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Make Reaction atom_map a list of atom maps #718

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Make Reaction atom_map a list of atom maps #718

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72c701c
Minor: Style modifications to AM driver
alongd Aug 21, 2023
efe2c65
Minor: Style modification in rmgdb tests
alongd Dec 4, 2023
c0011d9
Make Reaction atom_map a list of atom maps
alongd Sep 13, 2023
917db87
Tests: Adapt reaction and heuristics tests to reaction .atom_maps
alongd Sep 13, 2023
cf3c557
Adapted check_atom_map() in engine to the .atom_maps attribute change
alongd Sep 13, 2023
6443c71
Extracted two specialized functions out of map_two_species()
alongd Sep 13, 2023
4896592
Consider all RMG reacctions when mapping in driver
alongd Sep 13, 2023
5549385
Run GCN for all atom maps
alongd Sep 13, 2023
03ee005
Tests: Organised reaction tests of atom mapping into smaller unit tests
alongd Sep 13, 2023
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80 changes: 44 additions & 36 deletions arc/job/adapters/ts/gcn_ts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -274,46 +274,53 @@ def execute_gcn(self, exe_type: str = 'incore'):
charge=rxn.charge,
multiplicity=rxn.multiplicity,
)
write_sdf_files(rxn=rxn,
reactant_path=self.reactant_path,
product_path=self.product_path,
)
if exe_type == 'queue':
input_dict = {'reactant_path': self.reactant_path,
'product_path': self.product_path,
'local_path': self.local_path,
'yml_out_path': self.yml_out_path,
'repetitions': self.repetitions,
}
save_yaml_file(path=self.yml_in_path, content=input_dict)
self.legacy_queue_execution()
elif exe_type == 'incore':
for _ in range(self.repetitions):
run_subprocess_locally(direction='F',
reactant_path=self.reactant_path,
product_path=self.product_path,
ts_path=self.ts_fwd_path,
local_path=self.local_path,
ts_species=rxn.ts_species,
)
run_subprocess_locally(direction='R',
reactant_path=self.product_path,
product_path=self.reactant_path,
ts_path=self.ts_rev_path,
local_path=self.local_path,
ts_species=rxn.ts_species,
)
if len(self.reactions) < 5:
successes = len([tsg for tsg in rxn.ts_species.ts_guesses if tsg.success and 'gcn' in tsg.method])
if successes:
logger.info(f'GCN successfully found {successes} TS guesses for {rxn.label}.')
else:
logger.info(f'GCN did not find any successful TS guesses for {rxn.label}.')
for i in range(len(rxn.atom_maps)):
try:
write_sdf_files(rxn=rxn,
reactant_path=self.reactant_path,
product_path=self.product_path,
am_index=i,
)
except IndexError:
logger.warning(f'GCN adapter could not write SDF files for {rxn.label} with atom map {i}.')
continue
if exe_type == 'queue':
input_dict = {'reactant_path': self.reactant_path,
'product_path': self.product_path,
'local_path': self.local_path,
'yml_out_path': self.yml_out_path,
'repetitions': self.repetitions,
}
save_yaml_file(path=self.yml_in_path, content=input_dict)
self.legacy_queue_execution()
elif exe_type == 'incore':
for _ in range(self.repetitions):
run_subprocess_locally(direction='F',
reactant_path=self.reactant_path,
product_path=self.product_path,
ts_path=self.ts_fwd_path,
local_path=self.local_path,
ts_species=rxn.ts_species,
)
run_subprocess_locally(direction='R',
reactant_path=self.product_path,
product_path=self.reactant_path,
ts_path=self.ts_rev_path,
local_path=self.local_path,
ts_species=rxn.ts_species,
)
if len(self.reactions) < 5:
successes = len([tsg for tsg in rxn.ts_species.ts_guesses if tsg.success and 'gcn' in tsg.method])
if successes:
logger.info(f'GCN successfully found {successes} TS guesses for {rxn.label}.')
else:
logger.info(f'GCN did not find any successful TS guesses for {rxn.label}.')


def write_sdf_files(rxn: 'ARCReaction',
reactant_path: str,
product_path: str,
am_index: int = 0,
):
"""
Write reactant and product SDF files using RDKit.
