def test_get_highest_int():
# iterable expected, but not a str
with pytest.raises(TypeError):
RuleBurner._get_highest_int('123')
assert RuleBurner._get_highest_int((1, 2, 3)) == 3
assert RuleBurner._get_highest_int(('1', 2, '3')) == 3
assert RuleBurner._get_highest_int((1, '2', 'a')) == 2
def test_handle_result():
tuple_raw = (
Chem.MolFromSmiles('[H][O][C](=[O])[C]([H])([O][P](=[O])([O][H])[O][H])[C]([H])([H])[H]'),
Chem.MolFromSmiles('[H][N]=[c]1[n][c]([O][H])[c]2[n][c]([H])[n]([C]3([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][H])[C]([H])([O][H])[C]3([H])[O][H])[c]2[n]1[H]')
)
rb = RuleBurner()
tuple_tuple_rdmol, tuple_tuple_failed = rb._standardize_results(tuple_tuple_rdmol=(tuple_raw,),
with_hs=True, with_stereo=False)
rdmols, inchikeys, inchis, smiles = rb._handle_results(list_list_rdmol=tuple_tuple_rdmol)
# Check number products
assert len(inchikeys) == len(inchis) == len(smiles) == 1 # Only one set of result
assert len(inchikeys[0]) == len(inchis[0]) == len(smiles[0]) == 2 # 2 products
# Check Inchikeys
assert inchikeys[0][0] == 'CSZRNWHGZPKNKY-UHFFFAOYSA-N'
assert inchikeys[0][1] == 'QGWNDRXFNXRZMB-UHFFFAOYSA-N'
# Check Inchis
assert inchis[0][0] == 'InChI=1S/C3H7O6P/c1-2(3(4)5)9-10(6,7)8/h2H,1H3,(H,4,5)(H2,6,7,8)'
assert inchis[0][1] == 'InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)'
# Check SMILES #1
assert smiles[0][0] == '[H]OC(=O)C([H])(OP(=O)(O[H])O[H])C([H])([H])[H]'
rdmol = Chem.MolFromSmiles(smiles[0][0])
rdmol = Chem.AddHs(rdmol)
assert Chem.MolToSmiles(rdmol, allHsExplicit=True) == '[H][O][C](=[O])[C]([H])([O][P](=[O])([O][H])[O][H])[C]([H])([H])[H]'
# Check SMILES #2
assert smiles[0][1] == '[H]N=c1nc(O[H])c2nc([H])n(C3([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])O[H])C([H])(O[H])C3([H])O[H])c2n1[H]'
rdmol = Chem.MolFromSmiles(smiles[0][1])
rdmol = Chem.AddHs(rdmol)
assert Chem.MolToSmiles(rdmol, allHsExplicit=True) == '[H][N]=[c]1[n][c]([O][H])[c]2[n][c]([H])[n]([C]3([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][H])[C]([H])([O][H])[C]3([H])[O][H])[c]2[n]1[H]'
def test_standardize_chemical_3():
# Data
rb = RuleBurner()
wrong_smiles = '[H]OC(=O)C([H])([H])C([H])([H])C([H])(N=C(O[H])C([H])([H])C([H])([H])C([H])(N=C(O[H])C([H])(OP(=O)(O[H])OC([H])([H])C([H])(O[H])C([H])(O[H])C([H])(O[H])C([H])([H])n1c2nc(=O)nc(O[H])c-2c([H])c2c([H])c([H])c(OP(=O)(OC([H])([H])C(C([H])([H])[H])(C([H])([H])[H])C([H])(O[H])C(=NC([H])([H])C([H])([H])C(=NC([H])([H])C([H])([H])SC(=O)C([H])([H])C([H])([H])C([H])([H])C([H])(C(=C([H])[H])C([H])([H])[H])C([H])([H])C(=O)O[H])O[H])O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4[c]([H])n([H])[c]5[c](N([H])[H])[n][c]([H])[n][c]54)C([H])(O[H])C3([H])OP(=O)(O[H])O[H])c([H])c21)C([H])([H])[H])C(=O)O[H])C(=O)O[H]'
