From 50b5bb6092bc61b4204e8b3b918b4e120251ea65 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 22 Feb 2024 13:30:29 +0000
Subject: [PATCH] Recover missing molecule0 and molecule1 properties. [closes
 #248]

---
 .../Exscientia/_SireWrappers/_molecule.py     | 28 ++++---------------
 python/BioSimSpace/_SireWrappers/_molecule.py | 28 ++++---------------
 2 files changed, 12 insertions(+), 44 deletions(-)

diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py
index 80ed3de08..7da921f96 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py
@@ -80,13 +80,16 @@ def __init__(self, molecule):
         if isinstance(molecule, _SireMol._Mol.Molecule):
             super().__init__(molecule)
             if self._sire_object.hasProperty("is_perturbable"):
-                self._convertFromMergedMolecule()
+                # Flag that the molecule is perturbable.
+                self._is_perturbable = True
+
+                # Extract the end states.
                 if molecule.hasProperty("molecule0"):
-                    self._molecule = Molecule(molecule.property("molecule0"))
+                    self._molecule0 = Molecule(molecule.property("molecule0"))
                 else:
                     self._molecule0, _ = self._extractMolecule()
                 if molecule.hasProperty("molecule1"):
-                    self._molecule = Molecule(molecule.property("molecule1"))
+                    self._molecule1 = Molecule(molecule.property("molecule1"))
                 else:
                     self._molecule1, _ = self._extractMolecule(is_lambda1=True)
 
@@ -1565,25 +1568,6 @@ def _getPropertyMap1(self):
 
         return property_map
 
-    def _convertFromMergedMolecule(self):
-        """Convert from a merged molecule."""
-
-        # Extract the components of the merged molecule.
-        try:
-            mol0 = self._sire_object.property("molecule0")
-            mol1 = self._sire_object.property("molecule1")
-        except:
-            raise _IncompatibleError(
-                "The merged molecule doesn't have the required properties!"
-            )
-
-        # Store the components.
-        self._molecule0 = Molecule(mol0)
-        self._molecule1 = Molecule(mol1)
-
-        # Flag that the molecule is perturbable.
-        self._is_perturbable = True
-
     def _fixCharge(self, property_map={}):
         """
         Make the molecular charge an integer value.
diff --git a/python/BioSimSpace/_SireWrappers/_molecule.py b/python/BioSimSpace/_SireWrappers/_molecule.py
index 02b662c14..44af7619c 100644
--- a/python/BioSimSpace/_SireWrappers/_molecule.py
+++ b/python/BioSimSpace/_SireWrappers/_molecule.py
@@ -80,13 +80,16 @@ def __init__(self, molecule):
         if isinstance(molecule, _SireMol._Mol.Molecule):
             super().__init__(molecule)
             if self._sire_object.hasProperty("is_perturbable"):
-                self._convertFromMergedMolecule()
+                # Flag that the molecule is perturbable.
+                self._is_perturbable = True
+
+                # Extract the end states.
                 if molecule.hasProperty("molecule0"):
-                    self._molecule = Molecule(molecule.property("molecule0"))
+                    self._molecule0 = Molecule(molecule.property("molecule0"))
                 else:
                     self._molecule0, _ = self._extractMolecule()
                 if molecule.hasProperty("molecule1"):
-                    self._molecule = Molecule(molecule.property("molecule1"))
+                    self._molecule1 = Molecule(molecule.property("molecule1"))
                 else:
                     self._molecule1, _ = self._extractMolecule(is_lambda1=True)
 
@@ -1521,25 +1524,6 @@ def _getPropertyMap1(self):
 
         return property_map
 
-    def _convertFromMergedMolecule(self):
-        """Convert from a merged molecule."""
-
-        # Extract the components of the merged molecule.
-        try:
-            mol0 = self._sire_object.property("molecule0")
-            mol1 = self._sire_object.property("molecule1")
-        except:
-            raise _IncompatibleError(
-                "The merged molecule doesn't have the required properties!"
-            )
-
-        # Store the components.
-        self._molecule0 = Molecule(mol0)
-        self._molecule1 = Molecule(mol1)
-
-        # Flag that the molecule is perturbable.
-        self._is_perturbable = True
-
     def _fixCharge(self, property_map={}):
         """
         Make the molecular charge an integer value.