Merge pull request #23 from molssi-seamm/dev

Bugfix: incorrectly creating configurations
molssi-seamm · Nov 10, 2023 · 644f09f · 644f09f
2 parents 1554482 + 5b5b423
commit 644f09f
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,10 @@
 History
 =======
 
+2023.11.10 -- Bugfix: New configurations created incorrectly
+    * New configurations made from other systems could remove the atoms in those
+      systems.
+
 2023.11.9.1 -- Removed using structure names when perceiving type
     * Using structure names is too dangerous to use by perceiving if text is a name of
       SMILES and there is no easy test for valid SMILES. So change to only using names

diff --git a/from_smiles_step/from_smiles.py b/from_smiles_step/from_smiles.py
@@ -102,7 +102,7 @@ def run(self):
         notation = P["notation"]
 
         # Get the system
-        system, configuration = self.get_system_configuration(P)
+        system, configuration = self.get_system_configuration(P, same_as=None)
 
         # Create the structure in the given configuration
         text = P["smiles string"]