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Experimental App Domain (#43)

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Backend App Domain done, Frontend missing

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#43
This commit is contained in:
jebus
2025-08-08 20:52:21 +12:00
parent 280ddc7205
commit 579cd519d0
14 changed files with 1094 additions and 574 deletions
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66
utilities/chem.py
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@ -131,6 +131,24 @@ class FormatConverter(object):
# TODO call to AMBIT Service
return smiles
@staticmethod
def ep_standardize(smiles):
change = True
while change:
change = False
for standardizer in MATCH_STANDARDIZER:
tmp_smiles = standardizer.standardize(smiles)
if tmp_smiles != smiles:
print(f"change {smiles} to {tmp_smiles}")
change = True
smiles = tmp_smiles
if change is False:
print(f"nothing changed")
return smiles
@staticmethod
def standardize(smiles):
# Taken from https://bitsilla.com/blog/2021/06/standardizing-a-molecule-using-rdkit/
@ -180,54 +198,6 @@ class FormatConverter(object):
atom.UpdatePropertyCache()
return mol
# @staticmethod
# def apply(smiles, smirks, preprocess_smiles=True, bracketize=False, standardize=True):
# logger.debug(f'Applying {smirks} on {smiles}')
#
# if bracketize:
# smirks = smirks.split('>>')[0] + ">>(" + smirks.split('>>')[1] + ")"
#
# res = set()
# try:
# rxn = rdChemReactions.ReactionFromSmarts(smirks)
# mol = Chem.MolFromSmiles(smiles)
#
# # Inplace
# if preprocess_smiles:
# Chem.SanitizeMol(mol)
# mol = Chem.AddHs(mol)
#
# # apply!
# reacts = rxn.RunReactants((mol,))
# if len(reacts):
# # Sanitize mols
# for product_set in reacts:
# prod_set = list()
# for product in product_set:
# # Fixes
# # [2025-01-30 23:00:50] ERROR chem - Sanitizing and converting failed:
# # non-ring atom 3 marked aromatic
# # But does not improve overall performance
# #
# # for a in product.GetAtoms():
# # if (not a.IsInRing()) and a.GetIsAromatic():
# # a.SetIsAromatic(False)
# # for b in product.GetBonds():
# # if (not b.IsInRing()) and b.GetIsAromatic():
# # b.SetIsAromatic(False)
#
# try:
# Chem.SanitizeMol(product)
# prod_set.append(FormatConverter.standardize(Chem.MolToSmiles(product)))
# except ValueError as e:
# logger.error(f'Sanitizing and converting failed:\n{e}')
# continue
# res.add(tuple(list(set(prod_set))))
# except Exception as e:
# logger.error(f'Applying {smirks} on {smiles} failed:\n{e}')
#
# return list(res)
@staticmethod
def is_valid_smirks(smirks: str) -> bool:
try: