rcsb-embedding-model 0.0.29__py3-none-any.whl → 0.0.31__py3-none-any.whl

rcsb_embedding_model/__init__.py

@@ -1,4 +1,9 @@
-
+from importlib_metadata import version, PackageNotFoundError
 from rcsb_embedding_model.rcsb_structure_embedding import RcsbStructureEmbedding
 
-__all__ = ["RcsbStructureEmbedding"]
+try:
+    __version__ = version("rcsb-embedding-model")
+except PackageNotFoundError:
+    __version__ = "0.0.0"
+
+__all__ = ["RcsbStructureEmbedding", "__version__"]

rcsb_embedding_model/cli/inference.py

@@ -3,6 +3,7 @@ from typing import Annotated, List
 
 import typer
 
+from rcsb_embedding_model import __version__
 from rcsb_embedding_model.cli.args_utils import arg_devices
 from rcsb_embedding_model.types.api_types import StructureFormat, Accelerator, SrcLocation, SrcProteinFrom, \
     StructureLocation, SrcAssemblyFrom, SrcTensorFrom, OutFormat
@@ -437,5 +438,22 @@ def complete_embedding(
     )
 
 
+def version_callback(value: bool):
+    if value:
+        typer.echo(f"{__version__}")
+        raise typer.Exit()
+
+@app.callback()
+def main(
+        version: bool = typer.Option(
+            None,
+            "--version",
+            callback=version_callback,
+            is_eager=True,
+            help="Show the version and exit",
+        )
+):
+    pass
+
 if __name__ == "__main__":
     app()

rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py

@@ -1,3 +1,4 @@
+import argparse
 import sys
 
 import pandas as pd
@@ -76,12 +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/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-0.0.29.dist-info → rcsb_embedding_model-0.0.31.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rcsb-embedding-model
-Version: 0.0.29
+Version: 0.0.31
 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
@@ -11,6 +11,7 @@ Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.10
 Requires-Dist: esm>=3.2.0
+Requires-Dist: importlib-metadata>=8.7.0
 Requires-Dist: lightning>=2.5.0
 Requires-Dist: typer>=0.15.0
 Description-Content-Type: text/markdown

{rcsb_embedding_model-0.0.29.dist-info → rcsb_embedding_model-0.0.31.dist-info}/RECORD

@@ -1,11 +1,11 @@
-rcsb_embedding_model/__init__.py,sha256=r3gLdeBIXkQEQA_K6QcRPO-TtYuAQSutk6pXRUE_nas,120
+rcsb_embedding_model/__init__.py,sha256=7YfYO-V-u__19eAZfQ3t5Gf2qrhd_gwQB8rHO0J0puw,306
 rcsb_embedding_model/rcsb_structure_embedding.py,sha256=dKp9hXQO0JAnO4SEfjJ_mG_jHu3UxAPguv6jkOjp-BI,4487
 rcsb_embedding_model/cli/args_utils.py,sha256=7nP2q8pL5dWK_U7opxtWmoFcYVwasky6elHk-dASFaI,165
-rcsb_embedding_model/cli/inference.py,sha256=tfMvHAhkUIzJ2RbTtQjq7eWmOUrSyVfH5bjTkCCSIS8,19500
+rcsb_embedding_model/cli/inference.py,sha256=67_Tr3LWeA3T4KS5mkjq6tw77Ypy0R8IwMxEG2FwVqQ,19901
 rcsb_embedding_model/dataset/esm_prot_from_chain.py,sha256=l8pRgRpz-8gEzR6QsNcmdnX_KkgvgF1vdqNAsP8Lrc8,3960
 rcsb_embedding_model/dataset/esm_prot_from_structure.py,sha256=3HzXCCc-UqmZNbJaeXHyUsSIZZxMc2erbxAPGIxSmfE,2621
 rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py,sha256=69h1VkrIXesHZi1cG3BOMMytSDeRzcBBP0_Z3Xz3dM8,2869
-rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py,sha256=R-_WY8YJ6qNBjWvY9IzCRThAA42GJ71hzwZBMnkMhOg,3519
+rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py,sha256=Hd9oH-IVgY6d7Dxy5VfiwHvSaK-Wwhk6ccUBgOwl0TU,3740
 rcsb_embedding_model/dataset/residue_embedding_from_structure.py,sha256=1jmeEcCK41cAi2ZnqQkd667NWCAIGS3k6jGDF-WxtTk,2854
 rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py,sha256=4OPaw55yGKHjY2iPpCnemcfwfmTZ4j5VrGQ2oIMQw6A,1343
 rcsb_embedding_model/inference/assembly_inferece.py,sha256=8fPJjEXy1WsM5XB5U7KfdO5-Du6nEsawsaAjmWoXA9I,2329
@@ -20,11 +20,11 @@ rcsb_embedding_model/modules/structure_module.py,sha256=4js02XzKvhc_G26ELsGhJ9SC
 rcsb_embedding_model/types/api_types.py,sha256=SCwALwvEb0KRKaoWKbuN7JyfOH-1whsI0Z4ki41dht8,1235
 rcsb_embedding_model/utils/data.py,sha256=BOjYdIRHrFqk8qFuKGrgCtVyfDupzgOVmH_0C-ecMvg,3813
 rcsb_embedding_model/utils/model.py,sha256=xr3p02ohOgJ5UInwdIupN68Oq4yvNFhxobZRacS1adg,953
-rcsb_embedding_model/utils/structure_parser.py,sha256=IWMQ8brlEMe6_ND-DBESOli8vlqHxladTssjbM9RSKw,2751
+rcsb_embedding_model/utils/structure_parser.py,sha256=eq1Jpmeo5oqqo_kzYbyIrqDysBAZR3II0mZK3ygaYhs,2754
 rcsb_embedding_model/utils/structure_provider.py,sha256=eWtxjkPpmRfmil_DKR1J6miaXR3lQ28DF5O0qrqSgGA,786
 rcsb_embedding_model/writer/batch_writer.py,sha256=rTFNasB0Xp4-XCNTXKeEWZxSrb7lvZytoRldJUWn9Jg,3312
-rcsb_embedding_model-0.0.29.dist-info/METADATA,sha256=R3z_Non64xek0bqI40DAoqejy2BtSuHqYuAni2R-eFA,5310
-rcsb_embedding_model-0.0.29.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-rcsb_embedding_model-0.0.29.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
-rcsb_embedding_model-0.0.29.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
-rcsb_embedding_model-0.0.29.dist-info/RECORD,,
+rcsb_embedding_model-0.0.31.dist-info/METADATA,sha256=OasAMt9K5tnejFpXPrub63YorBeBsLo8BS7L68lkvyw,5351
+rcsb_embedding_model-0.0.31.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+rcsb_embedding_model-0.0.31.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
+rcsb_embedding_model-0.0.31.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
+rcsb_embedding_model-0.0.31.dist-info/RECORD,,