alterlab-medchem

name	alterlab-medchem
description	Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PAINS or reactive groups, or assessing drug-likeness of candidate molecules. Part of the AlterLab Academic Skills suite.
license	Apache-2.0
allowed-tools	Read Write Edit Bash(python:*) Bash(uv:*)
compatibility	Self-contained — runs under `uv run python` with the skill's Python package installed; no API key or account required.
metadata	{"skill-author":"AlterLab","version":"1.1.0"}

Medchem

Overview

Medchem (datamol-io/medchem) is a Python library for molecular filtering and prioritization in drug-discovery workflows: medicinal-chemistry rules, structural alerts (ChEMBL/NIBR/PAINS), chemical-group detection, complexity metrics, and a query DSL. Rules and filters are context-specific guidelines, not hard truth — combine with domain expertise.

Verified against medchem==2.0.5 (RDKit 2026.3.x, Python 3.12). API names below are checked against this version; earlier docs/blog posts described a different surface.

When to Use This Skill

This skill should be used when:

• Applying drug-likeness rules (Lipinski, Veber, etc.) to compound libraries
• Filtering molecules by structural alerts or PAINS patterns
• Prioritizing compounds for lead optimization
• Assessing compound quality and medicinal chemistry properties
• Detecting reactive or problematic functional groups
• Calculating molecular complexity metrics

Installation

uv pip install medchem    # PyPI; pulls rdkit + datamol

Two features need extra native deps that PyPI cannot provide:

• Lilly demerits (lilly_demerit_filter) shells out to compiled binaries — install via conda: mamba install -c conda-forge lilly-medchem-rules. Without them, the call raises ImportError.
• The ChemAxon rule (rule_of_chemaxon_druglikeness) needs a licensed ChemAxon install.

Everything else (RuleFilters, CommonAlerts, NIBR, complexity, groups, query) works from the PyPI wheel alone.

Core Capabilities

Conventions that hold across medchem. Filters take mols (a sequence of SMILES strings or RDKit mols), default to n_jobs=-1 (all cores), and accept progress=True. The medchem.structural / medchem.rules filter classes return a pandas DataFrame (one row per input mol); the medchem.functional.* helpers return a NumPy boolean array where True = the molecule passes / is kept. Get the canonical rule and alert names from mc.rules.RuleFilters.list_available_rules() and mc.structural.CommonAlertsFilters.list_default_available_alerts() rather than guessing.

1. Medicinal Chemistry Rules — medchem.rules

Single rule — medchem.rules.basic_rules.* functions take one mol (SMILES or RDKit) and return a plain bool:

import medchem as mc

smi = "CC(=O)OC1=CC=CC=C1C(=O)O"  # aspirin
mc.rules.basic_rules.rule_of_five(smi)   # -> True
mc.rules.basic_rules.rule_of_veber(smi)  # -> True
mc.rules.basic_rules.rule_of_cns(smi)

Available rules (subset; full list via mc.rules.RuleFilters.list_available_rules()): rule_of_five, rule_of_five_beyond, rule_of_four, rule_of_three, rule_of_three_extended, rule_of_two, rule_of_ghose, rule_of_veber, rule_of_reos, rule_of_egan, rule_of_pfizer_3_75, rule_of_gsk_4_400, rule_of_oprea, rule_of_xu, rule_of_cns, rule_of_respiratory, rule_of_zinc, rule_of_leadlike_soft, rule_of_druglike_soft, rule_of_generative_design, rule_of_chemaxon_druglikeness (needs ChemAxon).

There is no rule_of_drug, rule_of_leadlike_strict, golden_triangle, or pains_filter function in 2.0.5. PAINS lives in the alert system (HASALERT("pains") or CommonAlertsFilters(alerts_set=["PAINS"])). For lead-likeness use rule_of_leadlike_soft or rule_of_oprea.

Multiple rules — RuleFilters returns a DataFrame with columns mol, pass_all, pass_any, and one boolean column per rule:

import datamol as dm
import medchem as mc

mols = [dm.to_mol(s) for s in smiles_list]
rfilter = mc.rules.RuleFilters(rule_list=["rule_of_five", "rule_of_veber", "rule_of_cns"])
df = rfilter(mols=mols, n_jobs=-1, progress=True)
# df["pass_all"] -> bool per molecule; df["rule_of_five"] -> per-rule bool
clean = [m for m, ok in zip(mols, df["pass_all"]) if ok]

Property windows — there is no all-in-one "Constraints(mw_range=...)" object (see note in section 7). Build custom property cutoffs with mc.rules.in_range over descriptor names from mc.rules.list_descriptors() (mw, clogp, tpsa, n_lipinski_hbd, n_lipinski_hba, n_rotatable_bonds, n_rings, ...), or use the query DSL (HASPROP, section 8).

2. Structural Alert Filters — medchem.structural

Two filter classes ship in medchem.structural: CommonAlertsFilters and NIBRFilters. (Lilly demerits is reached through medchem.functional, see section 3 — its class lives under medchem.structural.lilly_demerits and needs external binaries.)

Common alerts — curated alert sets from ChEMBL (Glaxo, Dundee, BMS, PAINS, SureChEMBL, ...). Returns a DataFrame with mol, pass_filter (bool), status (ok/exclude), reasons (matched alert names, ;-joined):

import medchem as mc

caf = mc.structural.CommonAlertsFilters()                 # all default sets
caf_pains = mc.structural.CommonAlertsFilters(alerts_set=["PAINS"])  # PAINS only
df = caf(mols=mol_list, n_jobs=-1, progress=True)
clean = df[df["pass_filter"]]
# discover sets: mc.structural.CommonAlertsFilters.list_default_available_alerts()

NIBR filters — Novartis filter set. Returns a DataFrame including mol, pass_filter, severity, status, reasons:

nibr = mc.structural.NIBRFilters()
df = nibr(mols=mol_list, n_jobs=-1)

3. Functional API — medchem.functional

One-call helpers that return a NumPy boolean array (True = keep). Pass return_idx=True to get indices of passing mols instead:

import medchem as mc

mc.functional.rules_filter(mol_list, rules=["rule_of_five", "rule_of_veber"], n_jobs=-1)
mc.functional.alert_filter(mol_list, alerts=["pains"], n_jobs=-1)   # alert names are lowercase here
mc.functional.nibr_filter(mol_list, max_severity=10, n_jobs=-1)
mc.functional.complexity_filter(mol_list, complexity_metric="bertz", limit="99", n_jobs=-1)
mc.functional.chemical_group_filter(mol_list, chemical_group=mc.groups.ChemicalGroup(groups=["hinge_binders"]))

Lilly demerits — requires the external Lilly binaries (see Installation); raises ImportError if missing. Molecules above max_demerits (default 160) are rejected:

keep = mc.functional.lilly_demerit_filter(mol_list, max_demerits=160, n_jobs=-1)  # NumPy bool array

4. Chemical Groups Detection — medchem.groups

ChemicalGroup matches curated group catalogs. List valid catalog names with mc.groups.list_default_chemical_groups() (e.g. hinge_binders, electrophilic_warheads_for_kinases, common_warhead_covalent_inhibitors, privileged_kinase_inhibitor_scaffolds, aggregator). Per-mol functional-group names (for the query DSL HASGROUP) come from mc.groups.list_functional_group_names().

import medchem as mc

group = mc.groups.ChemicalGroup(groups=["hinge_binders"])
group.has_match(mol)        # bool for one mol
group.get_matches(mol)      # detailed matches
# batch: mc.functional.chemical_group_filter(mols, chemical_group=group)

phosphate_binders, michael_acceptors, and reactive_groups are not default catalog names. For reactive/electrophilic motifs use electrophilic_warheads_for_kinases / common_warhead_covalent_inhibitors, the alert filters (section 2), or a custom SMARTS catalog (mc.catalogs.catalog_from_smarts).

5. Named Catalogs — medchem.catalogs

import medchem as mc

mc.catalogs.list_named_catalogs()      # available catalog names
cat = mc.catalogs.NamedCatalogs.pains()  # e.g. a PAINS RDKit FilterCatalog
mc.catalogs.catalog_from_smarts(...)   # build a catalog from custom SMARTS

6. Molecular Complexity — medchem.complexity

ComplexityFilter flags molecules whose complexity exceeds a percentile threshold derived from a reference set (default ZINC). It is called per molecule and returns a bool (True = within limit / keep). Metrics: bertz, whitlock (WhitlockCT), barone (BaroneCT), smcm (SMCM), twc (TWC).

import medchem as mc

cflt = mc.complexity.ComplexityFilter(limit="99", complexity_metric="bertz")
keep = [cflt(m) for m in mol_list]
# or batch: mc.functional.complexity_filter(mol_list, complexity_metric="bertz", limit="99")

There is no mc.complexity.calculate_complexity(...) and ComplexityFilter takes limit/complexity_metric/threshold_stats_file, not max_complexity. For a raw score use the metric classes directly (mc.complexity.TWC, etc.).

7. Substructure Constraints — medchem.constraints

mc.constraints.Constraints(core, constraint_fns, prop_name="query") enforces substructure / R-group constraints around a query core (via has_match / validate) — it is not a physchem property-window filter. For MW/logP/TPSA windows, use RuleFilters + in_range (section 1) or the query DSL HASPROP (section 8).