# Test
wrong_mol = Chem.MolFromSmiles(wrong_smiles, sanitize=False)
with pytest.raises(Exception):
rb._standardize_chemical(wrong_mol)
def test_task_fire(mocker):
# raises RuleFireError
with pytest.raises(RuleFireError):
RuleBurner._task_fire('dummy', 'dummy', with_hs=False, with_stereo=False)
# goes well
mol = Chem.MolFromInchi(substrate_inchi)
rule = AllChem.ReactionFromSmarts(reaction_smarts)
mocker.patch.object(RuleBurner, '_handle_results')
RuleBurner._task_fire(rule, mol, with_hs=False, with_stereo=False)
def test_standardize_results_1():
tuple_tuple_raw = ((
Chem.MolFromSmiles('[H][O][C](=[O])[C]([H])([O][P](=[O])([O][H])[O][H])[C]([H])([H])[H]'),
Chem.MolFromSmiles('[H][N]=[c]1[n][c]([O][H])[c]2[n][c]([H])[n]([C]3([H])[O][C]([H])([C]([H])([H])[O][P](=[O])([O][H])[O][P](=[O])([O][H])[O][H])[C]([H])([O][H])[C]3([H])[O][H])[c]2[n]1[H]')
),(
Chem.MolFromInchi('InChI=1S/C5H6N5O/c6-5-9-3-2(4(11)10-5)7-1-8-3/h1H,9H2,(H,7,8)(H2,6,10,11)')
))
rb = RuleBurner()
tuple_tuple_rdmol, tuple_index_failed = rb._standardize_results(tuple_tuple_raw, with_hs=True, with_stereo=False)
assert len(tuple_tuple_rdmol) == 1
assert tuple_index_failed == [1]
def test_compute(smarts, inchi, expected_inchi):
# Things that are expected to return results
rb = RuleBurner(with_hs=True)
rb.insert_rsmarts([reaction_smarts])
rb.insert_inchi([substrate_inchi])
rb.compute(rule_mol='*')
result = [x for x in rb.compute(rule_mol='*')][0]
assert all(x in result for x in ['rule_id', 'substrate_id', 'product_list', 'product_inchikeys', 'product_inchis', 'product_smiles']), result
assert result['product_inchis'][0].sort() == expected_inchi.sort()
def test_init_rdkit_rule():
rb = RuleBurner()
with pytest.raises(RuleConversionError):
rb._init_rdkit_rule('DUMB')
rb._init_rdkit_rule('[C:1]>>[C:1]-[C]')
rb._init_rdkit_rule(reaction_smarts)
def test_gen_chemicals(valid_inputs):
rb = RuleBurner()
with pytest.raises(TypeError):
rb._gen_chemicals() # value is mandatory
rb.insert_inchi(valid_inputs)
list(rb._gen_chemicals(None))
ans = list(rb._gen_chemicals(list(valid_inputs.keys())))
assert len(ans) == len(valid_inputs)
def test_compute_wrong_chemical(caplog):
# Wrong chemical depiction should be caught and logged by RuleBurner
with caplog.at_level(logging.ERROR):
rb = RuleBurner()
rb.insert_rsmarts([reaction_smarts])
rb.insert_inchi(['DUMMY'])
result = [x for x in rb.compute(rule_mol='*')]
assert "CHEM-CONVERSION-ERROR" in caplog.text, (result, caplog.text)
def test_compute_timeout(caplog):
# Timeout should be logged
rsmarts = "([#6&v4:1](=[#6&v4:2](-[#6&v4:3])-[#6&v4:4](-[#6&v4:5](-[#6&v4:6](=[#6&v4:7](-[#6&v4:8])-[#6&v4:9](-[#6&v4:10](-[#6&v4:11](=[#6&v4:12](-[#6&v4:13])-[#6&v4:14](-[#6&v4:15](-[#6&v4:16](=[#6&v4:17](-[#6&v4:18])-[#6&v4:19](-[#6&v4:20](-[#6&v4:21](=[#6&v4:22](-[#6&v4:23])-[#6&v4:24](-[#6&v4:25](-[#6&v4:26](=[#6&v4:27](-[#6&v4:28])-[#6&v4:29](-[#6&v4:30](-[#6&v4:31](=[#6&v4:32])-[#1&v1:33])(-[#1&v1:34])-[#1&v1:35])(-[#1&v1:36])-[#1&v1:37])-[#1&v1:38])(-[#1&v1:39])-[#1&v1:40])(-[#1&v1:41])-[#1&v1:42])-[#1&v1:43])(-[#1&v1:44])-[#1&v1:45])(-[#1&v1:46])-[#1&v1:47])-[#1&v1:48])(-[#1&v1:49])-[#1&v1:50])(-[#1&v1:51])-[#1&v1:52])-[#1&v1:53])(-[#1&v1:54])-[#1&v1:55])(-[#1&v1:56])-[#1&v1:57])-[#1&v1:58])(-[#1&v1:59])-[#1&v1:60])(-[#1&v1:61])-[#1&v1:62])(-[#6&v4:63](-[#6&v4:64](-[#6&v4:65](=[#6&v4:66](-[#6&v4:67](-[#6&v4:68](-[#6&v4:69](=[#6&v4:70](-[#6&v4:71](-[#6&v4:72](-[#6&v4:73](=[#6&v4:74](-[#6&v4:75](-[#6&v4:76](-[#6&v4:77](=[#6&v4:78](-[#6&v4:79](-[#6&v4:80](-[#6&v4:81](=[#6&v4:82](-[#6&v4:83](-[#8&v2:84]-[#15&v5:85])(-[#1&v1:86])-[#1&v1:87])-[#1&v1:88])-[#6&v4:89])(-[#1&v1:90])-[#1&v1:91])(-[#1&v1:92])-[#1&v1:93])-[#1&v1:94])-[#6&v4:95])(-[#1&v1:96])-[#1&v1:97])(-[#1&v1:98])-[#1&v1:99])-[#1&v1:100])-[#6&v4:101])(-[#1&v1:102])-[#1&v1:103])(-[#1&v1:104])-[#1&v1:105])-[#1&v1:106])-[#6&v4:107])(-[#1&v1:108])-[#1&v1:109])(-[#1&v1:110])-[#1&v1:111])-[#1&v1:112])-[#6&v4:113])(-[#1&v1:114])-[#1&v1:115])(-[#1&v1:116])-[#1&v1:117])-[#1&v1:118])>>([#15&v5:85]-[#8&v2:84]-[#6&v4:83](-[#6&v4:29](-[#6&v4:27](=[#6&v4:26](-[#1&v1:38])-[#1&v1])-[#6&v4:28])(-[#1&v1:36])-[#1&v1:37])(-[#1&v1:86])-[#1&v1:87].[#6&v4:30](-[#6&v4:31](=[#6&v4:32])-[#1&v1:33])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:34])-[#1&v1:35].[#6&v4:82](=[#6&v4:81](-[#6&v4:89])-[#6&v4:80](-[#6&v4:79](-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:92])-[#1&v1:93])(-[#1&v1:90])-[#1&v1:91])(-[#1&v1:88])-[#1&v1].[#6&v4:78](=[#6&v4:77](-[#6&v4:95])-[#6&v4:76](-[#6&v4:75](-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:98])-[#1&v1:99])(-[#1&v1:96])-[#1&v1:97])(-[#1&v1:94])-[#1&v1].[#6&v4:74](=[#6&v4:73](-[#6&v4:101])-[#6&v4:72](-[#6&v4:71](-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:104])-[#1&v1:105])(-[#1&v1:102])-[#1&v1:103])(-[#1&v1:100])-[#1&v1].