bugfix: reading topology file

checking of last word of topology file block was .lower() == "END" - changed now to .lower() == "end"
MolarVerse · May 31, 2024 · 45e78ed · 45e78ed
1 parent d63a63b
commit 45e78ed
Showing 1 changed file with 30 additions and 31 deletions.
diff --git a/PQAnalysis/io/topology_file/topology_file_reader.py b/PQAnalysis/io/topology_file/topology_file_reader.py
@@ -90,7 +90,7 @@ def _get_definitions(self) -> dict[str, List[str]]:
             lines = [line for line in lines if line.strip()]
 
             # check if last line is END else raise error
-            if lines[-1].strip() != "END":
+            if lines[-1].strip().lower() != "end":
                 self.logger.error(
                     "Something went wrong. Each block should end with 'END'",
                     exception=TopologyFileError,
@@ -100,7 +100,7 @@ def _get_definitions(self) -> dict[str, List[str]]:
             blocks = []
             block = []
             for line in lines:
-                if line.strip().lower() == "END":
+                if line.strip().lower() == "end":
                     blocks.append(block)
                     block = []
                 else:
@@ -163,8 +163,7 @@ def _parse_blocks(self, blocks: dict[str, List[str]]) -> BondedTopology:
                 impropers = self._parse_impropers(value)
             else:
                 self.logger.error(
-                    f"Unknown block {key}",
-                    exception=TopologyFileError
+                    f"Unknown block {key}", exception=TopologyFileError
                 )
 
         return BondedTopology(
@@ -217,10 +216,10 @@ def _parse_bonds(self, block: List[str]) -> List[Bond]:
 
             bonds.append(
                 Bond(
-                index1=int(index),
-                index2=int(target_index),
-                bond_type=int(bond_type),
-                is_linker=is_linker,
+                    index1=int(index),
+                    index2=int(target_index),
+                    bond_type=int(bond_type),
+                    is_linker=is_linker,
                 )
             )
 
@@ -267,11 +266,11 @@ def _parse_angles(self, block: List[str]) -> List[Angle]:
 
             angles.append(
                 Angle(
-                index1=int(index1),
-                index2=int(index2),
-                index3=int(index3),
-                angle_type=int(angle_type),
-                is_linker=is_linker,
+                    index1=int(index1),
+                    index2=int(index2),
+                    index3=int(index3),
+                    angle_type=int(angle_type),
+                    is_linker=is_linker,
                 )
             )
 
@@ -318,12 +317,12 @@ def _parse_dihedrals(self, block: List[str]) -> List[Dihedral]:
 
             dihedrals.append(
                 Dihedral(
-                index1=int(index1),
-                index2=int(index2),
-                index3=int(index3),
-                index4=int(index4),
-                dihedral_type=int(dihedral_type),
-                is_linker=is_linker,
+                    index1=int(index1),
+                    index2=int(index2),
+                    index3=int(index3),
+                    index4=int(index4),
+                    dihedral_type=int(dihedral_type),
+                    is_linker=is_linker,
                 )
             )
 
@@ -370,13 +369,13 @@ def _parse_impropers(self, block: List[str]) -> List[Dihedral]:
 
             dihedrals.append(
                 Dihedral(
-                index1=int(index1),
-                index2=int(index2),
-                index3=int(index3),
-                index4=int(index4),
-                dihedral_type=int(dihedral_type),
-                is_linker=is_linker,
-                is_improper=True,
+                    index1=int(index1),
+                    index2=int(index2),
+                    index3=int(index3),
+                    index4=int(index4),
+                    dihedral_type=int(dihedral_type),
+                    is_linker=is_linker,
+                    is_improper=True,
                 )
             )
 
@@ -418,11 +417,11 @@ def _parse_shake(self, block: List[str]) -> List[Bond]:
 
             shake_bonds.append(
                 Bond(
-                index1=int(index),
-                index2=int(target_index),
-                equilibrium_distance=float(distance),
-                is_linker=is_linker,
-                is_shake=True,
+                    index1=int(index),
+                    index2=int(target_index),
+                    equilibrium_distance=float(distance),
+                    is_linker=is_linker,
+                    is_shake=True,
                 )
             )