TMP

ReactionMechanismGenerator · Jul 11, 2024 · 3b94e7b · 3b94e7b
1 parent 591c682
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Showing 10 changed files with 483 additions and 312 deletions.
diff --git a/arc/checks/ts.py b/arc/checks/ts.py
@@ -19,9 +19,7 @@
                         )
 from arc.imports import settings
 from arc.species.converter import check_xyz_dict, displace_xyz, xyz_to_dmat
-from arc.mapping.engine import (get_atom_indices_of_labeled_atoms_in_an_rmg_reaction,
-                                get_rmg_reactions_from_arc_reaction,
-                                )
+from arc.mapping.engine import get_atom_indices_of_labeled_atoms_in_a_reaction
 from arc.statmech.factory import statmech_factory
 
 if TYPE_CHECKING:
@@ -330,8 +328,7 @@ def check_normal_mode_displacement(reaction: 'ARCReaction',
                                            bond_lone_hydrogens=bond_lone_hs)
         got_expected_changing_bonds = False
         for i, rmg_reaction in enumerate(rmg_reactions):
-            r_label_dict = get_atom_indices_of_labeled_atoms_in_an_rmg_reaction(arc_reaction=reaction,
-                                                                                rmg_reaction=rmg_reaction)[0]
+            r_label_dict = get_atom_indices_of_labeled_atoms_in_a_reaction(arc_reaction=reaction)[0]
             if r_label_dict is None:
                 continue
             expected_breaking_bonds, expected_forming_bonds = reaction.get_expected_changing_bonds(r_label_dict=r_label_dict)

diff --git a/arc/job/adapters/ts/heuristics.py b/arc/job/adapters/ts/heuristics.py
@@ -33,7 +33,7 @@
 from arc.job.factory import register_job_adapter
 from arc.plotter import save_geo
 from arc.species.converter import compare_zmats, relocate_zmat_dummy_atoms_to_the_end, zmat_from_xyz, zmat_to_xyz
-from arc.mapping.engine import map_arc_rmg_species, map_two_species
+from arc.mapping.engine import map_two_species
 from arc.species.species import ARCSpecies, TSGuess, colliding_atoms
 from arc.species.zmat import get_parameter_from_atom_indices, remove_1st_atom, up_param
 

diff --git a/arc/mapping/driver.py b/arc/mapping/driver.py
@@ -14,8 +14,7 @@
                                 create_qc_mol,
                                 flip_map,
                                 fingerprint,
-                                get_atom_indices_of_labeled_atoms_in_an_rmg_reaction,
-                                get_rmg_reactions_from_arc_reaction,
+                                get_atom_indices_of_labeled_atoms_in_a_reaction,
                                 glue_maps,
                                 label_species_atoms,
                                 make_bond_changes,
@@ -26,28 +25,27 @@
                                 find_all_bdes,
                                 cut_species_based_on_atom_indices,
                                 update_xyz,
-                                RESERVED_FINGERPRINT_KEYS,)
+                                RESERVED_FINGERPRINT_KEYS,
+                                )
 from arc.common import logger
 
 from rmgpy.exceptions import ActionError, AtomTypeError
 
 if TYPE_CHECKING:
-    from rmgpy.data.rmg import RMGDatabase
     from arc.reaction import ARCReaction
 
 
 def map_reaction(rxn: 'ARCReaction',
                  backend: str = 'ARC',
-                 db: Optional['RMGDatabase'] = None,
-                 flip = False
+                 flip: bool = False
                  ) -> Optional[List[int]]:
     """
     Map a reaction.
 
     Args:
         rxn (ARCReaction): An ARCReaction object instance.
         backend (str, optional): Whether to use ``'QCElemental'`` or ``ARC``'s method as the backend.
-        db (RMGDatabase, optional): The RMG database instance.
+        flip (bool, optional): Whether to attempts fliping the reaction.
 
     Returns:
         Optional[List[int]]:
@@ -57,35 +55,31 @@ def map_reaction(rxn: 'ARCReaction',
     if flip:
         logger.warning(f"The requested ARC reaction {rxn} could not be atom mapped using {backend}. Trying again with the flipped reaction.")
         try:
-            _map = flip_map(map_rxn(rxn.flip_reaction(), backend=backend, db=db))
+            _map = flip_map(map_rxn(rxn.flip_reaction(), backend=backend))
         except ValueError:
             return None
         return _map
     else:
         if rxn.family is None:
             logger.warning(f'Could not determine the reaction family for {rxn.label}. '
                            f'Mapping as a general or isomerization reaction.')
-            _map = map_general_rxn(rxn, backend=backend)
-            return _map if _map is not None else map_reaction(rxn, backend=backend, db=db, flip=True)
+            _map = map_general_rxn(rxn)
+            return _map if _map is not None else map_reaction(rxn, backend=backend, flip=True)
         try:
-            _map = map_rxn(rxn, backend=backend, db=db)
-        except ValueError as e:
-            return map_reaction(rxn, backend=backend, db=db, flip=True)
-        return _map if _map is not None else map_reaction(rxn, backend=backend, db=db, flip=True)
+            _map = map_rxn(rxn, backend=backend)
+        except ValueError:
+            return map_reaction(rxn, backend=backend, flip=True)
+        return _map if _map is not None else map_reaction(rxn, backend=backend, flip=True)
 
 
 def map_general_rxn(rxn: 'ARCReaction',
-                    backend: str = 'ARC',
-                    db: Optional['RMGDatabase'] = None,
                     ) -> Optional[List[int]]:
     """
     Map a general reaction (one that was not categorized into a reaction family by RMG).
     The general method isn't great, a family-specific method should be implemented where possible.
 
     Args:
         rxn (ARCReaction): An ARCReaction object instance.
-        backend (str, optional): Whether to use ``'QCElemental'`` or ``ARC``'s method as the backend.
-        db (RMGDatabase, optional): The RMG database instance.
 
     Returns:
         Optional[List[int]]:
@@ -121,7 +115,6 @@ def map_isomerization_reaction(rxn: 'ARCReaction',
     Args:
         rxn (ARCReaction): An ARCReaction object instance.
         backend (str, optional): Whether to use ``'QCElemental'`` or ``ARC``'s method as the backend.
-        db (RMGDatabase, optional): The RMG database instance.
 
     Returns:
         Optional[List[int]]:
@@ -209,7 +202,6 @@ def map_isomerization_reaction(rxn: 'ARCReaction',
 
 def map_rxn(rxn: 'ARCReaction',
             backend: str = 'ARC',
-            db: Optional['RMGDatabase'] = None,
             ) -> Optional[List[int]]:
     """
     A wrapper function for mapping reaction, uses databases for mapping with the correct reaction family parameters.
@@ -224,26 +216,16 @@ def map_rxn(rxn: 'ARCReaction',
     Args:
         rxn (ARCReaction): An ARCReaction object instance that belongs to the RMG H_Abstraction reaction family.
         backend (str, optional): Whether to use ``'QCElemental'`` or ``ARC``'s method as the backend.
-        db (RMGDatabase, optional): The RMG database instance.
         
     Returns:
         Optional[List[int]]:
             Entry indices are running atom indices of the reactants,
             corresponding entry values are running atom indices of the products.
     """
-    # step 1:
-    rmg_reactions = get_rmg_reactions_from_arc_reaction(arc_reaction=rxn, backend=backend)
-
-    if not rmg_reactions:
-        return None
-
-    r_label_dict, p_label_dict = get_atom_indices_of_labeled_atoms_in_an_rmg_reaction(arc_reaction=rxn,
-                                                                                      rmg_reaction=rmg_reactions[0])
+    r_label_dict, p_label_dict = get_atom_indices_of_labeled_atoms_in_a_reaction(arc_reaction=rxn)
 
-    # step 2:
     assign_labels_to_products(rxn, p_label_dict)
-
-    #step 3:
+
     reactants, products = copy_species_list_for_mapping(rxn.r_species), copy_species_list_for_mapping(rxn.p_species)
     label_species_atoms(reactants), label_species_atoms(products)
 
@@ -259,13 +241,10 @@ def map_rxn(rxn: 'ARCReaction',
 
     r_cuts, p_cuts = update_xyz(r_cuts), update_xyz(p_cuts)
 
-    #step 4:
     pairs_of_reactant_and_products = pairing_reactants_and_products_for_mapping(r_cuts, p_cuts)
     if len(p_cuts):
         logger.error(f"Could not find isomorphism for scissored species: {[cut.mol.smiles for cut in p_cuts]}")
         return None
-    # step 5:
     maps = map_pairs(pairs_of_reactant_and_products)
 
-    #step 6:
     return glue_maps(maps, pairs_of_reactant_and_products)
diff --git a/arc/mapping/driver_test.py b/arc/mapping/driver_test.py
@@ -99,8 +99,8 @@ def setUpClass(cls):
                                   (-0.8942590, -0.8537420, 0.0000000)),
                        'isotopes': (16, 16, 1), 'symbols': ('O', 'O', 'H')}
         cls.nh2_xyz = """N       0.00022972    0.40059496    0.00000000
-                     H      -0.83174214   -0.19982058    0.00000000
-                     H       0.83151242   -0.20077438    0.00000000"""
+                         H      -0.83174214   -0.19982058    0.00000000
+                         H       0.83151242   -0.20077438    0.00000000"""
         cls.n2h4_xyz = """N      -0.67026921   -0.02117571   -0.25636419
                           N       0.64966276    0.05515705    0.30069593
                           H      -1.27787600    0.74907557    0.03694453
@@ -481,7 +481,6 @@ def test_map_abstractions(self):
         self.assertIn(atom_map[5], [4, 5])
         self.assertTrue(check_atom_map(rxn))
 