[#6&v4:70](=[#6&v4:69](-[#6&v4:107])-[#6&v4:68](-[#6&v4:67](-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:110])-[#1&v1:111])(-[#1&v1:108])-[#1&v1:109])(-[#1&v1:106])-[#1&v1].[#6&v4:66](=[#6&v4:65](-[#6&v4:113])-[#6&v4:64](-[#6&v4:63](-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:116])-[#1&v1:117])(-[#1&v1:114])-[#1&v1:115])(-[#1&v1:112])-[#1&v1].[#6&v4:1](=[#6&v4:2](-[#6&v4:3])-[#6&v4:4](-[#6&v4:5](-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:59])-[#1&v1:60])(-[#1&v1:61])-[#1&v1:62])(-[#1&v1:118])-[#1&v1].[#6&v4:6](=[#6&v4:7](-[#6&v4:8])-[#6&v4:9](-[#6&v4:10](-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:54])-[#1&v1:55])(-[#1&v1:56])-[#1&v1:57])(-[#1&v1:58])-[#1&v1].[#6&v4:11](=[#6&v4:12](-[#6&v4:13])-[#6&v4:14](-[#6&v4:15](-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:49])-[#1&v1:50])(-[#1&v1:51])-[#1&v1:52])(-[#1&v1:53])-[#1&v1].[#6&v4:16](=[#6&v4:17](-[#6&v4:18])-[#6&v4:19](-[#6&v4:20](-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:44])-[#1&v1:45])(-[#1&v1:46])-[#1&v1:47])(-[#1&v1:48])-[#1&v1].[#6&v4:21](=[#6&v4:22](-[#6&v4:23])-[#6&v4:24](-[#6&v4:25](-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(-[#8&v2]-[#15&v5](-[#8&v2]-[#1&v1])(=[#8&v2])-[#8&v2]-[#1&v1])=[#8&v2])(-[#1&v1:39])-[#1&v1:40])(-[#1&v1:41])-[#1&v1:42])(-[#1&v1:43])-[#1&v1])"
inchi = "InChI=1S/C70H116O7P2/c1-57(2)29-16-30-58(3)31-17-32-59(4)33-18-34-60(5)35-19-36-61(6)37-20-38-62(7)39-21-40-63(8)41-22-42-64(9)43-23-44-65(10)45-24-46-66(11)47-25-48-67(12)49-26-50-68(13)51-27-52-69(14)53-28-54-70(15)55-56-76-79(74,75)77-78(71,72)73/h29,31,33,35,37,39,41,43,45,47,49,51,53,55H,16-28,30,32,34,36,38,40,42,44,46,48,50,52,54,56H2,1-15H3,(H,74,75)(H2,71,72,73)"
with caplog.at_level(logging.WARNING):
rb = RuleBurner(with_hs=True)
rb.insert_rsmarts([rsmarts])
rb.insert_inchi([inchi])
result = [x for x in rb.compute(rule_mol='*', timeout=0.1)]
assert "timed-out" in caplog.text, (result, caplog.text)
def test_standardize_chemical_1():
# Without Hs
rb = RuleBurner()
rdmol = Chem.MolFromSmiles('[H][O][C](=[O])[C]([H])([O][H])[C]([H])([H])[H]')
rdmol_std_1 = rb._standardize_chemical(rdmol, with_hs=False, with_stereo=False)
assert Chem.MolToSmiles(rdmol_std_1) == 'CC(O)C(=O)O'
# With Hs
rb = RuleBurner()
rdmol_std_2 = rb._standardize_chemical(rdmol, with_hs=True, with_stereo=False)
assert Chem.MolToSmiles(rdmol_std_2, allHsExplicit=True) == '[H][O][C](=[O])[C]([H])([O][H])[C]([H])([H])[H]'
def __infile_mode(args):
"""
Execution mode to be used when rules and chemicals are provided
in CSV files.
