<jupyter_start><jupyter_text>Used [`openff-benchmark`82 ](https://github.com/openforcefield/openff-benchmark/pull/82) for the following, git commit `3c8e123cdfb28870e98a2df95a1a464bcb9f468e`<jupyter_code>!openff-benchmark optimize export --help
!openff-benchmark optimize export -p 12 -u 'https://api.qcarchive.molssi.org:443' -d 'OpenFF Industry Benchmark Season 1 v1.1' -o data/results-qm<jupyter_output>... 'JNS-00396-2' : exported COMPLETE
... 'JNS-00396-3' : exported COMPLETE
... 'JNS-00396-1' : exported COMPLETE
... 'JNS-00211-9' : exported COMPLETE
... 'JNS-00396-6' : exported COMPLETE
... 'JNS-01574-0' : exported COMPLETE
... 'JNS-00396-5' : exported COMPLETE
... 'JNS-00396-4' : exported COMPLETE
... 'JNS-01574-6' : exported COMPLETE
... 'JNS-01574-5' : exported COMPLETE
... 'JNS-01574-1' : exported COMPLETE
... 'JNS-01574-3' : exported COMPLETE
... 'JNS-01574-8' : exported COMPLETE
... 'JNS-01574-4' : exported COMPLETE
... 'JNS-01574-7' : exported COMPLETE
... 'JNS-00296-0' : exported COMPLETE
... 'JNS-00296-1' : exported COMPLETE
... 'JNS-00296-3' : exported COMPLETE
... 'JNS-00956-1' : exported COMPLETE
... 'JNS-01574-2' : exported COMPLETE
... 'JNS-00296-6' : exported COMPLETE
... 'JNS-00956-0' : exported COMPLETE
... 'JNS-00296-7' : exported COMPLETE
... 'JNS-00296-5' : exported COMPLETE
... 'JNS-00956-3' : exported COMPLETE
... 'JNS-00956-2' : exported COMPLETE
... 'JNS-009[...]<jupyter_text>Create submittable MM dataset from endpoints of QM dataset<jupyter_code>!openff-benchmark optimize create-submittable -o "dataset-mm.json.bz2" --dataset-name "OpenFF Industry Benchmark Season 1 - MM v1.1" --season "1:2" data/results-qm/default/<jupyter_output>[13:38:53] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:38:53] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:38:53] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:38:53] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:38:54] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:38:54] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:38:54] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:38:54] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:38:54] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:38:54] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:38:54] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:39:02] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:39:02] Warning: molecule is tagged as 3D, but all Z coords are zero
[13:39:02] Warning: molecule is tagged as 3D, but all Z coords a[...]<jupyter_text>Stats on dataset<jupyter_code>import json
from openff.qcsubmit.datasets import OptimizationDataset
from openff.qcsubmit.serializers import deserialize
ds = deserialize('dataset-mm.json.bz2')
optds = OptimizationDataset.parse_obj(ds)
full_dataset = optds
from rdkit.Chem import Descriptors
import numpy as np
confs = np.array([len(mol.conformers) for mol in full_dataset.molecules])
elements = set()
for entry in full_dataset.dataset.values():
    elements.update(entry.initial_molecules[0].symbols)

print("Unique list of elements          ", elements)
print("Number of unique molecules       ", full_dataset.n_molecules)
print("Number of optimizations         ", full_dataset.n_records)
print("Number of conformers min mean max",
      confs.min(), "{:6.2f}".format(confs.mean()), confs.max())

masses = []
for molecule in full_dataset.molecules:
    rd_mol = molecule.to_rdkit()
    mass = Descriptors.ExactMolWt(rd_mol)
    masses.append(mass)

print(f'Mean molecular weight: {np.mean(np.array(masses)):.2f}')
print(f'Max molecular weight: {np.max(np.array(masses)):.2f}')
print("Charges:", sorted(set(m.total_charge/m.total_charge.unit for m in full_dataset.molecules)))

{key: value.dict() for key, value in optds.qc_specifications.items()}
optds.scf_properties
optds.molecules_to_file("dataset.smi", "smi")<jupyter_output><empty_output><jupyter_text>Metadata edits<jupyter_code>import openforcefield
import openff.benchmark
import rdkit
openff.benchmark.__version__
optds.metadata.dataset_name = optds.dataset_name
optds.metadata.dataset_name
# change the metadata
full_dataset.metadata.submitter = "dotsdl"
full_dataset.metadata.long_description_url = ("https://github.com/openforcefield/qca-dataset-submission/tree/master/"
                                                "submissions/"
                                                "2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1")
full_dataset.metadata.elements = elements
full_dataset.provenance = {"openff-qcsubmit": openff.qcsubmit.__version__,
                            "openff-toolkit": openforcefield.__version__,
                            "rdkit": rdkit.__version__,
                            "openff-benchmark": "2021.04.09.0+27.ga4304fe.dirty"}

full_dataset.metadata.long_description = 'MM combination of all publicly chosen compound sets by industry partners from the OpenFF season 1 industry benchmark.'
full_dataset.metadata.short_description = "The public molecules from the OpenFF Industry Benchmark, MM optimizations following QM."
optds.metadata.dict()
optds.export_dataset("dataset.json.bz2")<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.12803158488437677, 'fraction_numerical': 0.06241774769693551, 'mean_word_length': 4.0283553875236295, 'pattern_counts': {'":': 4, '<': 15, '<?xml version=': 0, '>': 15, 'https://': 3, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 1, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '4', 'dir': 'jupyter-structured-clean-dedup', 'id': '572178', 'license': 'BSD-3-Clause', 'n_tokens_mistral': 2063, 'n_tokens_neox': 1808, 'n_words': 469, 'path': 'submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/Industry Dataset - MM.ipynb', 'repo_name': 'openforcefield/qca-dataset-submission', 'size': '5319'}