RNApolis 0.6.0__tar.gz → 0.6.1__tar.gz

{rnapolis-0.6.0/src/RNApolis.egg-info → rnapolis-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RNApolis
-Version: 0.6.0
+Version: 0.6.1
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.6.0 → rnapolis-0.6.1}/setup.py

@@ -5,7 +5,7 @@ with open("README.md") as f:
 
 setup(
     name="RNApolis",
-    version="0.6.0",
+    version="0.6.1",
     packages=["rnapolis"],
     package_dir={"": "src"},
     author="Tomasz Zok",

{rnapolis-0.6.0 → rnapolis-0.6.1/src/RNApolis.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RNApolis
-Version: 0.6.0
+Version: 0.6.1
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.6.0 → rnapolis-0.6.1}/src/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")