Expand All @@ -322,9 +329,10 @@ def write_sdf_files(rxn: 'ARCReaction',
rxn (ARCReaction): The relevant reaction.
reactant_path (str): The path to the reactant SDF file.
product_path (str): The path to the product SDF file.
am_index (int, optional): The atom map index. Default: 0.
"""
reactant_rdkit_mol = rdkit_conf_from_mol(rxn.r_species[0].mol, rxn.r_species[0].get_xyz())[1]
mapped_product = rxn.get_single_mapped_product_xyz()
mapped_product = rxn.get_single_mapped_product_xyz(am_index)
product_rdkit_mol = rdkit_conf_from_mol(mapped_product.mol, mapped_product.get_xyz())[1]
w = Chem.SDWriter(reactant_path)
w.write(reactant_rdkit_mol)
Expand Down
54 changes: 27 additions & 27 deletions arc/job/adapters/ts/heuristics_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -302,10 +302,10 @@ def test_heuristics_for_h_abstraction(self):
products=[Species(smiles='[CH3]'), Species(smiles='[H][H]')]))
rxn4.determine_family(rmg_database=self.rmgdb)
self.assertEqual(rxn4.family.label, 'H_Abstraction')
self.assertEqual(rxn4.atom_map[0], 0)
self.assertEqual(rxn4.atom_maps[0][0], 0)
for index in [1, 2, 3, 4]:
self.assertIn(rxn4.atom_map[index], [1, 2, 3, 4, 5])
self.assertIn(rxn4.atom_map[5], [4, 5])
self.assertIn(rxn4.atom_maps[0][index], [1, 2, 3, 4, 5])
self.assertIn(rxn4.atom_maps[0][5], [4, 5])
heuristics_4 = HeuristicsAdapter(job_type='tsg',
reactions=[rxn4],
testing=True,
Expand Down Expand Up @@ -926,13 +926,13 @@ def test_keeping_atom_order_in_ts(self):
p_species=[ARCSpecies(label='C2H5', smiles='C[CH2]', xyz=self.c2h5_xyz),
ARCSpecies(label='CCOOH', smiles='CCOO', xyz=self.ccooh_xyz)])
rxn_1.determine_family(rmg_database=self.rmgdb)
self.assertIn(rxn_1.atom_map[0], [0, 1])
self.assertIn(rxn_1.atom_map[1], [0, 1])
self.assertIn(rxn_1.atom_maps[0][0], [0, 1])
self.assertIn(rxn_1.atom_maps[0][1], [0, 1])
for index in [2, 3, 4, 5, 6, 7]:
self.assertIn(rxn_1.atom_map[index], [2, 3, 4, 5, 6, 16])
self.assertEqual(rxn_1.atom_map[8:12], [7, 8, 9, 10])
self.assertIn(tuple(rxn_1.atom_map[12:15]), itertools.permutations([13, 11, 12]))
self.assertIn(rxn_1.atom_map[15:], [[14, 15], [15, 14]])
self.assertIn(rxn_1.atom_maps[0][index], [2, 3, 4, 5, 6, 16])
self.assertEqual(rxn_1.atom_maps[0][8:12], [7, 8, 9, 10])
self.assertIn(tuple(rxn_1.atom_maps[0][12:15]), itertools.permutations([13, 11, 12]))
self.assertIn(rxn_1.atom_maps[0][15:], [[14, 15], [15, 14]])
heuristics_1 = HeuristicsAdapter(job_type='tsg',
reactions=[rxn_1],
testing=True,
Expand All @@ -952,12 +952,12 @@ def test_keeping_atom_order_in_ts(self):
ARCSpecies(label='C2H5', smiles='C[CH2]', xyz=self.c2h5_xyz)])
rxn_2.determine_family(rmg_database=self.rmgdb)
self.assertEqual(rxn_2.family.label, 'H_Abstraction')
self.assertEqual(rxn_2.atom_map[:2], [11, 10])
self.assertIn(tuple(rxn_2.atom_map[2:5]), itertools.permutations([9, 16, 15]))
self.assertIn(tuple(rxn_2.atom_map[5:8]), itertools.permutations([12, 13, 14]))
self.assertEqual(rxn_2.atom_map[8:12], [0, 1, 2, 3])
self.assertIn(tuple(rxn_2.atom_map[12:15]), itertools.permutations([4, 5, 6]))
self.assertIn(tuple(rxn_2.atom_map[15:]), itertools.permutations([7, 8]))
self.assertEqual(rxn_2.atom_maps[0][:2], [11, 10])
self.assertIn(tuple(rxn_2.atom_maps[0][2:5]), itertools.permutations([9, 16, 15]))
self.assertIn(tuple(rxn_2.atom_maps[0][5:8]), itertools.permutations([12, 13, 14]))
self.assertEqual(rxn_2.atom_maps[0][8:12], [0, 1, 2, 3])
self.assertIn(tuple(rxn_2.atom_maps[0][12:15]), itertools.permutations([4, 5, 6]))
self.assertIn(tuple(rxn_2.atom_maps[0][15:]), itertools.permutations([7, 8]))
heuristics_2 = HeuristicsAdapter(job_type='tsg',
reactions=[rxn_2],
testing=True,
Expand All @@ -976,12 +976,12 @@ def test_keeping_atom_order_in_ts(self):
p_species=[ARCSpecies(label='C2H5', smiles='C[CH2]', xyz=self.c2h5_xyz),
ARCSpecies(label='CCOOH', smiles='CCOO', xyz=self.ccooh_xyz)])
rxn_3.determine_family(rmg_database=self.rmgdb)
self.assertEqual(rxn_3.atom_map[:4], [7, 8, 9, 10])
self.assertIn(tuple(rxn_3.atom_map[4:7]), itertools.permutations([11, 12, 13]))
self.assertIn(tuple(rxn_3.atom_map[7:9]), itertools.permutations([14, 15]))
self.assertEqual(rxn_3.atom_map[9:11], [1, 0])
self.assertIn(tuple(rxn_3.atom_map[11:14]), itertools.permutations([16, 5, 6]))
self.assertIn(tuple(rxn_3.atom_map[14:]), itertools.permutations([3, 4, 2]))
self.assertEqual(rxn_3.atom_maps[0][:4], [7, 8, 9, 10])
self.assertIn(tuple(rxn_3.atom_maps[0][4:7]), itertools.permutations([11, 12, 13]))
self.assertIn(tuple(rxn_3.atom_maps[0][7:9]), itertools.permutations([14, 15]))
self.assertEqual(rxn_3.atom_maps[0][9:11], [1, 0])
self.assertIn(tuple(rxn_3.atom_maps[0][11:14]), itertools.permutations([16, 5, 6]))
self.assertIn(tuple(rxn_3.atom_maps[0][14:]), itertools.permutations([3, 4, 2]))

heuristics_3 = HeuristicsAdapter(job_type='tsg',
reactions=[rxn_3],
Expand All @@ -1001,12 +1001,12 @@ def test_keeping_atom_order_in_ts(self):
p_species=[ARCSpecies(label='CCOOH', smiles='CCOO', xyz=self.ccooh_xyz),
ARCSpecies(label='C2H5', smiles='C[CH2]', xyz=self.c2h5_xyz)])
rxn_4.determine_family(rmg_database=self.rmgdb)
self.assertEqual(rxn_4.atom_map[:4], [0, 1, 2, 3])
self.assertIn(tuple(rxn_4.atom_map[4:7]), itertools.permutations([4, 5, 6]))
self.assertIn(tuple(rxn_4.atom_map[7:9]), itertools.permutations([7, 8]))
self.assertEqual(rxn_4.atom_map[9:11], [11, 10])
self.assertIn(tuple(rxn_4.atom_map[11:14]), itertools.permutations([9, 15, 16]))
self.assertIn(tuple(rxn_4.atom_map[14:]), itertools.permutations([12, 13, 14 ]))
self.assertEqual(rxn_4.atom_maps[0][:4], [0, 1, 2, 3])
self.assertIn(tuple(rxn_4.atom_maps[0][4:7]), itertools.permutations([4, 5, 6]))
self.assertIn(tuple(rxn_4.atom_maps[0][7:9]), itertools.permutations([7, 8]))
self.assertEqual(rxn_4.atom_maps[0][9:11], [11, 10])
self.assertIn(tuple(rxn_4.atom_maps[0][11:14]), itertools.permutations([9, 15, 16]))
self.assertIn(tuple(rxn_4.atom_maps[0][14:]), itertools.permutations([12, 13, 14 ]))
heuristics_4 = HeuristicsAdapter(job_type='tsg',
reactions=[rxn_4],
testing=True,
Expand Down
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