The standardiser inappropriately removes organic compounds that are sometimes used as organic solvents. For example, the important metabolite glutamate is removed:
from rdkit import Chem
from standardiser import standardise
smiles = 'NC(CCC(=O)O)C(=O)O' # glutamate
mol = Chem.MolFromSmiles(smiles, sanitize=False)
clean_mol = standardise.apply(mol) # throws no_non_salt exception
One approach to resolving this issue would be allow organic solvents if they are the only organic fragment in the molecule. Here is code that does this:
organic_salt_frags = []
non_salt_frags = []
mol = break_bonds.apply(mol)
for n, frag in enumerate(Chem.GetMolFrags(mol, asMols=True), 1):
logger.debug("Starting fragment {n} '{smi}'...".format(n=n, smi=Chem.MolToSmiles(frag)))
logger.debug("1) Check for non-organic elements...")
if unsalt.is_nonorganic(frag): continue
logger.debug("2) Attempting to neutralise (first pass)...")
frag = neutralise.apply(frag)
logger.debug("3) Applying rules...")
frag = rules.apply(frag, output_rules_applied=output_rules_applied, verbose=verbose)
logger.debug("4) Attempting to neutralise (second pass)...")
frag = neutralise.apply(frag)
logger.debug("5) Checking if frag is a salt/solvate...")
if unsalt.is_salt(frag):
organic_salt_frags.append(frag)
continue
logger.debug("...fragment kept.")
non_salt_frags.append(frag)
if len(non_salt_frags) == 0:
logger.debug("No non-salt frags. If there is a single organic salt frag take it.")
if len(organic_salt_frags) == 1:
parent = organic_salt_frags[0]
else:
raise StandardiseException("no_non_salt")
elif len(non_salt_frags) > 1:
raise StandardiseException("multi_component")
else:
parent = non_salt_frags[0]
The standardiser inappropriately removes organic compounds that are sometimes used as organic solvents. For example, the important metabolite glutamate is removed:
One approach to resolving this issue would be allow organic solvents if they are the only organic fragment in the molecule. Here is code that does this: