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TorsionDrive Datasets¶
An individual TorsionDrive is specific workflow in the QCArchive ecosystem that computes the energy profile of rotatable dihedral (torsion) for use in Force Field fitting. This workflow has been developed by the QCArchive Team in conjunction with:
Chaya Stern
Yudong Qiu
The top-level TorsionDrive code can be found here.
The TorsionDrive Dataset organizes many TorsionDrives together for data exploration, analysis, and methodology comparison. To begin, we can connect to the MolSSI QCArchive server and query all known TorsionDrive Datasets:
[1]:
import qcportal as ptl
client = ptl.FractalClient()
client
[1]:
FractalClient
- Server: The MolSSI QCArchive Server
- Address: https://api.qcarchive.molssi.org:443/
- Username: None
[2]:
client.list_collections("TorsionDriveDataset")
[2]:
| tagline | ||
|---|---|---|
| collection | name | |
| TorsionDriveDataset | Fragment Stability Benchmark | None |
| OpenFF Fragmenter Phenyl Benchmark | Phenyl substituent torsional barrier heights. | |
| OpenFF Full TorsionDrive Benchmark 1 | None | |
| OpenFF Group1 Torsions | None | |
| OpenFF Primary TorsionDrive Benchmark 1 | None | |
| OpenFF Substituted Phenyl Set 1 | None | |
| Pfizer Discrepancy Torsion Dataset 1 | None | |
| SMIRNOFF Coverage Torsion Set 1 | None | |
| TorsionDrive Paper | None |
One of the datasets can be obtained in the canonical manner:
[3]:
ds = client.get_collection("TorsionDriveDataset", "OpenFF Fragmenter Phenyl Benchmark")
Exploring the Dataset¶
Each row of the dataset is comprised of a Entry which contains a list of starting molecules for the TorsionDrive, the dihedral of interest (in this case zero-indexed), and the scan resolution of the dihedral. For the purposes of the underlying DataFrame each row is the name of this Entry.
[4]:
ds.df.head()
[4]:
| c1c[cH:1][c:2](cc1)[C:3](=[O:4])O |
| c1[cH:1][c:2](cnc1)[C:3](=[O:4])O |
| [cH:1]1cncc[c:2]1[C:3](=[O:4])O |
| [cH:1]1cc(nc[c:2]1[C:3](=[O:4])O)[O-] |
| Cc1c[cH:1][c:2](cn1)[C:3](=[O:4])O |
New computations are based off specifications which contain many additional parameters to tune the torsiondrive as well as the underlying computational method. Here, we can list all specifications that are attributed to this dataset.
[5]:
ds.list_specifications()
[5]:
| Description | |
|---|---|
| Name | |
| UFF | UFF gradient evaluation with RDKit |
| B3LYP-D3 | B3LYP-D3 evaluation with Psi4 |
As we can see, we have several specifications at different levels of theory. It is important to recall that these Collections are “live”: new specifications can be added and individual TorsionDrives can be under computation. To see the current status of each specification the status function is provided:
[6]:
ds.status(["uff", "b3lyp-d3"])
[6]:
| UFF | B3LYP-D3 | |
|---|---|---|
| COMPLETE | 165 | 226 |
| INCOMPLETE | 62 | 1 |
[7]:
ds.status(["b3lyp-d3"], collapse=False, status="COMPLETE").head()
[7]:
| B3LYP-D3 | |
|---|---|
| c1c[cH:1][c:2](cc1)[C:3](=[O:4])O | COMPLETE |
| c1[cH:1][c:2](cnc1)[C:3](=[O:4])O | COMPLETE |
| [cH:1]1cncc[c:2]1[C:3](=[O:4])O | COMPLETE |
| [cH:1]1cc(nc[c:2]1[C:3](=[O:4])O)[O-] | COMPLETE |
| Cc1c[cH:1][c:2](cn1)[C:3](=[O:4])O | COMPLETE |
Visualizing the TorsionDrives¶
TorsionDrives can be visualized via the visualize command. Multiple torsiondrives can be plotted on the same graph for comparison.
[8]:
ds.visualize(["[CH3:4][O:3][c:2]1[cH:1]cccc1", "[CH3:4][O:3][c:2]1[cH:1]ccnc1"], "B3LYP-D3", units="kJ / mol")
Computational Requirements¶
We can check the number of optimizations and individual gradient evaluations by using the count method. By default, the count method shows the number of individual geometry optimizations:
[9]:
ds.counts(["[CH3:4][O:3][c:2]1[cH:1]cccc1", "[CH3:4][O:3][c:2]1[cH:1]ccnc1"])
[9]:
| UFF | B3LYP-D3 | |
|---|---|---|
| [CH3:4][O:3][c:2]1[cH:1]cccc1 | 49 | 49 |
| [CH3:4][O:3][c:2]1[cH:1]ccnc1 | 49 | 53 |
In addition to individual optimization runs, we can also find a sum of how many gradient evaluations were performed in the course of the run.
