diff --git a/proteinshake/backbone/backend/adapters/alphafold.py b/proteinshake/backend/adapters/alphafold.py similarity index 100% rename from proteinshake/backbone/backend/adapters/alphafold.py rename to proteinshake/backend/adapters/alphafold.py diff --git a/proteinshake/backbone/backend/adapters/pdb.py b/proteinshake/backend/adapters/pdb.py similarity index 100% rename from proteinshake/backbone/backend/adapters/pdb.py rename to proteinshake/backend/adapters/pdb.py diff --git a/proteinshake/backbone/backend/adapters/uniprot.py b/proteinshake/backend/adapters/uniprot.py similarity index 100% rename from proteinshake/backbone/backend/adapters/uniprot.py rename to proteinshake/backend/adapters/uniprot.py diff --git a/proteinshake/backbone/backend/collection.py b/proteinshake/backend/collection.py similarity index 100% rename from proteinshake/backbone/backend/collection.py rename to proteinshake/backend/collection.py diff --git a/proteinshake/backbone/backend/database.py b/proteinshake/backend/database.py similarity index 100% rename from proteinshake/backbone/backend/database.py rename to proteinshake/backend/database.py diff --git a/proteinshake/backbone/backend/structure.py b/proteinshake/backend/structure.py similarity index 100% rename from proteinshake/backbone/backend/structure.py rename to proteinshake/backend/structure.py diff --git a/proteinshake/backbone/frontend/dataloader.py b/proteinshake/datasets/alphafold.py similarity index 100% rename from proteinshake/backbone/frontend/dataloader.py rename to proteinshake/datasets/alphafold.py diff --git a/proteinshake/backbone/frontend/dataset.py b/proteinshake/datasets/enzymes.py similarity index 100% rename from proteinshake/backbone/frontend/dataset.py rename to proteinshake/datasets/enzymes.py diff --git a/proteinshake/backbone/frontend/tasks/task.py b/proteinshake/datasets/gene_ontology.py similarity index 100% rename from proteinshake/backbone/frontend/tasks/task.py rename to proteinshake/datasets/gene_ontology.py diff --git a/proteinshake/backbone/utils/io.py b/proteinshake/datasets/xray.py similarity index 100% rename from proteinshake/backbone/utils/io.py rename to proteinshake/datasets/xray.py diff --git a/proteinshake/datasets/GeneOntology.py b/proteinshake/frontend/dataloader.py similarity index 100% rename from proteinshake/datasets/GeneOntology.py rename to proteinshake/frontend/dataloader.py diff --git a/proteinshake/transforms/frameworks/torch.py b/proteinshake/frontend/datasets/dataset.py similarity index 100% rename from proteinshake/transforms/frameworks/torch.py rename to proteinshake/frontend/datasets/dataset.py diff --git a/proteinshake/transforms/representations/graph.py b/proteinshake/frontend/evaluators/classification.py similarity index 100% rename from proteinshake/transforms/representations/graph.py rename to proteinshake/frontend/evaluators/classification.py diff --git a/proteinshake/frontend/evaluators/regression.py b/proteinshake/frontend/evaluators/regression.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/frontend/evaluators/retrieval.py b/proteinshake/frontend/evaluators/retrieval.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/frontend/splitters/from_existing.py b/proteinshake/frontend/splitters/from_existing.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/frontend/splitters/random.py b/proteinshake/frontend/splitters/random.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/frontend/splitters/sequence_similarity.py b/proteinshake/frontend/splitters/sequence_similarity.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/frontend/splitters/structure_similarity.py b/proteinshake/frontend/splitters/structure_similarity.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/frontend/tasks/pairwise_protein.py b/proteinshake/frontend/tasks/pairwise_protein.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/frontend/tasks/pairwise_residue.py b/proteinshake/frontend/tasks/pairwise_residue.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/frontend/tasks/protein.py b/proteinshake/frontend/tasks/protein.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/frontend/tasks/residue.py b/proteinshake/frontend/tasks/residue.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/frontend/tasks/task.py b/proteinshake/frontend/tasks/task.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/tasks/GeneOntology.py b/proteinshake/tasks/gene_ontology_classification.py similarity index 100% rename from proteinshake/tasks/GeneOntology.py rename to proteinshake/tasks/gene_ontology_classification.py diff --git a/proteinshake/transforms/framework/torch.py b/proteinshake/transforms/framework/torch.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/transforms/post_framework/note.md b/proteinshake/transforms/post_framework/note.md new file mode 100644 index 00000000..7ba87cd3 --- /dev/null +++ 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) + +""" \ No newline at end of file diff --git a/proteinshake/transforms/post_representation/add_node_degree.py b/proteinshake/transforms/post_representation/add_node_degree.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/transforms/pre_framework/random_residue_masking.py b/proteinshake/transforms/pre_framework/random_residue_masking.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/transforms/pre_representation/residue_level.py b/proteinshake/transforms/pre_representation/residue_level.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/transforms/representation/point.py b/proteinshake/transforms/representation/point.py new file mode 100644 index 00000000..e69de29b diff --git a/proteinshake/utils/io.py b/proteinshake/utils/io.py new file mode 100644 index 00000000..e69de29b