bio-applied-molecular-modeling

bio-applied-molecular-modeling is a skill for Claude Code, Codex from Pavel-Kravchenko/Bioinformatics. It costs 65 tokens per session (2,295 once invoked), scanned A, original, no licence file.

A NumPy toolkit for checking molecular models and calculating their physical energy terms, such as bond, van der Waals, and electrostatic energy.

In plain words
What is it for?
Use it for energy minimization and for validating molecular-dynamics or homology models with measures such as RMSD, RMSF, and Ramachandran plots.
Why use it?
It helps identify unstable or unrealistic molecular structures and measure whether model refinement improves them.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it for energy minimization and for validating molecular-dynamics or homology models with measures such as RMSD, RMSF, and Ramachandran plots.

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Install with agentmods
npx agentmods add skills/pavel-kravchenko/bioinformatics/bio-applied-molecular-modeling
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add Pavel-Kravchenko/Bioinformatics --skill bio-applied-molecular-modeling
Clone the repo
git clone --depth 1 https://github.com/Pavel-Kravchenko/Bioinformatics

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for bio-applied-molecular-modeling

README.md
[![agentmods](https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/bio-applied-molecular-modeling/github.svg)](https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/bio-applied-molecular-modeling)
Your own site
<a href="https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/bio-applied-molecular-modeling"><img src="https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/bio-applied-molecular-modeling/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for bio-applied-molecular-modeling

Your own site · 80×15
<a href="https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/bio-applied-molecular-modeling"><img src="https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/bio-applied-molecular-modeling.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 65 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,295 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00065 $0.02295
Opus 5 $0.00032 $0.01148
Sonnet 5 $0.00013 $0.00459
Haiku 4.5 $0.00006 $0.00230

Measured 9d ago against content hash d0447a2d7d02, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

bio-applied-molecular-modeling scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Skills/bio-applied-molecular-modeling/SKILL.md · 167 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 9d ago First seen · 167 lines · 65 tokens per session scan A d0447a2d7d02

Subscribe to this mod's changes

bio-applied-molecular-modeling is a skill published in the GitHub repository Pavel-Kravchenko/Bioinformatics (5 stars, last pushed 2mo ago), with no licence file. It adds 65 tokens to every session and 2,295 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.