RNApolis 0.4.2__py3-none-any.whl → 0.4.3__py3-none-any.whl

{RNApolis-0.4.2.dist-info → RNApolis-0.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.2
+Version: 0.4.3
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{RNApolis-0.4.2.dist-info → RNApolis-0.4.3.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=ya7A2HyhPZSbA4rC8E43-mRIhR73-AeBuLE2GRpOTxk,20347
+rnapolis/tertiary.py,sha256=kysCb3U93Cpxxsfq5uwFxvcI_biwMiRJgWsNZxrXcaA,20501
 rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
 rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-RNApolis-0.4.2.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.4.2.dist-info/METADATA,sha256=1rZv7syiOsppxC9PAy0kYmgBXABKCX4gWZaqdtpbvis,54322
-RNApolis-0.4.2.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-RNApolis-0.4.2.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.4.2.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.4.2.dist-info/RECORD,,
+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/tertiary.py

@@ -497,24 +497,27 @@ class Mapping2D3D:
 
     @cached_property
     def strands_sequences(self) -> List[Tuple[str, str]]:
-        result = defaultdict(list)
+        nucleotides = list(filter(lambda r: r.is_nucleotide, self.structure3d.residues))
 
-        for i, residue in enumerate(
-            filter(lambda r: r.is_nucleotide, self.structure3d.residues)
-        ):
-            if i > 0 and self.find_gaps:
-                previous = self.structure3d.residues[i - 1]
+        if not nucleotides:
+            return []
 
-                if (
-                    not previous.is_connected(residue)
-                    and previous.chain == residue.chain
-                ):
-                    for k in range(residue.number - previous.number - 1):
-                        result[residue.chain].append("?")
+        result = [(nucleotides[0].chain, [nucleotides[0].one_letter_name])]
+
+        for i in range(1, len(nucleotides)):
+            previous = nucleotides[i - 1]
+            residue = nucleotides[i]
 
-            result[residue.chain].append(residue.one_letter_name)
+            if residue.chain != previous.chain:
+                result.append((residue.chain, [residue.one_letter_name]))
+            else:
+                if self.find_gaps:
+                    if not previous.is_connected(residue):
+                        for k in range(residue.number - previous.number - 1):
+                            result[-1][1].append("?")
+                result[-1][1].append(residue.one_letter_name)
 
-        return [(chain, "".join(sequence)) for chain, sequence in result.items()]
+        return [(chain, "".join(sequence)) for chain, sequence in result]
 
     @cached_property
     def bpseq(self) -> BpSeq: