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Check for explicit hydrogens #21

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Merged
tduigou merged 1 commit into from
Sep 23, 2025
Merged

Check for explicit hydrogens #21

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12 changes: 6 additions & 6 deletions retropath2_wrapper/RetroPath2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -381,7 +381,7 @@ def format_files_for_knime(
return files

def sniff_rules(path: str, logger: Logger = getLogger(__name__)) -> str:
hydrogen_implicit_patterns = ["[H", "!H", ",H", ";H", "&H"]
hydrogen_explicit_patterns = ["[#1"]
n = 10
lines = []
# --- Gzip compressed single file ---
Expand Down Expand Up @@ -427,9 +427,9 @@ def sniff_rules(path: str, logger: Logger = getLogger(__name__)) -> str:
lines.append(line.rstrip())

for line in lines:
for pattern in hydrogen_implicit_patterns:
for pattern in hydrogen_explicit_patterns:
if pattern in line:
logger.info("Detect implicit hydrogens in reaction rules")
return "implicit"
logger.info("Detect explicit hydrogen in reaction rules")
return "explicit"
logger.info("Detect explicit hydrogens in reaction rules")
return "explicit"
logger.info("Detect implicit hydrogen in reaction rules")
return "implicit"
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