-
         # H + CH3NH2 <=> H2 + CH2NH2
         ch3nh2_xyz = {'coords': ((-0.5734111454228507, 0.0203516083213337, 0.03088703933770556),
                                  (0.8105595891860601, 0.00017446498908627427, -0.4077728757313545),
@@ -560,7 +559,6 @@ def test_map_abstractions(self):
         self.assertTrue(any(atom_map[r_index] in [6, 7, 8] for r_index in [5, 6, 7, 8]))
         self.assertTrue(check_atom_map(rxn))
 
-
         # CH3OO + CH3CH2OH <=> CH3OOH + CH3CH2O  / peroxyl to alkoxyl, modified atom and product order
         r_1 = ARCSpecies(
             label="CH3OO",
@@ -669,7 +667,6 @@ def test_map_abstractions(self):
         self.assertEqual(atom_map[23],23)
         self.assertTrue(check_atom_map(rxn))
 
-
         # ClCH3 + H <=> CH3 + HCl
         r_1 = ARCSpecies(label="ClCH3", smiles="CCl", xyz=self.ch3cl_xyz)
         r_2 = ARCSpecies(label="H", smiles="[H]", xyz=self.h_rad_xyz)
@@ -714,23 +711,23 @@ def test_map_abstractions(self):
             (0.3717352549047681, -1.308596593192221, 0.7750989547682503),
             (-2.0374518517222544, -0.751480024679671, 0.37217669645466245))}
 
-        p_1_xyz = {'symbols': ('O', 'Cl', 'H'), 'isotopes': (16, 35, 1), 'coords': (
-        (-0.3223044372303026, 0.4343354356368888, 0.0), (1.2650242694442462, -0.12042710381137228, 0.0),
-        (-0.9427198322139436, -0.3139083318255167, 0.0))}
+        p_1_xyz = {'symbols': ('O', 'Cl', 'H'), 'isotopes': (16, 35, 1),
+                   'coords': ((-0.3223044372303026, 0.4343354356368888, 0.0),
+                              (1.2650242694442462, -0.12042710381137228, 0.0),
+                              (-0.9427198322139436, -0.3139083318255167, 0.0))}
 
         p_2_xyz = {'symbols': ('C', 'C', 'C', 'Cl', 'Cl', 'H', 'H', 'H', 'H', 'H'),
-                   'isotopes': (12, 12, 12, 35, 35, 1, 1, 1, 1, 1), 'coords': (
-            (-1.3496376883278178, -0.020445981649800302, -0.1995184115269273),
-            (-0.051149096449292386, -0.3885500107837139, 0.4222976979623008),
-            (1.217696701041357, 0.15947991928242372, -0.1242718714010236),
-            (1.7092794464102241, 1.570982412202936, 0.8295196720275746),
-            (2.474584210365428, -1.0919019396606517, -0.06869614478411318),
-            (-1.6045061896547035, 1.0179450876989615, 0.03024632893682861),
-            (-1.3137314500783486, -0.14754777860704252, -1.2853589013330937),
-            (-2.1459595425475264, -0.6625965540242661, 0.188478021031359),
-            (-0.044412318929613885, -0.9093853981117669, 1.373599947353138),
-            (1.1078359281702537, 0.47202024365290884, -1.1662963382659064))}
-
+                   'isotopes': (12, 12, 12, 35, 35, 1, 1, 1, 1, 1),
+                   'coords': ((-1.3496376883278178, -0.020445981649800302, -0.1995184115269273),
+                              (-0.051149096449292386, -0.3885500107837139, 0.4222976979623008),
+                              (1.217696701041357, 0.15947991928242372, -0.1242718714010236),
+                              (1.7092794464102241, 1.570982412202936, 0.8295196720275746),
+                              (2.474584210365428, -1.0919019396606517, -0.06869614478411318),
+                              (-1.6045061896547035, 1.0179450876989615, 0.03024632893682861),
+                              (-1.3137314500783486, -0.14754777860704252, -1.2853589013330937),
+                              (-2.1459595425475264, -0.6625965540242661, 0.188478021031359),
+                              (-0.044412318929613885, -0.9093853981117669, 1.373599947353138),
+                              (1.1078359281702537, 0.47202024365290884, -1.1662963382659064))}
         r_1 = ARCSpecies(label='r1', smiles=smiles[0],xyz=r_1_xyz )
         r_2 = ARCSpecies(label='r2', smiles=smiles[1],xyz=r_2_xyz)
         p_1 = ARCSpecies(label='p1', smiles=smiles[2],xyz=p_1_xyz)
@@ -750,7 +747,6 @@ def test_map_abstractions(self):
         self.assertTrue(check_atom_map(rxn))
 
