Add optional ligand_indices input to RandomLigandRotationMove

Allows users to explicitly specify ligand atom indices via the new  argument, avoiding reliance on residue name parsing. If provided,  overrides the default selection based on

Author: stevenayoub

blues/moves.py

@@ -160,7 +160,8 @@ class RandomLigandRotationMove(Move):
         ParmEd Structure object of the relevant system to be moved.
     random_state : integer or numpy.RandomState, optional
         The generator used for random numbers. If an integer is given, it fixes the seed. Defaults to the global numpy random number generator.
-
+    ligand_indices : list of int, optional
+        List of atom indices identifying the ligand to be rotated. If provided, overrides `resname` selection.
     Attributes
     ----------
     structure : parmed.Structure
@@ -190,17 +191,21 @@ class RandomLigandRotationMove(Move):
         'LIG'
     """
 
-    def __init__(self, structure, resname='LIG', random_state=None):
+    def __init__(self, structure, resname='LIG', ligand_indices=None, random_state=None):
         self.structure = structure
         self.resname = resname
         self.random_state = random_state
         self.atom_indices = self.getAtomIndices(structure, self.resname)
-        atom_indices_1based = [i + 1 for i in self.atom_indices]
-        self.topology = structure[atom_indices_1based].topology
+        self.ligand_indices = ligand_indices
+        self.topology = structure[self.atom_indices].topology
         self.totalmass = 0
         self.masses = []
         self.center_of_mass = None
-        self.positions = structure[atom_indices_1based].positions
+        self.positions = structure[self.atom_indices].positions
+        if self.ligand_indices:
+            self.topology = structure[self.ligand_indices].topology
+            self.positions = structure[self.ligand_indices].positions
+
         self._calculateProperties()
 
     def getAtomIndices(self, structure, resname):