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@atgctg
atgctg / compound.json
Last active September 14, 2022 06:06
Example PubChem Compound
{
"commonchem": { "version": 10 },
"defaults": {
"atom": {
"z": 6,
"impHs": 0,
"chg": 0,
"nRad": 0,
"isotope": 0,
"stereo": "unspecified"
@atgctg
atgctg / openbioml_datasets.md
Last active September 12, 2022 05:49
Sample run of process_data.py
  • Took around an hour on an M1 Mac
  • Memory use ~13GB at the end

Compound_000000001_000500000.jsonl

{"commonchem": {"version": 10}, "defaults": {"atom": {"z": 6, "impHs": 0, "chg": 0, "nRad": 0, "isotope": 0, "stereo": "unspecified"}, "bond": {"bo": 1, "stereo": "unspecified"}}, "molecules": [{"name": "1", "atoms": [{"z": 8}, {"z": 8, "chg": -1}, {"z": 8}, {"z": 8}, {"z": 7, "chg": 1}, {"impHs": 2}, {"impHs": 1}, {"impHs": 3}, {"impHs": 3}, {"impHs": 3}, {"impHs": 2}, {}, {}, {"impHs": 3}], "bonds": [{"atoms": [0, 6]}, {"atoms": [0, 12]}, {"atoms": [1, 11]}, {"bo": 2, "atoms": [2, 11]}, {"bo": 2, "atoms": [3, 12]}, {"atoms": [4, 5]}, {"atoms": [4, 7]}, {"atoms": [4, 8]}, {"atoms": [4, 9]}, {"atoms": [5, 6]}, {"atoms": [6, 10]}, {"atoms": [10, 11]}, {"atoms": [12, 13]}], "conformers": [{"dim": 2, "coords": [[2.866, 0.75], [2.866, -2.25], [2.0, -0.75], [3.732, 2.25], [5.4641, 0.25], [4.5981, 0.75], [3.732, 0.25], [6.3301, -0.25], [5.9641, 1.116], [4.9641, -0.616], [3.732, -0.75], [2.866, -1.25]