kntkb / rna-bgsu Goto Github PK

Corresponding notebook:
qca-dataset-submission_TEST/generate-dataset.ipynb

Issue:
I get the following error when I try to create a dataset for QCArchive submission using small portion of my structure (pdb/sdf) data. I'm able to successfully create a dataset for some part of my data, for example sample/AAA/*.pdb, but fails for others.

Deduplication : 62%|██████▉ | 30/48 [00:00<00:00, 31.90it/s]
---------------------------------------------------------------------------
AssertionError Traceback (most recent call last)
Input In [101], in <cell line: 1>()
----> 1 dataset = factory.create_dataset(dataset_name="RNA Single Point Dataset v1.0",
2 molecules=mols,
3 tagline="QM dataset for ML",
4 description="Data source: https://github.com/kntkb/rna_bgsu")

File ~/mambaforge/envs/qcarchive-user-submit/lib/python3.10/site-packages/openff/qcsubmit/factories.py:438, in >BaseDatasetFactory.create_dataset(self, dataset_name, molecules, description, tagline, metadata, processors, toolkit_registry, >verbose)
435 toolkit_registry = GLOBAL_TOOLKIT_REGISTRY
437 # create an initial component result
--> 438 workflow_molecules = self._create_initial_component_result(
439 molecules=molecules, toolkit_registry=toolkit_registry
440 )
442 # create the dataset
443 # first we need to instance the dataset and assign the metadata
444 object_meta = self.dict(exclude={"workflow", "type"})

File ~/mambaforge/envs/qcarchive-user-submit/lib/python3.10/site-packages/openff/qcsubmit/factories.py:374, in >BaseDatasetFactory._create_initial_component_result(self, molecules, toolkit_registry)
364 workflow_molecules = ComponentResult(
365 component_name=self.type,
366 component_description={"type": self.type},
(...)
370 ],
371 )
373 else:
--> 374 workflow_molecules = ComponentResult(
375 component_name=self.type,
376 component_description={"type": self.type},
377 component_provenance=self.provenance(toolkit_registry=toolkit_registry),
378 molecules=molecules,
379 )
381 return workflow_molecules

File ~/mambaforge/envs/qcarchive-user-submit/lib/python3.10/site->packages/openff/qcsubmit/workflow_components/utils.py:631, in ComponentResult.init(self, component_name, >component_description, component_provenance, molecules, input_file, input_directory, skip_unique_check, verbose)
623 if molecules is not None:
624 for molecule in tqdm.tqdm(
625 molecules,
626 total=len(molecules),
(...)
629 disable=not verbose,
630 ):
--> 631 self.add_molecule(molecule)

File ~/mambaforge/envs/qcarchive-user-submit/lib/python3.10/site->packages/openff/qcsubmit/workflow_components/utils.py:727, in ComponentResult.add_molecule(self, molecule)
717 if not self.skip_unique_check and molecule_hash in self._molecules:
718 # we need to align the molecules and transfer the coords and properties
719 # get the mapping, drop some comparisons to match inchikey
720 isomorphic, mapping = off.Molecule.are_isomorphic(
721 molecule,
722 self._molecules[molecule_hash],
(...)
725 bond_order_matching=False,
726 )
--> 727 assert isomorphic is True
728 # transfer any torsion indexes for similar fragments
729 if "dihedrals" in molecule.properties:
730 # we need to transfer the properties; get the current molecule dihedrals indexer
731 # if one is missing create a new one

AssertionError:

Create additional datasets:

• experimental structures (BGSU).
• OptimizationDataset with ConformationGenerator