RNApolis 0.4.13__py3-none-any.whl → 0.4.15__py3-none-any.whl

{RNApolis-0.4.13.dist-info → RNApolis-0.4.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: RNApolis
-Version: 0.4.13
+Version: 0.4.15
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok
@@ -26,6 +26,15 @@ Requires-Dist: pulp
 Requires-Dist: requests
 Requires-Dist: scipy
 Requires-Dist: viennarna
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: summary
 
 # RNApolis
 

{RNApolis-0.4.13.dist-info → RNApolis-0.4.15.dist-info}/RECORD

@@ -1,17 +1,17 @@
-rnapolis/annotator.py,sha256=_hsSX2VHFvIQ47l_EA7lwGFXLiVLbhFPEsOQzBKbjRk,22100
+rnapolis/annotator.py,sha256=hRRzRmneYxbg2tvwVHMWLfzmJb4szV0JL_6EOC09Gwg,22101
 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=1TDEIy2rgWXXqXxI21vjaElWExCFZlmCHWxwCfNehaM,9152
+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/parser.py,sha256=3g4mtFvpiEENFcSBBtx_E_x1vJPF9BujWnts0kb9XjE,16340
 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-0.4.13.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.4.13.dist-info/METADATA,sha256=wzV8Xvo09Qv02NfCKaLTID2Sm9k07aKsSZzqVWaNwf8,54323
-RNApolis-0.4.13.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-RNApolis-0.4.13.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.4.13.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.4.13.dist-info/RECORD,,
+RNApolis-0.4.15.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+RNApolis-0.4.15.dist-info/METADATA,sha256=qLYXvmGt9gT0KsEnD-303D8EqqpVz5-hZYCekAOAn1E,54516
+RNApolis-0.4.15.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+RNApolis-0.4.15.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
+RNApolis-0.4.15.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+RNApolis-0.4.15.dist-info/RECORD,,

{RNApolis-0.4.13.dist-info → RNApolis-0.4.15.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

rnapolis/annotator.py

@@ -11,6 +11,8 @@ import numpy
 import numpy.typing
 import orjson
 from ordered_set import OrderedSet
+from scipy.spatial import KDTree
+
 from rnapolis.common import (
     BR,
     BaseInteractions,
@@ -42,7 +44,6 @@ from rnapolis.tertiary import (
     torsion_angle,
 )
 from rnapolis.util import handle_input_file
-from scipy.spatial import KDTree
 
 HYDROGEN_BOND_MAX_DISTANCE = 4.0
 HYDROGEN_BOND_ANGLE_RANGE = (50.0, 130.0)  # 90 degrees is ideal, so allow +- 40 degrees

rnapolis/molecule_filter.py

@@ -156,7 +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()
 
@@ -187,13 +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.
 
@@ -228,6 +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/parser.py

@@ -218,7 +218,9 @@ def parse_cif(
                     )
 
                 if entity_id and pdbx_seq_one_letter_code_can:
-                    sequence_by_entity[entity_id] = pdbx_seq_one_letter_code_can
+                    sequence_by_entity[entity_id] = (
+                        pdbx_seq_one_letter_code_can.replace("\n", "")
+                    )
 
         if entity:
             for row in entity.getRowList():
@@ -234,7 +236,16 @@ def parse_cif(
 
                     if type_:
                         is_nucleic_acid_by_entity[entity_id] = (
-                            is_nucleic_acid_by_entity.get(entity_id, type_)
+                            is_nucleic_acid_by_entity.get(
+                                entity_id,
+                                type_
+                                in (
+                                    "peptide nucleic acid",
+                                    "polydeoxyribonucleotide",
+                                    "polydeoxyribonucleotide/polyribonucleotide hybrid",
+                                    "polyribonucleotide",
+                                ),
+                            )
                         )
 
     atoms = filter_clashing_atoms(atoms_to_process)