generative-design

name	generative-design
description	Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.
license	MIT

Version Compatibility

Reference examples tested with: REINVENT 4.0+, RDKit 2024.09+, PyTorch 2.1+, MolMIM (NVIDIA BioNeMo), chemprop 2.0+.

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Generative Molecular Design

Hard rules

1. No fabricated citations. Every cited work must resolve to a verifiable
2. No claim without provenance. Every quantitative or factual claim
3. No silent failure. Every script invocation, API call, or tool use must declare its exit status and what to do on non-zero. A skill that silently swallows errors is a violation.

When to use

Load this skill when the user asks a question that matches its declared trigger conditions (see the frontmatter description for the most common ones). Do not load it for questions outside its scope — defer to the appropriate ORS skill instead.

When NOT to use

Do not load this skill if the question is in a sibling skill's domain (see ## Cross-references), if the user explicitly asks for a different tool, or if the task is outside the skill's declared category.

Generator Mode Taxonomy

Mode	Input	Output	Use case	Fails when
De novo	Empty seed or training set	Novel molecules	Wide chemical space exploration	Synthetic feasibility weak
Scaffold decoration	Scaffold + attachment points	Decorated molecules	Series expansion	Diversity limited by scaffold
Linker design	2 fragments	Linker molecules	PROTAC, ternary complex	Few linker geometric options
R-group replacement	Scaffold + existing R-groups	New R-group set	Optimize one position	Single-position only
Molecular optimization	Lead molecule	Improved analogs	Lead optimization	Improvement window narrow
Constrained generation	Hard constraints (MW, fragments)	Compliant molecules	Patent / IP design	Constraints overly restrictive

Learning Algorithm Taxonomy

Algorithm	Use	Pro	Con
Transfer learning (TL)	Adapt prior model to focused training set	Stable, simple	Limited optimization power
Reinforcement learning (RL)	Reward-driven generation	Powerful for MPO	Reward hacking risk
Curriculum learning (CL)	Gradual constraint introduction	Better convergence	Slower; tuning sensitive

Decision Tree by Scenario

Scenario	Generator	Algorithm	Scoring
New target, no SAR	De novo	RL on docking score	Glide / Vina + QED
Series expansion	Scaffold decoration	TL on series + RL	QSAR ensemble + QED
PROTAC linker	Linker design	RL on ternary complex	DC50 surrogate
Lead optimization MPO	Molecular optimization	CL with staged constraints	Multi-task: activity + ADMET
Diverse hit set	De novo with diversity bonus	RL + Tanimoto distance to known	Activity + diversity
Patent space carve-out	Constrained de novo	RL + structural constraints	Activity + novelty
Hit-to-lead	R-group replacement	TL on lead + RL	Activity + Lipinski
ADMET-aware design	De novo or optimization	RL	hERG + CYP + AMES + QED

REINVENT 4 Setup

REINVENT 4 uses a TOML configuration file specifying generator, algorithm, prior model, and scoring functions.

[parameters]"
prior_file = "priors/reinvent.prior"
agent_file = "priors/reinvent.prior"
batch_size = 64
unique_sequences = true

[[stage]]
max_steps = 1000
chkpt_file = "checkpoints/agent.chkpt"

[[stage.scoring.component]]
name = "QED"

[[stage.scoring.component]]
name = "custom_activity"
weight = 1.0

Multi-Parameter Optimization (MPO)

The art of generative design lies in the scoring function. Common components:

Component	Purpose	Reference
QED	Drug-likeness	Bickerton 2012
SAScore	Synthetic accessibility	Ertl 2009
Activity QSAR	Target binding	chemprop model
hERG	Cardiotox	ADMETlab 3.0
Lipinski	Rule of 5	Lipinski 1997
Tanimoto distance	Diversity from known actives	RDKit

Critical pitfall: Reward hacking. If activity model is biased, generator produces structures that exploit the bias. Mitigations:

• Use ensemble of models (5+)
• Constrain to chemically reasonable substructures
• Validate top-100 by orthogonal in silico methods (docking, FEP)

MolMIM (NVIDIA BioNeMo)

MolMIM is a property-guided latent-variable model:

from molmint import MolMIM
from rdkit import Chem

model = MolMIM()
smiles = 'CCO'
optimized = model.optimize(smiles, target_logp=2.5, target_sas=2.0)
mol = Chem.MolFromSmiles(optimized)

Strength: Continuous property optimization in latent space. Weakness: Latent space not always semantically meaningful.

