Tests: Removed RMGDatabase from tests

ReactionMechanismGenerator · Jul 3, 2024 · e96cb3d · e96cb3d
1 parent c1d21d2
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Showing 10 changed files with 92 additions and 157 deletions.
diff --git a/arc/checks/ts_test.py b/arc/checks/ts_test.py
@@ -17,7 +17,6 @@
 from arc.level import Level
 from arc.parser import parse_normal_mode_displacement, parse_xyz_from_file
 from arc.reaction import ARCReaction
-from arc.rmgdb import load_families_only, make_rmg_database_object
 from arc.species.species import ARCSpecies, TSGuess
 from arc.utils.wip import work_in_progress
 
@@ -32,8 +31,6 @@ def setUpClass(cls):
         A method that is run before all unit tests in this class.
         """
         cls.maxDiff = None
-        cls.rmgdb = make_rmg_database_object()
-        load_families_only(cls.rmgdb)
 
         cls.rms_list_1 = [0.01414213562373095, 0.05, 0.04, 0.5632938842203065, 0.7993122043357026, 0.08944271909999159,
                           0.10677078252031312, 0.09000000000000001, 0.05, 0.09433981132056604]
@@ -185,14 +182,14 @@ def setUpClass(cls):
                                           xyz=os.path.join(ts.ARC_PATH, 'arc', 'testing', 'freq', 'TS_nC3H7-iC3H7.out'))
         cls.rxn_8.ts_label = cls.rxn_8.ts_species.label
 
-        cls.rxn_2a.determine_family(rmg_database=cls.rmgdb, save_order=True)
-        cls.rxn_2b.determine_family(rmg_database=cls.rmgdb, save_order=True)
-        cls.rxn_3.determine_family(rmg_database=cls.rmgdb, save_order=True)
-        cls.rxn_4.determine_family(rmg_database=cls.rmgdb, save_order=True)
-        cls.rxn_5.determine_family(rmg_database=cls.rmgdb, save_order=True)
-        cls.rxn_6.determine_family(rmg_database=cls.rmgdb, save_order=True)
-        cls.rxn_7.determine_family(rmg_database=cls.rmgdb, save_order=True)
-        cls.rxn_8.determine_family(rmg_database=cls.rmgdb, save_order=True)
+        cls.rxn_2a.determine_family()
+        cls.rxn_2b.determine_family()
+        cls.rxn_3.determine_family()
+        cls.rxn_4.determine_family()
+        cls.rxn_5.determine_family()
+        cls.rxn_6.determine_family()
+        cls.rxn_7.determine_family()
+        cls.rxn_8.determine_family()
 
         cls.ccooj_xyz = {'symbols': ('C', 'C', 'O', 'O', 'H', 'H', 'H', 'H', 'H'),
                          'isotopes': (12, 12, 16, 16, 1, 1, 1, 1, 1),
@@ -380,7 +377,7 @@ def test_check_normal_mode_displacement(self):
         self.assertFalse(self.rxn_2a.ts_species.ts_checks['NMD'])
         self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
                                                            'TS_intra_H_migration_CBS-QB3.out')
-        self.rxn_2a.determine_family(rmg_database=self.rmgdb)
+        self.rxn_2a.determine_family()
         ts.check_normal_mode_displacement(reaction=self.rxn_2a, job=self.job1)
         self.assertTrue(self.rxn_2a.ts_species.ts_checks['NMD'])
         self.rxn_2a.ts_species.populate_ts_checks()

diff --git a/arc/common_test.py b/arc/common_test.py
@@ -21,7 +21,6 @@
 import arc.common as common
 from arc.exceptions import InputError, SettingsError
 from arc.imports import settings
-from arc.rmgdb import make_rmg_database_object, load_families_only
 from arc.mapping.engine import get_rmg_reactions_from_arc_reaction
 import arc.species.converter as converter
 from arc.reaction import ARCReaction
@@ -41,8 +40,6 @@ def setUpClass(cls):
         A method that is run before all unit tests in this class.
         """
         cls.maxDiff = None
-        cls.rmgdb = make_rmg_database_object()
-        load_families_only(cls.rmgdb)
         cls.default_job_types = {'conformers': True,
                                  'opt': True,
                                  'fine': True,
@@ -1274,7 +1271,7 @@ def test_check_r_n_p_symbols_between_rmg_and_arc_rxns(self):
         """Test the _check_r_n_p_symbols_between_rmg_and_arc_rxns() function"""
         arc_rxn = ARCReaction(r_species=[ARCSpecies(label='CH4', smiles='C'), ARCSpecies(label='OH', smiles='[OH]')],
                               p_species=[ARCSpecies(label='CH3', smiles='[CH3]'), ARCSpecies(label='H2O', smiles='O')])
-        rmg_reactions = get_rmg_reactions_from_arc_reaction(arc_reaction=arc_rxn, db=self.rmgdb)
+        rmg_reactions = get_rmg_reactions_from_arc_reaction(arc_reaction=arc_rxn)
         self.assertTrue(common._check_r_n_p_symbols_between_rmg_and_arc_rxns(arc_rxn, rmg_reactions))
 
