Fix jaxtyping syntax error (#312)

* add PSW to nonstandard residues

* improve insertion and non-standard residue handling

* refactor chain selection

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* remove unused verbosity arg

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fix chain selection in tests

* fix chain selection in tutorial notebook

* fix notebook chain selection

* fix chain selection typehint

* Update changelog

* Add NLW to non-standard residues

* add .ent support

* add entry for construction from dataframe

* add missing stage arg

* improve obsolete mapping retrieving to include entries with no replacement

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* update changelog

* add transforms to foldcomp datasets

* fix jaxtyping syntax

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Update changelog

* fix double application of transforms

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

CHANGELOG.md

@@ -6,6 +6,7 @@
 
 #### Bugfixes
 * Adds missing `stage` parameter to `graphein.ml.datasets.foldcomp_data.FoldCompDataModule.setup()`. [#310](https://github.com/a-r-j/graphein/pull/310)
+* Fixes incorrect jaxtyping syntax for variable size dimensions [#312](https://github.com/a-r-j/graphein/pull/312)
 
 #### Other Changes
 * Adds entry point for biopandas dataframes in `graphein.protein.tensor.io.protein_to_pyg`. [#310](https://github.com/a-r-j/graphein/pull/310)
@@ -14,7 +15,7 @@
 * Adds the ability to store a dictionary of HETATM positions in `Data`/`Protein` objects created in the `graphein.protein.tensor` module. [#307](https://github.com/a-r-j/graphein/pull/307)
 * Improved handling of non-standard residues in the `graphein.protein.tensor` module. [#307](https://github.com/a-r-j/graphein/pull/307)
 * Insertions retained by default in the `graphein.protein.tensor` module. I.e. `insertions=True` is now the default behaviour.[#307](https://github.com/a-r-j/graphein/pull/307)
-
+* Adds transform composition to FoldComp Dataset [#312](https://github.com/a-r-j/graphein/pull/312)
 
 
 ### 1.7.0 - UNRELEASED

graphein/ml/datasets/foldcomp_dataset.py

@@ -6,17 +6,17 @@
 # Code Repository: https://github.com/a-r-j/graphein
 
 import asyncio
-import contextlib
 import os
 import random
 import shutil
 from pathlib import Path
-from typing import Callable, List, Optional, Union
+from typing import Callable, Dict, Iterable, List, Optional, Union
 
 import pandas as pd
 from biopandas.pdb import PandasPdb
 from loguru import logger as log
 from sklearn.model_selection import train_test_split
+from torch_geometric import transforms as T
 from torch_geometric.data import Data, Dataset
 from torch_geometric.loader import DataLoader
 from tqdm import tqdm
@@ -76,7 +76,7 @@ def __init__(
         exclude_ids: Optional[List[str]] = None,
         fraction: float = 1.0,
         use_graphein: bool = True,
-        transform: Optional[List[GraphTransform]] = None,
+        transform: Optional[T.BaseTransform] = None,
     ):
         """Dataset class for FoldComp databases.
 
@@ -124,7 +124,7 @@ def __init__(
         ]
         self._get_indices()
         super().__init__(
-            root=self.root, transform=None, pre_transform=None  # type: ignore
+            root=self.root, transform=self.transform, pre_transform=None  # type: ignore
         )
 
     @property
@@ -232,14 +232,7 @@ def get(self, idx) -> Union[Data, Protein]:
             idx = self.protein_to_idx[idx]
         name, pdb = self.db[idx]
 
-        out = self.process_pdb(pdb, name)
-
-        # Apply transforms, if any
-        if self.transform is not None:
-            for transform in self.transform:
-                out = transform(out)
-
-        return out
+        return self.process_pdb(pdb, name)
 
 
 class FoldCompLightningDataModule(L.LightningDataModule):
@@ -252,7 +245,7 @@ def __init__(
         train_split: Optional[Union[List[str], float]] = None,
         val_split: Optional[Union[List[str], float]] = None,
         test_split: Optional[Union[List[str], float]] = None,
-        transform: Optional[List[GraphTransform]] = None,
+        transform: Optional[Iterable[Callable]] = None,
         num_workers: int = 4,
         pin_memory: bool = True,
     ) -> None:
@@ -281,7 +274,7 @@ def __init__(
             ``Data``/``Protein`` object and return a transformed version.
             The data object will be transformed before every access.
             (default: ``None``).
-        :type transform: Optional[List[GraphTransform]]
+        :type transform: Optional[Iterable[Callable]]
         :param num_workers: Number of workers to use for data loading, defaults
             to ``4``.
         :type num_workers: int, optional
@@ -297,7 +290,12 @@ def __init__(
         self.train_split = train_split
         self.val_split = val_split
         self.test_split = test_split
-        self.transform = transform
+        self.transform = (
+            self._compose_transforms(transform)
+            if transform is not None
+            else None
+        )
+
         if (
             isinstance(train_split, float)
             and isinstance(val_split, float)
@@ -311,6 +309,12 @@ def __init__(
         self.num_workers = num_workers
         self.pin_memory = pin_memory
 
