tdc

Genentech · Jul 15, 2024 · c4a1a48 · c4a1a48
1 parent 00d5fc9
commit c4a1a48
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diff --git a/docs/reference/beignet.io.md b/docs/reference/beignet.io.md
@@ -1,3 +1 @@
-# beignet.io
-
 ::: beignet.io.ThreadSafeFile
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -67,7 +67,7 @@ nav:
             - "Transformations": "reference/features/geometry/transformations.md"
     - "beignet.func":
         - "Molecular dynamics": "reference/func/molecular-dynamics.md"
-    - "beignet.io": "reference/operators.io.md"
+    - "beignet.io": "reference/beignet.io.md"
     - "beignet.transforms":
         - "General-purpose": "reference/transforms/general-purpose.md"
 plugins:

diff --git a/src/beignet/datasets/_astrazeneca_clearance_dataset.py b/src/beignet/datasets/_astrazeneca_clearance_dataset.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Callable
 
-from torch.utils.data import Dataset
-
 from beignet.transforms import Transform
 
+from ._tdc_dataset import TDCDataset
+
 
-class AstraZenecaClearanceDataset(Dataset):
+class AstraZenecaClearanceDataset(TDCDataset):
     def __init__(
         self,
         root: str | Path,
@@ -32,10 +32,14 @@ def __init__(
         target_transform : Callable | Transform | None
             Transforms the target.
         """
-        raise NotImplementedError
-
-    def __getitem__(self, index: int):
-        raise NotImplementedError
-
-    def __len__(self) -> int:
-        raise NotImplementedError
+        super().__init__(
+            root=root,
+            download=download,
+            identifier=0,
+            suffix="",
+            checksum="",
+            x_keys=[""],
+            y_keys=[""],
+            transform=transform,
+            target_transform=target_transform,
+        )
diff --git a/src/beignet/datasets/_astrazeneca_lipophilicity_dataset.py b/src/beignet/datasets/_astrazeneca_lipophilicity_dataset.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Callable
 
-from torch.utils.data import Dataset
-
 from beignet.transforms import Transform
 
+from ._tdc_dataset import TDCDataset
+
 
-class AstraZenecaLipophilicityDataset(Dataset):
+class AstraZenecaLipophilicityDataset(TDCDataset):
     def __init__(
         self,
         root: str | Path,
@@ -32,10 +32,14 @@ def __init__(
         target_transform : Callable | Transform | None
             Transforms the target.
         """
-        raise NotImplementedError
-
-    def __getitem__(self, index: int):
-        raise NotImplementedError
-
-    def __len__(self) -> int:
-        raise NotImplementedError
+        super().__init__(
+            root=root,
+            download=download,
+            identifier=0,
+            suffix="",
+            checksum="",
+            x_keys=[""],
+            y_keys=[""],
+            transform=transform,
+            target_transform=target_transform,
+        )
diff --git a/src/beignet/datasets/_astrazeneca_plasma_protein_binding_rate_dataset.py b/src/beignet/datasets/_astrazeneca_plasma_protein_binding_rate_dataset.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Callable
 
-from torch.utils.data import Dataset
-
 from beignet.transforms import Transform
 
+from ._tdc_dataset import TDCDataset
+
 
-class AstraZenecaPlasmaProteinBindingRateDataset(Dataset):
+class AstraZenecaPlasmaProteinBindingRateDataset(TDCDataset):
     def __init__(
         self,
         root: str | Path,
@@ -32,10 +32,14 @@ def __init__(
         target_transform : Callable | Transform | None
             Transforms the target.
         """
-        raise NotImplementedError
-
-    def __getitem__(self, index: int):
-        raise NotImplementedError
-
-    def __len__(self) -> int:
-        raise NotImplementedError
+        super().__init__(
+            root=root,
+            download=download,
+            identifier=0,
+            suffix="",
+            checksum="",
+            x_keys=[""],
+            y_keys=[""],
+            transform=transform,
+            target_transform=target_transform,
+        )
diff --git a/src/beignet/datasets/_bindingdb_dataset.py b/src/beignet/datasets/_bindingdb_dataset.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Callable
 
-from torch.utils.data import Dataset
-
 from beignet.transforms import Transform
 
+from ._tdc_dataset import TDCDataset
+
 
-class BindingDBDataset(Dataset):
+class BindingDBDataset(TDCDataset):
     def __init__(
         self,
         root: str | Path,
@@ -32,10 +32,14 @@ def __init__(
         target_transform : Callable | Transform | None
             Transforms the target.
         """
-        raise NotImplementedError
-
-    def __getitem__(self, index: int):
-        raise NotImplementedError
-
-    def __len__(self) -> int:
-        raise NotImplementedError
+        super().__init__(
+            root=root,
+            download=download,
+            identifier=0,
+            suffix="",
+            checksum="",
+            x_keys=[""],
+            y_keys=[""],
+            transform=transform,
+            target_transform=target_transform,
+        )
diff --git a/src/beignet/datasets/_broccatelli_p_glycoprotein_inhibition_dataset.py b/src/beignet/datasets/_broccatelli_p_glycoprotein_inhibition_dataset.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Callable
 
-from torch.utils.data import Dataset
-
 from beignet.transforms import Transform
 
+from ._tdc_dataset import TDCDataset
+
 
-class BroccatelliPGlycoproteinInhibitionDataset(Dataset):
+class BroccatelliPGlycoproteinInhibitionDataset(TDCDataset):
     def __init__(
         self,
         root: str | Path,
@@ -32,10 +32,14 @@ def __init__(
         target_transform : Callable | Transform | None
             Transforms the target.
         """
-        raise NotImplementedError
-
-    def __getitem__(self, index: int):
-        raise NotImplementedError
-
-    def __len__(self) -> int:
-        raise NotImplementedError
+        super().__init__(
+            root=root,
+            download=download,
+            identifier=0,
+            suffix="",
+            checksum="",
+            x_keys=[""],
+            y_keys=[""],
+            transform=transform,
+            target_transform=target_transform,
+        )
diff --git a/src/beignet/datasets/_carbon_mangels_cytochrome_p450_2c9_substrate_dataset.py b/src/beignet/datasets/_carbon_mangels_cytochrome_p450_2c9_substrate_dataset.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Callable
 
-from torch.utils.data import Dataset
-
 from beignet.transforms import Transform
 
+from ._tdc_dataset import TDCDataset
+
 
-class CarbonMangelsCytochromeP4502C9SubstrateDataset(Dataset):
+class CarbonMangelsCytochromeP4502C9SubstrateDataset(TDCDataset):
     def __init__(
         self,
         root: str | Path,
@@ -32,10 +32,14 @@ def __init__(
         target_transform : Callable | Transform | None
             Transforms the target.
         """
-        raise NotImplementedError
-
-    def __getitem__(self, index: int):
-        raise NotImplementedError
-
-    def __len__(self) -> int:
-        raise NotImplementedError
+        super().__init__(
+            root=root,
+            download=download,
+            identifier=0,
+            suffix="",
+            checksum="",
+            x_keys=[""],
+            y_keys=[""],
+            transform=transform,
+            target_transform=target_transform,
+        )
diff --git a/src/beignet/datasets/_carbon_mangels_cytochrome_p450_2d6_substrate_dataset.py b/src/beignet/datasets/_carbon_mangels_cytochrome_p450_2d6_substrate_dataset.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Callable
 
-from torch.utils.data import Dataset
-
 from beignet.transforms import Transform
 
+from ._tdc_dataset import TDCDataset
+
 
-class CarbonMangelsCytochromeP4502D6SubstrateDataset(Dataset):
+class CarbonMangelsCytochromeP4502D6SubstrateDataset(TDCDataset):
     def __init__(
         self,
         root: str | Path,
@@ -32,10 +32,14 @@ def __init__(
         target_transform : Callable | Transform | None
             Transforms the target.
         """
-        raise NotImplementedError
-
-    def __getitem__(self, index: int):
-        raise NotImplementedError
-
-    def __len__(self) -> int:
-        raise NotImplementedError
+        super().__init__(
+            root=root,
+            download=download,
+            identifier=0,
+            suffix="",
+            checksum="",
+            x_keys=[""],
+            y_keys=[""],
+            transform=transform,
+            target_transform=target_transform,
+        )
diff --git a/src/beignet/datasets/_carbon_mangels_cytochrome_p450_3a4_substrate_dataset.py b/src/beignet/datasets/_carbon_mangels_cytochrome_p450_3a4_substrate_dataset.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Callable
 
-from torch.utils.data import Dataset
-
 from beignet.transforms import Transform
 
+from ._tdc_dataset import TDCDataset
+
 
-class CarbonMangelsCytochromeP4503A4SubstrateDataset(Dataset):
+class CarbonMangelsCytochromeP4503A4SubstrateDataset(TDCDataset):
     def __init__(
         self,
         root: str | Path,
@@ -32,10 +32,14 @@ def __init__(
         target_transform : Callable | Transform | None
             Transforms the target.
         """
-        raise NotImplementedError
-
-    def __getitem__(self, index: int):
-        raise NotImplementedError
-
-    def __len__(self) -> int:
-        raise NotImplementedError
+        super().__init__(
+            root=root,
+            download=download,
+            identifier=0,
+            suffix="",
+            checksum="",
+            x_keys=[""],
+            y_keys=[""],
+            transform=transform,
+            target_transform=target_transform,
+        )
diff --git a/src/beignet/datasets/_clintox_dataset.py b/src/beignet/datasets/_clintox_dataset.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Callable
 
-from torch.utils.data import Dataset
-
 from beignet.transforms import Transform
 
+from ._tdc_dataset import TDCDataset
+
 
-class ClinToxDataset(Dataset):
+class ClinToxDataset(TDCDataset):
     def __init__(
         self,
         root: str | Path,
@@ -32,10 +32,14 @@ def __init__(
         target_transform : Callable | Transform | None
             Transforms the target.
         """
-        raise NotImplementedError
-
-    def __getitem__(self, index: int):
-        raise NotImplementedError
-
-    def __len__(self) -> int:
-        raise NotImplementedError
+        super().__init__(
+            root=root,
+            download=download,
+            identifier=0,
+            suffix="",
+            checksum="",
+            x_keys=[""],
+            y_keys=[""],
+            transform=transform,
+            target_transform=target_transform,
+        )
diff --git a/src/beignet/datasets/_davis_dataset.py b/src/beignet/datasets/_davis_dataset.py
@@ -1,12 +1,12 @@
 from pathlib import Path
 from typing import Callable
 
-from torch.utils.data import Dataset
-
 from beignet.transforms import Transform
 
+from ._tdc_dataset import TDCDataset
+
 
-class DAVISDataset(Dataset):
+class DAVISDataset(TDCDataset):
     def __init__(
         self,
         root: str | Path,
@@ -32,10 +32,14 @@ def __init__(
         target_transform : Callable | Transform | None
             Transforms the target.
         """
-        raise NotImplementedError
-
-    def __getitem__(self, index: int):
-        raise NotImplementedError
-
-    def __len__(self) -> int:
-        raise NotImplementedError
+        super().__init__(
+            root=root,
+            download=download,
+            identifier=0,
+            suffix="",
+            checksum="",
+            x_keys=[""],
+            y_keys=[""],
+            transform=transform,
+            target_transform=target_transform,
+        )