Merge pull request #2574 from hwpang/fix_fragment_regression

Compatibility of `regression.py` with fragment
ReactionMechanismGenerator · Nov 8, 2023 · ffeb7bb · ffeb7bb
2 parents e9eca53 + f898372
commit ffeb7bb
Show file tree

Hide file tree

Showing 3 changed files with 5 additions and 12 deletions.
diff --git a/rmgpy/tools/regression.py b/rmgpy/tools/regression.py
@@ -40,6 +40,7 @@
 from rmgpy.molecule import Molecule
 from rmgpy.quantity import Quantity
 from rmgpy.species import Species
+from rmgpy.rmg.input import fragment_adj, fragment_smiles, smiles, adjacency_list
 from rmgpy.tools.canteramodel import CanteraCondition
 from rmgpy.tools.observablesregression import ObservablesTestCase
 
@@ -74,9 +75,11 @@ def read_input_file(path):
         'True': True,
         'False': False,
         'observable': observable,
-        'SMILES': SMILES,
+        'SMILES': smiles,
+        'fragment_adj': fragment_adj,
+        'fragment_SMILES': fragment_smiles,
         'species': species,
-        'adjacencyList': adjacencyList,
+        'adjacencyList': adjacency_list,
         'reactorSetups': reactorSetups,
         'options': options,
     }
@@ -122,14 +125,6 @@ def reactorSetups(reactorTypes, temperatures, pressures, initialMoleFractionsLis
     setups = [reactorTypes, temperatures, pressures, initialMoleFractionsList, terminationTimes]
 
 
-def SMILES(string):
-    return Molecule().from_smiles(string)
-
-
-def adjacencyList(string):
-    return Molecule().from_adjacency_list(string)
-
-
 def options(title='', tolerance=0.05):
     global casetitle, tol
     casetitle = title

diff --git a/test/regression/RMS_constantVIdealGasReactor_fragment/regression_input.py b/test/regression/RMS_constantVIdealGasReactor_fragment/regression_input.py
@@ -48,7 +48,6 @@
 
 species(
     label="RCCCC",
-    reactive=True,
     structure=fragment_adj(
         """1  C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
 2  C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}

diff --git a/test/regression/fragment/regression_input.py b/test/regression/fragment/regression_input.py
@@ -48,7 +48,6 @@
 
 species(
     label="RCCCC",
-    reactive=True,
     structure=fragment_adj(
         """1  C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
 2  C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}