datasets

Genentech · Jul 19, 2024 · 3ac91a3 · 3ac91a3
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diff --git a/docs/reference/beignet.datasets.md b/docs/reference/beignet.datasets.md
@@ -0,0 +1,80 @@
+::: beignet.datasets.ATOM3DDataset
+::: beignet.datasets.ATOM3DMSPDataset
+::: beignet.datasets.ATOM3DPPIDataset
+::: beignet.datasets.ATOM3DPSRDataset
+::: beignet.datasets.ATOM3DRESDataset
+::: beignet.datasets.ATOM3DRSRDataset
+::: beignet.datasets.ATOM3DSMPDataset
+::: beignet.datasets.AqSolDBSolubilityDataset
+::: beignet.datasets.AstraZenecaClearanceDataset
+::: beignet.datasets.AstraZenecaLipophilicityDataset
+::: beignet.datasets.AstraZenecaPlasmaProteinBindingRateDataset
+::: beignet.datasets.BindingDBIC50Dataset
+::: beignet.datasets.BindingDBKdDataset
+::: beignet.datasets.BindingDBKiDataset
+::: beignet.datasets.BroccatelliPGlycoproteinInhibitionDataset
+::: beignet.datasets.CarbonMangelsCytochromeP4502C9SubstrateDataset
+::: beignet.datasets.CarbonMangelsCytochromeP4502D6SubstrateDataset
+::: beignet.datasets.CarbonMangelsCytochromeP4503A4SubstrateDataset
+::: beignet.datasets.ChEMBLDataset
+::: beignet.datasets.ClinToxDataset
+::: beignet.datasets.DAVISDataset
+::: beignet.datasets.DataFrameDataset
+::: beignet.datasets.DisGeNETDataset
+::: beignet.datasets.DrugCombDataset
+::: beignet.datasets.FASTADataset
+::: beignet.datasets.FreeSolvDataset
+::: beignet.datasets.GDSC1Dataset
+::: beignet.datasets.GDSC2Dataset
+::: beignet.datasets.HDF5TrajectoryDataset
+::: beignet.datasets.HouHumanIntestinalAbsorptionDataset
+::: beignet.datasets.HuRIDataset
+::: beignet.datasets.JespersenIEDBDataset
+::: beignet.datasets.JespersenPDBDataset
+::: beignet.datasets.KIBADataset
+::: beignet.datasets.LMDBDataset
+::: beignet.datasets.LombardoVolumeOfDistributionAtSteadyStateDataset
+::: beignet.datasets.MOSESDataset
+::: beignet.datasets.MaBioavailabilityDataset
+::: beignet.datasets.MartinsBloodBrainBarrierDataset
+::: beignet.datasets.NCATSPAMPAPermeabilityDataset
+::: beignet.datasets.ObachHalfLifeDataset
+::: beignet.datasets.PDB70Dataset
+::: beignet.datasets.PDBTrajectoryDataset
+::: beignet.datasets.PDBbindDataset
+::: beignet.datasets.ParquetDataset
+::: beignet.datasets.QM7Dataset
+::: beignet.datasets.QM7bDataset
+::: beignet.datasets.QM8Dataset
+::: beignet.datasets.QM9Dataset
+::: beignet.datasets.REALDatabaseDataset
+::: beignet.datasets.RandomEulerAngleDataset
+::: beignet.datasets.RandomQuaternionDataset
+::: beignet.datasets.RandomRotationDataset
+::: beignet.datasets.RandomRotationMatrixDataset
+::: beignet.datasets.RandomRotationVectorDataset
+::: beignet.datasets.SAbDabDataset
+::: beignet.datasets.SKEMPIDataset
+::: beignet.datasets.SequenceDataset
+::: beignet.datasets.SizedSequenceDataset
+::: beignet.datasets.SwissProtDataset
+::: beignet.datasets.TDCDataset
+::: beignet.datasets.TherapeuticAntibodyProfilerDataset
+::: beignet.datasets.Tox21Dataset
+::: beignet.datasets.ToxCastDataset
+::: beignet.datasets.TrEMBLDataset
+::: beignet.datasets.TrajectoryDataset
+::: beignet.datasets.USPTODataset
+::: beignet.datasets.USPTOReactionProductDataset
+::: beignet.datasets.UniProtDataset
+::: beignet.datasets.UniRef100Dataset
+::: beignet.datasets.UniRef50Dataset
+::: beignet.datasets.UniRef90Dataset
+::: beignet.datasets.VeithCytochromeP4501A2InhibitionDataset
+::: beignet.datasets.VeithCytochromeP4502C19InhibitionDataset
