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molclaw-rgroup-sampling

Decorate molecular scaffolds with R-groups at [*:N] attachment points using LibInvent.

28|2|Updated Mar 31, 2026
Search Tags:#scaffold#smiles#virtual-screening#sar#molecule-generation#libinvent#r-group
One-click install
npx skills add https://github.com/InternScience/MolClaw --skill molclaw-rgroup-sampling
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molclaw-rgroup-sampling
Source: https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-rgroup-sampling
Command: npx skills add https://github.com/InternScience/MolClaw --skill molclaw-rgroup-sampling

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Generate new molecules by decorating a fixed molecular scaffold with R-groups at specified attachment points using LibInvent, enabling systematic exploration of substituents without manual enumeration.

Core Features & Use Cases

  • Custom scaffold decoration: Accepts user-provided scaffold SMILES with R-group positions marked as [*:N] to generate fully-decorated molecules.
  • Predefined scaffold library: Sample from common drug scaffolds by name (e.g., pyrimidine, indole, biphenyl) for rapid library enumeration.
  • Filtering and validation: Supports configurable filter presets and Lipinski checks, and outputs results as a saved CSV plus a list of SMILES for downstream analysis.
  • Use Case: Run large-scale SAR exploration by sampling hundreds of R-group variants from a single scaffold to identify promising substitution patterns.

Quick Start

Generate 100 decorated molecules from scaffold c1ccc([:1])cc1C(=O)N[:2] using LibInvent with default filters and save the output CSV.

Frequently Asked Questions about molclaw-rgroup-sampling

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate molecules by decorating a fixed scaffold with R-groups for SAR exploration?▼

To decorate a scaffold, provide an RDKit-parseable SMILES with attachment points marked as [*:N], configure the sampling count, and apply filter presets. The Skill generates decorated molecules and returns SMILES lists plus a saved CSV of results.

What is the SMILES syntax for marking attachment points in scaffold-constrained library enumeration?▼

Attachment points are marked using the [*:N] syntax in the scaffold SMILES, where N denotes the R-group position. This tells the molecule generator exactly where to attach substituents during scaffold decoration.

Can I use predefined drug scaffolds like pyrimidine or indole for rapid library enumeration?▼

Yes, predefined scaffolds like pyrimidine, indole, and biphenyl can be selected by name for rapid library enumeration. This bypasses the need to manually provide scaffold SMILES for R-group sampling.

Does LibInvent support Lipinski checks and filter presets when generating decorated molecules?▼

Yes, LibInvent supports configurable filter presets and Lipinski checks during scaffold decoration. This validates generated molecules for drug-likeness before returning the decorated SMILES lists and saved CSV.

How many R-group variants can I sample from a single scaffold for virtual screening?▼

You can configure the sampling count to generate hundreds of R-group variants from a single scaffold for virtual screening. This allows large-scale SAR exploration to identify promising substitution patterns.

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