def test_get_compound_hash_two_blocks():
smiles = "C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O"
assert utils.get_compound_hash(smiles, "Starting Compound", inchi_blocks=2) == (
"Cf95a3c17f908e427c3127b4e8c3d8575c286d6ce",
"WQZGKKKJIJFFOK-DVKNGEFBSA-N",
)
assert utils.get_compound_hash(smiles, "Starting Compound", inchi_blocks=1) == (
"C9ab1a08d72c90a8167d1f3a668d8f1138e534a07",
"WQZGKKKJIJFFOK-DVKNGEFBSA-N",
)
def test_get_compound_hash():
"""Test compound to hash."""
assert utils.get_compound_hash("CCO", "Coreactant") == (
"Xa41fe8492d86f214ba494e3d04da2f0854c0e2ea",
"LFQSCWFLJHTTHZ",
)
assert utils.get_compound_hash("CCO", "Predicted") == (
"Ca41fe8492d86f214ba494e3d04da2f0854c0e2ea",
"LFQSCWFLJHTTHZ-UHFFFAOYSA-N",
)
assert utils.get_compound_hash("CCO", "Starting Compound") == (
"Ca41fe8492d86f214ba494e3d04da2f0854c0e2ea",
"LFQSCWFLJHTTHZ-UHFFFAOYSA-N",
)
def import_mol_dir(mine_db: MINE,
target: str,
name_field: str = "Name",
overwrite: bool = False) -> None:
"""Imports a directory of molfiles as a MINE database.
Parameters
----------
mine_db : MINE
The database to export.
target : str
Directory in which to place the files.
name_field : str, optional
Field for the compound name, by default "Name".
overwrite : bool, optional
Replace old compounds with new ones if a collision happens, by default False.
"""
# For each .mol file in the directory of the target folder (path):
for file in os.listdir(target):
if ".mol" in file:
# MolFromMolFile (rdkit) generates Mol objects from .mol files
mol = AllChem.MolFromMolFile(target + "/" + file)
# Mol object name becomes name of mol file without .mol extension
name = file.rstrip(".mol")
# Check that Mol object is successfully generated
if mol:
# Create hashkey for the compound
cpdhash = utils.get_compound_hash(mol)
# If we don't want to overwrite, and the compound (cpdhash)
# already exists, then add an extra cpdhash for that molecule
if not overwrite and mine_db.compounds.count({"_id": cpdhash}):
mine_db.compounds.update({"_id": cpdhash},
{"$addToSet": {
name_field: name
}})
# If we don't care about overwriting, just insert the new
# compound into the database
else:
mine_db.insert_compound(
mol,
compound_dict={
name_field: [name],
"Generation": 0
},
pubchem_db=None,
kegg_db=None,
modelseed_db=None,
)
# Add to log file (metadata)
mine_db.meta_data.insert({
"Timestamp": datetime.datetime.now(),
"Action": "MolFiles Imported",
"Filepath": target,
})
def _gen_compound(mol):
rkl.DisableLog("rdApp.*")
try:
if explicit_h:
mol = RemoveHs(mol)
# resolve potential tautomers and choose first one
mol_smiles = MolToSmiles(mol, True)
if "n" in mol_smiles:
mol_smiles = utils.postsanitize_smiles([mol_smiles])[0][0]
mol = MolFromSmiles(mol_smiles)
SanitizeMol(mol)
# TODO: logger
# Get lots of "Explicit valence greater than permitted" errors here
# This is for predicted compounds that are infeasible, so we throw them out
except BaseException:
return None
rkl.EnableLog("rdApp.*")
mol_smiles = MolToSmiles(mol, True)
if "." in mol_smiles:
return None
cpd_id, inchi_key = utils.get_compound_hash(mol_smiles, "Predicted")
if cpd_id:
if cpd_id not in local_cpds:
cpd_dict = {
"ID": None,
"_id": cpd_id,
"SMILES": mol_smiles,
"InChI_key": inchi_key,
"Type": "Predicted",
"Generation": generation,
"atom_count": utils.get_atom_count(mol),
"Reactant_in": [],
"Product_of": [],
"Expand": True,
"Formula": CalcMolFormula(mol),
"last_tani": 0,
}
else:
cpd_dict = local_cpds[cpd_id]
return cpd_dict
else:
return None
def parse_comps(field):
atoms = collections.Counter()
compounds = collections.Counter(field.split(' // '))
half_rxn = []
for comp, stoich in compounds.items():
if comp in metacyc2hash:
mol = metacyc2hash[comp]
for pair in re.findall('([A-Z][a-z]*)(\d*)',
AllChem.CalcMolFormula(mol)):
if pair[1]:
atoms[pair[0]] += int(pair[1]) * stoich
else:
atoms[pair[0]] += 1 * stoich
if comp not in inserted:
mine_db.insert_compound(mol, {'Generation': 0})
inserted.add(comp)
half_rxn.append(
utils.stoich_tuple(stoich, utils.get_compound_hash(mol)))
else:
raise ValueError('Undefined Compound: %s' % comp)
return half_rxn, atoms