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Release sage 2.0.0 #418

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merged 11 commits into from
Dec 18, 2024
Merged

Release sage 2.0.0 #418

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9263334
Initial files
jaclark5 Dec 12, 2024
b7bdc14
Generate dataset descriptive files
jaclark5 Dec 13, 2024
e1bfb89
Update method to use requests to pull relevant file from github
jaclark5 Dec 13, 2024
ba25628
Update files after running with RDKit
jaclark5 Dec 13, 2024
b74805b
Update README table
jaclark5 Dec 13, 2024
8b2dfb0
Add openeye installation to instructions
jaclark5 Dec 16, 2024
09f9af4
Address dataset formatting feedback
jaclark5 Dec 16, 2024
9e646d0
Use OpenEyeToolkit
jaclark5 Dec 17, 2024
346194f
Run black, clean up generate-combined-dataset file
jaclark5 Dec 17, 2024
2b3de02
Added forcefield table
jaclark5 Dec 18, 2024
39351b7
Update repo README table
jaclark5 Dec 18, 2024
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4 changes: 2 additions & 2 deletions submissions/2024-12-12-OpenFF-Sage-2.0.0-Training-Optimization-Dataset-v1.0/dataset.json.bz2
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15 changes: 8 additions & 7 deletions ...4-12-12-OpenFF-Sage-2.0.0-Training-Optimization-Dataset-v1.0/generate-combined-dataset.py
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Original file line number Diff line number Diff line change
@@ -1,18 +1,19 @@

import numpy as np
import requests
import logging
logging.getLogger("openff").setLevel(logging.ERROR)

from openff.qcsubmit.results import OptimizationResultCollection
from openff.qcsubmit.datasets import OptimizationDataset
from openff.qcsubmit.factories import OptimizationDatasetFactory
from openff.qcsubmit.common_structures import MoleculeAttributes
import numpy as np

from openff.toolkit.utils import OpenEyeToolkitWrapper, ToolkitRegistry
from openff.units import unit
import logging
logging.getLogger("openff").setLevel(logging.ERROR)

filtered_and_combined = OptimizationResultCollection.parse_file(
"/Users/jennifer.clark/bin/openff-sage/data-set-curation/quantum-chemical/data-sets/1-2-0-opt-set-v3.json",
# "/Users/jennifer.clark/bin/openff-sage/data-set-curation/quantum-chemical/data-sets/1-2-0-td-set.json",
)
file = requests.get("https://raw.githubusercontent.com/openforcefield/openff-sage/refs/heads/main/data-set-curation/quantum-chemical/data-sets/1-2-0-opt-set-v3.json")
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If you want to super, super pedantic, you can use the GitHub permalink: https://raw.githubusercontent.com/openforcefield/openff-sage/37a36e7eeaf6cdca795847089a288bdff168c08a/data-set-curation/quantum-chemical/data-sets/1-2-0-opt-set-v3.json. It's kinda annoying to get this (click the ... in the upper right, copy permalink, then click raw for the raw file at the permalink), but it should always point to this exact file version instead of whatever main happens to be. This is especially unlikely to matter here because this repo is basically an archive anyway, though.

filtered_and_combined = OptimizationResultCollection.parse_raw(file.content)
rec_and_mol = filtered_and_combined.to_records()

print('Number of results: ',filtered_and_combined.n_results,flush=True)
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