RNApolis 0.4.12__tar.gz → 0.4.14__tar.gz

{rnapolis-0.4.12/src/RNApolis.egg-info → rnapolis-0.4.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.12
+Version: 0.4.14
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.4.12 → rnapolis-0.4.14}/setup.py

@@ -5,7 +5,7 @@ with open("README.md") as f:
 
 setup(
     name="RNApolis",
-    version="0.4.12",
+    version="0.4.14",
     packages=["rnapolis"],
     package_dir={"": "src"},
     author="Tomasz Zok",

{rnapolis-0.4.12 → rnapolis-0.4.14/src/RNApolis.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.12
+Version: 0.4.14
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.4.12 → rnapolis-0.4.14}/src/rnapolis/molecule_filter.py

@@ -21,6 +21,7 @@ ENTITY_POLY_TYPES = [
 ]
 
 CATEGORIES_WITH_ENTITY_ID = [
+    ("entity", "id"),
     ("atom_site", "label_entity_id"),
     ("entity_keywords", "entity_id"),
     ("entity_name_com", "entity_id"),
@@ -155,7 +156,9 @@ def select_category_by_id(
 
 
 def filter_by_poly_types(
-    file_content: str, entity_poly_types: Iterable[str] = ["polyribonucleotide"]
+    file_content: str,
+    entity_poly_types: Iterable[str] = ["polyribonucleotide"],
+    retain_categories: Iterable[str] = [],
 ) -> str:
     adapter = IoAdapterPy()
 
@@ -186,13 +189,20 @@ def filter_by_poly_types(
                 obj = DataCategory(category, attributes, rows)
                 output.append(obj)
 
+    for category in retain_categories:
+        obj = data[0].getObj(category)
+        if obj:
+            output.append(obj)
+
     with tempfile.NamedTemporaryFile("rt+") as tmp:
         adapter.writeFile(tmp.name, [output])
         tmp.seek(0)
         return tmp.read()
 
 
-def filter_by_chains(file_content: str, chains: Iterable[str]) -> str:
+def filter_by_chains(
+    file_content: str, chains: Iterable[str], retain_categories: Iterable[str] = []
+) -> str:
     """
     Filter a PDBx/mmCIF file by chain IDs. The function returns a new PDBx/mmCIF file.
 
@@ -227,6 +237,11 @@ def filter_by_chains(file_content: str, chains: Iterable[str]) -> str:
                 obj = DataCategory(category, attributes, rows)
                 output.append(obj)
 
+    for category in retain_categories:
+        obj = data[0].getObj(category)
+        if obj:
+            output.append(obj)
+
     with tempfile.NamedTemporaryFile("rt+") as tmp:
         adapter.writeFile(tmp.name, [output])
         tmp.seek(0)

{rnapolis-0.4.12 → rnapolis-0.4.14}/tests/test_molecule_filter.py

@@ -1,3 +1,4 @@
+import re
 import tempfile
 
 from rnapolis.molecule_filter import filter_by_chains, filter_by_poly_types
@@ -8,7 +9,9 @@ def test_filter_by_poly_types():
     with open("tests/1a9n.cif") as f:
         content = f.read()
 
-    filtered = filter_by_poly_types(content, ["polyribonucleotide"])
+    filtered = filter_by_poly_types(content, ["polyribonucleotide"], ["chem_comp"])
+    assert re.search(r"^_entity\.id", filtered, re.MULTILINE) is not None
+    assert re.search(r"^_chem_comp\.id", filtered, re.MULTILINE) is not None
 
     with tempfile.NamedTemporaryFile("rt+") as f:
         f.write(filtered)
@@ -23,7 +26,9 @@ def test_filter_by_chains():
     with open("tests/1a9n.cif") as f:
         content = f.read()
 
-    filtered = filter_by_chains(content, ["A", "C"])
+    filtered = filter_by_chains(content, ["A", "C"], ["chem_comp"])
+    assert re.search(r"^_entity\.id", filtered, re.MULTILINE) is not None
+    assert re.search(r"^_chem_comp\.id", filtered, re.MULTILINE) is not None
 
     with tempfile.NamedTemporaryFile("rt+") as f:
         f.write(filtered)