rcsb-embedding-model 0.0.11__py3-none-any.whl → 0.0.13__py3-none-any.whl

rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py

@@ -37,7 +37,7 @@ class ResidueAssemblyDatasetFromStructure(ResidueAssemblyEmbeddingFromTensorFile
         super().__init__(
             src_stream=self.__get_assemblies(src_stream),
             res_embedding_location=res_embedding_location,
-            src_location=src_location,
+            src_location=SrcLocation.stream,
             structure_location=structure_location,
             structure_format=structure_format,
             min_res_n=min_res_n,
@@ -60,9 +60,9 @@ class ResidueAssemblyDatasetFromStructure(ResidueAssemblyEmbeddingFromTensorFile
         )).iterrows():
             src_name = row[ResidueAssemblyDatasetFromStructure.STREAM_NAME_ATTR]
             src_structure = row[ResidueAssemblyDatasetFromStructure.STREAM_ATTR]
-            src_structure = stringio_from_url(src_structure) if self.structure_location == StructureLocation.remote else src_structure
+            structure = stringio_from_url(src_structure) if self.structure_location == StructureLocation.remote else src_structure
             item_name = row[ResidueAssemblyDatasetFromStructure.ITEM_NAME_ATTR]
-            for assembly_id in get_assemblies(src_structure=src_structure, structure_format=self.structure_format):
+            for assembly_id in get_assemblies(structure=structure, structure_format=self.structure_format):
                 assemblies.append((src_name, src_structure, str(assembly_id), f"{item_name}.{assembly_id}"))
 
         return tuple(assemblies)

rcsb_embedding_model/utils/data.py

@@ -44,6 +44,7 @@ def stringio_from_url(url):
         print(f"Error fetching URL: {e}")
         return None
 
+
 def concatenate_tensors(file_list, max_residues, dim=0):
     """
     Concatenates a list of tensors stored in individual files along a specified dimension.

rcsb_embedding_model/utils/structure_parser.py

@@ -37,13 +37,13 @@ def get_protein_chains(structure, min_res_n=0):
     return tuple(chain_ids)
 
 
-def get_assemblies(src_structure, structure_format="mmcif"):
+def get_assemblies(structure, structure_format="mmcif"):
     if structure_format == "pdb":
-        return tuple(list_pdb_assemblies(PDBFile.read(src_structure)))
+        return tuple(list_pdb_assemblies(PDBFile.read(structure)))
     elif structure_format == "mmcif":
-        return tuple(list_assemblies(CIFFile.read(src_structure)).keys())
+        return tuple(list_assemblies(CIFFile.read(structure)).keys())
     elif structure_format == "binarycif":
-        return tuple(list_assemblies(BinaryCIFFile.read(src_structure)))
+        return tuple(list_assemblies(BinaryCIFFile.read(structure)))
     else:
         raise RuntimeError(f"Unknown file format {structure_format}")
 

{rcsb_embedding_model-0.0.11.dist-info → rcsb_embedding_model-0.0.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rcsb-embedding-model
-Version: 0.0.11
+Version: 0.0.13
 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
@@ -18,7 +18,7 @@ Description-Content-Type: text/markdown
 
 # RCSB Embedding Model
 
-**Version** 0.0.11
+**Version** 0.0.13
 
 
 ## Overview

{rcsb_embedding_model-0.0.11.dist-info → rcsb_embedding_model-0.0.13.dist-info}/RECORD

@@ -4,7 +4,7 @@ rcsb_embedding_model/cli/args_utils.py,sha256=7nP2q8pL5dWK_U7opxtWmoFcYVwasky6el
 rcsb_embedding_model/cli/inference.py,sha256=0DZHw4QeAi2f6xdfoEPzYb_gQhCWc_IPA1QgnckcUIg,12916
 rcsb_embedding_model/dataset/esm_prot_from_chain.py,sha256=dBD2N0Y-GoN6p3z2yLnOvv6JGn-skAxwgbOYhXKDngc,3487
 rcsb_embedding_model/dataset/esm_prot_from_structure.py,sha256=9IvurGr7PGjfAABoGoMlG08zn6mC6iVAjgExGSrDVdQ,2552
-rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py,sha256=nvBBQzEgHOj4XwoTfzSUiahWKXMDuc11lhKszl_HaF0,2873
+rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py,sha256=10NUHnjTE5xSXPFVTfeuL8MpOhqk-f3ZIG7EbWR49B4,2867
 rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py,sha256=KXiohnPjjfZEFbPZQ46HGE8eEYWrVX8bfbTz4zPlo7o,3451
 rcsb_embedding_model/dataset/residue_embedding_from_structure.py,sha256=9MfgKvFAxYr9RU8kwvHnEZBH35gukx8hRPeoBXfyNXo,2797
 rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py,sha256=mDCqJrpnu2GXmp75zOPTH8ogL3GWDqc3iEH62JuyHVs,1275
@@ -18,13 +18,13 @@ rcsb_embedding_model/modules/chain_module.py,sha256=sDSPXJmWuU2C3lt1NorlbUVWZvRS
 rcsb_embedding_model/modules/esm_module.py,sha256=CTHGOATXiarqZsBsZ8oxGJBj20A73186Slpr0EzMJsE,770
 rcsb_embedding_model/modules/structure_module.py,sha256=dEtDNdWo1j2sSDa0JiOHQfEfQzIWqSLEKpvOX0GrXZ4,1048
 rcsb_embedding_model/types/api_types.py,sha256=JSHd5Rq7dm6uWNzy1UZnLkWKxfjsKB7gRRTCSqS4r7c,1156
-rcsb_embedding_model/utils/data.py,sha256=x6ca_bVdBXEAp9ugCi1rVEQ-G5nGTFKpzDKqZKpkFBE,2933
+rcsb_embedding_model/utils/data.py,sha256=ODz6GG6IAhgAlLh3tcIP6-JVHX8Bb_-E745Lvc_oR84,2934
 rcsb_embedding_model/utils/model.py,sha256=rpZa-gfm3cEtbBd7UXMHrZv3x6f0AC8TJT3gtrSxr5I,852
-rcsb_embedding_model/utils/structure_parser.py,sha256=q_MmuU1AokZ-x-6ATxknJr_D6Sn3ZuaZ2yoJAIL-VIU,2767
+rcsb_embedding_model/utils/structure_parser.py,sha256=IWMQ8brlEMe6_ND-DBESOli8vlqHxladTssjbM9RSKw,2751
 rcsb_embedding_model/utils/structure_provider.py,sha256=eWtxjkPpmRfmil_DKR1J6miaXR3lQ28DF5O0qrqSgGA,786
 rcsb_embedding_model/writer/batch_writer.py,sha256=ekgzFZyoKpcnZ3IDP9hfOWBpuHxUQ31P35ViDAi-Edw,2843
-rcsb_embedding_model-0.0.11.dist-info/METADATA,sha256=J_7XzyvG_Dd-kz4oSS90fVnmMKf97BL015Qe5XMtCd4,5368
-rcsb_embedding_model-0.0.11.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-rcsb_embedding_model-0.0.11.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
-rcsb_embedding_model-0.0.11.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
-rcsb_embedding_model-0.0.11.dist-info/RECORD,,
+rcsb_embedding_model-0.0.13.dist-info/METADATA,sha256=wB8Ww1bRnvU9Fl_fvsobKz1xl8g2kyEftPyZ01646QA,5368
+rcsb_embedding_model-0.0.13.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+rcsb_embedding_model-0.0.13.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
+rcsb_embedding_model-0.0.13.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
+rcsb_embedding_model-0.0.13.dist-info/RECORD,,