+    def _compose_transforms(self, transforms: Iterable[Callable]) -> T.Compose:
+        try:
+            return T.Compose(list(transforms.values()))
+        except Exception:
+            return T.Compose(transforms)
+
     def setup(self, stage: Optional[str] = None):
         self.train_dataset()
         self.val_dataset()

graphein/protein/tensor/types.py

@@ -9,11 +9,11 @@
 # Code Repository: https://github.com/a-r-j/graphein
 from typing import NewType, Optional, Union
 
-from jaxtyping import Float
+from jaxtyping import Float, Int
 from torch import Tensor
 
 # Positions
-AtomTensor = NewType("AtomTensor", Float[Tensor, "-1 37 3"])
+AtomTensor = NewType("AtomTensor", Float[Tensor, "residues 37 3"])
 """
 ``torch.float[-1, 37, 3]``
 
@@ -24,7 +24,7 @@
 .. seealso:: :class:`ResidueTensor` :class:`CoordTensor`
 """
 
-BackboneTensor = NewType("BackboneTensor", Float[Tensor, "-1 4 3"])
+BackboneTensor = NewType("BackboneTensor", Float[Tensor, "residues 4 3"])
 """
 ``torch.float[-1, 4, 3]``
 
@@ -49,7 +49,7 @@
 """
 
 
-CoordTensor = NewType("CoordTensor", Float[Tensor, "-1 3"])
+CoordTensor = NewType("CoordTensor", Float[Tensor, "nodes 3"])
 """
 ``torch.float[-1, 3]``
 
@@ -68,7 +68,9 @@
 """
 
 # Represenations
-BackboneFrameTensor = NewType("BackboneFrameTensor", Float[Tensor, "-1 3 3"])
+BackboneFrameTensor = NewType(
+    "BackboneFrameTensor", Float[Tensor, "residues 3 3"]
+)
 """
 ``torch.float[-1, 3, 3]``
 
@@ -89,9 +91,9 @@
 
 
 # Rotations
-EulerAngleTensor = NewType("EulerAngleTensor", Float[Tensor, "-1 3"])
+EulerAngleTensor = NewType("EulerAngleTensor", Float[Tensor, "nodes 3"])
 
-QuaternionTensor = NewType("QuaternionTensor", Float[Tensor, "-1 4"])
+QuaternionTensor = NewType("QuaternionTensor", Float[Tensor, "nodes 4"])
 """
 ``torch.float[-1, 4]``
 
@@ -102,7 +104,7 @@
 """
 
 
-TransformTensor = NewType("TransformTensor", Float[Tensor, "-1 4 4"])
+TransformTensor = NewType("TransformTensor", Float[Tensor, "nodes 4 4"])
 
 
 RotationMatrix2D = NewType("RotationMatrix2D", Float[Tensor, "2 2"])
@@ -135,7 +137,9 @@
 """
 
 
-RotationMatrixTensor = NewType("RotationMatrixTensor", Float[Tensor, "-1 3 3"])
+RotationMatrixTensor = NewType(
+    "RotationMatrixTensor", Float[Tensor, "nodes 3 3"]
+)
 
 RotationTensor = NewType(
     "RotationTensor", Union[QuaternionTensor, RotationMatrixTensor]
@@ -144,7 +148,8 @@
 
 # Angles
 DihedralTensor = NewType(
-    "DihedralTensor", Union[Float[Tensor, "-1 3"], Float[Tensor, "-1 6"]]
+    "DihedralTensor",
+    Union[Float[Tensor, "residues 3"], Float[Tensor, "residues 6"]],
 )
 """
 ``Union[torch.float[-1, 3], torch.float[-1, 6]]``
@@ -161,7 +166,8 @@
 """
 
 TorsionTensor = NewType(
-    "TorsionTensor", Union[Float[Tensor, "-1 4"], Float[Tensor, "-1 8"]]
+    "TorsionTensor",
+    Union[Float[Tensor, "residues 4"], Float[Tensor, "residues 8"]],
 )
 """
 ``Union[torch.float[-1, 4], torch.float[-1, 8]]``
@@ -177,7 +183,9 @@
 
 """
 
-BackboneFrameTensor = NewType("BackboneFrameTensor", Float[Tensor, "-1 3 3"])
+BackboneFrameTensor = NewType(
+    "BackboneFrameTensor", Float[Tensor, "residues 3 3"]
+)
 """
 ``torch.float[-1, 3, 3]``
 
@@ -198,12 +206,12 @@
 .. seealso:: :class:`BackboneFrameTensor`
 """
 
-EdgeTensor = NewType("EdgeTensor", Float[Tensor, "2 -1"])
+EdgeTensor = NewType("EdgeTensor", Int[Tensor, "2 edges"])
 
 
-OrientationTensor = NewType("OrientationTensor", Float[Tensor, "-1 2 3"])
+OrientationTensor = NewType("OrientationTensor", Float[Tensor, "nodes 2 3"])
 
 
-ScalarTensor = NewType("ScalarTensor", Float[Tensor, "-1"])
+ScalarTensor = NewType("ScalarTensor", Float[Tensor, "nodes"])
 
 OptTensor = NewType("OptTensor", Optional[Tensor])