8. Query DSL — medchem.query

QueryFilter evaluates a boolean expression over rules, properties, alerts, and groups. Operators: AND, OR, NOT, comparisons < > <= >= == !=. Primitives: MATCHRULE("..."), HASPROP("<descriptor>" < value), HASALERT("<lowercase set>"), HASGROUP("..."), HASSUBSTRUCTURE/HASSUPERSTRUCTURE, LIKE.

import medchem as mc

qf = mc.query.QueryFilter('MATCHRULE("rule_of_five") AND HASPROP("mw" < 500) AND NOT HASALERT("pains")')
keep = qf(mol_list, n_jobs=-1)   # NumPy bool array

The syntax is the structured DSL above — not free-form text like "rule_of_five AND NOT common_alerts". There is no mc.query.parse(); construct mc.query.QueryFilter(query_string) and call it on the mols. Alert names inside HASALERT are lowercase (pains, tox, nih, ...).

Workflow Patterns

Pattern 1: Initial Triage of Compound Library

Filter a large collection to drug-like candidates, dropping anything with structural alerts.

import datamol as dm
import medchem as mc
import pandas as pd

df = pd.read_csv("compounds.csv")
mols = [dm.to_mol(smi) for smi in df["smiles"]]

# Rule filter -> DataFrame with pass_all + per-rule columns
rule_df = mc.rules.RuleFilters(rule_list=["rule_of_five", "rule_of_veber"])(
    mols=mols, n_jobs=-1, progress=True
)

# Structural alerts -> DataFrame with pass_filter (True = clean)
alert_df = mc.structural.CommonAlertsFilters()(mols=mols, n_jobs=-1, progress=True)

df["passes_rules"] = rule_df["pass_all"].to_numpy()
df["no_alerts"] = alert_df["pass_filter"].to_numpy()
df["drug_like"] = df["passes_rules"] & df["no_alerts"]

df[df["drug_like"]].to_csv("filtered_compounds.csv", index=False)

Pattern 2: Lead Optimization Filtering

Stack stricter filters and keep only molecules passing every stage. The functional.* helpers all return aligned NumPy bool arrays, so intersecting them is straightforward.

import numpy as np
import medchem as mc

f = mc.functional
keep = (
    f.rules_filter(candidate_mols, rules=["rule_of_oprea"], n_jobs=-1)
    & f.nibr_filter(candidate_mols, n_jobs=-1)
    & f.complexity_filter(candidate_mols, complexity_metric="bertz", limit="99", n_jobs=-1)
)
# Add lilly_demerit_filter(...) too if the Lilly binaries are installed.
survivors = [m for m, ok in zip(candidate_mols, keep) if ok]

Pattern 3: Identify Specific Chemical Groups

Flag molecules containing a target scaffold/motif (validate names with mc.groups.list_default_chemical_groups()).

import medchem as mc

group = mc.groups.ChemicalGroup(groups=["hinge_binders"])
keep = mc.functional.chemical_group_filter(mol_list, chemical_group=group)
with_group = [m for m, ok in zip(mol_list, keep) if ok]

Best Practices

1. Context Matters: Don't blindly apply filters. Understand the biological target and chemical space.

2. Combine Multiple Filters: Use rules, structural alerts, and domain knowledge together for better decisions.

3. Use Parallelization: For large datasets (>1000 molecules), always use n_jobs=-1 for parallel processing.

4. Iterative Refinement: Start with broad filters (Ro5), then apply more specific criteria (CNS, leadlike) as needed.

5. Document Filtering Decisions: Track which molecules were filtered out and why for reproducibility.

6. Validate Results: Remember that marketed drugs often fail standard filters—use these as guidelines, not absolute rules.

7. Consider Prodrugs: Molecules designed as prodrugs may intentionally violate standard medicinal chemistry rules.

Resources

references/api_guide.md

Comprehensive API reference covering all medchem modules with detailed function signatures, parameters, and return types.

references/rules_catalog.md

Complete catalog of available rules, filters, and alerts with descriptions, thresholds, and literature references.

scripts/filter_molecules.py

Batch filtering CLI. Supports CSV/TSV, SDF, and plain-SMILES .txt input, configurable filter combinations, and a summary report.

Usage:

uv run python scripts/filter_molecules.py input.csv \
    --rules rule_of_five,rule_of_cns --nibr --output filtered.csv

Flags are individual switches (--nibr, --common-alerts, --lilly, --pains), not --alerts <name>. --lilly needs the external Lilly binaries.

Documentation

Official documentation: https://medchem-docs.datamol.io/ GitHub repository: https://github.com/datamol-io/medchem