Diffusion-Based Generators (DiffSMol, DiGress)

Diffusion models generate molecules by iteratively denoising:

# DiffSMol / DiGress pseudo-API; verify against current release.
# from diffsmol import generate
# mols = generate(n_samples=1000, scaffold='aryl_sulfonamide')

Strength: State-of-the-art sample quality on MOSES benchmark. Weakness: Slower than RL; harder to condition on multiple objectives.

JT-VAE (Latent-Space Optimization)

Junction Tree VAE optimizes in latent space then decodes:

# Pseudo-API
# from jtvae import optimize
# best_mol = optimize(smiles='CCO', target='activity', iterations=100)

Strength: Smooth latent space for optimization. Weakness: Outdated vs transformers; reconstruction quality lower.

Per-Tool Failure Modes

REINVENT -- reward hacking

Trigger: Generated molecules score high but don't bind target.

Mechanism: Generator exploits QSAR model weaknesses (e.g., simple features that correlate spuriously).

Symptom: Top-100 in silico but 0% hit rate in vitro.

Fix: Ensemble of 5+ scoring models; structural diversity constraint; orthogonal validation (docking).

Scaffold decoration -- diversity loss

Trigger: After 1000 REINVENT steps, all generated molecules are near-same scaffold.

Mechanism: Generator converges to local optimum.

Symptom: Generated SMILES have Tanimoto > 0.9 to scaffold.

Fix: Add Tanimoto distance to known actives as bonus; restart with new seed; increase stochasticity.

Generative vs docking mismatch

Trigger: Generated molecules have high predicted QED but Vina score = 0.

Mechanism: Generator not aware of binding pocket geometry.

Symptom: Synthesizable but non-binders.

Fix: Add docking score (Vina or GNINA) to scoring function; dock top candidates as filter.

MolMIM -- discontinuous objective

Trigger: Optimizing a property with sharp boundaries (e.g., exactly 1 sulfonamide).

Mechanism: Latent-space optimization uses smooth gradient; sharp objectives don't have it.

Symptom: Generator oscillates around target.

Fix: Use reward-style scoring instead of property-distance; post-filter for hard constraints.

Common Errors

Symptom	Cause	Fix
reinvent exits with OOM	Prior model too large for GPU	Use smaller prior; CPU mode
All generated molecules identical	Mode collapse	Reset agent; add diversity bonus
Generated SMILES invalid	Tokenizer mismatch	Update reinvent to latest version; validate SMILES post-gen
MPO components all zero	Components missing from TOML	Re-check TOML section names
QED 1.0 but no synthesis	QED rewards unrealistic features	Add SAScore; run retrosynthesis filter

References

• Loeffler et al., J. Cheminform. -- REINVENT 4.
• Sanchez-Lengeling et al., ACS Cent. Sci. -- generative chemistry review.
• Jin et al. -- JT-VAE.

Related Skills

• chemoinformatics/qsar-modeling - Scoring models
• chemoinformatics/retrosynthesis - Synthetic feasibility
• chemoinformatics/reaction-enumeration - Library enumeration alternative
• chemoinformatics/protac-degraders - Linker design for PROTACs

Cross-references

Other skills in this category:

• admet-prediction
• conformer-generation
• covalent-design
• docking-rescoring
• free-energy-calculations
• molecular-descriptors
• molecular-io
• molecular-standardization
• pharmacophore-modeling
• pose-validation
• protac-degraders
• qsar-modeling
• retrosynthesis
• scaffold-analysis
• shape-similarity
• similarity-searching
• substructure-search
• virtual-screening

Changelog

• 1.1.0 (migration) — Bulk-migrated to v0.4.0 schema: canonical metadata block, base Hard rules, Cross-references. Body content unchanged; author should review and fill in any domain-specific extensions to the Hard rules.
• 1.0.0 — Initial release.