From 4f9e11d130fa77be0c933c21290b99e6de971aa1 Mon Sep 17 00:00:00 2001
From: kfir4444 <kfir.k4@gmail.com>
Date: Thu, 21 Sep 2023 13:55:24 +0300
Subject: [PATCH] Added copy_species_list_for_mapping function

This due to issue #675, this function also moved the atom indices when copying.(https://github.com/ReactionMechanismGenerator/ARC/issues/675)
---
 arc/mapping/engine.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/arc/mapping/engine.py b/arc/mapping/engine.py
index 5ff2fdcdd5..50c1a3fb02 100644
--- a/arc/mapping/engine.py
+++ b/arc/mapping/engine.py
@@ -1291,3 +1291,18 @@ def cut_species_based_on_atom_indices(species: List["ARCSpecies"], bdes: List[Tu
                 break
                 
     return species
+
+
+def copy_species_list_for_mapping(species: List["ARCSpecies"]) -> List["ARCSpecies"]:
+    """
+    A helper function for copying the species list for mapping. Also keeps the atom indices when copying.
+    Args:
+        species (List[ARCSpecies]): The species list to be copied.
+    Returns:
+        List[ARCSpecies]: The copied species list.
+    """
+    copies = [spc.copy() for spc in species]
+    for copy, spc in zip(copies, species):
+        for atom1, atom2 in zip(copy.mol.atoms, spc.mol.atoms):
+            atom1.label = atom2.label
+    return copies