01-Gaussian Parse and Inspect¶

Parse a real Gaussian log fixture with AutoParser, inspect frame status, and output a compact, verifiable summary.

In [1]:

import os
from pathlib import Path

os.environ.setdefault("TQDM_DISABLE", "1")

from molop.io import AutoParser


def find_repo_root(start: Path | None = None) -> Path:
    current = (start or Path.cwd()).resolve()
    for parent in [current, *current.parents]:
        if (parent / "pyproject.toml").exists():
            return parent
    raise FileNotFoundError("Could not find repository root containing pyproject.toml")


repo_root = find_repo_root()
fixture_path = repo_root / "tests/test_files/g16log/2-TS1-Opt.log"
relative_fixture_path = fixture_path.relative_to(repo_root)

batch = AutoParser(fixture_path.as_posix(), n_jobs=1)
parsed_file = batch[0]
last_frame = parsed_file[-1]

print("summary_snippet:")
parsed_file.to_summary_df()

import os from pathlib import Path os.environ.setdefault("TQDM_DISABLE", "1") from molop.io import AutoParser def find_repo_root(start: Path | None = None) -> Path: current = (start or Path.cwd()).resolve() for parent in [current, *current.parents]: if (parent / "pyproject.toml").exists(): return parent raise FileNotFoundError("Could not find repository root containing pyproject.toml") repo_root = find_repo_root() fixture_path = repo_root / "tests/test_files/g16log/2-TS1-Opt.log" relative_fixture_path = fixture_path.relative_to(repo_root) batch = AutoParser(fixture_path.as_posix(), n_jobs=1) parsed_file = batch[0] last_frame = parsed_file[-1] print("summary_snippet:") parsed_file.to_summary_df()

MolOP parsing with single process:   0%|          | 0/1 [00:00<?, ?it/s]

summary_snippet:

Out[1]:

	DiskStorage		General					Calc Parameter						Environment				Status
	FilePath	FileFormat	Charge	Multiplicity	CanonicalSMILES	NumAtoms	FrameID	Software	Version	Method	...	Functional	Keywords	SolventModel	Solvent	Temperature (kelvin)	Pressure (standard_atmosphere)	IsError	IsNormal	IsTS	IsOptimized
0	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	0	Gaussian	ES64L-G16RevC.01	DFT	...	RB3LYP-GD3BJ	# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdi...	None	None	298.15 kelvin	1.0 standard_atmosphere	False	True	False	False
1	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	1	Gaussian	ES64L-G16RevC.01	DFT	...	RB3LYP-GD3BJ	# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdi...	None	None	298.15 kelvin	1.0 standard_atmosphere	False	True	False	False
2	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	2	Gaussian	ES64L-G16RevC.01	DFT	...	RB3LYP-GD3BJ	# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdi...	None	None	298.15 kelvin	1.0 standard_atmosphere	False	True	False	False
3	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	3	Gaussian	ES64L-G16RevC.01	DFT	...	RB3LYP-GD3BJ	# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdi...	None	None	298.15 kelvin	1.0 standard_atmosphere	False	True	False	False
4	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	4	Gaussian	ES64L-G16RevC.01	DFT	...	RB3LYP-GD3BJ	# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdi...	None	None	298.15 kelvin	1.0 standard_atmosphere	False	True	False	False
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
101	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	101	Gaussian	ES64L-G16RevC.01	DFT	...	RB3LYP-GD3BJ	# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdi...	None	None	298.15 kelvin	1.0 standard_atmosphere	False	True	False	False
102	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	102	Gaussian	ES64L-G16RevC.01	DFT	...	RB3LYP-GD3BJ	# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdi...	None	None	298.15 kelvin	1.0 standard_atmosphere	False	True	False	False
103	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	103	Gaussian	ES64L-G16RevC.01	DFT	...	RB3LYP-GD3BJ	# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdi...	None	None	298.15 kelvin	1.0 standard_atmosphere	False	True	False	True
104	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	104	Gaussian	ES64L-G16RevC.01	DFT	...	RB3LYP-GD3BJ	# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdi...	None	None	298.15 kelvin	1.0 standard_atmosphere	False	True	False	False
105	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	105	Gaussian	ES64L-G16RevC.01	DFT	...	RB3LYP	#N Geom=AllCheck Guess=TCheck SCRF=Check GenCh...	None	None	298.15 kelvin	1.0 standard_atmosphere	False	True	True	False

106 rows × 21 columns

A richer summary can be obtained by setting brief=False.

In [2]:

parsed_file.to_summary_df(brief=False)

parsed_file.to_summary_df(brief=False)

Out[2]:

	DiskStorage		General					Calc Parameter			...	Thermal								Vibration
	FilePath	FileFormat	Charge	Multiplicity	CanonicalSMILES	NumAtoms	FrameID	Software	Version	Method	...	TCH (kilocalorie / mole)	TCG (kilocalorie / mole)	U_0 (kilocalorie / mole)	U_T (kilocalorie / mole)	H_T (kilocalorie / mole)	G_T (kilocalorie / mole)	S (calorie / kelvin / mole)	C_V (calorie / kelvin / mole)	num_imaginary	num_vibrations
0	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	0	Gaussian	ES64L-G16RevC.01	DFT	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
1	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	1	Gaussian	ES64L-G16RevC.01	DFT	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
2	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	2	Gaussian	ES64L-G16RevC.01	DFT	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
3	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	3	Gaussian	ES64L-G16RevC.01	DFT	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
4	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	4	Gaussian	ES64L-G16RevC.01	DFT	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
101	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	101	Gaussian	ES64L-G16RevC.01	DFT	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
102	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	102	Gaussian	ES64L-G16RevC.01	DFT	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
103	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	103	Gaussian	ES64L-G16RevC.01	DFT	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
104	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	104	Gaussian	ES64L-G16RevC.01	DFT	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
105	/Users/tmj/Documents/proj/MolOP/tests/test_fil...	.log	0	1	CC1=C=C2[CH-]C=CC=C2C=C1.Cc1ccc(C[N+]2[C@H](C[...	101	105	Gaussian	ES64L-G16RevC.01	DFT	...	536.632297	444.716592	-2301115.979432	-2301081.95775	-2301081.365382	-2301173.280459	208.673	308.286	1	297

106 rows × 41 columns

File Information¶

In [3]:

parsed_file

parsed_file

Out[3]:

frames=106, G16LogFileDisk(charge=0, multiplicity=1, qm_software='Gaussian', qm_software_version='ES64L-G16RevC.01', keywords='# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdiis) freq b3lyp/genecp em=gd3bj', method='DFT', basis_set='pseudopotential', functional='RB3LYP-GD3BJ', resources_raw='', solvent=None, temperature=<Quantity(298.15, 'kelvin')>, pressure=<Quantity(1.0, 'standard_atmosphere')>, running_time=<Quantity(1065479.2, 'second')>, status=Status(scf_converged=True, normal_terminated=True), geometry_optimization_status=None, options='%nprocs=32\n%mem=80GB', title_card='Title Card Required', job_type='FTS', filename='2-TS1-Opt.log')

In [4]:

parsed_file.model_dump()

parsed_file.model_dump()

Out[4]:

{'charge': 0,
 'multiplicity': 1,
 'qm_software': 'Gaussian',
 'qm_software_version': 'ES64L-G16RevC.01',
 'keywords': '# opt=(calcfc,ts,noeigen,maxstep=1,notrust,gdiis) freq b3lyp/genecp em=gd3bj',
 'method': 'DFT',
 'basis_set': 'pseudopotential',
 'functional': 'RB3LYP-GD3BJ',
 'resources_raw': '',
 'solvent': None,
 'temperature': <Quantity(298.15, 'kelvin')>,
 'pressure': <Quantity(1.0, 'standard_atmosphere')>,
 'running_time': <Quantity(1065479.2, 'second')>,
 'status': {'scf_converged': True, 'normal_terminated': True},
 'geometry_optimization_status': None,
 'options': '%nprocs=32\n%mem=80GB',
 'title_card': 'Title Card Required',
 'job_type': 'FTS',
 'standard_orientation_transformation_matrix': array([[ 1.00000000e+00, -7.15316281e-08,  9.67269248e-08,
          2.43332149e-07],
        [ 7.15316216e-08,  1.00000000e+00,  6.57111532e-08,
         -1.92074856e-07],
        [-9.67269293e-08, -6.57111463e-08,  1.00000000e+00,
          1.30262744e-07],
        [ 0.00000000e+00,  0.00000000e+00,  0.00000000e+00,
          1.00000000e+00]]),
 'file_path': '/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/2-TS1-Opt.log',
 'detected_format_id': 'g16log',
 'filename': '2-TS1-Opt.log'}

Properties with units are represented with pint and support unit conversion.

In [5]:

parsed_file.running_time

parsed_file.running_time

Out[5]:

1065479.2 second

In [6]:

parsed_file.running_time.to("h")

parsed_file.running_time.to("h")

Out[6]:

295.96644444444445 hour

Frame Object Information¶

MolOP integrates rdkit-dof. The default RDKit molecule rendering includes a depth-of-field effect. If you don't like this style, you can disable it via the global configuration.

from molop.config import molopconfig
molopconfig.set_dof_effect_drawer(False)

In [7]:

last_frame.rdmol

last_frame.rdmol

Out[7]:

Accessing Data in a Frame¶

In [8]:

last_frame.model_dump().keys()

last_frame.model_dump().keys()

Out[8]:

dict_keys(['atoms', 'coords', 'charge', 'multiplicity', 'bonds', 'formal_charges', 'formal_num_radicals', 'frame_id', 'qm_software', 'qm_software_version', 'keywords', 'method', 'basis_set', 'functional', 'resources_raw', 'solvent', 'temperature', 'pressure', 'forces', 'hessian', 'rotation_constants', 'energies', 'thermal_informations', 'molecular_orbitals', 'vibrations', 'charge_spin_populations', 'polarizability', 'bond_orders', 'total_spin', 'single_point_properties', 'status', 'geometry_optimization_status', 'running_time', 'options', 'title_card', 'job_type', 'standard_orientation_transformation_matrix', 'standard_coords', 'file_path', 'detected_format_id', 'smiles', 'canonical_smiles', 'is_error', 'is_normal', 'is_TS', 'is_optimized', 'filename'])

If multiple energy levels are available, total_energy automatically selects the highest-level energy.

In [9]:

last_frame.energies.model_dump()

last_frame.energies.model_dump()

Out[9]:

{'electronic_energy': None,
 'scf_energy': <Quantity(-3667.86175, 'hartree')>,
 'mp2_energy': None,
 'mp3_energy': None,
 'mp4_energy': None,
 'ccsd_energy': None,
 'total_energy': <Quantity(-3667.86175, 'hartree')>}

Thermal properties

In [10]:

last_frame.thermal_informations.model_dump()

last_frame.thermal_informations.model_dump()

Out[10]:

{'ZPVE': <Quantity(502.017619, 'kilocalorie / mole')>,
 'TCE': <Quantity(536.039928, 'kilocalorie / mole')>,
 'TCH': <Quantity(536.632297, 'kilocalorie / mole')>,
 'TCG': <Quantity(444.716592, 'kilocalorie / mole')>,
 'U_0': <Quantity(-2301115.98, 'kilocalorie / mole')>,
 'U_T': <Quantity(-2301081.96, 'kilocalorie / mole')>,
 'H_T': <Quantity(-2301081.37, 'kilocalorie / mole')>,
 'G_T': <Quantity(-2301173.28, 'kilocalorie / mole')>,
 'S': <Quantity(208.673, 'calorie / mole / kelvin')>,
 'C_V': <Quantity(308.286, 'calorie / mole / kelvin')>}

Optimization status

In [11]:

last_frame.geometry_optimization_status.model_dump()

last_frame.geometry_optimization_status.model_dump()

Out[11]:

{'geometry_optimized': False,
 'rms_force_threshold': 0.0003,
 'max_force_threshold': 0.00045,
 'rms_displacement_threshold': 0.0012,
 'max_displacement_threshold': 0.0018,
 'energy_change': -2.689102e-08,
 'rms_force': 4e-06,
 'max_force': 3.7e-05,
 'rms_displacement': 0.001014,
 'max_displacement': 0.004373,
 'energy_change_converged': None,
 'rms_force_converged': True,
 'max_force_converged': True,
 'rms_displacement_converged': True,
 'max_displacement_converged': False}

