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Fix wildcart (*) uses in SMILES #33

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Fix wildcart (*) uses in SMILES #33

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0856c1c
Fix dummy processing
Feb 20, 2024
d22e587
Black + simple test
Feb 20, 2024
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8 changes: 7 additions & 1 deletion safe/converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -332,7 +332,13 @@ def encoder(
val = str(starting_num) if starting_num < 10 else f"%{starting_num}"
# we cannot have anything of the form "\([@=-#-$/\]*\d+\)"
attach_regexp = re.compile(r"(" + re.escape(attach) + r")")
scaffold_str = attach_regexp.sub(val, scaffold_str)
# check if we have at least 2 matches, if not, we have a dummy
n_matches = len(attach_regexp.findall(scaffold_str))
scaffold_str = (
attach_regexp.sub(val, scaffold_str)
if n_matches > 1
else scaffold_str.replace(attach, "*")
)
starting_num += 1
# now we need to remove all the parenthesis around digit only number
wrong_attach = re.compile(r"\(([\%\d]*)\)")
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1 change: 1 addition & 0 deletions tests/test_safe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,7 @@ def test_rdkit_smiles_parser_issues():
"c1cc2c(cc1[C@@H]1CCC[NH2+]1)OCCO2",
"[13C]1CCCCC1C[238U]C[NH3+]",
"COC[CH2:1][CH2:2]O[CH:2]C[OH:3]",
"C1*CCC1COO",
],
)
def test_bracket_smiles_issues(input_sm):
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