molclaw-mol-basic-metrics

Compute molecular formula, weights, atom counts, and formal charge from SMILES strings.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Provide reliable, per-molecule basic property calculations from SMILES strings to support data curation, quality control, and downstream screening or optimization workflows, while detecting inconsistencies between reported formula and computed mass.

Core Features & Use Cases

  • Batch SMILES processing: Accepts a list of SMILES strings and returns per-molecule metrics.
  • Key metrics computed: molecular formula, exact and average molecular weights, heavy and total atom counts, bond counts, valence electrons, and formal charge.
  • Validation guidance: Includes a molecular weight vs formula consistency check to flag parsing errors and prompt SMILES re-validation.
  • Use Cases: Dataset QC before model training, preprocessing for virtual screening, and sanity-checking molecules produced by generative models.

Quick Start

Use molclaw-mol-basic-metrics to compute formulas, exact and average molecular weights, atom and bond counts, valence electrons, and formal charge for the provided list of SMILES and report any MW/formula inconsistencies.

Frequently Asked Questions about molclaw-mol-basic-metrics

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

FAQPage Schema
How do I compute molecular weight and formula from a list of SMILES strings?

You can compute molecular weight and formula from SMILES strings by batch processing the list to return per-molecule metrics including exact and average molecular weights, molecular formula, atom counts, and valence electrons.

What basic molecular properties can I calculate from SMILES for dataset curation?

Calculating basic molecular properties from SMILES for dataset curation yields molecular formula, exact and average molecular weights, heavy and total atom counts, bond counts, valence electron counts, and formal charge per molecule.

How do I validate SMILES strings and check molecular weight vs formula consistency?

Validating SMILES strings and checking molecular weight vs formula consistency involves computing metrics from the SMILES and flagging any parsing errors or MW/formula inconsistencies to prompt re-validation.

Can I batch process SMILES to get heavy atom counts and valence electrons for virtual screening?

Yes, you can batch process SMILES to get heavy atom counts and valence electrons for virtual screening by submitting a list of SMILES strings and receiving per-molecule metrics for preprocessing.

What is the best way to perform quality control on molecules generated by generative models?

The best way to perform quality control on molecules generated by generative models is to compute core molecular metrics from their SMILES and run MW/formula consistency checks to detect parsing errors and invalid structures.

Why does my computed molecular weight not match the expected formula during cheminformatics preprocessing?

Computed molecular weight not matching the expected formula during cheminformatics preprocessing indicates a SMILES parsing error, which consistency checks flag to prompt SMILES re-validation and correct the structural representation.