Or view it as a table

In [12]:

last_frame.geometry_optimization_status.to_df()

last_frame.geometry_optimization_status.to_df()

Out[12]:

	value	threshold	converged
energy_change	-2.689102e-08	NaN	None
rms_force	4.000000e-06	0.00030	True
max_force	3.700000e-05	0.00045	True
rms_displacement	1.014000e-03	0.00120	True
max_displacement	4.373000e-03	0.00180	False

Polarizability-related information

In [13]:

last_frame.polarizability.model_dump()

last_frame.polarizability.model_dump()

Out[13]:

{'electronic_spatial_extent': <Quantity(32064.5204, 'bohr ** 2')>,
 'isotropic_polarizability': <Quantity(567.607, 'bohr ** 3')>,
 'anisotropic_polarizability': <Quantity(151.035, 'bohr ** 3')>,
 'polarizability_tensor': <Quantity([604.564   32.9301 583.745  -56.4015 -33.4024 514.513 ], 'bohr ** 3')>,
 'dipole': <Quantity([ 3.68616  -0.880583  2.95738 ], 'debye')>,
 'quadrupole': <Quantity([-349.5223 -319.1229 -351.3398   -7.7821  -26.9199  -17.9296], 'debye * angstrom')>,
 'traceless_quadrupole': <Quantity([ -9.5273  20.8721 -11.3448  -7.7821 -26.9199 -17.9296], 'debye * angstrom')>,
 'octapole': <Quantity([ 83.6646 -58.9773  74.3053 -25.8942 -43.5558  65.9372  30.8367  34.1059
    6.7378 -16.6707], 'debye * angstrom ** 2')>,
 'hexadecapole': <Quantity([-1.73940777e+04 -1.25671001e+04 -1.14539245e+04  4.65876000e+01
  -1.53457800e+02  2.62174600e+02 -7.24701000e+01 -1.91710500e+02
  -2.66604000e+01 -5.09340340e+03 -4.82498970e+03 -3.94426940e+03
  -1.91343500e+02  4.34870000e+00 -4.70990000e+00], 'debye * angstrom ** 3')>}

molecular_orbitals can be indexed like a list to access a specific orbital. MolOP also provides shortcuts for commonly used orbitals, for example:

In [14]:

last_frame.molecular_orbitals.model_dump().keys()

last_frame.molecular_orbitals.model_dump().keys()

Out[14]:

dict_keys(['electronic_state', 'alpha_energies', 'beta_energies', 'alpha_occupancies', 'beta_occupancies', 'alpha_symmetries', 'beta_symmetries', 'coefficients', 'HOMO_id', 'LUMO_id', 'beta_HOMO_id', 'beta_LUMO_id', 'SOMO_ids', 'NHOMO_id', 'SLUMO_id', 'HOMO_energy', 'LUMO_energy', 'NHOMO_energy', 'SLUMO_energy', 'HOMO_LUMO_gap', 'beta_HOMO_energy', 'beta_LUMO_energy', 'beta_HOMO_LUMO_gap', 'beta_NHOMO_id', 'beta_NHOMO_energy', 'beta_SLUMO_id', 'beta_SLUMO_energy'])

In [15]:

last_frame.molecular_orbitals[0].model_dump()

last_frame.molecular_orbitals[0].model_dump()

Out[15]:

{'alpha_energy': <Quantity(-89.0746, 'hartree')>,
 'beta_energy': None,
 'alpha_occupancy': True,
 'alpha_symmetry': '(A)',
 'beta_occupancy': None,
 'beta_symmetry': None,
 'coefficient': None}

In [16]:

last_frame.molecular_orbitals.HOMO.model_dump()

last_frame.molecular_orbitals.HOMO.model_dump()

Out[16]:

{'alpha_energy': <Quantity(-0.18767, 'hartree')>,
 'beta_energy': None,
 'alpha_occupancy': True,
 'alpha_symmetry': '(A)',
 'beta_occupancy': None,
 'beta_symmetry': None,
 'coefficient': None}

