rcsb-embedding-model 0.0.28__tar.gz → 0.0.30__tar.gz

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/.gitignore

@@ -2,4 +2,5 @@
 /rcsb-embedding-model.iml
 /dist/
 /.pypi.rc
-__pycache__
+__pycache__
+/tests/resources/tmp

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rcsb-embedding-model
-Version: 0.0.28
+Version: 0.0.30
 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

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rcsb-embedding-model"
-version = "0.0.28"
+version = "0.0.30"
 authors = [
     { name="Joan Segura", email="joan.segura@rcsb.org" },
 ]

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/src/rcsb_embedding_model/dataset/esm_prot_from_chain.py

@@ -59,10 +59,10 @@ class EsmProtFromChain(Dataset):
         return len(self.data)
 
     def __getitem__(self, idx):
-        src_name = self.data.loc[idx, EsmProtFromChain.STREAM_NAME_ATTR]
-        src_structure = self.data.loc[idx, EsmProtFromChain.STREAM_ATTR]
-        chain_id = self.data.loc[idx, EsmProtFromChain.CH_ATTR]
-        item_name = self.data.loc[idx, EsmProtFromChain.ITEM_NAME_ATTR]
+        src_name = self.data.iloc[idx][EsmProtFromChain.STREAM_NAME_ATTR]
+        src_structure = self.data.iloc[idx][EsmProtFromChain.STREAM_ATTR]
+        chain_id = self.data.iloc[idx][EsmProtFromChain.CH_ATTR]
+        item_name = self.data.iloc[idx][EsmProtFromChain.ITEM_NAME_ATTR]
         structure = self.__structure_provider.get_structure(
             src_name=src_name,
             src_structure=stringio_from_url(src_structure) if self.structure_location == StructureLocation.remote else src_structure,
@@ -87,7 +87,7 @@ if __name__ == '__main__':
         src_stream=args.file_list,
         src_location=SrcLocation.file,
         structure_location=StructureLocation.remote,
-        structure_format=StructureFormat.mmcif,
+        structure_format=StructureFormat.bciff,
     )
 
     esm3 = ESM3.from_pretrained(

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/src/rcsb_embedding_model/dataset/esm_prot_from_structure.py

@@ -40,7 +40,7 @@ class EsmProtFromStructure(EsmProtFromChain):
 
     def __get_chains(self, src_stream):
         chains = []
-        for idx, row in (pd.DataFrame(
+        data = pd.DataFrame(
             src_stream,
             dtype=str,
             columns=EsmProtFromStructure.COLUMNS
@@ -50,7 +50,9 @@ class EsmProtFromStructure(EsmProtFromChain):
             index_col=None,
             dtype=str,
             names=EsmProtFromStructure.COLUMNS
-        )).iterrows():
+        )
+        data = data.sort_values(by=data.columns[0])
+        for idx, row in data.iterrows():
             src_name = row[EsmProtFromStructure.STREAM_NAME_ATTR]
             src_structure = row[EsmProtFromStructure.STREAM_ATTR]
             item_name = row[EsmProtFromStructure.ITEM_NAME_ATTR]

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/src/rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py

@@ -33,7 +33,6 @@ class ResidueAssemblyDatasetFromStructure(ResidueAssemblyEmbeddingFromTensorFile
         self.structure_format = structure_format
         self.min_res_n = min_res_n
         self.max_res_n = max_res_n
-        self.__structure_provider = structure_provider
         super().__init__(
             src_stream=self.__get_assemblies(src_stream),
             res_embedding_location=res_embedding_location,
@@ -47,17 +46,19 @@ class ResidueAssemblyDatasetFromStructure(ResidueAssemblyEmbeddingFromTensorFile
 
     def __get_assemblies(self, src_stream):
         assemblies = []
-        for idx, row in (pd.DataFrame(
-                src_stream,
-                dtype=str,
-                columns=ResidueAssemblyDatasetFromStructure.COLUMNS
+        data = pd.DataFrame(
+            src_stream,
+            dtype=str,
+            columns=ResidueAssemblyDatasetFromStructure.COLUMNS
         ) if self.src_location == SrcLocation.stream else pd.read_csv(
             src_stream,
             header=None,
             index_col=None,
             dtype=str,
             names=ResidueAssemblyDatasetFromStructure.COLUMNS
-        )).iterrows():
+        )
+        data = data.sort_values(by=data.columns[0])
+        for idx, row in data.iterrows():
             src_name = row[ResidueAssemblyDatasetFromStructure.STREAM_NAME_ATTR]
             src_structure = row[ResidueAssemblyDatasetFromStructure.STREAM_ATTR]
             structure = stringio_from_url(src_structure) if self.structure_location == StructureLocation.remote else src_structure

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/src/rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py

