rcsb-embedding-model 0.0.25__tar.gz → 0.0.27__tar.gz

rcsb_embedding_model-0.0.27/.dockerignore

@@ -0,0 +1,36 @@
+# Only list files that could be under version control or could be created in CI/CD.
+
+# Note: Patterns are absolute, like `.prettierignore` but unlike `.gitignore`.
+
+# Gitignored files
+**/.*
+**/[~#$]*
+**/*[~#$]
+
+# Gitignored directories
+node_modules/
+
+# Directories
+/dist/
+/tests/
+/assets/
+/examples/
+
+# Files in the root directory
+/*.md
+/*.txt
+/CITATION.cff
+/compose.yaml
+/justfile
+/mkdocs.yaml
+
+# Keep README.md (needed for build)
+!/README.md
+
+# Keep .dockerignore and .gitignore
+!/.dockerignore
+!/.gitignore
+
+# Keep legal files
+!/LICENSE.*
+!/NOTICE.txt

{rcsb_embedding_model-0.0.25 → rcsb_embedding_model-0.0.27}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rcsb-embedding-model
-Version: 0.0.25
+Version: 0.0.27
 Summary: Protein Embedding Model for Structure Search
 Project-URL: Homepage, https://github.com/rcsb/rcsb-embedding-model
 Project-URL: Issues, https://github.com/rcsb/rcsb-embedding-model/issues
@@ -17,7 +17,7 @@ Description-Content-Type: text/markdown
 
 # RCSB Embedding Model
 
-**Version** 0.0.25
+**Version** 0.0.26
 
 
 ## Overview

{rcsb_embedding_model-0.0.25 → rcsb_embedding_model-0.0.27}/README.md

@@ -1,6 +1,6 @@
 # RCSB Embedding Model
 
-**Version** 0.0.25
+**Version** 0.0.26
 
 
 ## Overview

{rcsb_embedding_model-0.0.25 → rcsb_embedding_model-0.0.27}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rcsb-embedding-model"
-version = "0.0.25"
+version = "0.0.27"
 authors = [
     { name="Joan Segura", email="joan.segura@rcsb.org" },
 ]

{rcsb_embedding_model-0.0.25 → rcsb_embedding_model-0.0.27}/src/rcsb_embedding_model/dataset/esm_prot_from_chain.py

@@ -53,6 +53,7 @@ class EsmProtFromChain(Dataset):
             dtype=str,
             names=EsmProtFromChain.COLUMNS
         )
+        self.data = self.data.sort_values(by=self.data.columns[0])
 
     def __len__(self):
         return len(self.data)
@@ -83,7 +84,10 @@ if __name__ == '__main__':
     args = parser.parse_args()
 
     dataset = EsmProtFromChain(
-        args.file_list
+        src_stream=args.file_list,
+        src_location=SrcLocation.file,
+        structure_location=StructureLocation.remote,
+        structure_format=StructureFormat.mmcif,
     )
 
     esm3 = ESM3.from_pretrained(

{rcsb_embedding_model-0.0.25 → rcsb_embedding_model-0.0.27}/src/rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py

@@ -52,6 +52,7 @@ class ResidueAssemblyEmbeddingFromTensorFile(Dataset):
             dtype=str,
             names=ResidueAssemblyEmbeddingFromTensorFile.COLUMNS
         )
+        self.data = self.data.sort_values(by=self.data.columns[0])
 
     def __len__(self):
         return len(self.data)

{rcsb_embedding_model-0.0.25 → rcsb_embedding_model-0.0.27}/src/rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py

@@ -33,6 +33,7 @@ class ResidueEmbeddingFromTensorFile(Dataset):
             index_col=None,
             names=ResidueEmbeddingFromTensorFile.COLUMNS
         )
+        self.data = self.data.sort_values(by=self.data.columns[0])
 
     def __len__(self):
         return len(self.data)

{rcsb_embedding_model-0.0.25 → rcsb_embedding_model-0.0.27}/src/rcsb_embedding_model/inference/chain_inference.py

@@ -1,3 +1,4 @@
+import torch
 from torch.utils.data import DataLoader
 from lightning import Trainer
 
@@ -53,7 +54,9 @@ def predict(
         )
     )
 
-    aggregator_model = get_aggregator_model()
+    aggregator_model = get_aggregator_model(
+        device=torch.device("cpu")
+    )
     module = ChainModule(
         model=aggregator_model
     )

{rcsb_embedding_model-0.0.25 → rcsb_embedding_model-0.0.27}/src/rcsb_embedding_model/inference/esm_inference.py

@@ -1,3 +1,4 @@
+import torch
 from torch.utils.data import DataLoader
 from lightning import Trainer
 
@@ -47,7 +48,9 @@ def predict(
         collate_fn=lambda _: _
     )
 
-    esm_model = get_residue_model()
+    esm_model = get_residue_model(
+        device=torch.device("cpu")
+    )
     module = EsmModule(
         model=esm_model
     )

{rcsb_embedding_model-0.0.25 → rcsb_embedding_model-0.0.27}/src/rcsb_embedding_model/inference/structure_inference.py

@@ -1,3 +1,4 @@
+import torch
 from torch.utils.data import DataLoader
 from lightning import Trainer
 
@@ -46,8 +47,12 @@ def predict(
         collate_fn=lambda _: _
     )
 
-    res_model = get_residue_model()
-    aggregator_model = get_aggregator_model()
+    res_model = get_residue_model(
+        device=torch.device("cpu")
+    )
+    aggregator_model = get_aggregator_model(
+        device=torch.device("cpu")
+    )
     module = StructureModule(
         res_model=res_model,
         aggregator_model=aggregator_model