"""
import csv
with open(args.rfile, 'r') as ifh:
reader = csv.DictReader(ifh, delimiter='\t')
rsmarts = {row['rule_id']: row['rule_smarts'] for row in reader}
with open(args.cfile, 'r') as ifh:
reader = csv.DictReader(ifh, delimiter='\t')
inchis = {row['chem_id']: row['inchi'] for row in reader}
r = RuleBurner(with_hs=args.with_hs, with_stereo=args.with_stereo)
r.insert_rsmarts(rsmarts)
r.insert_inchi(inchis)
return [x for x in r.compute(rule_mol='*', timeout=args.fire_timeout)]
def __inline_mode(args):
"""Execution mode to be used when a single rule and a single chemical
are provided through CLI.
"""
r = RuleBurner(with_hs=args.with_hs, with_stereo=args.with_stereo)
if args.rid:
r.insert_rsmarts({args.rid: args.rsmarts})
else:
r.insert_rsmarts([args.rsmarts])
if args.cid:
r.insert_inchi({args.cid: args.inchi})
else:
r.insert_inchi([args.inchi])
return [x for x in r.compute(rule_mol='*', timeout=args.fire_timeout)]
def _create_db_from_retrorules_v1_0_5(path_retrosmarts_tsv, db_path, with_hs,
with_stereo):
def helper_metabolite(store, cid, smiles):
if cid not in store:
store[cid] = smiles
elif store[cid] != smiles:
logger.warning(
f"Metabolite {cid} is suspiciously associated to distinct SMILES. "
f"Only the first one will be considered: {store[cid]} and {smiles}"
)
rules = {}
metabolites = {} # both substrate and products
results = set(
) # all "obvious" results that directly come from the reaction database (no promiscuity)
pgroup = {} # index of a solution rid vs. cid
# Load all valuable data in-memory
# NB: is this file small enough that we do not need to chunk it?
with open(path_retrosmarts_tsv) as hdl:
for row in csv.DictReader(hdl, delimiter='\t'):
# each row is a reaction rule automatically generated from a known metabolic reaction
# each row contains 1 rule...
# NB: rule identifier may be duplicated over several rows but must match the same RSMARTS
rid = row["# Rule_ID"]
rsmarts = row["Rule_SMARTS"]
diameter = int(row["Diameter"])
direction = row["Rule_usage"] # -1, 0, 1 ==> retro, both, forward
if direction == "both":
direction = 0
elif direction == "retro":
direction = -1
elif direction == "forward":
direction = 1
else:
raise ValueError(
f"Found an unexpected direction for rule {rid}: {direction}"
)
if rid not in rules:
# warning: keys must match database schema
rules[rid] = {
'rd_rule': rsmarts,
'diameter': diameter,
'direction': direction
}
else:
assert rules[rid]['rd_rule'] == rsmarts, f"UNEXPECTED: rule {rid} from {path_retrosmarts_tsv} has " \
f"mismatching RSMARTS: {rules[rid]} and {rsmarts}"
# ... and 1 substrate ...
sid = row["Substrate_ID"]
helper_metabolite(metabolites, sid, row["Substrate_SMILES"])
# ... and N coproducts
smiles_list = row["Product_SMILES"].split('.')
