medchem

name	medchem
description	Filter molecules using CommonAlertsFilters from medchem library. Detect structural alerts and problematic functional groups in molecules for drug discovery filtering.

Medchem: Common Alerts Filter

Overview

Use CommonAlertsFilters from the medchem library to detect problematic functional groups (structural alerts) in molecules. Write the number of alerts and pass/fail status to output.

Installation

uv pip install medchem datamol

Workflow

Step 1: Load Library and Create Filter

import medchem as mc

alert_filter = mc.structural.CommonAlertsFilters()

Step 2: Read Input SMILES

with open("/root/input.txt") as f:
    smiles = f.read().strip()

Step 3: Convert to Molecule and Check

import datamol as dm

mol = dm.to_mol(smiles)
has_alerts, details = alert_filter.check_mol(mol)

Step 4: Determine Status and Pass/Fail

if not has_alerts:
    num_alerts = 0
    status = "ok"
    passes = "yes"
else:
    num_alerts = len(details.get("alert_types", []))
    if num_alerts == 0:
        status = "annotations"
        passes = "yes"
    else:
        status = "alert"
        passes = "no"

Step 5: Write Output

with open("/root/output.txt", "w") as f:
    f.write(f"Common alerts: {num_alerts}\n")
    f.write(f"Status: {status}\n")
    f.write(f"Pass: {passes}\n")

Complete Script

import datamol as dm
import medchem as mc

# Read SMILES from input
with open("/root/input.txt") as f:
    smiles = f.read().strip()

# Create CommonAlertsFilters
alert_filter = mc.structural.CommonAlertsFilters()

# Convert SMILES to molecule object
mol = dm.to_mol(smiles)

# Check for structural alerts
has_alerts, details = alert_filter.check_mol(mol)

# Determine number of alerts and status
if not has_alerts:
    num_alerts = 0
    status = "ok"
    passes = "yes"
else:
    num_alerts = len(details.get("alert_types", []))
    if num_alerts == 0:
        status = "annotations"
        passes = "yes"
    else:
        status = "alert"
        passes = "no"

# Write results
with open("/root/output.txt", "w") as f:
    f.write(f"Common alerts: {num_alerts}\n")
    f.write(f"Status: {status}\n")
    f.write(f"Pass: {passes}\n")

Output Format

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

Status values:

• ok: No alerts found
• annotations: Alerts present but flagged as annotations (0 alert reasons)
• alert: Structural alerts detected

Pass/Fail:

• yes: Molecule passes (no alerts, or annotations with 0 alert reasons)
• no: Molecule has structural alerts

Key Reference

• mc.structural.CommonAlertsFilters() — Create common alerts filter
• alert_filter.check_mol(mol) — Returns (has_alerts, details) tuple
• datamol.to_mol(smiles) — Convert SMILES string to molecule object
• Pass if status == "ok" or status == "annotations" with 0 alert reasons