RNApolis 0.4.12__py3-none-any.whl → 0.4.14__py3-none-any.whl

{RNApolis-0.4.12.dist-info → RNApolis-0.4.14.dist-info}/METADATA

@@ -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.dist-info → RNApolis-0.4.14.dist-info}/RECORD

@@ -2,16 +2,16 @@ rnapolis/annotator.py,sha256=_hsSX2VHFvIQ47l_EA7lwGFXLiVLbhFPEsOQzBKbjRk,22100
 rnapolis/clashfinder.py,sha256=i95kp0o6OWNqmJDBr-PbsZd7RY2iJtBDr7QqolJSuAQ,8513
 rnapolis/common.py,sha256=LY6Uz96Br8ki_gA8LpfatgtvVbt9jOTkwgagayqTgf8,31251
 rnapolis/metareader.py,sha256=I1-cXc2YNBPwa3zihAnMTjEsAo79tEKzSmWu5yvN1Pk,2071
-rnapolis/molecule_filter.py,sha256=F_xkAe7q2NZAaDpRaeikv-twUvbNflWdlLte7oFn2Ms,9130
+rnapolis/molecule_filter.py,sha256=_7zrF-AH56vXI4vhFtfaU9wr-X7aeOL6DsXbX6_9vPQ,9497
 rnapolis/motif_extractor.py,sha256=Lfn1iEkhkP9eZD3GPEWNAfy00QO7QPCc8wM_XS1ory8,1147
 rnapolis/parser.py,sha256=lHI6LyFbEEPdHOzbged1-Ov0tl6MpSungIPacip0Py0,15838
 rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
 rnapolis/tertiary.py,sha256=6t9ZB4w33-5n_M3sns1RoFXCOTgVAgGH4WDNG5OG9Kg,23426
 rnapolis/transformer.py,sha256=aC0nBmHHJf5TyLvBIV57Jj3tlwpvHbPo347opfAOlQA,3844
 rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-RNApolis-0.4.12.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.4.12.dist-info/METADATA,sha256=fPrlpVrM83UYwPYwaeymBP7SeVLMv7XftCZOl7hUnes,54323
-RNApolis-0.4.12.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-RNApolis-0.4.12.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.4.12.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.4.12.dist-info/RECORD,,
+RNApolis-0.4.14.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+RNApolis-0.4.14.dist-info/METADATA,sha256=MY6ulJgbaM4qJggOEswGUArvP0IsIMBX-zeoebjqjzk,54323
+RNApolis-0.4.14.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+RNApolis-0.4.14.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
+RNApolis-0.4.14.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+RNApolis-0.4.14.dist-info/RECORD,,

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)