In [17]:

last_frame.molecular_orbitals.LUMO.model_dump()

last_frame.molecular_orbitals.LUMO.model_dump()

Out[17]:

{'alpha_energy': <Quantity(-0.06315, 'hartree')>,
 'beta_energy': None,
 'alpha_occupancy': False,
 'alpha_symmetry': '(A)',
 'beta_occupancy': None,
 'beta_symmetry': None,
 'coefficient': None}

vibrations can also be indexed like a list to access information for a specific vibrational mode, for example:

In [18]:

last_frame.vibrations.model_dump().keys()

last_frame.vibrations.model_dump().keys()

Out[18]:

dict_keys(['frequencies', 'reduced_masses', 'force_constants', 'IR_intensities', 'vibration_modes'])

In [19]:

last_frame.vibrations[0].model_dump()

last_frame.vibrations[0].model_dump()

Out[19]:

{'frequency': <Quantity(-44.2376, 'reciprocal_centimeter')>,
 'reduced_mass': <Quantity(9.5785, 'unified_atomic_mass_unit')>,
 'force_constant': <Quantity(0.011, 'millidyne / angstrom')>,
 'IR_intensity': <Quantity(19.3851, 'kilometer / mole')>,
 'vibration_mode': <Quantity([[-0.04353013 -0.0568171  -0.01688054]
  [ 0.01008565 -0.0033201   0.2121684 ]
  [-0.0093313   0.00927325  0.18452081]
  [-0.00480192 -0.0812717  -0.01543192]
  [-0.02312481 -0.05325445  0.04998448]
  [-0.01445755 -0.07534108 -0.00233244]
  [-0.00480192 -0.0812717  -0.01543192]
  [-0.0141281  -0.06995574  0.01074004]
  [-0.00531579 -0.0904913  -0.01927053]
  [-0.00428806 -0.0720521  -0.01159332]
  [-0.02458769 -0.07634687 -0.02461177]
  [-0.04488732 -0.08064165 -0.03763022]
  [-0.01445755 -0.07534108 -0.00233244]
  [-0.05505681 -0.08393063 -0.02836933]
  [-0.05538627 -0.08931597 -0.04144181]
  [-0.01445755 -0.07534108 -0.00233244]
  [ 0.00602648 -0.06721204  0.00145214]
  [-0.03475718 -0.07963586 -0.01535089]
  [-0.06485749 -0.07955109 -0.03757619]
  [-0.00414301 -0.07050102  0.01071303]
  [-0.04441281 -0.07370524 -0.0022514 ]
  [-0.0146026  -0.07689215 -0.02463878]
  [-0.00601406 -0.10354517 -0.01387526]
  [-0.02286169 -0.0448538  -0.02232984]
  [-0.00480192 -0.0812717  -0.01543192]
  [ 0.0027589  -0.12636392 -0.0123456 ]
  [-0.02234783 -0.03563419 -0.01849124]
  [-0.03214851 -0.03125465 -0.0276981 ]
  [-0.01357488 -0.05845295 -0.01696158]
  [ 0.00448489 -0.09487085 -0.01006367]
  [-0.03112078 -0.01281544 -0.02002089]
  [-0.01306101 -0.04923334 -0.01312298]
  [-0.04342444 -0.05754922  0.03696603]
  [-0.0249565  -0.0840154  -0.00614403]
  [-0.01515582 -0.08839495  0.00306283]
  [-0.02514091 -0.08784967  0.00308985]
  [-0.02514091 -0.08784967  0.00308985]
  [-0.01548528 -0.09378029 -0.01000964]
  [-0.02462705 -0.07863006  0.00692845]
  [-0.02462705 -0.07863006  0.00692845]
  [-0.02532532 -0.09168393  0.01232372]
  [-0.01515582 -0.08839495  0.00306283]
  [-0.02481145 -0.08246433  0.01616232]
  [-0.02481145 -0.08246433  0.01616232]
  [-0.04342444 -0.05754922  0.03696603]
  [-0.0437539  -0.06293456  0.02389355]
  [-0.04356949 -0.0591003   0.01465968]
  [-0.0437539  -0.06293456  0.02389355]
