molclaw-mol-structure-metrics

Compute molecular structure complexity metrics for SMILES lists.

28|2|Updated Mar 31, 2026
One-click install
npx skills add https://github.com/InternScience/MolClaw --skill molclaw-mol-structure-metrics
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: molclaw-mol-structure-metrics
Source: https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-mol-structure-metrics
Command: npx skills add https://github.com/InternScience/MolClaw --skill molclaw-mol-structure-metrics

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Calculates comprehensive molecular structure complexity descriptors for lists of SMILES so users can quickly quantify and compare structural features across molecules for screening, filtering, or feature engineering.

Core Features & Use Cases

  • Per-molecule metrics: Returns rotatable bond counts, total/aromatic/aliphatic/saturated ring counts, heteroatom counts, fraction of sp3 carbons (Fsp³), and bridgehead atom counts for each SMILES.
  • Batch processing: Accepts lists of SMILES and yields a structured metrics array suitable for downstream filtering, scoring, or ML feature assembly.
  • Use case: Filter a screening library by Fsp³ and ring complexity to prioritize synthesizable, drug-like candidates or generate descriptors for a QSAR model.

Quick Start

Calculate molecular structure complexity metrics for the SMILES list ["NC@@HC(=O)O","CC(C)C1=CC=CC=C1"] and return a metrics array containing rotatable bonds, ring counts, heteroatom counts, Fsp3, and bridgehead atom counts.

Frequently Asked Questions about molclaw-mol-structure-metrics

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

FAQPage Schema
How do I calculate molecular complexity metrics like Fsp3 and rotatable bonds from a SMILES list?

To calculate molecular complexity metrics from a SMILES list, you can process the strings to extract structural descriptors including rotatable bonds, ring counts, heteroatom counts, Fsp3, and bridgehead atom counts for each molecule. This yields a structured metrics array suitable for cheminformatics preprocessing or feature engineering.

What is Fsp3 and why is it used in cheminformatics virtual screening filters?

Fsp3, or fraction of sp3 carbons, is a molecular descriptor used in cheminformatics to quantify structural complexity and saturation. It helps filter screening libraries to prioritize synthesizable, drug-like candidates by measuring the carbon saturation of the molecules.

How do I extract ring counts and heteroatom counts for molecular property modeling?

You can extract ring counts and heteroatom counts for molecular property modeling by computing structural complexity descriptors from SMILES strings. This process generates per-molecule metrics including total, aromatic, aliphatic, and saturated ring counts alongside heteroatom totals for dataset feature extraction.

Can I batch process SMILES strings to generate a descriptors array for QSAR models?

Yes, you can batch process SMILES strings to generate a descriptors array for QSAR models. This approach accepts lists of SMILES and yields a structured metrics array containing rotatable bonds, ring counts, and Fsp3 values suitable for direct machine learning feature assembly.

What are bridgehead atom counts and when do I need them for dataset feature extraction?

Bridgehead atom counts measure the number of shared ring junction atoms in a molecular structure. You need them for dataset feature extraction when quantifying polycyclic structural complexity to filter screening libraries or assemble comprehensive cheminformatics descriptors for molecular property modeling.