tmp_results = []
pid_stoichio = {}
for idx, pid in enumerate(row["Product_IDs"].split('.')):
if pid in pid_stoichio:
pid_stoichio[pid] += 1
else:
pid_stoichio[pid] = 1
helper_metabolite(metabolites, pid, smiles_list[idx])
tmp_results.append(
(rid, sid, pid)
) # TODO: bug, there can be several solutions for the same rule x mol couple
# each row is also a distinct solution of "1 rule applied on 1 metabolite"... but there can be many
# especially at low diameters!
if (rid, sid) not in pgroup:
pgroup[(rid, sid)] = -1
else:
pgroup[(rid, sid)] -= 1
# record the results of this row (1 by distinct product)
for rid, sid, pid in tmp_results:
results.add(
(sid, rid, pid, pid_stoichio[pid], pgroup[(rid, sid)]))
# Create the database
o = RuleBurner(db_path=db_path, with_hs=with_hs, with_stereo=with_stereo)
o.insert_rsmarts(rules)
o.insert_smiles(metabolites)
o.db.executemany("INSERT INTO results VALUES (?,?,?,?,?);", list(results))
o.create_indexes()
def test_standardize_chemical_2():
# Data
violacein_smiles = 'OC1=NC(=C\\C1=C1/C(O)=NC2=CC=CC=C12)C1=CNC2=C1C=C(O)C=C2'
violacein_mol = Chem.MolFromSmiles(violacein_smiles, sanitize=False)
# Test simplest case
rb = RuleBurner()
std_mol_1 = rb._standardize_chemical(violacein_mol, with_hs=False, with_stereo=True)
assert Chem.MolToSmiles(std_mol_1) == 'OC1=NC(c2c[nH]c3ccc(O)cc23)=C/C1=C1\\C(O)=Nc2ccccc21'
# Test adding Hs
rb = RuleBurner()
std_mol_2 = rb._standardize_chemical(violacein_mol, with_hs=True, with_stereo=True)
assert Chem.MolToSmiles(std_mol_2) == '[H]OC1=NC(c2c([H])n([H])c3c([H])c([H])c(O[H])c([H])c23)=C([H])/C1=C1\\C(O[H])=Nc2c([H])c([H])c([H])c([H])c21'
# Test removing stereo
rb = RuleBurner()
std_mol_3 = rb._standardize_chemical(violacein_mol, with_hs=False, with_stereo=False)
assert Chem.MolToSmiles(std_mol_3) == 'O=C1NC(c2c[nH]c3ccc(O)cc23)=CC1=C1C(=O)Nc2ccccc21'
# Test adding Hs + removing stereo
rb = RuleBurner()
std_mol_4 = rb._standardize_chemical(violacein_mol, with_hs=True, with_stereo=False)
assert Chem.MolToSmiles(std_mol_4) == '[H]Oc1c([H])c([H])c2c(c1[H])c(C1=C([H])C(=C3C(=O)N([H])c4c([H])c([H])c([H])c([H])c43)C(=O)N1[H])c([H])n2[H]'
def test_init_rdkit_mol_from_smiles(valid_smiles):
rb = RuleBurner()
with pytest.raises(ChemConversionError):
rb._init_rdkit_mol_from_smiles('DUMB')
rb._init_rdkit_mol_from_smiles(valid_smiles)
def test_gen_rules(valid_ids):
rb = RuleBurner()
rb.insert_rsmarts(reaction_smarts)
with pytest.raises(TypeError):
rb._gen_rules() # value is mandatory
list(rb._gen_rules(valid_ids))
def test_init_1():
# Empty is OK
rb = RuleBurner() # Empty is OK
with pytest.raises(TypeError):
rb.compute() # Missing argument rule_mol
rb.compute(rule_mol=((), ()))
def test_rules():
# Rules to be considered
rb = RuleBurner()
rb.insert_rsmarts({'rid1': reaction_smarts, 'rid2': reaction_smarts})
assert sorted(rb.rules) == ['rid1', 'rid2']
def test_chemicals():
# Chemicals to be considered
rb = RuleBurner()
rb.insert_inchi({'cid1': substrate_inchi, 'cid2': substrate_inchi})
assert sorted(rb.chemicals) == ['cid1', 'cid2']
def test_init_2():
# Stereo support not implemented
with pytest.raises(NotImplementedError):
RuleBurner(with_stereo=True)