@@ -1,3 +1,4 @@
+import argparse
 import sys
 
 import pandas as pd
@@ -58,11 +59,10 @@ class ResidueAssemblyEmbeddingFromTensorFile(Dataset):
         return len(self.data)
 
     def __getitem__(self, idx):
-        src_name = self.data.loc[idx, ResidueAssemblyEmbeddingFromTensorFile.STREAM_NAME_ATTR]
-        src_structure = self.data.loc[idx, ResidueAssemblyEmbeddingFromTensorFile.STREAM_ATTR]
-        assembly_id = self.data.loc[idx, ResidueAssemblyEmbeddingFromTensorFile.ASSEMBLY_ATTR]
-        item_name = self.data.loc[idx, ResidueAssemblyEmbeddingFromTensorFile.ITEM_NAME_ATTR]
-
+        src_name = self.data.iloc[idx][ResidueAssemblyEmbeddingFromTensorFile.STREAM_NAME_ATTR]
+        src_structure = self.data.iloc[idx][ResidueAssemblyEmbeddingFromTensorFile.STREAM_ATTR]
+        assembly_id = self.data.iloc[idx][ResidueAssemblyEmbeddingFromTensorFile.ASSEMBLY_ATTR]
+        item_name = self.data.iloc[idx][ResidueAssemblyEmbeddingFromTensorFile.ITEM_NAME_ATTR]
         structure = self.__structure_provider.get_structure(
             src_name=src_name,
             src_structure=stringio_from_url(src_structure) if self.structure_location == StructureLocation.remote else src_structure,
@@ -77,12 +77,17 @@ class ResidueAssemblyEmbeddingFromTensorFile(Dataset):
 
 if __name__ == "__main__":
 
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--file_list', type=argparse.FileType('r'), required=True)
+    parser.add_argument('--res_embeddings_path', required=True)
+    args = parser.parse_args()
+
     dataset = ResidueAssemblyEmbeddingFromTensorFile(
-        src_stream="/Users/joan/tmp/assembly-test.csv",
-        res_embedding_location="/Users/joan/tmp",
+        src_stream=args.file_list,
+        res_embedding_location=args.res_embeddings_path,
         src_location=SrcLocation.file,
-        structure_location=StructureLocation.local,
-        structure_format=StructureFormat.mmcif
+        structure_location=StructureLocation.remote,
+        structure_format=StructureFormat.bciff
     )
 
     dataloader = DataLoader(

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/src/rcsb_embedding_model/dataset/residue_embedding_from_structure.py

@@ -42,17 +42,19 @@ class ResidueEmbeddingFromStructure(ResidueEmbeddingFromTensorFile):
 
     def __get_chains(self, src_stream):
         chains = []
-        for idx, row in (pd.DataFrame(
-                src_stream,
-                dtype=str,
-                columns=ResidueEmbeddingFromStructure.COLUMNS
+        data = pd.DataFrame(
+            src_stream,
+            dtype=str,
+            columns=ResidueEmbeddingFromStructure.COLUMNS
         ) if self.src_location == SrcLocation.stream else pd.read_csv(
             src_stream,
             header=None,
             index_col=None,
             dtype=str,
             names=ResidueEmbeddingFromStructure.COLUMNS
-        )).iterrows():
+        )
+        data = data.sort_values(by=data.columns[0])
+        for idx, row in data.iterrows():
             src_name = row[ResidueEmbeddingFromStructure.STREAM_NAME_ATTR]
             src_structure = row[ResidueEmbeddingFromStructure.STREAM_ATTR]
             item_name = row[ResidueEmbeddingFromStructure.ITEM_NAME_ATTR]

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/src/rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py

@@ -39,6 +39,6 @@ class ResidueEmbeddingFromTensorFile(Dataset):
         return len(self.data)
 
     def __getitem__(self, idx):
-        embedding_src = self.data.loc[idx, ResidueEmbeddingFromTensorFile.FILE_ATTR]
-        item_name = self.data.loc[idx, ResidueEmbeddingFromTensorFile.ITEM_NAME_ATTR]
+        embedding_src = self.data.iloc[idx][ResidueEmbeddingFromTensorFile.FILE_ATTR]
+        item_name = self.data.iloc[idx][ResidueEmbeddingFromTensorFile.ITEM_NAME_ATTR]
         return torch.load(embedding_src, map_location=torch.device('cpu')), item_name

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/src/rcsb_embedding_model/utils/structure_parser.py

@@ -32,7 +32,7 @@ def get_protein_chains(structure, min_res_n=0):
     for atom_ch in chain_iter(structure):
         atom_res = atom_ch[filter_polymer(atom_ch)]
         atom_res = atom_res[filter_amino_acids(atom_res)]
-        if len(atom_res) > 0 and len(get_residues(atom_res)) > min_res_n:
+        if len(atom_res) > 0 and len(get_residues(atom_res)[0]) > min_res_n:
             chain_ids.append(str(get_chains(atom_res)[0]))
     return tuple(chain_ids)
 

rcsb_embedding_model-0.0.30/tests/resources/src_stream/assembly-complete-test.csv

@@ -0,0 +1,7 @@
+1A21,https://models.rcsb.org/1A21.bcif.gz,1,1A21-1
+1A21,https://models.rcsb.org/1A21.bcif.gz,2,1A21-2
+1A3J,https://models.rcsb.org/1A3J.bcif.gz,1,1A3J-1
+1A3X,https://models.rcsb.org/1A3X.bcif.gz,1,1A3X-1
+1A3X,https://models.rcsb.org/1A3X.bcif.gz,2,1A3X-2
+1AIV,https://models.rcsb.org/1AIV.bcif.gz,1,1AIV-1
+1AU1,https://models.rcsb.org/1AU1.bcif.gz,1,1AU1-1

rcsb_embedding_model-0.0.30/tests/resources/src_stream/instance-complete-test.csv

@@ -0,0 +1,10 @@
+1A21,https://models.rcsb.org/1A21.bcif.gz,A,1A21.A
+1A21,https://models.rcsb.org/1A21.bcif.gz,B,1A21.B
+1A3J,https://models.rcsb.org/1A3J.bcif.gz,A,1A3J.A
+1A3J,https://models.rcsb.org/1A3J.bcif.gz,B,1A3J.B
+1A3J,https://models.rcsb.org/1A3J.bcif.gz,C,1A3J.C
+1A3X,https://models.rcsb.org/1A3X.bcif.gz,A,1A3X.A
+1A3X,https://models.rcsb.org/1A3X.bcif.gz,B,1A3X.B
+1AIV,https://models.rcsb.org/1AIV.bcif.gz,A,1AIV.A
+1AU1,https://models.rcsb.org/1AU1.bcif.gz,A,1AU1.A
+1AU1,https://models.rcsb.org/1AU1.bcif.gz,B,1AU1.B

rcsb_embedding_model-0.0.30/tests/resources/src_stream/instance.csv

@@ -0,0 +1,2 @@
+1acb,https://models.rcsb.org/1acb.bcif.gz,A,1acb.A
+2uzi,https://models.rcsb.org/2uzi.bcif.gz,A,2uzi.A

rcsb_embedding_model-0.0.30/tests/test_cli_inference.py

@@ -0,0 +1,53 @@
+
+import os
+import shutil
+import unittest
+
+from rcsb_embedding_model.types.api_types import OutFormat, StructureLocation, StructureFormat, Accelerator
+
+
+
+
+
+class TestCliInference(unittest.TestCase):
+    __test_path = os.path.dirname(__file__)
+
+    def test_complete_inference(self):
+        _remove_files_in_directory(f"{self.__test_path}/resources/tmp")
+        from rcsb_embedding_model.cli.inference import complete_embedding
+        complete_embedding(
+            src_chain_file=f"{self.__test_path}/resources/src_stream/instance-complete-test.csv",
+            src_assembly_file=f"{self.__test_path}/resources/src_stream/assembly-complete-test.csv",
+            output_res_path=f"{self.__test_path}/resources/tmp",
+            output_chain_path=f"{self.__test_path}/resources/tmp",
+            output_assembly_path=f"{self.__test_path}/resources/tmp",
+            output_format=OutFormat.grouped,
+            output_chain_name="instance-inference",
+            output_assembly_name="assembly-inference",
+            structure_location=StructureLocation.remote,
+            structure_format=StructureFormat.bciff,
+            min_res_n=0,
+            batch_size_res=1,
+            num_workers_res=0,
+            batch_size_chain=1,
+            num_workers_chain=0,
+            batch_size_assembly=1,
+            num_workers_assembly=0,
+            num_nodes=1,
+            accelerator=Accelerator.cpu
+        )
+        self.assertTrue(os.path.exists(f"{self.__test_path}/resources/tmp/instance-inference.json.gz"))
+        self.assertTrue(os.path.exists(f"{self.__test_path}/resources/tmp/assembly-inference.json.gz"))
+
+
+def _remove_files_in_directory(directory_path):
+    os.makedirs(directory_path, exist_ok=True)
+    for filename in os.listdir(directory_path):
+        file_path = os.path.join(directory_path, filename)
+        try:
+            if os.path.isfile(file_path):
+                os.unlink(file_path)
+            elif os.path.isdir(file_path):
+                shutil.rmtree(file_path)
+        except Exception as e:
+            print(f"Failed to delete {file_path}. Reason: {e}")

{rcsb_embedding_model-0.0.28 → rcsb_embedding_model-0.0.30}/tests/test_remote_inference.py

@@ -50,6 +50,24 @@ class TestRemoteInference(unittest.TestCase):
             self.assertEqual(tuple(esm_embeddings[idx][0][0].shape), shape)
 
 
+    def test_esm_inference_from_csv_bcif_gz(self):
+        from rcsb_embedding_model.inference.esm_inference import predict
+
+        esm_embeddings = predict(
+            src_stream=f"{self.__test_path}/resources/src_stream/instance.csv",
+            src_location=SrcLocation.file,
+            src_from=SrcProteinFrom.chain,
+            structure_location=StructureLocation.remote,
+            structure_format=StructureFormat.bciff,
+            accelerator=Accelerator.cpu
+        )
+
+        self.assertEqual(len(esm_embeddings), 2)
+        shapes = ((243, 1536), (116, 1536))
+        for idx, shape in enumerate(shapes):
+            self.assertEqual(tuple(esm_embeddings[idx][0][0].shape), shape)
+
+
     def test_esm_inference_from_cif_gz(self):
         from rcsb_embedding_model.inference.esm_inference import predict