rcsb-embedding-model 0.0.31__tar.gz → 0.0.32__tar.gz

{rcsb_embedding_model-0.0.31 → rcsb_embedding_model-0.0.32}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rcsb-embedding-model
-Version: 0.0.31
+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

{rcsb_embedding_model-0.0.31 → rcsb_embedding_model-0.0.32}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rcsb-embedding-model"
-version = "0.0.31"
+version = "0.0.32"
 authors = [
     { name="Joan Segura", email="joan.segura@rcsb.org" },
 ]

{rcsb_embedding_model-0.0.31 → rcsb_embedding_model-0.0.32}/src/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-0.0.31 → rcsb_embedding_model-0.0.32}/src/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,