RNApolis 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

rnapolis/aligner.py

@@ -43,22 +43,38 @@ def main():
             elif line.startswith("pdb2"):
                 pdb2_aligned.append(line.split()[1])
 
-    pdb1_aligned = " ".join(pdb1_aligned)
-    pdb2_aligned = " ".join(pdb2_aligned)
+    pdb1_aligned = "".join(pdb1_aligned)
+    pdb2_aligned = "".join(pdb2_aligned)
     residues_to_remove = {"pdb1": [], "pdb2": []}
 
-    for i, (c1, c2) in enumerate(zip(pdb1_aligned, pdb2_aligned)):
+    i, j = 0, 0
+    for c1, c2 in zip(pdb1_aligned, pdb2_aligned):
+        if c1 == c2 == "-":
+            continue  # Should not happen to have gap aligned to gap, but just in case
+
         if c1 == c2:
+            i += 1
+            j += 1
             continue
+
         if c1 == "-":
-            residues_to_remove["pdb2"].append(i)
-        elif c2 == "-":
+            residues_to_remove["pdb2"].append(j)
+            j += 1
+            continue
+
+        if c2 == "-":
             residues_to_remove["pdb1"].append(i)
-        elif c1 != c2:
+            i += 1
+            continue
+
+        if c1 != c2:
             residues_to_remove["pdb1"].append(i)
-            residues_to_remove["pdb2"].append(i)
-        else:
-            raise ValueError("This should not happen!")
+            residues_to_remove["pdb2"].append(j)
+            i += 1
+            j += 1
+            continue
+
+        raise ValueError("This should not happen!")
 
     if not residues_to_remove["pdb1"] and not residues_to_remove["pdb2"]:
         print("Structures are already aligned")

rnapolis/unifier.py

@@ -73,6 +73,7 @@ def main():
 
         structures.append((path, residues))
 
+    residues_to_remove = set()
     for path, residues in structures:
         ref_path, ref_residues = structures[0]
 
@@ -92,7 +93,6 @@ def main():
                 sys.exit(1)
 
         # Find residues with different number of atoms
-        residues_to_remove = set()
         for i, (residue, ref_residue) in enumerate(zip(residues, ref_residues)):
             if len(residue.atoms) != len(ref_residue.atoms):
                 print(

{rnapolis-0.6.0.dist-info → rnapolis-0.6.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RNApolis
-Version: 0.6.0
+Version: 0.6.2
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.6.0.dist-info → rnapolis-0.6.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-rnapolis/aligner.py,sha256=oJ81FrjlEEzqJcYJdZUE1PrPjabIOT7j0idwAHXVQMI,3156
+rnapolis/aligner.py,sha256=o7rQyjAZ3n4VXcnSPY3HVB8nLNRkVbl552O3NVh0mfg,3429
 rnapolis/annotator.py,sha256=hRRzRmneYxbg2tvwVHMWLfzmJb4szV0JL_6EOC09Gwg,22101
 rnapolis/clashfinder.py,sha256=AC9_tIx7QIk57sELq_aKfU1u3UMOXbgcccQeGHhMR6c,8517
 rnapolis/common.py,sha256=LY6Uz96Br8ki_gA8LpfatgtvVbt9jOTkwgagayqTgf8,31251
@@ -16,11 +16,11 @@ rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
 rnapolis/tertiary.py,sha256=6t9ZB4w33-5n_M3sns1RoFXCOTgVAgGH4WDNG5OG9Kg,23426
 rnapolis/tertiary_v2.py,sha256=I1uyHWIUePNGO5m-suoL4ibtz02qAJUMvYm0BUKUygY,22480
 rnapolis/transformer.py,sha256=aC0nBmHHJf5TyLvBIV57Jj3tlwpvHbPo347opfAOlQA,3844
-rnapolis/unifier.py,sha256=bXscX3lxeSxT4K1fm2UEURcU9_0JA0HdTbd8ZoHZFAY,5442
+rnapolis/unifier.py,sha256=DR1_IllgaAYT9_FUE6XC9B-2wgqbBHs2D1MjyZT2j2g,5438
 rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-rnapolis-0.6.0.dist-info/licenses/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-rnapolis-0.6.0.dist-info/METADATA,sha256=TcGmjLlYH8jPvWJr48a2ce-UhIIl_dAO_wygm4ZPrKY,54537
-rnapolis-0.6.0.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-rnapolis-0.6.0.dist-info/entry_points.txt,sha256=kS_Ji3_6UaomxkOaYpGHh4aZKaIh9CAfzoexbaS3y50,372
-rnapolis-0.6.0.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-rnapolis-0.6.0.dist-info/RECORD,,
+rnapolis-0.6.2.dist-info/licenses/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+rnapolis-0.6.2.dist-info/METADATA,sha256=2epFKLVBOoNmJHGZSSSF4bNEdOq2eB_KpWKmannB7rY,54537
+rnapolis-0.6.2.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+rnapolis-0.6.2.dist-info/entry_points.txt,sha256=kS_Ji3_6UaomxkOaYpGHh4aZKaIh9CAfzoexbaS3y50,372
+rnapolis-0.6.2.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+rnapolis-0.6.2.dist-info/RECORD,,