Skip to content

Make Reaction atom_map a list of atom maps #718

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 9 commits into
base: main
Choose a base branch
from
+427 −436
Draft

Make Reaction atom_map a list of atom maps #718

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
80 changes: 44 additions & 36 deletions arc/job/adapters/ts/gcn_ts.py
View file
Open in desktop
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
View file
Open in desktop
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
Loading