From 76ca9e4a2accffe7b539962c9075b6a12caa4911 Mon Sep 17 00:00:00 2001
From: Alon Grinberg Dana <alon@technion.ac.il>
Date: Thu, 10 Oct 2024 15:33:24 +0300
Subject: [PATCH] Send original_molecule in Species when calling
 molecules_from_xyz()

---
 arc/species/species.py | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/arc/species/species.py b/arc/species/species.py
index 91db9f9ab8..6bb763fdc4 100644
--- a/arc/species/species.py
+++ b/arc/species/species.py
@@ -1385,7 +1385,7 @@ def set_dihedral(self,
             return None
         mol = self.mol
         if mol is None:
-            mols = molecules_from_xyz(xyz, multiplicity=self.multiplicity, charge=self.charge)
+            mols = molecules_from_xyz(xyz, multiplicity=self.multiplicity, charge=self.charge, original_molecule=mol)
             mol = mols[1] or mols[0]
         if chk_rotor_list:
             for rotor in self.rotors_dict.values():
@@ -1595,7 +1595,9 @@ def mol_from_xyz(self,
             # self.mol should have come from another source, e.g., SMILES or yml.
             mol_s, mol_b = molecules_from_xyz(xyz=xyz,
                                               multiplicity=self.multiplicity,
-                                              charge=self.charge)
+                                              charge=self.charge,
+                                              original_molecule=self.mol,
+                                              )
             perceived_mol = mol_b or mol_s
             if perceived_mol is not None:
                 allow_nonisomorphic_2d = self.charge \
@@ -1615,7 +1617,11 @@ def mol_from_xyz(self,
                 if not self.keep_mol:
                     self.mol = perceived_mol
         else:
-            mol_s, mol_b = molecules_from_xyz(xyz, multiplicity=self.multiplicity, charge=self.charge)
+            mol_s, mol_b = molecules_from_xyz(xyz,
+                                              multiplicity=self.multiplicity,
+                                              charge=self.charge,
+                                              original_molecule=self.mol,
+                                              )
             if mol_b is not None and len(mol_b.atoms) == self.number_of_atoms:
                 self.mol = mol_b
             elif mol_s is not None and len(mol_s.atoms) == self.number_of_atoms:
@@ -1788,7 +1794,11 @@ def check_xyz_isomorphism(self,
 
             # 1. Perceive
             try:
-                s_mol, b_mol = molecules_from_xyz(xyz, multiplicity=self.multiplicity, charge=self.charge)
+                s_mol, b_mol = molecules_from_xyz(xyz,
+                                                  multiplicity=self.multiplicity,
+                                                  charge=self.charge,
+                                                  original_molecule=mol,
+                                                  )
             except Exception as e:
                 if verbose:
                     logger.error(f'Could not perceive the Cartesian coordinates of species {self.label}. This '