RNApolis 0.4.3__py3-none-any.whl → 0.4.4__py3-none-any.whl

{RNApolis-0.4.3.dist-info → RNApolis-0.4.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.3
+Version: 0.4.4
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{RNApolis-0.4.3.dist-info → RNApolis-0.4.4.dist-info}/RECORD

@@ -6,12 +6,12 @@ rnapolis/molecule_filter.py,sha256=hB6-nXgjmw7FAsQ3bj0cZ2FvuW2I1PXunEfcdwEUB1o,7
 rnapolis/motif_extractor.py,sha256=duHvpi9Ulcny9K60E6VBpz5RpJZw-KdTB4_Ph0iP478,774
 rnapolis/parser.py,sha256=wCA9rXqt51iLECgeBqOShFpuT8JwanNkHYD5uXYvLzU,13988
 rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
-rnapolis/tertiary.py,sha256=kysCb3U93Cpxxsfq5uwFxvcI_biwMiRJgWsNZxrXcaA,20501
+rnapolis/tertiary.py,sha256=SQyiYWA0RJhAK70f88CKZvS4EzGKHQ2RoL1s4MueEDQ,21657
 rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
 rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-RNApolis-0.4.3.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.4.3.dist-info/METADATA,sha256=24AO4oRKx840RqJLNOF_SrT4xHNtu26s0Nx3URw0NZI,54322
-RNApolis-0.4.3.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-RNApolis-0.4.3.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.4.3.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.4.3.dist-info/RECORD,,
+RNApolis-0.4.4.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+RNApolis-0.4.4.dist-info/METADATA,sha256=irtWJbeg1LWun2r3WtnsnDDSHlLvru0hO9wz1e67cIE,54322
+RNApolis-0.4.4.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+RNApolis-0.4.4.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
+RNApolis-0.4.4.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+RNApolis-0.4.4.dist-info/RECORD,,

{RNApolis-0.4.3.dist-info → RNApolis-0.4.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (72.2.0)
+Generator: setuptools (74.1.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

rnapolis/tertiary.py

@@ -7,6 +7,7 @@ from typing import Dict, List, Optional, Set, Tuple, Union
 
 import numpy
 import numpy.typing
+
 from rnapolis.common import (
     BasePair,
     BpSeq,
@@ -16,6 +17,7 @@ from rnapolis.common import (
     Residue,
     ResidueAuth,
     ResidueLabel,
+    Saenger,
     Stacking,
 )
 
@@ -521,13 +523,47 @@ class Mapping2D3D:
 
     @cached_property
     def bpseq(self) -> BpSeq:
-        return self.__generate_bpseq(
-            [
-                base_pair
-                for base_pair in self.base_pairs
-                if base_pair.is_canonical and base_pair.nt1 < base_pair.nt2
-            ]
-        )
+        def pair_scoring_function(pair: BasePair3D) -> int:
+            if pair.saenger is not None:
+                if pair.saenger in (Saenger.XIX, Saenger.XX):
+                    return 0, pair.nt1, pair.nt2
+                else:
+                    return 1, pair.nt1, pair.nt2
+
+            sequence = "".join(
+                sorted(
+                    [
+                        pair.nt1_3d.one_letter_name.upper(),
+                        pair.nt2_3d.one_letter_name.upper(),
+                    ]
+                )
+            )
+            if sequence in ("AU", "AT", "CG"):
+                return 0, pair.nt1, pair.nt2
+            return 1, pair.nt1, pair.nt2
+
+        canonical = [
+            base_pair
+            for base_pair in self.base_pairs
+            if base_pair.is_canonical and base_pair.nt1 < base_pair.nt2
+        ]
+
+        while True:
+            matches = defaultdict(set)
+
+            for base_pair in canonical:
+                matches[base_pair.nt1_3d].add(base_pair)
+                matches[base_pair.nt2_3d].add(base_pair)
+
+            for pairs in matches.values():
+                if len(pairs) > 1:
+                    pairs = sorted(pairs, key=pair_scoring_function)
+                    canonical.remove(pairs[-1])
+                    break
+            else:
+                break
+
+        return self.__generate_bpseq(canonical)
 
     def __generate_bpseq(self, base_pairs):
         result: Dict[int, List] = {}