         # Br abstraction
-
         # OH + CH3Br <=> HOBr + CH3
         r_1_xyz = {'symbols': ('O', 'H'), 'isotopes': (16, 1),
                    'coords': ((0.48890386738601, 0.0, 0.0), (-0.48890386738601, 0.0, 0.0))}
@@ -788,22 +784,22 @@ def test_map_abstractions(self):
         # [H] + CC(=O)Br <=> [H][Br] + C[C](=O)
         r_1_xyz = {'symbols': ('H',), 'isotopes': (1,), 'coords': ((0.0, 0.0, 0.0),)}
 
-        r_2_xyz = {'symbols': ('C', 'C', 'O', 'Br', 'H', 'H', 'H'), 'isotopes': (12, 12, 16, 79, 1, 1, 1), 'coords': (
-        (-0.7087772076387326, -0.08697184565826255, 0.08295914062572969),
-        (0.7238141593293749, 0.2762480677183181, -0.14965326856248656),
-        (1.1113560248255752, 1.3624373452907719, -0.554840372311578),
-        (2.0636725443687616, -1.041297021241265, 0.20693447296577364),
-        (-0.9844931733249197, -0.9305935329026733, -0.5546432084044857),
-        (-0.8586221633621384, -0.3455305862905263, 1.134123935245044),
-        (-1.3469501841979155, 0.7657075730836449, -0.16488069955797996))}
+        r_2_xyz = {'symbols': ('C', 'C', 'O', 'Br', 'H', 'H', 'H'), 'isotopes': (12, 12, 16, 79, 1, 1, 1),
+                   'coords': ((-0.7087772076387326, -0.08697184565826255, 0.08295914062572969),
+                              (0.7238141593293749, 0.2762480677183181, -0.14965326856248656),
+                              (1.1113560248255752, 1.3624373452907719, -0.554840372311578),
+                              (2.0636725443687616, -1.041297021241265, 0.20693447296577364),
+                              (-0.9844931733249197, -0.9305935329026733, -0.5546432084044857),
+                              (-0.8586221633621384, -0.3455305862905263, 1.134123935245044),
+                              (-1.3469501841979155, 0.7657075730836449, -0.16488069955797996))}
 
-        p_1_xyz = {'symbols': ('C', 'C', 'O', 'H', 'H', 'H'), 'isotopes': (12, 12, 16, 1, 1, 1), 'coords': (
-        (-0.4758624005470258, 0.015865899777425058, -0.11215987340300927),
-        (0.9456990856850401, -0.031530842469194666, 0.2228995599390481),
-        (2.0897646616994816, -0.06967555524967288, 0.492553667108967),
-        (-1.08983188764878, -0.06771143046366379, 0.7892594299969324),
-        (-0.7261604551815313, 0.9578749227991876, -0.6086176800339509),
-        (-0.7436090040071672, -0.8048229943940851, -0.7839351036079769))}
+        p_1_xyz = {'symbols': ('C', 'C', 'O', 'H', 'H', 'H'), 'isotopes': (12, 12, 16, 1, 1, 1),
+                   'coords': ((-0.4758624005470258, 0.015865899777425058, -0.11215987340300927),
+                              (0.9456990856850401, -0.031530842469194666, 0.2228995599390481),
+                              (2.0897646616994816, -0.06967555524967288, 0.492553667108967),
+                              (-1.08983188764878, -0.06771143046366379, 0.7892594299969324),
+                              (-0.7261604551815313, 0.9578749227991876, -0.6086176800339509),
+                              (-0.7436090040071672, -0.8048229943940851, -0.7839351036079769))}
 
         p_2_xyz = {'symbols': ('Br', 'H'), 'isotopes': (79, 1),
                    'coords': ((0.7644788559644482, 0.0, 0.0), (-0.7644788559644482, 0.0, 0.0))}
@@ -819,7 +815,7 @@ def test_map_abstractions(self):
         self.assertIn(tuple(atom_map[5:]), permutations([5, 6, 7]))
         self.assertTrue(check_atom_map(rxn))
 
-        #Change Order [H] + CC(=O)Br <=> C[C](=O) + [H][Br]
+        # Change Order [H] + CC(=O)Br <=> C[C](=O) + [H][Br]
         r_1 = ARCSpecies(label='r1', smiles='[H]', xyz=r_1_xyz)
         r_2 = ARCSpecies(label='r2', smiles='CC(=O)Br', xyz=r_2_xyz)
         p_1 = ARCSpecies(label='p1', smiles='C[C](=O)', xyz=p_1_xyz)