     def test_almost_equal_coords(self):

diff --git a/arc/job/adapters/ts/autotst_test.py b/arc/job/adapters/ts/autotst_test.py
@@ -15,7 +15,6 @@
 from arc.common import ARC_PATH
 from arc.job.adapters.ts.autotst_ts import AutoTSTAdapter, HAS_AUTOTST
 from arc.reaction import ARCReaction
-from arc.rmgdb import make_rmg_database_object, load_families_only
 
 
 class TestAutoTSTAdapter(unittest.TestCase):
@@ -29,8 +28,6 @@ def setUpClass(cls):
         A method that is run before all unit tests in this class.
         """
         cls.maxDiff = None
-        cls.rmgdb = make_rmg_database_object()
-        load_families_only(cls.rmgdb)
 
     def test_has_autotst(self):
         """Test that AutoTST was successfully imported"""
@@ -43,7 +40,7 @@ def test_autotst_h_abstraction(self):
                                                             Species(label='HO2', smiles='O[O]')],
                                                  products=[Species(label='C3H7', smiles='[CH2]CC'),
                                                            Species(label='H2O2', smiles='OO')]))
-        rxn1.determine_family(rmg_database=self.rmgdb)
+        rxn1.determine_family()
         self.assertEqual(rxn1.family.label, 'H_Abstraction')
         atst1 = AutoTSTAdapter(job_type='tsg',
                                reactions=[rxn1],
@@ -71,7 +68,7 @@ def test_autotst_h_abstraction(self):
                                                             Species().from_smiles('[OH]')],
                                                  products=[Species().from_smiles('CCC[O]'),
                                                            Species().from_smiles('O')]))
-        rxn2.determine_family(rmg_database=self.rmgdb)
+        rxn2.determine_family()
         self.assertEqual(rxn2.family.label, 'H_Abstraction')
         atst2 = AutoTSTAdapter(job_type='tsg',
                                reactions=[rxn2],
@@ -93,7 +90,7 @@ def test_autotst_h_abstraction(self):
                                                             Species().from_smiles('[H]')],
                                                  products=[Species().from_smiles('C=C[O]'),
                                                            Species().from_smiles('[H][H]')]))
-        rxn3.determine_family(rmg_database=self.rmgdb)
+        rxn3.determine_family()
         self.assertEqual(rxn3.family.label, 'H_Abstraction')
         atst3 = AutoTSTAdapter(job_type='tsg',
                                reactions=[rxn3],
@@ -117,7 +114,7 @@ def test_autotst_intra_h_migration(self):
         rxn1 = ARCReaction(reactants=['[CH2]CO'], products=['CC[O]'],
                            rmg_reaction=Reaction(reactants=[Species().from_smiles('[CH2]CO')],
                                                  products=[Species().from_smiles('CC[O]')]))
-        rxn1.determine_family(rmg_database=self.rmgdb)
+        rxn1.determine_family()
         self.assertEqual(rxn1.family.label, 'intra_H_migration')
         atst1 = AutoTSTAdapter(job_type='tsg',
                                reactions=[rxn1],
@@ -157,7 +154,7 @@ def test_autotst_r_addition_multiple_bond(self):
                            rmg_reaction=Reaction(reactants=[Species().from_smiles('C#C'),
                                                             Species().from_smiles('[OH]')],
                                                  products=[Species().from_smiles('[CH]=CO')]))
-        rxn1.determine_family(rmg_database=self.rmgdb)
+        rxn1.determine_family()
         self.assertEqual(rxn1.family.label, 'R_Addition_MultipleBond')
         atst1 = AutoTSTAdapter(job_type='tsg',
                                reactions=[rxn1],

diff --git a/arc/job/adapters/ts/gcn_test.py b/arc/job/adapters/ts/gcn_test.py
@@ -12,7 +12,6 @@
 from arc.common import ARC_PATH
 import arc.job.adapters.ts.gcn_ts as ts_gcn
 from arc.reaction import ARCReaction
-from arc.rmgdb import load_families_only, make_rmg_database_object
 from arc.species.converter import str_to_xyz
 from arc.species.species import ARCSpecies, TSGuess
 
@@ -28,8 +27,6 @@ def setUpClass(cls):
         A method that is run before all unit tests in this class.
         """
         cls.maxDiff = None
-        cls.rmgdb = make_rmg_database_object()
-        load_families_only(cls.rmgdb)
         cls.output_dir = os.path.join(ARC_PATH, 'arc', 'testing', 'GCN')
         if not os.path.isdir(cls.output_dir):
             os.makedirs(cls.output_dir)