From f09177f22fb769f6816581240421134ca682d470 Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Mon, 25 May 2026 10:32:07 -0700 Subject: [PATCH 1/8] Try removing nomkl from all envs --- devtools/conda-envs/conda.yaml | 2 -- devtools/conda-envs/openeye-examples.yaml | 2 -- devtools/conda-envs/rdkit-examples.yaml | 2 -- devtools/conda-envs/test_env.yaml | 2 -- 4 files changed, 8 deletions(-) diff --git a/devtools/conda-envs/conda.yaml b/devtools/conda-envs/conda.yaml index c80600afa..70275378a 100644 --- a/devtools/conda-envs/conda.yaml +++ b/devtools/conda-envs/conda.yaml @@ -12,5 +12,3 @@ dependencies: - numpy <2.3 # https://github.com/openforcefield/openff-toolkit/issues/2150 - xmltodict <=1.0.2 - # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821 - - nomkl diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml index d43f0f69e..8f015aa1d 100644 --- a/devtools/conda-envs/openeye-examples.yaml +++ b/devtools/conda-envs/openeye-examples.yaml @@ -19,8 +19,6 @@ dependencies: - openff-units - openff-utilities >=0.1.5 - openff-interchange-base >=0.5 - # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821 - - nomkl - openff-nagl-base >=0.4.0 - openff-nagl-models >=0.3.0 - typing_extensions diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml index dbb60133e..6ac9bf115 100644 --- a/devtools/conda-envs/rdkit-examples.yaml +++ b/devtools/conda-envs/rdkit-examples.yaml @@ -18,8 +18,6 @@ dependencies: - openff-units - openff-utilities >=0.1.5 - openff-interchange-base >=0.5 - # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821 - - nomkl - openff-nagl-base >=0.4.0 - openff-nagl-models >=0.3.0 - typing_extensions diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index 65da06d64..29c16d47b 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -46,5 +46,3 @@ dependencies: - nglview - mdtraj - nbval - # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821 - - nomkl From df399ba94916e0d35ed6962238a04e0c21ff0a82 Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Mon, 25 May 2026 10:38:09 -0700 Subject: [PATCH 2/8] disable mypy checks --- .github/workflows/CI.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 98db567a4..f62b50ef8 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -126,14 +126,14 @@ jobs: micromamba list pip list - - name: Run mypy - # When possible re-enable this with OE+RDK=True, but for now rdkit builds often have bugs - # in stubs and there are other subtleties (in the source code and builds) that reduce the number - # of available builds. - # See ex https://github.com/rdkit/rdkit/issues/7221 - # and https://github.com/rdkit/rdkit/issues/7583 - if: ${{ matrix.rdkit == false && matrix.openeye == true }} - run: mypy -p "openff.toolkit" + #- name: Run mypy + # # When possible re-enable this with OE+RDK=True, but for now rdkit builds often have bugs + # # in stubs and there are other subtleties (in the source code and builds) that reduce the number + # # of available builds. + # # See ex https://github.com/rdkit/rdkit/issues/7221 + # # and https://github.com/rdkit/rdkit/issues/7583 + # if: ${{ matrix.rdkit == false && matrix.openeye == true }} + # run: mypy -p "openff.toolkit" - name: Run unit tests run: | From 1d61e001cd23379e4eb01390d0badcf2d61a5797 Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Mon, 25 May 2026 12:04:18 -0700 Subject: [PATCH 3/8] pin qcengine+qcelemental <0.50 --- devtools/conda-envs/openeye-examples.yaml | 4 ++-- devtools/conda-envs/openeye.yaml | 4 ++-- devtools/conda-envs/rdkit-examples.yaml | 4 ++-- devtools/conda-envs/rdkit.yaml | 4 ++-- devtools/conda-envs/test_env.yaml | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml index 8f015aa1d..74d43b3ab 100644 --- a/devtools/conda-envs/openeye-examples.yaml +++ b/devtools/conda-envs/openeye-examples.yaml @@ -33,9 +33,9 @@ dependencies: - toml - bson - msgpack-python - - qcelemental + - qcelemental <0.50 - qcportal >=0.50 - - qcengine + - qcengine <0.50 - mdtraj - nbval - pdbfixer diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml index 61f75e468..39806acf5 100644 --- a/devtools/conda-envs/openeye.yaml +++ b/devtools/conda-envs/openeye.yaml @@ -34,9 +34,9 @@ dependencies: - bson - msgpack-python - pydantic - - qcelemental + - qcelemental <0.50 - qcportal >=0.50 - - qcengine + - qcengine <0.50 - mdtraj - nglview - mypy =1.18 diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml index 6ac9bf115..a5439202c 100644 --- a/devtools/conda-envs/rdkit-examples.yaml +++ b/devtools/conda-envs/rdkit-examples.yaml @@ -34,9 +34,9 @@ dependencies: - toml - bson - msgpack-python - - qcelemental + - qcelemental <0.50 - qcportal >=0.50 - - qcengine + - qcengine <0.50 - nbval - mdtraj - pdbfixer diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml index 6f1d980ce..f52fe5a61 100644 --- a/devtools/conda-envs/rdkit.yaml +++ b/devtools/conda-envs/rdkit.yaml @@ -35,7 +35,7 @@ dependencies: - bson - msgpack-python - pydantic - - qcelemental + - qcelemental <0.50 - qcportal >=0.50 - - qcengine + - qcengine <0.50 - nglview diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index 29c16d47b..7e5688af6 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -40,9 +40,9 @@ dependencies: - bson - msgpack-python - pydantic - - qcelemental + - qcelemental <0.50 - qcportal >=0.50 - - qcengine + - qcengine <0.50 - nglview - mdtraj - nbval From 6da0e076814a58f9b5693288e31177fd261f7b46 Mon Sep 17 00:00:00 2001 From: Jeffrey Wagner Date: Mon, 25 May 2026 12:56:29 -0700 Subject: [PATCH 4/8] update QCA example for new qcschema version interpretation, unpin qcengine and qcelemental --- devtools/conda-envs/openeye-examples.yaml | 4 +- devtools/conda-envs/openeye.yaml | 4 +- devtools/conda-envs/rdkit-examples.yaml | 4 +- devtools/conda-envs/rdkit.yaml | 4 +- devtools/conda-envs/test_env.yaml | 4 +- .../QCarchive_interface.ipynb | 495 ++++++++++++------ 6 files changed, 336 insertions(+), 179 deletions(-) diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml index 74d43b3ab..8f015aa1d 100644 --- a/devtools/conda-envs/openeye-examples.yaml +++ b/devtools/conda-envs/openeye-examples.yaml @@ -33,9 +33,9 @@ dependencies: - toml - bson - msgpack-python - - qcelemental <0.50 + - qcelemental - qcportal >=0.50 - - qcengine <0.50 + - qcengine - mdtraj - nbval - pdbfixer diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml index 39806acf5..61f75e468 100644 --- a/devtools/conda-envs/openeye.yaml +++ b/devtools/conda-envs/openeye.yaml @@ -34,9 +34,9 @@ dependencies: - bson - msgpack-python - pydantic - - qcelemental <0.50 + - qcelemental - qcportal >=0.50 - - qcengine <0.50 + - qcengine - mdtraj - nglview - mypy =1.18 diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml index a5439202c..6ac9bf115 100644 --- a/devtools/conda-envs/rdkit-examples.yaml +++ b/devtools/conda-envs/rdkit-examples.yaml @@ -34,9 +34,9 @@ dependencies: - toml - bson - msgpack-python - - qcelemental <0.50 + - qcelemental - qcportal >=0.50 - - qcengine <0.50 + - qcengine - nbval - mdtraj - pdbfixer diff --git a/devtools/conda-envs/rdkit.yaml b/devtools/conda-envs/rdkit.yaml index f52fe5a61..6f1d980ce 100644 --- a/devtools/conda-envs/rdkit.yaml +++ b/devtools/conda-envs/rdkit.yaml @@ -35,7 +35,7 @@ dependencies: - bson - msgpack-python - pydantic - - qcelemental <0.50 + - qcelemental - qcportal >=0.50 - - qcengine <0.50 + - qcengine - nglview diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index 7e5688af6..29c16d47b 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -40,9 +40,9 @@ dependencies: - bson - msgpack-python - pydantic - - qcelemental <0.50 + - qcelemental - qcportal >=0.50 - - qcengine <0.50 + - qcengine - nglview - mdtraj - nbval diff --git a/examples/QCArchive_interface/QCarchive_interface.ipynb b/examples/QCArchive_interface/QCarchive_interface.ipynb index cb4915b0c..28b61dee1 100644 --- a/examples/QCArchive_interface/QCarchive_interface.ipynb +++ b/examples/QCArchive_interface/QCarchive_interface.ipynb @@ -14,165 +14,244 @@ { "cell_type": "code", "execution_count": 1, - "metadata": {}, + "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:15.496419Z", + "iopub.status.busy": "2026-05-25T19:46:15.496314Z", + "iopub.status.idle": "2026-05-25T19:46:21.504039Z", + "shell.execute_reply": "2026-05-25T19:46:21.503399Z", + "shell.execute_reply.started": "2026-05-25T19:46:15.496407Z" + }, + "scrolled": true + }, "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "678eea5ba7b04d1892b4a5e800deea61", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [] + }, + "metadata": {}, + "output_type": "display_data" + }, { "name": "stdout", "output_type": "stream", "text": [ - " id type name\n", - "---- ---------------- ----------------------------------------------------------------------------------\n", - " 35 torsiondrive OpenFF Fragmenter Phenyl Benchmark\n", - " 36 torsiondrive OpenFF Group1 Torsions\n", - " 41 optimization OpenFF Optimization Set 1\n", - " 42 torsiondrive Fragment Stability Benchmark\n", - " 43 optimization SMIRNOFF Coverage Set 1\n", - " 45 optimization OpenFF VEHICLe Set 1\n", - " 48 torsiondrive SMIRNOFF Coverage Torsion Set 1\n", - " 49 optimization OpenFF NCI250K Boron 1\n", - " 50 optimization OpenFF Discrepancy Benchmark 1\n", - " 57 torsiondrive OpenFF Substituted Phenyl Set 1\n", - " 68 optimization Pfizer Discrepancy Optimization Dataset 1\n", - " 69 optimization FDA Optimization Dataset 1\n", - " 70 torsiondrive Pfizer Discrepancy Torsion Dataset 1\n", - " 71 gridoptimization OpenFF Trivalent Nitrogen Set 1 (deprecated)\n", - " 148 reaction AlkIsod14\n", - " 149 reaction BHPERI26\n", - " 151 singlepoint OpenFF Optimization Set 1\n", - " 152 singlepoint OpenFF VEHICLe Set 1\n", - " 153 singlepoint OpenFF NCI250K Boron 1\n", - " 156 reaction CYCONF\n", - " 157 manybody DS14\n", - " 158 manybody FmH2O10\n", - " 159 singlepoint OpenFF Discrepancy Benchmark 1\n", - " 160 manybody NC15\n", - " 161 reaction Butanediol65\n", - " 162 manybody HB15\n", - " 163 reaction ACONF\n", - " 164 reaction HNBrBDE18\n", - " 165 reaction MPCONF196\n", - " 167 reaction AlkIsomer11\n", - " 168 manybody A21\n", - " 169 manybody A24\n", - " 170 reaction BSR36\n", - " 171 reaction BH76RC\n", - " 172 manybody AlkBind12\n", - " 173 reaction C20C24\n", - " 174 singlepoint SMIRNOFF Coverage Set 1\n", - " 194 torsiondrive OpenFF Primary TorsionDrive Benchmark 1\n", - " 195 torsiondrive OpenFF Full TorsionDrive Benchmark 1\n", - " 196 optimization OpenFF Primary Optimization Benchmark 1\n", - " 197 optimization OpenFF Full Optimization Benchmark 1\n", - " 213 singlepoint Solvated Protein Fragments\n", - " 217 torsiondrive TorsionDrive Paper\n", - " 231 gridoptimization OpenFF Trivalent Nitrogen Set 1\n", - " 232 optimization Kinase Inhibitors: WBO Distributions\n", - " 235 torsiondrive OpenFF Primary Benchmark 1 Torsion Set\n", - " 237 gridoptimization OpenFF Trivalent Nitrogen Set 2\n", - " 239 gridoptimization OpenFF Trivalent Nitrogen Set 3\n", - " 241 torsiondrive OpenFF Primary Benchmark 2 Torsion Set\n", - " 242 torsiondrive OpenFF Group1 Torsions 2\n", - " 243 torsiondrive OpenFF Group1 Torsions 3\n", - " 245 torsiondrive OpenFF Gen 2 Torsion Set 1 Roche\n", - " 246 torsiondrive OpenFF Gen 2 Torsion Set 2 Coverage\n", - " 247 torsiondrive OpenFF Gen 2 Torsion Set 3 Pfizer Discrepancy\n", - " 248 torsiondrive OpenFF Gen 2 Torsion Set 4 eMolecules Discrepancy\n", - " 249 torsiondrive OpenFF Gen 2 Torsion Set 5 Bayer\n", - " 250 torsiondrive OpenFF Gen 2 Torsion Set 6 Supplemental\n", - " 251 optimization OpenFF Gen 2 Opt Set 1 Roche\n", - " 253 optimization OpenFF Gen 2 Opt Set 2 Coverage\n", - " 254 optimization OpenFF Gen 2 Opt Set 4 eMolecules Discrepancy\n", - " 255 optimization OpenFF Gen 2 Opt Set 3 Pfizer Discrepancy\n", - " 256 torsiondrive OpenFF Gen 2 Torsion Set 1 Roche 2\n", - " 257 torsiondrive OpenFF Gen 2 Torsion Set 2 Coverage 2\n", - " 258 torsiondrive OpenFF Gen 2 Torsion Set 3 Pfizer Discrepancy 2\n", - " 259 torsiondrive OpenFF Gen 2 Torsion Set 4 eMolecules Discrepancy 2\n", - " 260 singlepoint OpenFF Gen 2 Opt Set 1 Roche\n", - " 262 singlepoint OpenFF Gen 2 Opt Set 2 Coverage\n", - " 263 singlepoint OpenFF Gen 2 Opt Set 3 Pfizer Discrepancy\n", - " 264 singlepoint OpenFF Gen 2 Opt Set 4 eMolecules Discrepancy\n", - " 265 torsiondrive OpenFF Gen 2 Torsion Set 5 Bayer 2\n", - " 266 torsiondrive OpenFF Gen 2 Torsion Set 6 Supplemental 2\n", - " 268 torsiondrive SiliconTX Torsion Benchmark Set 1\n", - " 270 optimization OpenFF Gen 2 Opt Set 5 Bayer\n", - " 272 singlepoint OpenFF Gen 2 Opt Set 5 Bayer\n", - " 275 torsiondrive Fragmenter paper\n", - " 278 torsiondrive OpenFF Fragmenter Validation 1.0\n", - " 279 optimization OpenFF Ehrman Informative Optimization v0.1\n", - " 281 optimization OpenFF Ehrman Informative Optimization v0.2\n", - " 282 torsiondrive OpenFF DANCE 1 eMolecules t142 v1.0\n", - " 283 torsiondrive OpenFF Rowley Biaryl v1.0\n", - " 284 optimization OpenFF Protein Fragments v1.0\n", - " 285 torsiondrive OpenFF Theory Benchmarking Set B3LYP-D3BJ DZVP v1.0\n", - " 286 torsiondrive OpenFF Theory Benchmarking Set B3LYP-D3BJ def2-TZVP v1.0\n", - " 287 torsiondrive OpenFF Theory Benchmarking Set B3LYP-D3BJ def2-TZVPD v1.0\n", - " 288 torsiondrive OpenFF Theory Benchmarking Set B3LYP-D3BJ def2-TZVPP v1.0\n", - " 289 torsiondrive OpenFF-benchmark-ligand-fragments-v1.0\n", - " 290 optimization OpenFF Protein Fragments v2.0\n", - " 291 torsiondrive OpenFF Protein Fragments TorsionDrives v1.0\n", - " 296 optimization OpenFF Sandbox CHO PhAlkEthOH v1.0\n", - " 297 optimization OpenFF Protein Peptide Fragments constrained v1.0\n", - " 298 optimization OpenFF Protein Peptide Fragments unconstrained v1.0\n", - " 299 torsiondrive OpenFF Theory Benchmarking Set B3LYP-D3BJ 6-31+Gss\n", - " 300 torsiondrive OpenFF Theory Benchmarking Set B3LYP-D3BJ def2-TZVPPD\n", - " 301 optimization OpenFF PEPCONF OptimizationDataset v1.0\n", - " 302 torsiondrive OpenFF Substituted Phenyl Set 1 v2.0\n", - " 303 singlepoint OpenFF BCC Refit Study COH v1.0\n", - " 304 optimization OpenFF Roche Opt Set With Protomers and Tautomers v1.0\n", - " 305 optimization Genentech PDB Ligand Expo whole optimization neutral v1.0\n", - " 307 optimization OpenFF Roche Opt Set With Protomers and Tautomers v1.1\n", - " 308 torsiondrive OpenFF WBO Conjugated Series v1.0\n", - " 309 torsiondrive OpenFF Theory Benchmarking Set v1.0\n", - " 310 optimization OpenFF Theory Benchmarking Constrained Optimization Set B3LYP-NL def2-TZVPD v1.0\n", - " 311 optimization OpenFF Theory Benchmarking Constrained Optimization Set MP2 heavy-aug-cc-pVTZ v1.0\n", - " 312 optimization OpenFF Theory Benchmarking Constrained Optimization Set WB97X-V def2-TZVPD v1.0\n", - " 313 optimization Genentech PDB Ligand Expo fragment optimization neutral v1.0\n", - " 314 torsiondrive OpenFF Amide Torsion Set v1.0\n", - " 315 optimization OpenFF Aniline Para Opt v1.0\n", - " 316 optimization OpenFF Industry Benchmark Season 1 v1.0\n", - " 317 torsiondrive OpenFF Gen3 Torsion Set v1.0\n", - " 318 torsiondrive OpenFF Aniline 2D Impropers v1.0\n", - " 319 optimization OpenFF Industry Benchmark Season 1 v1.1\n", - " 320 optimization OpenFF BCC Refit Study COH v2.0\n", - " 321 optimization OpenFF Theory Benchmarking Constrained Optimization Set MP2 heavy-aug-cc-pVTZ v1.1\n", - " 322 optimization OpenFF Industry Benchmark Season 1 - MM v1.1\n", - " 323 singlepoint OpenFF Theory Benchmarking Single Point Energies v1.0\n", - " 324 torsiondrive OpenFF-benchmark-ligand-fragments-v2.0\n", - " 326 optimization OpenFF RESP Polarizability Optimizations v1.0\n", - " 327 optimization OpenFF RESP Polarizability Optimizations v1.1\n", - " 329 singlepoint TorsionNet500 Single Points Dataset v1.0\n", - " 333 torsiondrive OpenFF Protein Dipeptide 2-D TorsionDrive v1.0\n", - " 344 torsiondrive OpenFF Protein Dipeptide 2-D TorsionDrive v1.1\n", - " 345 optimization OpenFF Gen2 Optimization Dataset Protomers v1.0\n", - " 346 torsiondrive OpenFF Protein Dipeptide 2-D TorsionDrive v2.0\n", - " 347 