RNApolis 0.4.0__py3-none-any.whl → 0.4.1__py3-none-any.whl

{RNApolis-0.4.0.dist-info → RNApolis-0.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.0
+Version: 0.4.1
 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-0.4.1.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=qk1te8GPDuvQsnm4rTiw96VDYyNoO5x4IPf98zDzxPw,20824
 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-0.4.1.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+RNApolis-0.4.1.dist-info/METADATA,sha256=EayMQbE4Y5raff-7pFMmeh4EB81JaLEEMrbvEA4mbAk,54322
+RNApolis-0.4.1.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+RNApolis-0.4.1.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
+RNApolis-0.4.1.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+RNApolis-0.4.1.dist-info/RECORD,,

rnapolis/tertiary.py

@@ -548,7 +548,20 @@ class Mapping2D3D:
         result: Dict[int, List] = {}
         residue_map: Dict[Residue3D, int] = {}
         i = 1
-        for residue in self.structure3d.residues:
+
+        for j, residue in enumerate(self.structure3d.residues):
+            if self.find_gaps and j > 0:
+                previous = self.structure3d.residues[j - 1]
+                if (
+                    previous.is_nucleotide
+                    and residue.is_nucleotide
+                    and previous.label
+                    and residue.label
+                    and previous.label.chain == residue.label.chain
+                ):
+                    for k in range(residue.label.number - previous.label.number - 1):
+                        result[i] = [i, "?", 0]
+                        i += 1
             if residue.is_nucleotide:
                 result[i] = [i, residue.one_letter_name, 0]
                 residue_map[residue] = i