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BorgwardtLab · Nov 24, 2023 · a9f4652 · a9f4652
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diff --git a/...ke/backbone/backend/adapters/alphafold.py → proteinshake/backend/adapters/alphafold.py b/...ke/backbone/backend/adapters/alphafold.py → proteinshake/backend/adapters/alphafold.py
diff --git a/...einshake/backbone/backend/adapters/pdb.py → proteinshake/backend/adapters/pdb.py b/...einshake/backbone/backend/adapters/pdb.py → proteinshake/backend/adapters/pdb.py
diff --git a/...hake/backbone/backend/adapters/uniprot.py → proteinshake/backend/adapters/uniprot.py b/...hake/backbone/backend/adapters/uniprot.py → proteinshake/backend/adapters/uniprot.py
diff --git a/proteinshake/backbone/backend/collection.py → proteinshake/backend/collection.py b/proteinshake/backbone/backend/collection.py → proteinshake/backend/collection.py
diff --git a/proteinshake/backbone/backend/database.py → proteinshake/backend/database.py b/proteinshake/backbone/backend/database.py → proteinshake/backend/database.py
diff --git a/proteinshake/backbone/backend/structure.py → proteinshake/backend/structure.py b/proteinshake/backbone/backend/structure.py → proteinshake/backend/structure.py
diff --git a/proteinshake/backbone/frontend/dataloader.py → proteinshake/datasets/alphafold.py b/proteinshake/backbone/frontend/dataloader.py → proteinshake/datasets/alphafold.py
diff --git a/proteinshake/backbone/frontend/dataset.py → proteinshake/datasets/enzymes.py b/proteinshake/backbone/frontend/dataset.py → proteinshake/datasets/enzymes.py
diff --git a/proteinshake/backbone/frontend/tasks/task.py → proteinshake/datasets/gene_ontology.py b/proteinshake/backbone/frontend/tasks/task.py → proteinshake/datasets/gene_ontology.py
diff --git a/proteinshake/backbone/utils/io.py → proteinshake/datasets/xray.py b/proteinshake/backbone/utils/io.py → proteinshake/datasets/xray.py
diff --git a/proteinshake/datasets/GeneOntology.py → proteinshake/frontend/dataloader.py b/proteinshake/datasets/GeneOntology.py → proteinshake/frontend/dataloader.py
diff --git a/proteinshake/transforms/frameworks/torch.py → proteinshake/frontend/datasets/dataset.py b/proteinshake/transforms/frameworks/torch.py → proteinshake/frontend/datasets/dataset.py
diff --git a/...shake/transforms/representations/graph.py → ...ake/frontend/evaluators/classification.py b/...shake/transforms/representations/graph.py → ...ake/frontend/evaluators/classification.py
diff --git a/proteinshake/frontend/evaluators/regression.py b/proteinshake/frontend/evaluators/regression.py
diff --git a/proteinshake/frontend/evaluators/retrieval.py b/proteinshake/frontend/evaluators/retrieval.py
diff --git a/proteinshake/frontend/splitters/from_existing.py b/proteinshake/frontend/splitters/from_existing.py
diff --git a/proteinshake/frontend/splitters/random.py b/proteinshake/frontend/splitters/random.py
diff --git a/proteinshake/frontend/splitters/sequence_similarity.py b/proteinshake/frontend/splitters/sequence_similarity.py
diff --git a/proteinshake/frontend/splitters/structure_similarity.py b/proteinshake/frontend/splitters/structure_similarity.py
diff --git a/proteinshake/frontend/tasks/pairwise_protein.py b/proteinshake/frontend/tasks/pairwise_protein.py
diff --git a/proteinshake/frontend/tasks/pairwise_residue.py b/proteinshake/frontend/tasks/pairwise_residue.py
diff --git a/proteinshake/frontend/tasks/protein.py b/proteinshake/frontend/tasks/protein.py
diff --git a/proteinshake/frontend/tasks/residue.py b/proteinshake/frontend/tasks/residue.py
diff --git a/proteinshake/frontend/tasks/task.py b/proteinshake/frontend/tasks/task.py
diff --git a/proteinshake/tasks/GeneOntology.py → ...ake/tasks/gene_ontology_classification.py b/proteinshake/tasks/GeneOntology.py → ...ake/tasks/gene_ontology_classification.py
diff --git a/proteinshake/transforms/framework/torch.py b/proteinshake/transforms/framework/torch.py
diff --git a/proteinshake/transforms/post_framework/note.md b/proteinshake/transforms/post_framework/note.md
@@ -0,0 +1,11 @@
+"""
+Post-framework transforms will not be implemented in ProteinShake, but are responsibility of the respective framework.
+You can pass the framework-native transforms to the Dataset object though.
+
+Example:
+
+    from proteinshake.datasets import EnzymeDataset
+    from torch_geometric.transforms import AddSelfLoops
+    ds = EnzymeDataset(...).to_graph(...).pyg(..., post_transform=AddSelfLoops)
+
+"""
diff --git a/proteinshake/transforms/post_representation/add_node_degree.py b/proteinshake/transforms/post_representation/add_node_degree.py
diff --git a/proteinshake/transforms/pre_framework/random_residue_masking.py b/proteinshake/transforms/pre_framework/random_residue_masking.py
diff --git a/proteinshake/transforms/pre_representation/residue_level.py b/proteinshake/transforms/pre_representation/residue_level.py
diff --git a/proteinshake/transforms/representation/point.py b/proteinshake/transforms/representation/point.py
diff --git a/proteinshake/utils/io.py b/proteinshake/utils/io.py