+::: beignet.datasets.VeithCytochromeP4502C9InhibitionDataset
+::: beignet.datasets.VeithCytochromeP4502D6InhibitionDataset
+::: beignet.datasets.VeithCytochromeP4503A4InhibitionDataset
+::: beignet.datasets.WangEffectivePermeabilityDataset
+::: beignet.datasets.ZINCDataset
+::: beignet.datasets.ZhuAcuteToxicityLD50Dataset
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -35,31 +35,7 @@ nav:
               - "Laguerre polynomial": "reference/operators/special-functions/orthogonal-polynomials/laguerre-polynomial.md"
               - "Legendre polynomial": "reference/operators/special-functions/orthogonal-polynomials/legendre-polynomial.md"
       - "Thermodynamics": "reference/operators/thermodynamics.md"
-    - "beignet.datasets":
-        - "General-purpose": "reference/datasets/general-purpose.md"
-        - "Antibody affinity": "reference/datasets/antibody-affinity.md"
-        - "Catalyst": "reference/datasets/catalyst.md"
-        - "Drug interaction": "reference/datasets/drug-interaction.md"
-        - "Drug intolerance": "reference/datasets/drug-intolerance.md"
-        - "Epitope": "reference/datasets/epitope.md"
-        - "Geometry":
-          - "Transformations": "reference/datasets/geometry/transformations.md"
-        - "Gene-disease association": "reference/datasets/gene-disease-association.md"
-        - "Molecule": "reference/datasets/molecule.md"
-        - "Pharmacokinetic property":
-            - "Absorption": "reference/datasets/pharmacokinetic-property/absorption.md"
-            - "Distribution": "reference/datasets/pharmacokinetic-property/distribution.md"
-            - "Excretion": "reference/datasets/pharmacokinetic-property/excretion.md"
-            - "Metabolism": "reference/datasets/pharmacokinetic-property/metabolism.md"
-        - "Protein":
-          - "Protein sequence": "reference/datasets/protein/protein-sequence.md"
-          - "Protein structure": "reference/datasets/protein/protein-structure.md"
-        - "Protein–protein interaction": "reference/datasets/protein-protein-interaction.md"
-        - "Quantum mechanics": "reference/datasets/quantum-mechanics.md"
-        - "Reaction": "reference/datasets/reaction.md"
-        - "Retrosynthesis": "reference/datasets/retrosynthesis.md"
-        - "Toxicity": "reference/datasets/toxicity.md"
-        - "Sequences": "reference/datasets/sequences.md"
+    - "beignet.datasets": "reference/beignet.datasets.md"
     - "beignet.features":
         - "General-purpose": "reference/features/general-purpose.md"
         - "Geometry":

diff --git a/src/beignet/datasets/__init__.py b/src/beignet/datasets/__init__.py
@@ -54,7 +54,6 @@
 from ._ncats_pampa_permeability_dataset import NCATSPAMPAPermeabilityDataset
 from ._obach_half_life_dataset import ObachHalfLifeDataset
 from ._parquet_dataset import ParquetDataset
-from ._pdb_70_dataset import PDB70Dataset
 from ._pdb_trajectory_dataset import PDBTrajectoryDataset
 from ._pdbbind_dataset import PDBbindDataset
 from ._qm7_dataset import QM7Dataset
@@ -145,7 +144,6 @@
     "MartinsBloodBrainBarrierDataset",
     "NCATSPAMPAPermeabilityDataset",
     "ObachHalfLifeDataset",
-    "PDB70Dataset",
     "PDBTrajectoryDataset",
     "PDBbindDataset",
     "ParquetDataset",

diff --git a/src/beignet/datasets/_pdb_70_dataset.py b/src/beignet/datasets/_pdb_70_dataset.py