S}
7 H u0 p0 c0 {4,S}
8 H u0 p0 c0 {5,S}
""") # cannot read SMILES 'c1ncc[n]1' (but can generate them)
self.assertEqual(mol20.toSMILES(), 'C=C[CH]C=CC')
def test_molecules_from_xyz(self):
"""Tests that atom orders are preserved when converting xyz's into RMG Molecules"""
s_mol, b_mol = converter.molecules_from_xyz(self.xyz4)
# check that the atom order is the same
self.assertTrue(s_mol.atoms[0].isSulfur())
self.assertTrue(b_mol.atoms[0].isSulfur())
self.assertTrue(s_mol.atoms[1].isOxygen())
self.assertTrue(b_mol.atoms[1].isOxygen())
self.assertTrue(s_mol.atoms[2].isOxygen())
self.assertTrue(b_mol.atoms[2].isOxygen())
self.assertTrue(s_mol.atoms[3].isNitrogen())
self.assertTrue(b_mol.atoms[3].isNitrogen())
self.assertTrue(s_mol.atoms[4].isCarbon())
self.assertTrue(b_mol.atoms[4].isCarbon())
self.assertTrue(s_mol.atoms[5].isHydrogen())
self.assertTrue(b_mol.atoms[5].isHydrogen())
self.assertTrue(s_mol.atoms[6].isHydrogen())
self.assertTrue(b_mol.atoms[6].isHydrogen())
self.assertTrue(s_mol.atoms[7].isHydrogen())
self.assertTrue(b_mol.atoms[7].isHydrogen())
self.assertTrue(s_mol.atoms[8].isHydrogen())
self.assertTrue(b_mol.atoms[8].isHydrogen())
self.assertTrue(s_mol.atoms[9].isHydrogen())
self.assertTrue(b_mol.atoms[9].isHydrogen())
s_mol, b_mol = converter.molecules_from_xyz(self.xyz5)
self.assertTrue(s_mol.atoms[0].isOxygen())
self.assertTrue(b_mol.atoms[0].isOxygen())
self.assertTrue(s_mol.atoms[2].isCarbon())
self.assertTrue(b_mol.atoms[2].isCarbon())
expected_bonded_adjlist = """multiplicity 2
1 O u0 p2 c0 {6,S} {10,S}
2 O u0 p2 c0 {3,S} {28,S}
3 C u0 p0 c0 {2,S} {8,S} {14,S} {15,S}
4 C u0 p0 c0 {7,S} {16,S} {17,S} {18,S}
5 C u0 p0 c0 {7,S} {19,S} {20,S} {21,S}
6 C u0 p0 c0 {1,S} {22,S} {23,S} {24,S}
7 C u1 p0 c0 {4,S} {5,S} {9,S}
8 C u0 p0 c0 {3,S} {10,D} {11,S}
9 C u0 p0 c0 {7,S} {11,D} {12,S}
10 C u0 p0 c0 {1,S} {8,D} {13,S}
11 C u0 p0 c0 {8,S} {9,D} {25,S}
12 C u0 p0 c0 {9,S} {13,D} {26,S}
13 C u0 p0 c0 {10,S} {12,D} {27,S}
14 H u0 p0 c0 {3,S}
15 H u0 p0 c0 {3,S}
16 H u0 p0 c0 {4,S}
17 H u0 p0 c0 {4,S}
18 H u0 p0 c0 {4,S}
19 H u0 p0 c0 {5,S}
20 H u0 p0 c0 {5,S}
21 H u0 p0 c0 {5,S}
22 H u0 p0 c0 {6,S}
23 H u0 p0 c0 {6,S}
24 H u0 p0 c0 {6,S}
25 H u0 p0 c0 {11,S}
26 H u0 p0 c0 {12,S}
27 H u0 p0 c0 {13,S}
28 H u0 p0 c0 {2,S}
"""
expected_mol = Molecule().fromAdjacencyList(
str(expected_bonded_adjlist))
self.assertEqual(b_mol.toAdjacencyList(), expected_bonded_adjlist)
# the isIsomorphic test must come after the adjlist test since it changes the atom order
self.assertTrue(b_mol.isIsomorphic(expected_mol))
def save_conformers_file(project_directory,
label,
xyzs,
level_of_theory,
multiplicity=None,
charge=None,
is_ts=False,
energies=None,
ts_methods=None):
"""
Save the conformers before or after optimization.
If energies are given, the conformers are considered to be optimized.
Args:
project_directory (str): The path to the project's directory.
label (str): The species label.
xyzs (list): Entries are sting-format xyz coordinates of conformers.
level_of_theory (str): The level of theory used for the conformers optimization.
multiplicity (int, optional): The species multiplicity, used for perceiving the molecule.
charge (int, optional): The species charge, used for perceiving the molecule.
is_ts (bool, optional): Whether the species represents a TS. True if it does.
energies (list, optional): Entries are energies corresponding to the conformer list in kJ/mol.
If not given (None) then the Species.conformer_energies are used instead.
ts_methods (list, optional): Entries are method names used to generate the TS guess.
"""
spc_dir = 'rxns' if is_ts else 'Species'
geo_dir = os.path.join(project_directory, 'output', spc_dir, label,
'geometry', 'conformers')
if not os.path.exists(geo_dir):
os.makedirs(geo_dir)
if energies is not None and any(e is not None for e in energies):
optimized = True
min_e = min_list(energies)
conf_path = os.path.join(geo_dir, 'conformers_after_optimization.txt')
else:
optimized = False
conf_path = os.path.join(geo_dir, 'conformers_before_optimization.txt')
with open(conf_path, 'w') as f:
content = ''
if optimized:
content += 'Conformers for {0}, optimized at the {1} level:\n\n'.format(
label, level_of_theory)
for i, xyz in enumerate(xyzs):
content += 'conformer {0}:\n'.format(i)
if xyz is not None:
content += xyz + '\n'
if not is_ts:
try:
b_mol = molecules_from_xyz(xyz,
multiplicity=multiplicity,
charge=charge)[1]
except SanitizationError:
b_mol = None
smiles = b_mol.toSMILES(
) if b_mol is not None else 'Could not perceive molecule'
content += 'SMILES: {0}\n'.format(smiles)
elif ts_methods is not None:
content += 'TS guess method: {0}\n'.format(ts_methods[i])
if optimized:
if energies[i] == min_e:
content += 'Relative Energy: 0 kJ/mol (lowest)'
elif energies[i] is not None:
content += 'Relative Energy: {0:.3f} kJ/mol'.format(
energies[i] - min_e)
else:
# Failed to converge
if is_ts and ts_methods is not None:
content += 'TS guess method: ' + ts_methods[i] + '\n'
content += 'Failed to converge'
content += '\n\n\n'
f.write(str(content))