[10]:
ds.counts(["[CH3:4][O:3][c:2]1[cH:1]cccc1", "[CH3:4][O:3][c:2]1[cH:1]ccnc1"], count_gradients=True)
[10]:
| UFF | B3LYP-D3 | |
|---|---|---|
| [CH3:4][O:3][c:2]1[cH:1]cccc1 | 606 | 601 |
| [CH3:4][O:3][c:2]1[cH:1]ccnc1 | 538 | 680 |
Deep data inspection¶
The TorsionDriveDataset also allows exploration of every single computation and molecule created during the individual TorsionDrive executions. Examples below this point will only be for those who wish to explore all of the individual computations in a TorsionDrive Dataset.
These TorsionDrive Datasets are different from canonical ReactionDataset and Dataset collections as each item in the underlying Pandas DataFrame is a TorsionDriveRecord object which contains links to all data used in the TorsionDrive. We can observe the these in the underlying DataFrame:
[11]:
ds.df.head()
[11]:
| UFF | B3LYP-D3 | |
|---|---|---|
| c1c[cH:1][c:2](cc1)[C:3](=[O:4])O | id=1761595 hash_index=973a82dee50895e16d0a1099... | id=1761822 hash_index=028379f6fcec47dd5a41b7c4... |
| c1[cH:1][c:2](cnc1)[C:3](=[O:4])O | id=1761596 hash_index=52cd24c390a25eee94e2ce1b... | id=1761823 hash_index=205e930c36ae28eb2dd5153d... |
| [cH:1]1cncc[c:2]1[C:3](=[O:4])O | id=1761597 hash_index=50db63b5d61dbaa0b326d588... | id=1761824 hash_index=381175f46c75a36d1bdec6c2... |
| [cH:1]1cc(nc[c:2]1[C:3](=[O:4])O)[O-] | id=1761598 hash_index=aa028d05f9aac9984667e4e2... | id=1761825 hash_index=f11d261f1ba21ac280706a36... |
| Cc1c[cH:1][c:2](cn1)[C:3](=[O:4])O | id=1761599 hash_index=16aeb7c248405ebd9ea1d117... | id=1761826 hash_index=93cf4b08356a79aef7f70be6... |
We can then begin to explore an individual TorsionDriveRecord by first pulling it from the DataFrame:
[12]:
td = ds.df.loc["[CH3:4][O:3][c:2]1[cH:1]cccc1", "B3LYP-D3"]
We can then request a variety of attributes off this TorsionDriveRecord:
[13]:
print("Torsion of interest : {}".format(td.keywords.dihedrals))
print("Final optimization energy in hartree: {}".format(td.get_final_energies(180)))
Torsion of interest : [(3, 5, 7, 6)]
Final optimization energy in hartree: -346.5319986074462
[14]:
td.get_final_molecules(90)
The Molecule object has a measure attribute so that we check the dihedral angle is in fact 180 degrees.
[15]:
"3-5-7-6 dihedral in degrees: {}".format(td.get_final_molecules(180).measure([3, 5, 7, 6]))
[15]:
'3-5-7-6 dihedral in degrees: 179.99999995886662'
You can also get a dictionary of all final molecules:
[16]:
td.get_final_molecules()
[16]:
{(-90,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.40718507 -2.21840696 -0.22958297]
[ 4.97493788 -3.48334777 1.48334476]
[ 1.7716505 -0.3298455 0.63640014]
[ 4.90787611 -2.87176474 4.05190433]
[ 1.69441113 0.29082009 3.20260133]
[ 3.26680019 -0.98070424 4.91013927]
[ 1.5337185 -1.70492748 8.94696498]
[ 3.24498132 -0.32624151 7.42021119]
[ 3.46717648 -2.69676568 -2.23750076]
[ 6.26600112 -4.95093418 0.81459893]
[ 0.55229994 0.67321911 -0.69586245]
[ 6.13043938 -3.82147864 5.41754483]
[ 0.44593371 1.77186336 3.91617642]
[ 1.72079846 -0.98831032 10.88831694]
[ 1.96264592 -3.7518771 8.93520479]
[-0.44384326 -1.44836098 8.3163972 ]], name=C7H8O, identifiers={'molecule_hash': '34e0a1476c201686f17fe576609083dc7d8bb187', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=460608, extras=None),
(180,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.61027365e+00 -1.98030605e+00 -3.18740370e-01]
[ 5.52088757e+00 -3.08165509e+00 1.14994779e+00]
[ 1.54199251e+00 -8.74617230e-01 8.85238100e-01]
[ 5.36125372e+00 -3.07470080e+00 3.77580127e+00]
[ 1.35317133e+00 -8.52024700e-01 3.52622139e+00]
[ 3.27349763e+00 -1.95850076e+00 4.98449807e+00]
[ 1.25868666e+00 -9.66527320e-01 8.90037066e+00]
[ 3.28505965e+00 -2.04442029e+00 7.55013272e+00]
[ 3.73979950e+00 -1.98801841e+00 -2.37887261e+00]
[ 7.15429448e+00 -3.95597241e+00 2.35669430e-01]
[ 3.66345200e-02 -7.97205000e-03 -2.33700310e-01]
[ 6.82865599e+00 -3.92206287e+00 4.95325767e+00]
[-2.84620420e-01 2.56175000e-02 4.41539709e+00]
[ 1.66683083e+00 -1.25550003e+00 1.09153783e+01]
[-5.62174440e-01 -1.88506626e+00 8.44355628e+00]
[ 1.07941944e+00 1.08370374e+00 8.53662357e+00]], name=C7H8O, identifiers={'molecule_hash': '454b9110a607f34201c736a791f2a438ef7eab3b', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=458506, extras=None),
(135,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.71074266 -1.78005411 -0.28373136]
[ 5.60347076 -2.81108719 1.25014161]
[ 1.41712809 -1.04780261 0.80318487]
[ 5.2116725 -3.10100381 3.84211902]
[ 0.99788049 -1.34633653 3.39535384]
[ 2.89417641 -2.3994055 4.92058236]
[ 1.52117769 -0.80706242 8.90148939]
[ 2.60669985 -2.77544922 7.4566502 ]
[ 4.02516342 -1.54291228 -2.31039311]
[ 7.41160882 -3.37483763 0.42488076]
[-0.07297217 -0.23671814 -0.37601593]
[ 6.66649345 -3.88431511 5.0779687 ]
[-0.8050157 -0.78350122 4.22440334]
[ 1.86678347 -1.26394897 10.89874498]
[-0.5432106 -0.64765122 8.61880289]
[ 2.39551084 1.03754822 8.45893749]], name=C7H8O, identifiers={'molecule_hash': 'a181fc4f7143c3e59d6db6a67f68ec2d6dca7d01', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=458654, extras=None),
(165,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.65418749 -1.90093631 -0.31404815]
[ 5.56021506 -2.99808714 1.16271943]
[ 1.51514808 -0.91626636 0.87283114]
[ 5.32801018 -3.10570501 3.78188 ]
[ 1.25147303 -1.01602504 3.50484657]
[ 3.16118484 -2.13031622 4.97086769]
[ 1.31253922 -0.89145213 8.89765096]
[ 3.08963919 -2.33077078 7.53054258]
[ 3.84376413 -1.81267554 -2.36768675]
[ 7.25298638 -3.76720236 0.26197523]
[ 0.01480673 -0.0501931 -0.25324579]
[ 6.79530961 -3.94250746 4.9669548 ]
[-0.4400024 -0.23597809 4.38548001]
[ 1.7612165 -1.14516869 10.90913746]
[-0.64769987 -1.53804325 8.5690084 ]
[ 1.43117256 1.13977679 8.42246929]], name=C7H8O, identifiers={'molecule_hash': '2c67957d95a44c137d7746d2ecd1c4f28c655849', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=458889, extras=None),
(-165,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.56477391 -2.06268365 -0.31933034]
[ 5.46806545 -3.1646068 1.15740257]
[ 1.56234862 -0.83094627 0.87518466]
[ 5.36641548 -3.0359742 3.78393169]
[ 1.43705914 -0.68051491 3.51500416]
[ 3.35702811 -1.77598282 4.98183602]
[ 1.22152767 -1.05569795 8.89252899]
[ 3.42101743 -1.73127425 7.549176 ]
[ 3.64518515 -2.17194564 -2.37912539]
[ 7.04316019 -4.14656642 0.25010762]
[ 0.0611202 0.03347081 -0.2509852 ]
[ 6.82376306 -3.89074244 4.96846074]
[-0.14605238 0.29553537 4.40164763]
[ 1.62176362 -1.39719575 10.90124846]
[-0.42219723 -2.21053475 8.31784924]
[ 0.73508868 0.96218359 8.64722648]], name=C7H8O, identifiers={'molecule_hash': 'cf816486557e9146f6a71606f1c8ec975073de08', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=458861, extras=None),
(-135,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.491733 -2.17583439 -0.29637177]
[ 5.33054359 -3.30455675 1.23430153]
[ 1.62351776 -0.67457419 0.81459627]
[ 5.2991748 -2.94298239 3.84661412]
[ 1.58487459 -0.28523287 3.42824227]
[ 3.44443861 -1.4048686 4.9512827 ]
[ 1.26160538 -1.27722055 8.88669334]
[ 3.54307214 -1.08323406 7.50911694]
[ 3.51165624 -2.47088682 -2.33965283]
[ 6.79103733 -4.49672339 0.38935433]
[ 0.17567664 0.21298338 -0.36216721]
[ 6.70326276 -3.8180982 5.07954316]
[ 0.12784967 0.9028205 4.27685668]
[ 1.77954751 -1.42167327 10.89369992]
[ 0.17735948 -2.97500059 8.3345377 ]
[ 0.03575585 0.39865631 8.65060519]], name=C7H8O, identifiers={'molecule_hash': '8175d7667946055f7f16e5bb64997ab5fb0dfb17', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=458870, extras=None),
(150,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.68950957 -1.83192958 -0.30263301]
[ 5.58788714 -2.91449311 1.19197383]
[ 1.47651723 -0.96952926 0.84767887]
[ 5.27814438 -3.12904808 3.79899959]
[ 1.13585096 -1.18495302 3.46192866]
[ 3.03480466 -2.29331251 4.94542969]
[ 1.40141672 -0.85296282 8.89427796]
[ 2.86097753 -2.59344088 7.49456838]
[ 3.94144492 -1.65547154 -2.34397562]
[ 7.33843648 -3.57937644 0.31914596]
[-0.01672084 -0.11341923 -0.29527781]
[ 6.74037439 -3.94979797 5.00135427]
[-0.60798886 -0.50658543 4.32710875]
[ 1.88525221 -1.13551231 10.89457591]
[-0.65152006 -1.17180494 8.66612967]
[ 1.831008 1.11863797 8.35470128]], name=C7H8O, identifiers={'molecule_hash': '2afce2897a153d1f113c03a8839f12cac3ac0719', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=459105, extras=None),
(-150,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.52476149e+00 -2.12952483e+00 -3.12109620e-01]
[ 5.41127251e+00 -3.23366809e+00 1.18174239e+00]
[ 1.58752395e+00 -7.68590320e-01 8.53755290e-01]
[ 5.35958136e+00 -2.98227988e+00 3.80332133e+00]
[ 1.51990512e+00 -4.90890560e-01 3.48340437e+00]
[ 3.42886502e+00 -1.58133228e+00 4.96735537e+00]
[ 1.23691058e+00 -1.15109572e+00 8.88478749e+00]
[ 3.52325946e+00 -1.39670006e+00 7.53161235e+00]
[ 3.56322781e+00 -2.33889999e+00 -2.36548922e+00]
[ 6.92801398e+00 -4.32112774e+00 2.95604100e-01]
[ 9.88758100e-02 9.59362800e-02 -2.88856250e-01]
[ 6.80025429e+00 -3.84213567e+00 5.00437371e+00]
[-4.47220000e-03 5.84117900e-01 4.36108482e+00]
[ 1.68066939e+00 -1.50621313e+00 1.08828092e+01]
[-1.89240600e-01 -2.53460509e+00 8.24066372e+00]
[ 4.20982040e-01 7.66566550e-01 8.72640143e+00]], name=C7H8O, identifiers={'molecule_hash': 'f3b67ee06b6b817183b9c0f41a9c6e7ac631c146', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=459114, extras=None),
(105,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.69545538 -1.70634993 -0.23938507]
[ 5.58436954 -2.54998336 1.40623546]
[ 1.25836456 -1.25614547 0.68418211]
[ 5.04976205 -2.9314534 3.96508707]
[ 0.70724096 -1.64444833 3.23706462]
[ 2.60724282 -2.48633636 4.87951087]
[ 1.86172856 -0.77318807 8.93121643]
[ 2.08977467 -2.94052016 7.37904178]
[ 4.11789466 -1.4081985 -2.23853071]
[ 7.4899185 -2.91207376 0.69511821]
[-0.22967914 -0.61125939 -0.59562359]
[ 6.49168507 -3.5949349 5.28423518]
[-1.19362524 -1.33018691 3.97905554]
[ 1.41574336 -1.43372593 10.85002017]
[ 0.33246541 0.49775271 8.28516983]
[ 3.6428032 0.32145572 8.98528528]], name=C7H8O, identifiers={'molecule_hash': 'a72a6127282ba5336fb37ae76ef40ea1e446a21c', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=459232, extras=None),
(-105,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.42039406 -2.20354666 -0.25271686]
[ 5.09605067 -3.43333395 1.38060355]
[ 1.7185079 -0.4240417 0.71262135]
[ 5.06721158 -2.90095096 3.96800149]
[ 1.68677973 0.12628289 3.29486938]
[ 3.36694948 -1.11363064 4.92455346]
[ 1.41395078 -1.58524678 8.90830178]
[ 3.41029401 -0.55427638 7.4557179 ]
[ 3.44543837 -2.62362267 -2.27431064]
[ 6.43496313 -4.81991356 0.63721685]
[ 0.4146949 0.55441554 -0.55653123]
[ 6.36113935 -3.83233623 5.27864259]
[ 0.38996126 1.53278678 4.07115436]
[ 1.68407697 -0.94737393 10.86717504]
[ 1.43485456 -3.67596418 8.86458193]
[-0.45838733 -0.93599831 8.24185377]], name=C7H8O, identifiers={'molecule_hash': 'dda2cb6b2f0782068fc6a0a395c8631962bc24e0', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=459394, extras=None),
(120,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.68154157 -1.74990256 -0.24461527]
[ 5.58614604 -2.68218607 1.33400306]
[ 1.31356562 -1.16345525 0.77506458]
[ 5.13669762 -3.01249357 3.91491872]
[ 0.84241752 -1.50501605 3.35088957]
[ 2.75895471 -2.43763707 4.92670024]
[ 1.70964993 -0.7538 8.9503509 ]
[ 2.3670574 -2.86664598 7.44878031]
[ 4.03838228 -1.48541515 -2.26104614]
[ 7.44229936 -3.14542008 0.55413637]
[-0.18938282 -0.44590515 -0.44750504]
[ 6.59476681 -3.73210344 5.18542651]
[-1.01536662 -1.08131531 4.14394906]
[ 1.55620491 -1.42607057 10.91017616]
[-0.12115984 0.08733461 8.39660453]
[ 3.17380361 0.7350621 8.85419846]], name=C7H8O, identifiers={'molecule_hash': '2526a43946fc423be4f370a91480eb7d31cbd392', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=459538, extras=None),
(-120,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.45091577 -2.17571528 -0.26546162]
[ 5.21045061 -3.36877965 1.30595734]
[ 1.66970257 -0.52870746 0.78601954]
[ 5.18350251 -2.93404589 3.9102702 ]
[ 1.64081975 -0.06925252 3.38632468]
[ 3.40713121 -1.27216144 4.9545363 ]
[ 1.31775564 -1.46385389 8.91994316]
[ 3.49582237 -0.83122039 7.50330384]
[ 3.4695849 -2.52358983 -2.30063283]
[ 6.60916241 -4.65886601 0.50136998]
[ 0.2959696 0.42130221 -0.43001301]
[ 6.53386114 -3.84721516 5.17544277]
[ 0.2743827 1.24257482 4.20596625]
[ 1.75350877 -1.06837263 10.91245988]
[ 0.83775254 -3.48824763 8.71708563]
[-0.35272618 -0.33384423 8.37353198]], name=C7H8O, identifiers={'molecule_hash': '135dd920d0dbd5dcbbb668246becc22ea8f19dba', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=459600, extras=None),
(90,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.70026604 -1.68781217 -0.21473939]
[ 5.55971395 -2.42504226 1.5147141 ]
[ 1.20886204 -1.3472961 0.60288173]
[ 4.93860674 -2.81548453 4.05199411]
[ 0.57469777 -1.73382934 3.13764424]
[ 2.44233629 -2.47122049 4.8618902 ]
[ 2.0262802 -0.81298112 8.97297625]
[ 1.81054902 -2.91990197 7.33754827]
[ 4.19006652 -1.388848 -2.19839178]
[ 7.50634899 -2.70687967 0.88300624]
[-0.25363715 -0.78411793 -0.74315142]
[ 6.35677177 -3.41129129 5.42873571]
[-1.36184649 -1.49732344 3.81235793]
[ 1.46745331 -1.44403575 10.87215158]
[ 0.77398282 0.75470241 8.38281463]
[ 3.98719974 -0.08961615 9.04816579]], name=C7H8O, identifiers={'molecule_hash': 'a6601a8f8c024493170efc180fb7ce6a3f6ea552', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=461369, extras=None),
(75,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.70212325 -1.72466955 -0.21585801]
[ 5.51905339 -2.32444209 1.61008955]
[ 1.16923478 -1.46408046 0.49415964]
[ 4.81449559 -2.66039694 4.13241122]
[ 0.4522114 -1.78473091 3.01641573]
[ 2.27581552 -2.38406191 4.8372815 ]
[ 2.15535767 -0.85813513 9.03145663]
[ 1.52672714 -2.78611098 7.28616169]
[ 4.25856462 -1.4718899 -2.18825289]
[ 7.49871004 -2.54995062 1.06400225]
[-0.2610239 -1.00629602 -0.92454499]
[ 6.20785963 -3.16338765 5.57048426]
[-1.51425058 -1.59868966 3.61443722]
[ 1.4695119 -1.46795424 10.8955 ]
[ 1.24259402 0.95548078 8.53075546]
[ 4.21880374 -0.54221236 9.1461044 ]], name=C7H8O, identifiers={'molecule_hash': 'b0e45b3d9bfb9763487b040f0053eb857a2140ce', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=461425, extras=None),
(-75,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.43900598 -2.20071294 -0.22823573]
[ 4.86508261 -3.50716914 1.57581688]
[ 1.85180055 -0.22953493 0.53510663]
[ 4.70765322 -2.85320039 4.12901981]
[ 1.67473259 0.42691458 3.08785967]
[ 3.10410599 -0.88523154 4.88656201]
[ 1.63777454 -1.79343168 9.00470539]
[ 2.9808923 -0.15490425 7.37079048]
[ 3.57347597 -2.7115241 -2.22444734]
[ 6.12387823 -5.03664869 0.98911017]
[ 0.74084538 0.80565965 -0.86563389]
[ 5.83674841 -3.83404887 5.55225734]
[ 0.45497214 1.96371446 3.7278884 ]
[ 1.7397371 -0.9786394 10.9132759 ]
[ 2.46538192 -3.71275772 9.04941128]
[-0.36950472 -1.95935811 8.4422741 ]], name=C7H8O, identifiers={'molecule_hash': '6fe82700dc2bbb954cfa35bce052a43ef355e8c3', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=461459, extras=None),
(30,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.69600344 -1.85447301 -0.30101366]
[ 5.42957732 -1.96441247 1.68575814]
[ 1.10571549 -1.80496047 0.24404663]
[ 4.60860206 -2.02544662 4.19938437]
[ 0.26273043 -1.85146068 2.73915521]
[ 2.01117613 -1.95189563 4.73362008]
[ 2.47935475 -1.15790713 9.14730531]
[ 1.03798047 -2.10187281 7.10982174]
[ 4.35246849 -1.80992101 -2.25772808]
[ 7.4563067 -2.0155252 1.28725824]
[-0.27319083 -1.72058681 -1.29211501]
[ 5.9901253 -2.13100274 5.72583171]
[-1.74683847 -1.81374977 3.20562904]
[ 1.1989466 -1.02138253 10.77726717]
[ 3.26020365 0.7331975 8.72723948]
[ 4.05738793 -2.42970717 9.6581919 ]], name=C7H8O, identifiers={'molecule_hash': '5aba4f48598014250d3b37a70e119aa9d17b76b8', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=461723, extras=None),
(60,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.71828345 -1.76811666 -0.27338275]
[ 5.50089579 -2.20886409 1.62864783]
[ 1.15779938 -1.58361834 0.35850376]
[ 4.74133601 -2.46356402 4.14507752]
[ 0.38360523 -1.81737538 2.87169991]
[ 2.17400832 -2.25536827 4.7722983 ]
[ 2.28444156 -0.94953994 9.06682808]
[ 1.32018125 -2.59349763 7.19110947]
[ 4.32142939 -1.57815469 -2.23890818]
[ 7.50367599 -2.37607107 1.14971388]
[-0.25023734 -1.246811 -1.11528944]
[ 6.12828802 -2.84801683 5.62417659]
[-1.60352774 -1.68120413 3.41076772]
[ 1.31483482 -1.42137021 10.84263787]
[ 1.90592803 1.05132903 8.59565568]
[ 4.34048833 -1.17965735 9.35939703]], name=C7H8O, identifiers={'molecule_hash': '179c476f669865b56eebca36680d181929e6e5b7', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=461685, extras=None),
(-60,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.48556806 -2.18859899 -0.28454022]
[ 4.75712849 -3.55422444 1.58838991]
[ 1.95045647 -0.14980855 0.40552128]
[ 4.50247118 -2.8965478 4.13335644]
[ 1.67036486 0.50930549 2.9466371 ]
[ 2.94379439 -0.86431289 4.81779631]
[ 1.78466861 -1.85587089 9.04078282]
[ 2.71212821 -0.07793354 7.2717555 ]
[ 3.69732353 -2.7058812 -2.2721875 ]
[ 5.9768439 -5.13753051 1.06503382]
[ 0.95491809 0.93350363 -1.0447928 ]
[ 5.52697525 -3.93700323 5.5917871 ]
[ 0.48365833 2.09295743 3.53111283]
[ 1.62148788 -0.86984945 10.86215514]
[ 3.06567807 -3.48777783 9.28933466]
[-0.097693 -2.57462474 8.48502773]], name=C7H8O, identifiers={'molecule_hash': 'b44ad27c199728b72c05ba913385cb2bc642c8a8', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=461700, extras=None),
(-30,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.54750913 -2.12259724 -0.30742535]
[ 4.51078875 -3.62629947 1.63566464]
[ 2.11306417 0.0171931 0.30314439]
[ 4.05963677 -3.01927365 4.17022987]
[ 1.63838631 0.63602012 2.81911036]
[ 2.60133437 -0.88567949 4.76903241]
[ 2.06262868 -1.91409872 9.1259098 ]
[ 2.14806198 -0.09606409 7.17464836]
[ 3.91046327 -2.60827962 -2.28075711]
[ 5.64288319 -5.29531538 1.18645125]
[ 1.34830037 1.21278008 -1.19818872]
[ 4.84397415 -4.20537125 5.66280304]
[ 0.52497984 2.29437545 3.33637992]
[ 1.22301635 -0.98084951 10.78088872]
[ 3.96516229 -2.59916291 9.65479546]
[ 0.88871412 -3.55824497 8.59566222]], name=C7H8O, identifiers={'molecule_hash': 'c5c33ab70cf9df182831507c6ed5daea82827341', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=461731, extras=None),
(45,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.69639473 -1.79743864 -0.29873657]
[ 5.45928124 -2.05967591 1.65083976]
[ 1.11810236 -1.70428504 0.28674669]
[ 4.67054666 -2.22992127 4.16744948]
[ 0.3109718 -1.85413007 2.7927833 ]
[ 2.08514535 -2.10889291 4.74580389]
[ 2.40545302 -1.06954623 9.11534623]
[ 1.16885394 -2.37939496 7.14132671]
[ 4.32497976 -1.67092038 -2.26118922]
[ 7.47686639 -2.15019919 1.21495776]
[-0.27892714 -1.5030941 -1.22190147]
[ 6.05998786 -2.46332476 5.67393071]
[-1.68935396 -1.78551201 3.29413963]
[ 1.14500254 -1.13490653 10.76580932]
[ 2.76366218 0.92393291 8.60563825]
[ 4.22194341 -1.95474001 9.648864 ]], name=C7H8O, identifiers={'molecule_hash': 'a159c8d539fe8935046beac7fdeabf3a66465c1c', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=461819, extras=None),
(-45,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.49939228 -2.15330139 -0.30787911]
[ 4.60813322 -3.59922556 1.60454938]
[ 2.03333459 -0.04875028 0.34065581]
[ 4.26647776 -2.96167543 4.14644088]
[ 1.66490412 0.59404878 2.87150549]
[ 2.77323437 -0.86555735 4.78671794]
[ 1.94936593 -1.89691127 9.0917486 ]
[ 2.4517307 -0.06107251 7.21585974]
[ 3.77829643 -2.65860577 -2.29010662]
[ 5.7696973 -5.23780629 1.12013198]
[ 1.15934525 1.09887588 -1.13829112]
[ 5.16374776 -4.08568481 5.62496036]
[ 0.52934295 2.22651639 3.42188566]
[ 1.290692 -0.87441177 10.77628966]
[ 3.65100376 -2.98999082 9.6184854 ]
[ 0.46628521 -3.23341981 8.47832305]], name=C7H8O, identifiers={'molecule_hash': '5c9839877f910bb7dafc3694046103f7cee32e02', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=461827, extras=None),
(0,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.705481 -2.005779 -0.30916382]
[ 5.41340407 -1.8578246 1.69359705]
[ 1.10677377 -1.96699335 0.20622924]
[ 4.56869423 -1.67222782 4.19620825]
[ 0.23744147 -1.78335773 2.68235995]
[ 1.96387315 -1.63440946 4.69802417]
[ 2.54284232 -1.30378749 9.1626126 ]
[ 0.93684859 -1.46033225 7.04427198]
[ 4.38361058 -2.14990825 -2.25347798]
[ 7.44581918 -1.88579145 1.32253157]
[-0.25684224 -2.08140433 -1.34162258]
[ 5.94690775 -1.55958853 5.72300638]
[-1.77796083 -1.75024478 3.1236002 ]
[ 1.31441531 -1.17992622 10.8317381 ]
[ 3.76178701 0.39258319 9.09604855]
[ 3.76126299 -2.99182153 9.34675257]], name=C7H8O, identifiers={'molecule_hash': '30b86628fd1d834aa7ad1deeb50d962a82a0214d', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=463178, extras=None),
(-15,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.70444484 -2.08536058 -0.30602168]
[ 5.42171814 -1.81248734 1.67650045]
[ 1.10845069 -2.04737062 0.22011872]
[ 4.58579213 -1.50370096 4.16903174]
[ 0.24847747 -1.74870149 2.6892643 ]
[ 1.98334563 -1.48072909 4.68387251]
[ 2.54115462 -1.3800461 9.16114721]
[ 0.97332592 -1.13872669 7.02046597]
[ 4.37458448 -2.32456995 -2.24376515]
[ 7.45230012 -1.83222076 1.29503933]
[-0.26085794 -2.25792583 -1.31253249]
[ 5.96644644 -1.28397146 5.68249548]
[-1.76495913 -1.71423857 3.13922479]
[ 1.29951636 -1.2873653 10.82289062]
[ 3.94041723 0.16716183 9.29131427]
[ 3.56236256 -3.20285849 9.1733056 ]], name=C7H8O, identifiers={'molecule_hash': '6353c768493bd01d50a28569b04b0bd1faeccfb3', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=463335, extras=None),
(15,): Molecule(schema_name=qcschema_molecule, schema_version=2, validated=True, symbols=['C' 'C' 'C' 'C' 'C' 'C' 'C' 'O' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'H'], geometry=[[ 3.70448247 -1.92662444 -0.31778593]
[ 5.42169639 -1.90514381 1.68336373]
[ 1.10848889 -1.88548988 0.20812449]
[ 4.58571506 -1.84287149 4.19415947]
[ 0.24846249 -1.81664612 2.69429743]
[ 1.983275 -1.78854545 4.70667893]
[ 2.5411861 -1.22859275 9.14992915]
[ 0.97317763 -1.78202702 7.06812715]
[ 4.37466574 -1.97588365 -2.26960286]
[ 7.45227515 -1.94275871 1.3032283 ]
[-0.26077669 -1.90247038 -1.33886803]
[ 5.96632233 -1.83779682 5.72352584]
[-1.76497555 -1.78351301 3.14435528]
[ 1.29956022 -1.07481746 10.80714566]
[ 3.56322061 0.57564798 8.8933725 ]
[ 3.93975196 -2.74036093 9.50672658]], name=C7H8O, identifiers={'molecule_hash': '0fb2d9128eabf27a29c645d57a5ce4d64ce03dc4', 'molecular_formula': 'C7H8O', 'smiles': None, 'inchi': None, 'inchikey': None, 'canonical_explicit_hydrogen_smiles': None, 'canonical_isomeric_explicit_hydrogen_mapped_smiles': None, 'canonical_isomeric_explicit_hydrogen_smiles': None, 'canonical_isomeric_smiles': None, 'canonical_smiles': None}, comment=None, molecular_charge=0.0, molecular_multiplicity=1, masses=[12. 12. 12. 12. 12. 12.
