RNApolis 0.4.0__py3-none-any.whl → 0.4.2__py3-none-any.whl

{RNApolis-0.4.0.dist-info → RNApolis-0.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.0
+Version: 0.4.2
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{RNApolis-0.4.0.dist-info → RNApolis-0.4.2.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=iA5_ut1_nhwlbYpu2898h5li4pTEOc-iA_uK7vIvQ2o,20269
+rnapolis/tertiary.py,sha256=ya7A2HyhPZSbA4rC8E43-mRIhR73-AeBuLE2GRpOTxk,20347
 rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
 rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-RNApolis-0.4.0.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.4.0.dist-info/METADATA,sha256=kz7fPjyFm8j6HMwnDvtwlLkZGPpzw2Ce29XI1pVyIyU,54322
-RNApolis-0.4.0.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-RNApolis-0.4.0.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.4.0.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.4.0.dist-info/RECORD,,
+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/tertiary.py

@@ -497,42 +497,24 @@ class Mapping2D3D:
 
     @cached_property
     def strands_sequences(self) -> List[Tuple[str, str]]:
-        nucleotides = [
-            residue for residue in self.structure3d.residues if residue.is_nucleotide
-        ]
+        result = defaultdict(list)
 
-        if len(nucleotides) == 0:
-            return []
+        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]
 
-        result = []
-        strand = [nucleotides[0]]
-
-        for i in range(1, len(nucleotides)):
-            previous = strand[-1]
-            current = nucleotides[i]
-
-            if previous.chain == current.chain and (
-                self.find_gaps == False or previous.is_connected(current)
-            ):
-                strand.append(current)
-            else:
-                result.append(
-                    (
-                        previous.chain,
-                        "".join([residue.one_letter_name for residue in strand]),
-                    )
-                )
-                strand = [current]
+                if (
+                    not previous.is_connected(residue)
+                    and previous.chain == residue.chain
+                ):
+                    for k in range(residue.number - previous.number - 1):
+                        result[residue.chain].append("?")
 
-        if len(strand) > 0:
-            result.append(
-                (
-                    strand[0].chain,
-                    "".join([residue.one_letter_name for residue in strand]),
-                )
-            )
+            result[residue.chain].append(residue.one_letter_name)
 
-        return result
+        return [(chain, "".join(sequence)) for chain, sequence in result.items()]
 
     @cached_property
     def bpseq(self) -> BpSeq:
@@ -548,11 +530,24 @@ class Mapping2D3D:
         result: Dict[int, List] = {}
         residue_map: Dict[Residue3D, int] = {}
         i = 1
-        for residue in self.structure3d.residues:
-            if residue.is_nucleotide:
-                result[i] = [i, residue.one_letter_name, 0]
-                residue_map[residue] = i
-                i += 1
+
+        for j, residue in enumerate(
+            filter(lambda r: r.is_nucleotide, self.structure3d.residues)
+        ):
+            if self.find_gaps and j > 0:
+                previous = self.structure3d.residues[j - 1]
+
+                if (
+                    not previous.is_connected(residue)
+                    and previous.chain == residue.chain
+                ):
+                    for k in range(residue.number - previous.number - 1):
+                        result[i] = [i, "?", 0]
+                        i += 1
+
+            result[i] = [i, residue.one_letter_name, 0]
+            residue_map[residue] = i
+            i += 1
 
         for base_pair in base_pairs:
             j = residue_map.get(base_pair.nt1_3d, None)