singlepoint OpenFF ESP Fragment Conformers v1.0\n", - " 351 optimization OpenFF ESP Industry Benchmark Set v1.0\n", - " 352 torsiondrive OpenFF Protein Capped 1-mer Sidechains v1.0\n", - " 353 torsiondrive OpenFF Protein Dipeptide 2-D TorsionDrive v2.1\n", - " 357 singlepoint OpenFF ESP Industry Benchmark Set v1.1\n", - " 358 torsiondrive OpenFF Protein Capped 1-mer Sidechains v1.1\n", - " 359 torsiondrive OpenFF Protein Capped 1-mer Sidechains v1.2\n", - " 360 torsiondrive OpenFF Protein Capped 1-mer Sidechains v1.3\n", - " 363 optimization OpenFF multiplicity correction optimization set v1.0\n", - " 364 torsiondrive OpenFF multiplicity correction torsion drive data v1.0\n", - " 365 optimization OpenFF Protein Capped 1-mers 3-mers Optimization Dataset v1.0\n", - " 366 torsiondrive OpenFF Protein Capped 3-mer Backbones v1.0\n", - " 370 torsiondrive OpenFF multiplicity correction torsion drive data v1.1\n", - " 371 singlepoint RNA Single Point Dataset v1.0\n", - " 372 optimization OpenFF Iodine Chemistry Optimization Dataset v1.0\n", - " 373 singlepoint RNA Trinucleotide Single Point Dataset v1.0\n", - " 374 torsiondrive OpenFF Protein Capped 3-mer Omega v1.0\n", - " 375 singlepoint RNA Nucleoside Single Point Dataset v1.0\n", - " 376 optimization OpenFF multi-Br ESP Fragment Conformers v1.0\n", - " 377 singlepoint OpenFF multi-Br ESP Fragment Conformers v1.1\n", - " 378 torsiondrive XtalPi Shared Fragments TorsiondriveDataset v1.0\n", - " 379 optimization XtalPi Shared Fragments OptimizationDataset v1.0\n", - " 380 torsiondrive OpenFF Torsion Coverage Supplement v1.0\n", - " 381 torsiondrive OpenFF RNA Dinucleoside Monophosphate TorsionDrives v1.0\n", - " 382 torsiondrive XtalPi 20-percent Fragments TorsiondriveDataset v1.0\n", - " 383 optimization XtalPi 20-percent Fragments OptimizationDataset v1.0\n", - " 384 torsiondrive OpenFF Torsion Drive Supplement v1.0\n", - " 385 optimization OpenFF Torsion Benchmark Supplement v1.0\n" + " id type record_count name\n", + "---- ---------------- -------------- ---------------------------------------------------------------------------------------\n", + " 35 torsiondrive 454 OpenFF Fragmenter Phenyl Benchmark\n", + " 36 torsiondrive 820 OpenFF Group1 Torsions\n", + " 41 optimization 937 OpenFF Optimization Set 1\n", + " 42 torsiondrive 86 Fragment Stability Benchmark\n", + " 43 optimization 1132 SMIRNOFF Coverage Set 1\n", + " 45 optimization 25500 OpenFF VEHICLe Set 1\n", + " 48 torsiondrive 585 SMIRNOFF Coverage Torsion Set 1\n", + " 49 optimization 189 OpenFF NCI250K Boron 1\n", + " 50 optimization 19714 OpenFF Discrepancy Benchmark 1\n", + " 57 torsiondrive 795 OpenFF Substituted Phenyl Set 1\n", + " 68 optimization 352 Pfizer Discrepancy Optimization Dataset 1\n", + " 69 optimization 6670 FDA Optimization Dataset 1\n", + " 70 torsiondrive 227 Pfizer Discrepancy Torsion Dataset 1\n", + " 71 gridoptimization 311 OpenFF Trivalent Nitrogen Set 1 (deprecated)\n", + " 148 reaction 994 AlkIsod14\n", + " 149 reaction 1846 BHPERI26\n", + " 151 singlepoint 937 OpenFF Optimization Set 1\n", + " 152 singlepoint 48280 OpenFF VEHICLe Set 1\n", + " 153 singlepoint 189 OpenFF NCI250K Boron 1\n", + " 156 reaction 710 CYCONF\n", + " 159 singlepoint 18864 OpenFF Discrepancy Benchmark 1\n", + " 161 reaction 4544 Butanediol65\n", + " 163 reaction 1065 ACONF\n", + " 164 reaction 1278 HNBrBDE18\n", + " 165 reaction 12936 MPCONF196\n", + " 167 reaction 781 AlkIsomer11\n", + " 170 reaction 2556 BSR36\n", + " 171 reaction 2130 BH76RC\n", + " 173 reaction 426 C20C24\n", + " 174 singlepoint 1109 SMIRNOFF Coverage Set 1\n", + " 194 torsiondrive 31 OpenFF Primary TorsionDrive Benchmark 1\n", + " 195 torsiondrive 227 OpenFF Full TorsionDrive Benchmark 1\n", + " 196 optimization 1885 OpenFF Primary Optimization Benchmark 1\n", + " 197 optimization 26736 OpenFF Full Optimization Benchmark 1\n", + " 213 singlepoint 0 Solvated Protein Fragments\n", + " 217 torsiondrive 4 TorsionDrive Paper\n", + " 231 gridoptimization 311 OpenFF Trivalent Nitrogen Set 1\n", + " 232 optimization 6567 Kinase Inhibitors: WBO Distributions\n", + " 235 torsiondrive 259 OpenFF Primary Benchmark 1 Torsion Set\n", + " 237 gridoptimization 311 OpenFF Trivalent Nitrogen Set 2\n", + " 239 gridoptimization 126 OpenFF Trivalent Nitrogen Set 3\n", + " 241 torsiondrive 595 OpenFF Primary Benchmark 2 Torsion Set\n", + " 242 torsiondrive 19 OpenFF Group1 Torsions 2\n", + " 243 torsiondrive 6 OpenFF Group1 Torsions 3\n", + " 245 torsiondrive 65 OpenFF Gen 2 Torsion Set 1 Roche\n", + " 246 torsiondrive 93 OpenFF Gen 2 Torsion Set 2 Coverage\n", + " 247 torsiondrive 38 OpenFF Gen 2 Torsion Set 3 Pfizer Discrepancy\n", + " 248 torsiondrive 106 OpenFF Gen 2 Torsion Set 4 eMolecules Discrepancy\n", + " 249 torsiondrive 100 OpenFF Gen 2 Torsion Set 5 Bayer\n", + " 250 torsiondrive 7 OpenFF Gen 2 Torsion Set 6 Supplemental\n", + " 251 optimization 298 OpenFF Gen 2 Opt Set 1 Roche\n", + " 253 optimization 373 OpenFF Gen 2 Opt Set 2 Coverage\n", + " 254 optimization 2201 OpenFF Gen 2 Opt Set 4 eMolecules Discrepancy\n", + " 255 optimization 197 OpenFF Gen 2 Opt Set 3 Pfizer Discrepancy\n", + " 256 torsiondrive 142 OpenFF Gen 2 Torsion Set 1 Roche 2\n", + " 257 torsiondrive 157 OpenFF Gen 2 Torsion Set 2 Coverage 2\n", + " 258 torsiondrive 82 OpenFF Gen 2 Torsion Set 3 Pfizer Discrepancy 2\n", + " 259 torsiondrive 272 OpenFF Gen 2 Torsion Set 4 eMolecules Discrepancy 2\n", + " 260 singlepoint 298 OpenFF Gen 2 Opt Set 1 Roche\n", + " 262 singlepoint 352 OpenFF Gen 2 Opt Set 2 Coverage\n", + " 263 singlepoint 197 OpenFF Gen 2 Opt Set 3 Pfizer Discrepancy\n", + " 264 singlepoint 2181 OpenFF Gen 2 Opt Set 4 eMolecules Discrepancy\n", + " 265 torsiondrive 219 OpenFF Gen 2 Torsion Set 5 Bayer 2\n", + " 266 torsiondrive 22 OpenFF Gen 2 Torsion Set 6 Supplemental 2\n", + " 268 torsiondrive 1459 SiliconTX Torsion Benchmark Set 1\n", + " 270 optimization 1850 OpenFF Gen 2 Opt Set 5 Bayer\n", + " 272 singlepoint 1772 OpenFF Gen 2 Opt Set 5 Bayer\n", + " 275 torsiondrive 462 Fragmenter paper\n", + " 278 torsiondrive 440 OpenFF Fragmenter Validation 1.0\n", + " 279 optimization 3485 OpenFF Ehrman Informative Optimization v0.1\n", + " 281 optimization 3485 OpenFF Ehrman Informative Optimization v0.2\n", + " 282 torsiondrive 20 OpenFF DANCE 1 eMolecules t142 v1.0\n", + " 283 torsiondrive 87 OpenFF Rowley Biaryl v1.0\n", + " 284 optimization 576 OpenFF Protein Fragments v1.0\n", + " 285 torsiondrive 36 OpenFF Theory Benchmarking Set B3LYP-D3BJ DZVP v1.0\n", + " 286 torsiondrive 36 OpenFF Theory Benchmarking Set B3LYP-D3BJ def2-TZVP v1.0\n", + " 287 torsiondrive 36 OpenFF Theory Benchmarking Set B3LYP-D3BJ def2-TZVPD v1.0\n", + " 288 torsiondrive 36 OpenFF Theory Benchmarking Set B3LYP-D3BJ def2-TZVPP v1.0\n", + " 289 torsiondrive 3848 OpenFF-benchmark-ligand-fragments-v1.0\n", + " 290 optimization 6716 OpenFF Protein Fragments v2.0\n", + " 291 torsiondrive 845 OpenFF Protein Fragments TorsionDrives v1.0\n", + " 296 optimization 85897 OpenFF Sandbox CHO PhAlkEthOH v1.0\n", + " 297 optimization 6716 OpenFF Protein Peptide Fragments constrained v1.0\n", + " 298 optimization 6709 OpenFF Protein Peptide Fragments unconstrained v1.0\n", + " 299 torsiondrive 36 OpenFF Theory Benchmarking Set B3LYP-D3BJ 6-31+Gss\n", + " 300 torsiondrive 36 OpenFF Theory Benchmarking Set B3LYP-D3BJ def2-TZVPPD\n", + " 301 optimization 22680 OpenFF PEPCONF OptimizationDataset v1.0\n", + " 302 torsiondrive 780 OpenFF Substituted Phenyl Set 1 v2.0\n", + " 303 singlepoint 382 OpenFF BCC Refit Study COH v1.0\n", + " 304 optimization 1376 OpenFF Roche Opt Set With Protomers and Tautomers v1.0\n", + " 305 optimization 445 Genentech PDB Ligand Expo whole optimization neutral v1.0\n", + " 307 optimization 1376 OpenFF Roche Opt Set With Protomers and Tautomers v1.1\n", + " 308 torsiondrive 787 OpenFF WBO Conjugated Series v1.0\n", + " 309 torsiondrive 767 OpenFF Theory Benchmarking Set v1.0\n", + " 310 optimization 864 OpenFF Theory Benchmarking Constrained Optimization Set B3LYP-NL def2-TZVPD v1.0\n", + " 311 optimization 864 OpenFF Theory Benchmarking Constrained Optimization Set MP2 heavy-aug-cc-pVTZ v1.0\n", + " 312 optimization 864 OpenFF Theory Benchmarking Constrained Optimization Set WB97X-V def2-TZVPD v1.0\n", + " 313 optimization 2363 Genentech PDB Ligand Expo fragment optimization neutral v1.0\n", + " 314 torsiondrive 260 OpenFF Amide Torsion Set v1.0\n", + " 315 optimization 223 OpenFF Aniline Para Opt v1.0\n", + " 316 optimization 69672 OpenFF Industry Benchmark Season 1 v1.0\n", + " 317 torsiondrive 888 OpenFF Gen3 Torsion Set v1.0\n", + " 318 torsiondrive 24 OpenFF Aniline 2D Impropers v1.0\n", + " 319 optimization 539385 OpenFF Industry Benchmark Season 1 v1.1\n", + " 320 optimization 4650 OpenFF BCC Refit Study COH v2.0\n", + " 321 optimization 1416 OpenFF Theory Benchmarking Constrained Optimization Set MP2 heavy-aug-cc-pVTZ v1.1\n", + " 322 optimization 501585 OpenFF Industry Benchmark Season 1 - MM v1.1\n", + " 323 singlepoint 66552 OpenFF Theory Benchmarking Single Point Energies v1.0\n", + " 324 torsiondrive 8052 OpenFF-benchmark-ligand-fragments-v2.0\n", + " 326 optimization 735 OpenFF RESP Polarizability Optimizations v1.0\n", + " 327 optimization 735 OpenFF RESP Polarizability Optimizations v1.1\n", + " 329 singlepoint 24000 TorsionNet500 Single Points Dataset v1.0\n", + " 333 torsiondrive 5 OpenFF Protein Dipeptide 2-D TorsionDrive v1.0\n", + " 344 torsiondrive 5 OpenFF Protein Dipeptide 2-D TorsionDrive v1.1\n", + " 345 optimization 600 OpenFF Gen2 Optimization Dataset Protomers v1.0\n", + " 346 torsiondrive 26 OpenFF Protein Dipeptide 2-D TorsionDrive v2.0\n", + " 347 singlepoint 65116 OpenFF ESP Fragment Conformers v1.0\n", + " 351 optimization 56054 OpenFF ESP Industry Benchmark Set v1.0\n", + " 352 torsiondrive 46 OpenFF Protein Capped 1-mer Sidechains v1.0\n", + " 353 torsiondrive 26 OpenFF Protein Dipeptide 2-D TorsionDrive v2.1\n", + " 357 singlepoint 39983 OpenFF ESP Industry Benchmark Set v1.1\n", + " 358 torsiondrive 46 OpenFF Protein Capped 1-mer Sidechains v1.1\n", + " 359 torsiondrive 46 OpenFF Protein Capped 1-mer Sidechains v1.2\n", + " 360 torsiondrive 61 OpenFF Protein Capped 1-mer Sidechains v1.3\n", + " 363 optimization 400 OpenFF multiplicity correction optimization set v1.0\n", + " 364 torsiondrive 99 OpenFF multiplicity correction torsion drive data v1.0\n", + " 365 optimization 759 OpenFF Protein Capped 1-mers 3-mers Optimization Dataset v1.0\n", + " 366 torsiondrive 54 OpenFF Protein Capped 3-mer Backbones v1.0\n", + " 370 torsiondrive 131 OpenFF multiplicity correction torsion drive data v1.1\n", + " 371 singlepoint 13467 RNA Single Point Dataset v1.0\n", + " 372 optimization 327 OpenFF Iodine Chemistry Optimization Dataset v1.0\n", + " 373 singlepoint 81670 RNA Trinucleotide Single Point Dataset v1.0\n", + " 374 torsiondrive 26 OpenFF Protein Capped 3-mer Omega v1.0\n", + " 375 singlepoint 19110 RNA Nucleoside Single Point Dataset v1.0\n", + " 376 optimization 677 OpenFF multi-Br ESP Fragment Conformers v1.0\n", + " 377 singlepoint 650 OpenFF multi-Br ESP Fragment Conformers v1.1\n", + " 378 torsiondrive 169 XtalPi Shared Fragments TorsiondriveDataset v1.0\n", + " 379 optimization 2384 XtalPi Shared Fragments OptimizationDataset v1.0\n", + " 380 torsiondrive 43 OpenFF Torsion Coverage Supplement v1.0\n", + " 381 torsiondrive 192 OpenFF RNA Dinucleoside Monophosphate TorsionDrives v1.0\n", + " 382 torsiondrive 8737 XtalPi 20-percent Fragments TorsiondriveDataset v1.0\n", + " 383 optimization 128180 XtalPi 20-percent Fragments OptimizationDataset v1.0\n", + " 384 torsiondrive 18 OpenFF Torsion Drive Supplement v1.0\n", + " 385 optimization 51 OpenFF Torsion Benchmark Supplement v1.0\n", + " 386 torsiondrive 59 OpenFF Torsion Multiplicity Torsion Drive Coverage Supplement v1.0\n", + " 387 optimization 185 OpenFF Torsion Multiplicity Optimization Training Coverage Supplement v1.0\n", + " 388 optimization 451 OpenFF Torsion Multiplicity Optimization Benchmarking Coverage Supplement v1.0\n", + " 389 torsiondrive 318 OpenFF Phosphate Torsion Drives v1.0\n", + " 390 torsiondrive 192 OpenFF Alkane Torsion Drives v1.0\n", + " 391 singlepoint 137932 MLPepper RECAP Optimized Fragments v1.0\n", + " 392 optimization 531 OpenFF Iodine Fragment Opt v1.0\n", + " 393 optimization 899 OpenFF Sulfur Optimization Training Coverage Supplement v1.0\n", + " 394 singlepoint 1009 OpenFF NAGL2 ESP Timing Benchmark v1.0\n", + " 395 singlepoint 6054 OpenFF NAGL2 ESP Timing Benchmark v1.1\n", + " 396 optimization 319 OpenFF Sulfur Optimization Benchmarking Coverage Supplement v1.0\n", + " 397 singlepoint 899 OpenFF Sulfur Hessian Training Coverage Supplement v1.0\n", + " 398 singlepoint 223 OpenFF Aniline Para Hessian v1.0\n", + " 399 optimization 29770 OpenFF Lipid Optimization Training Supplement v1.0\n", + " 400 singlepoint 12262 MLPepper RECAP Optimized Fragments v1.0 Add Iodines\n", + " 401 singlepoint 899 OpenFF Sulfur Hessian Training Coverage Supplement v1.1\n", + " 402 singlepoint 327 OpenFF Iodine Chemistry Hessian Dataset v1.0\n", + " 403 singlepoint 597 OpenFF Gen2 Hessian Dataset Protomers v1.1\n", + " 404 singlepoint 223 OpenFF Aniline Para Hessian v1.1\n", + " 405 optimization 131185 OpenFF NAGL2 Training Optimization Dataset Part 1 v4.0\n", + " 406 optimization 2323 OpenFF NAGL2 Training Optimization Dataset Part 2 v4.0\n", + " 407 optimization 128281 OpenFF NAGL2 Training Optimization Dataset v4.0\n", + " 408 optimization 239 OpenFF Organometallics Exploratory Optimization Dataset v1.0\n", + " 410 optimization 677 SPICE Dipeptides Lowest E Conformer Optimization Dataset v4.0\n", + " 411 optimization 374 SPICE DES370k Monomers Lowest E Conformer Optimization Dataset v4.0\n", + " 412 optimization 8387 OpenFF Lipid Optimization Benchmark Supplement v1.0\n", + " 413 torsiondrive 82 OpenFF Cresset Additional Coverage TorsionDrives v4.0\n", + " 414 optimization 33850 SPICE Dipeptides Partial Relaxation Dataset v4.0\n", + " 415 optimization 393 OpenFF Cresset Additional Coverage Optimizations v4.0\n", + " 416 optimization 1000 OpenFF Protein PDB 4-mers v4.0\n", + " 417 optimization 18700 SPICE DES370k Monomers Partial Relaxation Dataset v4.0\n", + " 419 singlepoint 675204 Curated tmQM-xtb Dataset: T=100K Dataset Restricted to Pd, Zn, Fe, Cu v0.0\n", + " 420 optimization 411 PDB CCD Chemical Space A: Optimization Dataset v0.0\n", + " 421 singlepoint 393 OpenFF Cresset Additional Coverage Hessian v4.0\n", + " 422 optimization 633 TM Benchmark Optimization Dataset Step 1 v0.0\n", + " 423 torsiondrive 48 OpenFF Additional Generated Guanidine Amidine Derivative and O-Linker TorsionDrives 4.0\n", + " 424 torsiondrive 275 OpenFF Additional Generated ChEMBL TorsionDrives 4.0\n", + " 425 singlepoint 297934 OpenFF Optimization Hessians 2019-07 to 2025-03 v4.0\n", + " 426 optimization 2430 OpenFF Additional Generated ChEMBL Optimizations v4.0\n", + " 437 singlepoint 2938 OpenFF CX3-CX4 singlepoints v4.0\n", + " 445 torsiondrive 1300 OpenFF SMIRNOFF Sage 2.1.0\n", + " 446 optimization 5580 OpenFF SMIRNOFF Sage 2.1.0\n", + " 447 optimization 5126 OpenFF SMIRNOFF Sage 2.2.0\n", + " 448 torsiondrive 1290 OpenFF SMIRNOFF Sage 2.2.0\n", + " 449 torsiondrive 713 OpenFF SMIRNOFF Sage 2.0.0\n", + " 450 optimization 3663 OpenFF SMIRNOFF Sage 2.0.0\n", + " 452 singlepoint 150194 MLPepper RECAP Optimized Fragments v1.1\n", + " 453 optimization 74585 OpenFF Industry Benchmark Season 1 v1.2\n", + " 456 torsiondrive 78 OpenFF Lipid Torsion Drives v4.0\n", + " 462 singlepoint 306993 tmQM xtb Dataset T=100K low-mw high-coordinate mult=1 v0.0\n", + " 463 singlepoint 158905 tmQM xtb Dataset T=100K low-mw high-coordinate mult=5 v0.0\n", + " 464 singlepoint 206240 tmQM xtb Dataset T=100K low-mw high-coordinate mult=3 v0.0\n", + " 465 singlepoint 968 OpenFF TMC Atom Energies v0.0\n", + " 467 optimization 1968 TM Benchmark Optimization Dataset Step 2 v0.0\n", + " 468 singlepoint 68794 tmQM xtb Dataset T=100K low-mw high-coordinate geom-mult=3 v0.0\n", + " 469 singlepoint 102338 tmQM xtb Dataset T=100K low-mw high-coordinate geom-mult=1 v0.0\n", + " 470 torsiondrive 1371 OpenFF SMIRNOFF Sage 2.3.0\n", + " 471 optimization 4696 OpenFF SMIRNOFF Sage 2.3.0\n", + " 472 torsiondrive 500 TorsionNet500 Re-optimization TorsionDrives v4.0\n", + " 473 optimization 5820 OpenFF NSP Optimization Set 1 Phosphorus v4.0\n", + " 474 optimization 6780 OpenFF NSP Optimization Set 1 Nitrogen v4.0\n", + " 475 optimization 7940 OpenFF NSP Optimization Set 1 Sulfur v4.0\n", + " 476 torsiondrive 27 OpenFF Lipid Torsion Drives v4.1\n", + " 477 optimization 80972 OpenFF Organometallic Complexes Architector Minimum Energy Structures v0.0\n", + " 478 optimization 2350 OpenFF SPICE2 Subset Optimization Dataset v4.0\n" ] } ], @@ -196,7 +275,15 @@ { "cell_type": "code", "execution_count": 2, - "metadata": {}, + "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:21.504712Z", + "iopub.status.busy": "2026-05-25T19:46:21.504518Z", + "iopub.status.idle": "2026-05-25T19:46:21.588739Z", + "shell.execute_reply": "2026-05-25T19:46:21.588122Z", + "shell.execute_reply.started": "2026-05-25T19:46:21.504701Z" + } + }, "outputs": [], "source": [ "dataset = client.get_dataset(\n", @@ -215,7 +302,15 @@ { "cell_type": "code", "execution_count": 3, - "metadata": {}, + "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:21.589232Z", + "iopub.status.busy": "2026-05-25T19:46:21.589131Z", + "iopub.status.idle": "2026-05-25T19:46:21.913250Z", + "shell.execute_reply": "2026-05-25T19:46:21.912544Z", + "shell.execute_reply.started": "2026-05-25T19:46:21.589223Z" + } + }, "outputs": [], "source": [ "entry = dataset.get_entry(entry_name=dataset.entry_names[-1])" @@ -231,7 +326,15 @@ { "cell_type": "code", "execution_count": 4, - "metadata": {}, + "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:21.913688Z", + "iopub.status.busy": "2026-05-25T19:46:21.913583Z", + "iopub.status.idle": "2026-05-25T19:46:21.922641Z", + "shell.execute_reply": "2026-05-25T19:46:21.921956Z", + "shell.execute_reply.started": "2026-05-25T19:46:21.913678Z" + } + }, "outputs": [ { "data": { @@ -436,7 +539,8 @@ " 'provenance': {'creator': 'QCElemental',\n", " 'version': 'v0.11.1',\n", " 'routine': 'qcelemental.molparse.from_schema'},\n", - " 'id': 9590661},\n", + " 'id': 9590661,\n", + " 'extras': {}},\n", " 'additional_keywords': {},\n", " 'attributes': {'inchi_key': 'BCFGMOOMADDAQU-UHFFFAOYSA-N',\n", " 'provenance': 'cmiles_v0.1.5+1.gdbd63e8_openeye_2019.Apr.2',\n", @@ -471,7 +575,15 @@ { "cell_type": "code", "execution_count": 5, - "metadata": {}, + "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:21.923099Z", + "iopub.status.busy": "2026-05-25T19:46:21.922993Z", + "iopub.status.idle": "2026-05-25T19:46:22.098581Z", + "shell.execute_reply": "2026-05-25T19:46:22.097808Z", + "shell.execute_reply.started": "2026-05-25T19:46:21.923089Z" + } + }, "outputs": [], "source": [ "# first make a molecule using this record object\n", @@ -489,6 +601,13 @@ "cell_type": "code", "execution_count": 6, "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:22.099156Z", + "iopub.status.busy": "2026-05-25T19:46:22.099023Z", + "iopub.status.idle": "2026-05-25T19:46:22.184984Z", + "shell.execute_reply": "2026-05-25T19:46:22.184376Z", + "shell.execute_reply.started": "2026-05-25T19:46:22.099144Z" + }, "scrolled": true }, "outputs": [ @@ -496,7 +615,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "\n", + "\n", "6 6\n", "6 6\n", "6 6\n", @@ -592,7 +711,15 @@ { "cell_type": "code", "execution_count": 7, - "metadata": {}, + "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:22.185851Z", + "iopub.status.busy": "2026-05-25T19:46:22.185700Z", + "iopub.status.idle": "2026-05-25T19:46:22.200983Z", + "shell.execute_reply": "2026-05-25T19:46:22.200374Z", + "shell.execute_reply.started": "2026-05-25T19:46:22.185837Z" + } + }, "outputs": [ { "name": "stdout", @@ -635,13 +762,21 @@ }, { "cell_type": "code", - "execution_count": 12, - "metadata": {}, + "execution_count": 8, + "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:22.201533Z", + "iopub.status.busy": "2026-05-25T19:46:22.201425Z", + "iopub.status.idle": "2026-05-25T19:46:22.226037Z", + "shell.execute_reply": "2026-05-25T19:46:22.224987Z", + "shell.execute_reply.started": "2026-05-25T19:46:22.201523Z" + } + }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "18df6d74c6bd4b27a5269c69492be157", + "model_id": "e792d4ffed78496f8c91ab5f78effb6e", "version_major": 2, "version_minor": 0 }, @@ -661,12 +796,20 @@ { "cell_type": "code", "execution_count": 9, - "metadata": {}, + "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:22.226744Z", + "iopub.status.busy": "2026-05-25T19:46:22.226631Z", + "iopub.status.idle": "2026-05-25T19:46:22.247736Z", + "shell.execute_reply": "2026-05-25T19:46:22.246655Z", + "shell.execute_reply.started": "2026-05-25T19:46:22.226734Z" + } + }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "bb939d5eb8534e5eaf2cc06edac52e7b", + "model_id": "5d9fa5b8107c433e8d66f75114ea60a0", "version_major": 2, "version_minor": 0 }, @@ -699,7 +842,15 @@ { "cell_type": "code", "execution_count": 10, - "metadata": {}, + "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:22.248423Z", + "iopub.status.busy": "2026-05-25T19:46:22.248192Z", + "iopub.status.idle": "2026-05-25T19:46:22.653973Z", + "shell.execute_reply": "2026-05-25T19:46:22.653067Z", + "shell.execute_reply.started": "2026-05-25T19:46:22.248409Z" + } + }, "outputs": [], "source": [ "import qcengine\n", @@ -707,7 +858,6 @@ "# set up the RDKit task\n", "rdkit_task = {\n", " \"schema_name\": \"qcschema_input\",\n", - " \"schema_version\": 2,\n", " \"molecule\": qc_molecule,\n", " \"driver\": \"energy\",\n", " \"model\": {\"method\": \"uff\", \"basis\": None},\n", @@ -722,6 +872,13 @@ "cell_type": "code", "execution_count": 11, "metadata": { + "execution": { + "iopub.execute_input": "2026-05-25T19:46:22.654680Z", + "iopub.status.busy": "2026-05-25T19:46:22.654534Z", + "iopub.status.idle": "2026-05-25T19:46:22.658193Z", + "shell.execute_reply": "2026-05-25T19:46:22.657207Z", + "shell.execute_reply.started": "2026-05-25T19:46:22.654666Z" + }, "tags": [] }, "outputs": [ @@ -755,7 +912,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.10" + "version": "3.13.13" }, "widgets": { "application/vnd.jupyter.widget-state+json": { From 0a6d09c2e82f3e6162ca466ab02cd2fe0b469ddd Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Mon, 25 May 2026 15:23:02 -0700 Subject: [PATCH 5/8] fix mypy issues by folding in changes from https://github.com/openforcefield/openff-toolkit/pull/2181 --- openff/toolkit/topology/molecule.py | 2 +- pyproject.toml | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/openff/toolkit/topology/molecule.py b/openff/toolkit/topology/molecule.py index 24097677c..8e4ba4e2c 100644 --- a/openff/toolkit/topology/molecule.py +++ b/openff/toolkit/topology/molecule.py @@ -5654,7 +5654,7 @@ def _networkx_graph_to_hill_formula(graph: "nx.Graph[int]") -> str: if not isinstance(graph, nx.Graph): raise ValueError("The graph must be a NetworkX graph.") - atom_nums: list[int] = [atomic_number for (_, atomic_number) in graph.nodes(data="atomic_number", default=1)] + atom_nums: list[int] = [atomic_number for (_, atomic_number) in graph.nodes(data="atomic_number", default=1)] # type: ignore[misc] return _atom_nums_to_hill_formula(atom_nums) # type:ignore[arg-type] diff --git a/pyproject.toml b/pyproject.toml index 5ba267c84..eac6ca15f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,7 +44,6 @@ lint.isort.known-third-party = [ "openff.interchange", "openff.utilities", "open [tool.mypy] python_version = 3.12 -plugins = "numpy.typing.mypy_plugin" warn_unused_configs = true # would be nice to flip back to true warn_unused_ignores = false From d4d9c486d26f688d2d0fcf483580fa7645dd6782 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 25 May 2026 22:23:12 +0000 Subject: [PATCH 6/8] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- openff/toolkit/topology/molecule.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openff/toolkit/topology/molecule.py b/openff/toolkit/topology/molecule.py index 8e4ba4e2c..fee8216df 100644 --- a/openff/toolkit/topology/molecule.py +++ b/openff/toolkit/topology/molecule.py @@ -5654,7 +5654,7 @@ def _networkx_graph_to_hill_formula(graph: "nx.Graph[int]") -> str: if not isinstance(graph, nx.Graph): raise ValueError("The graph must be a NetworkX graph.") - atom_nums: list[int] = [atomic_number for (_, atomic_number) in graph.nodes(data="atomic_number", default=1)] # type: ignore[misc] + atom_nums: list[int] = [atomic_number for (_, atomic_number) in graph.nodes(data="atomic_number", default=1)] # type: ignore[misc] return _atom_nums_to_hill_formula(atom_nums) # type:ignore[arg-type] From e39eaf4cea2ec9c0fbf9b282f0c6fa0a4679ce92 Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Mon, 25 May 2026 15:23:53 -0700 Subject: [PATCH 7/8] Also move mypy to pip install --- devtools/conda-envs/openeye.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml index 61f75e468..0b932829e 100644 --- a/devtools/conda-envs/openeye.yaml +++ b/devtools/conda-envs/openeye.yaml @@ -39,9 +39,9 @@ dependencies: - qcengine - mdtraj - nglview - - mypy =1.18 - typing_extensions - pip: + - mypy ==2 - types-setuptools - types-toml - types-PyYAML From 2073a961b6d0b2017900a7c492e7581bf28ea02b Mon Sep 17 00:00:00 2001 From: Jeff Wagner Date: Fri, 29 May 2026 16:09:15 -0700 Subject: [PATCH 8/8] re enable mypy tests --- .github/workflows/CI.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index f62b50ef8..98db567a4 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -126,14 +126,14 @@ jobs: micromamba list pip list - #- name: Run mypy - # # When possible re-enable this with OE+RDK=True, but for now rdkit builds often have bugs - # # in stubs and there are other subtleties (in the source code and builds) that reduce the number - # # of available builds. - # # See ex https://github.com/rdkit/rdkit/issues/7221 - # # and https://github.com/rdkit/rdkit/issues/7583 - # if: ${{ matrix.rdkit == false && matrix.openeye == true }} - # run: mypy -p "openff.toolkit" + - name: Run mypy + # When possible re-enable this with OE+RDK=True, but for now rdkit builds often have bugs + # in stubs and there are other subtleties (in the source code and builds) that reduce the number + # of available builds. + # See ex https://github.com/rdkit/rdkit/issues/7221 + # and https://github.com/rdkit/rdkit/issues/7583 + if: ${{ matrix.rdkit == false && matrix.openeye == true }} + run: mypy -p "openff.toolkit" - name: Run unit tests run: |