  [-0.05373898 -0.06238928  0.02392056]
  [-0.04360885 -0.06138349  0.0461999 ]
  [-0.04379326 -0.06521775  0.05543377]
  [-0.04342444 -0.05754922  0.03696603]
  [-0.04412271 -0.07060309  0.0423613 ]
  [-0.03395322 -0.06731411  0.03310041]
  [-0.03413763 -0.07114837  0.04233428]
  [-0.01398305 -0.06840467  0.03304639]
  [-0.03325495 -0.05426024  0.02770514]
  [-0.03461213 -0.07808478  0.00695546]
  [-0.04511108 -0.08675911  0.00314387]
  [-0.06456739 -0.07644894  0.0070365 ]
  [-0.05542562 -0.09159916 -0.00990159]
  [-0.03494159 -0.08347012 -0.00611701]
  [-0.03498095 -0.08575331  0.02542321]
  [-0.03508664 -0.08502119 -0.02842336]
  [-0.02499586 -0.08629859  0.02539619]
  [-0.03516535 -0.08958758  0.03465708]
  [-0.02528596 -0.08940074 -0.0192165 ]
  [-0.03504728 -0.082738   -0.05996358]
  [-0.01482637 -0.08300961  0.01613531]
  [-0.02485081 -0.08474752  0.04770254]
  [-0.02543101 -0.09095181 -0.04152285]
  [-0.01482637 -0.08300961  0.01613531]
  [-0.01482637 -0.08300961  0.01613531]
  [-0.00521009 -0.09122342  0.03457604]
  [ 0.0051438  -0.08410017  0.01608128]
  [-0.04471529 -0.08438908  0.10160314]
  [-0.10345303 -0.06112712  0.13174876]
  [-0.08161181 -0.02917353  0.15628302]
  [ 0.00858342 -0.02869572  0.16911238]
  [ 0.06662289 -0.06501155  0.14436202]
  [ 0.03549485 -0.08336599  0.11445951]
  [-0.17059491 -0.00737787  0.14189699]
  [-0.06604264 -0.10712306  0.08090748]
  [-0.16387741 -0.06707503  0.12807224]
  [-0.13032511 -0.00417365  0.15486142]
  [ 0.13703235 -0.05960891  0.14801153]
  [ 0.07440747 -0.10398632  0.10667425]
  [-0.09882826  0.02184931  0.16629618]
  [-0.12929738  0.01426555  0.16253862]
  [-0.18799577  0.03981071  0.16114403]
  [-0.03980043  0.00168949  0.18076325]
  [-0.02122679 -0.0255088   0.19149976]
  [-0.06098273 -0.01949342  0.18237394]
  [-0.01894758  0.01748707  0.16608008]
  [ 0.02706374 -0.0475802  -0.0224649 ]
  [ 0.2817611  -0.14783608 -0.10232735]
  [-0.12317468 -0.0387557  -0.20590576]
  [ 0.09640612 -0.06289996  0.00504762]
  [ 0.13348705 -0.11428125 -0.05886613]
  [ 0.0280521  -0.03142419  0.01675252]
  [ 0.14639788 -0.06864168  0.09029935]], 'angstrom')>,
 'is_imaginary': True}

For other available fields, see Model Field Map.

TS-Specific Features¶

For transition states (TS), MolOP can use the imaginary frequency information for quick inspection to assess whether a TS is reasonable. Bonds that are likely changing connectivity are marked with dashed lines.

In [20]:

last_frame.to_diff_rdmol()

last_frame.to_diff_rdmol()

Out[20]:

MolOP successfully validated a reductive elimination step, where Ni changes oxidation state from +2 to +0.

In [21]:

from rdkit.Chem import Draw

Draw.MolsToGridImage(last_frame.possible_pre_post_ts(show_3D=True), molsPerRow=2, subImgSize=(500, 500))

from rdkit.Chem import Draw Draw.MolsToGridImage(last_frame.possible_pre_post_ts(show_3D=True), molsPerRow=2, subImgSize=(500, 500))

Out[21]:

In [ ]: