xushuwenn/redact/medchem-ro5-pass

Common Alerts Filter with medchem

When to Use

• Detect problematic functional groups in molecules
• Use medchem CommonAlertsFilters
• Follow task-specific implementation constraints exactly: use the required library/API directly, and do not substitute RDKit or another chemistry library unless the task explicitly allows it.
• Check if molecule passes safety criteria

Input

• /root/input.txt: SMILES input
• Do not assume exactly one molecule unless the file clearly contains only one record; if multiple non-empty molecule rows are present, process every row exactly once.

Output Format

To /root/output.txt:

Common alerts: N
Status: status
Pass: yes/no

A molecule PASSES if:

• status is "ok", OR
• status is "annotations" with 0 alert reasons

• If the task input contains multiple molecule records or IDs, emit one result block/line per input record in the required task format, and ensure the output covers all records.

New Section

Execution Checklist

• Write the required results to /root/output.txt before declaring completion.
• If /root/input.txt contains multiple molecule rows, process every non-empty record exactly once.
• Before finishing, verify output cardinality: the number of result blocks/lines matches the number of input records, and any summary totals agree.
• Follow task-level and system-level protocol exactly when present (required library/API, tool-call schema, or completion formatting). Higher-priority instructions override this skill's examples.
• If the environment requires an exact completion string (for example, ACTION: TASK_COMPLETE), output that exact string verbatim as the final chat message and nothing else.
• Do not summarize results in chat after writing the file unless the task explicitly asks for it.

Using medchem

from medchem._filters import CommonAlertsFilters
# Apply CommonAlertsFilters to molecule

Alert Detection

• CommonAlertsFilters detects problematic functional groups
• Count number of alerts
• Determine pass/fail based on status

• Process every molecule present in the input source.
• Before finishing, verify the number of output result blocks matches the number of input molecules/records.
• If you include totals or pass/fail counts, reconcile them against the full input set.

Tips

• Check status field to determine pass/fail
• Zero alerts means pass (yes)
• Handle different status return types

• Before coding, verify all hard constraints: required library, exact input/output paths, and exact output format.
• For batch inputs, count input records first and reconcile them with the final output.
• Re-read task-specific output requirements before finishing; if the task requires an exact completion string or response format, use it verbatim.
• Do not claim the result is fully compliant unless you checked all stated task and environment constraints.