rcsb-embedding-model 0.0.30__py3-none-any.whl → 0.0.32__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/esm_prot_from_chain.py

@@ -11,7 +11,7 @@ import pandas as pd
 
 from rcsb_embedding_model.types.api_types import StructureFormat, StructureLocation, SrcLocation
 from rcsb_embedding_model.utils.data import stringio_from_url
-from rcsb_embedding_model.utils.structure_parser import rename_atom_ch
+from rcsb_embedding_model.utils.structure_parser import rename_atom_ch, check_all_hetero, remove_hetero
 from rcsb_embedding_model.utils.structure_provider import StructureProvider
 
 
@@ -72,8 +72,14 @@ class EsmProtFromChain(Dataset):
         for atom_ch in chain_iter(structure):
             if len(atom_ch) == 0:
                 raise IOError(f"No atoms were found in structure chain {src_name}.{chain_id}")
-            protein_chain = ProteinChain.from_atomarray(rename_atom_ch(atom_ch))
-            return ESMProtein.from_protein_chain(protein_chain), item_name
+            if check_all_hetero(atom_ch):
+                atom_ch = remove_hetero(atom_ch)
+            atom_ch = rename_atom_ch(atom_ch)
+            protein_chain = ProteinChain.from_atomarray(atom_ch)
+            protein_chain = ESMProtein.from_protein_chain(protein_chain)
+            if len(protein_chain) == 0:
+                raise IOError(f"No atoms were found in structure chain {src_name}.{chain_id}")
+            return protein_chain, item_name
         raise IOError(f"No atoms were found in structure chain {src_name}.{chain_id}")
 
 

rcsb_embedding_model/utils/structure_parser.py

@@ -50,14 +50,24 @@ def get_assemblies(structure, structure_format="mmcif"):
 
 def rename_atom_ch(atom_ch, ch="A"):
     renamed_atom_ch = AtomArray(len(atom_ch))
-    n = 0
-    for atom in atom_ch:
+    for idx, atom in enumerate(atom_ch):
         atom.chain_id = ch
-        renamed_atom_ch[n] = atom
-        n += 1
+        renamed_atom_ch[idx] = atom
     return renamed_atom_ch
 
 
+def remove_hetero(atom_ch):
+    renamed_atom_ch = AtomArray(len(atom_ch))
+    for idx, atom in enumerate(atom_ch):
+        atom.hetero = False
+        renamed_atom_ch[idx] = atom
+    return renamed_atom_ch
+
+
+def check_all_hetero(atom_ch):
+    return sum(atom_ch.hetero) == len(atom_ch)
+
+
 def __get_pdb_structure(pdb_file, assembly_id=None):
     return get_pdb_structure(
         pdb_file,

{rcsb_embedding_model-0.0.30.dist-info → rcsb_embedding_model-0.0.32.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rcsb-embedding-model
-Version: 0.0.30
+Version: 0.0.32
 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-0.0.30.dist-info → rcsb_embedding_model-0.0.32.dist-info}/RECORD

@@ -1,8 +1,8 @@
-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/dataset/esm_prot_from_chain.py,sha256=l8pRgRpz-8gEzR6QsNcmdnX_KkgvgF1vdqNAsP8Lrc8,3960
+rcsb_embedding_model/cli/inference.py,sha256=67_Tr3LWeA3T4KS5mkjq6tw77Ypy0R8IwMxEG2FwVqQ,19901
+rcsb_embedding_model/dataset/esm_prot_from_chain.py,sha256=HuKII1zOnO0JF6wZXyqBykiGunSFXmhzBimsSpbEC1I,4291
 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=Hd9oH-IVgY6d7Dxy5VfiwHvSaK-Wwhk6ccUBgOwl0TU,3740
@@ -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=eq1Jpmeo5oqqo_kzYbyIrqDysBAZR3II0mZK3ygaYhs,2754
+rcsb_embedding_model/utils/structure_parser.py,sha256=z_Aid5QgGUAJkLL-fMzG2Uh2wPrHXmBdjhLn_YkPl-k,3035
 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-0.0.30.dist-info/METADATA,sha256=IjxTnTFbYAIGu99NNAH2MII46PvFMZXEkim5STOCNTU,5310
-rcsb_embedding_model-0.0.30.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-rcsb_embedding_model-0.0.30.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
-rcsb_embedding_model-0.0.30.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
-rcsb_embedding_model-0.0.30.dist-info/RECORD,,
+rcsb_embedding_model-0.0.32.dist-info/METADATA,sha256=JWSb2a_wZ2Y8YWzyM3vk_QG--ukrIGsI5Q1-R3bApjs,5351
+rcsb_embedding_model-0.0.32.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+rcsb_embedding_model-0.0.32.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
+rcsb_embedding_model-0.0.32.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
+rcsb_embedding_model-0.0.32.dist-info/RECORD,,