12. 15.99491462 1.00782503 1.00782503 1.00782503 1.00782503
1.00782503 1.00782503 1.00782503 1.00782503], real=[ True True True True True True True True True True True True
True True True True], atom_labels=['' '' '' '' '' '' '' '' '' '' '' '' '' '' '' ''], atomic_numbers=[6 6 6 6 6 6 6 8 1 1 1 1 1 1 1 1], mass_numbers=[12 12 12 12 12 12 12 16 1 1 1 1 1 1 1 1], connectivity=[(0, 2, 2.0), (0, 1, 1.0), (0, 8, 1.0), (1, 3, 2.0), (1, 9, 1.0), (2, 4, 1.0), (2, 10, 1.0), (3, 5, 1.0), (3, 11, 1.0), (4, 5, 2.0), (4, 12, 1.0), (5, 7, 1.0), (6, 7, 1.0), (6, 13, 1.0), (6, 14, 1.0), (6, 15, 1.0)], fragments=[array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
dtype=int32)], fragment_charges=[0.0], fragment_multiplicities=[1], fix_com=True, fix_orientation=True, fix_symmetry=None, provenance={'creator': 'QCElemental', 'version': 'v0.11.0', 'routine': 'qcelemental.molparse.from_schema'}, id=465210, extras=None)}
Exploring connection optimizations¶
If desired, we can pull each geometry optimization belonging to the torsiondrive with the get_history function. In this case, we will pull the lowest energy optimization for the 180 degree dihedral:
[17]:
opt = td.get_history(180, minimum=True)
opt
[17]:
OptimizationRecord(id=1701507, hash_index=effb8d6307ac3cc1a263e674e93342498f10219f, procedure=optimization, program=geometric, version=1, protocols={}, extras={}, stdout=228720, stderr=None, error=None, task_id=5c988a95b6a2de5fb9b9e33f, manager_name=None, status=COMPLETE, modified_on=2019-03-25 08:02:57.063000, created_on=2019-03-22 20:21:05.145000, provenance={'creator': 'geomeTRIC', 'version': '0.9.5', 'routine': 'geometric.run_json.geometric_run_json', 'wall_time': 111.76719880104065, 'qcengine_version': 'v0.6.4', 'cpu': 'Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz', 'username': 'lnaden', 'hostname': 'dt039'}, schema_version=1, initial_molecule=458443, qc_spec={'driver': <DriverEnum.gradient: 'gradient'>, 'method': 'b3lyp-d3', 'basis': 'def2-svp', 'keywords': '5c954fa6b6a2de5f188ea234', 'program': 'psi4'}, keywords={'coordsys': 'tric', 'enforce': 0.1, 'constraints': {'set': [{'type': 'dihedral', 'indices': [3, 5, 7, 6], 'value': 180}]}, 'program': 'psi4'}, energies=[-346.53147622614085, -346.53177915374135, -346.5318873591642, -346.53194287295247, -346.53197743434515, -346.5319973422999, -346.53199831291954, -346.53199826976714, -346.5319986074462], final_molecule=458506, trajectory=['594805', '594862', '594863', '594864', '594865', '594866', '594867', '594868', '594869'])
[18]:
opt.energies
[18]:
[-346.53147622614085,
-346.53177915374135,
-346.5318873591642,
-346.53194287295247,
-346.53197743434515,
-346.5319973422999,
-346.53199831291954,
-346.53199826976714,
-346.5319986074462]
Exploring individual gradient evaluations¶
We can go even deeper in the calculations to look at each gradient calculation of the Optimization calculation if we so choose and see even more details about how the TorsionDrive object was constructed.
[19]:
result = opt.get_trajectory()[-1]
[20]:
print("Program: {}".format(result.program))
print("Number of Basis Functions: {}".format(result.properties.calcinfo_nbasis))
print("Total execution time: {:.2f}s".format(result.provenance.wall_time))
Program: psi4
Number of Basis Functions: 152
Total execution time: 12.15s
This example also contains the Wiberg-Lowdin indices. As this is specific to Psi4, this data resides inside the extras tag rather than general properties. This data is not yet well curated and currently exists as a 1D list. We will first pull this data and transform it to a 2D array:
[21]:
import numpy as np
wiberg = np.array(result.extras["qcvars"]["WIBERG_LOWDIN_INDICES"]).reshape(-1, 16)
As this particular example is exploring the 3-5-7-6 dihedral, we would find the most use in the 5-7 bond. This can be acquired as follows:
[22]:
wiberg[5, 7]
[22]:
1.2700940280530457
We can continue to explore these results and even obtain the standard Psi4 logging information!
[23]:
print(result.get_stdout()[:1000])
Memory set to 60.800 GiB by Python driver.
gradient() will perform analytic gradient computation.
*** tstart() called on dt039
*** at Mon Mar 25 04:02:23 2019
=> Loading Basis Set <=
Name: DEF2-SVP
Role: ORBITAL
Keyword: BASIS
atoms 1-7 entry C line 90 file /home/lnaden/miniconda3/envs/qca/share/psi4/basis/def2-svp.gbs
atoms 8 entry O line 130 file /home/lnaden/miniconda3/envs/qca/share/psi4/basis/def2-svp.gbs
atoms 9-16 entry H line 15 file /home/lnaden/miniconda3/envs/qca/share/psi4/basis/def2-svp.gbs
---------------------------------------------------------
SCF
by Justin Turney, Rob Parrish, Andy Simmonett
and Daniel G. A. Smith
RKS Reference
6 Threads, 62259 MiB Core
---------------------------------------------------------
==> Geometry <==
Molecular