epistract-validate

A command that checks molecular identifiers in existing extraction files, including SMILES (text descriptions of chemical structures) and biological sequences.

In plain words
What is it for?
Use it on an extraction output directory created by the ingest or build commands to check compounds, sequences, and other identifiers.
Why use it?
It helps find invalid or unrecognised identifiers before you rely on extracted research data. It also reports which identifiers were found and whether they passed validation.

Command

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.

agentmods
npx agentmods add commands/usathyan/epistract/validate
Clone the repo
git clone --depth 1 https://github.com/usathyan/epistract
Per session 18 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 259 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin original 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 $0.00018 $0.00259
Opus 5 $0.00009 $0.00130
Sonnet 5 $0.00004 $0.00052
Haiku 4.5 $0.00002 $0.00026

Measured 2d ago against content hash 27822c641e93, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

epistract-validate 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 2d 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.

commands/validate.md · 37 lines

What it actually says

Run molecular validation on existing extractions.

python3 ${CLAUDE_PLUGIN_ROOT}/domains/drug-discovery/validate_molecules.py <output_dir>

Report: SMILES found/valid, sequences found/valid, other identifiers found. If RDKit or Biopython not installed, suggest installation commands.

Usage Guard

If invoked with no arguments or with --help: Display the following usage block verbatim and stop — do not run any pipeline steps.

Usage: /epistract:validate <output-dir>

Required:
  <output-dir>    Path to directory containing extraction JSON files (from /epistract:ingest or /epistract:build)

Examples:
  /epistract:validate ./epistract-output
  /epistract:validate ./my-output
python3 ${CLAUDE_PLUGIN_ROOT}/domains/drug-discovery/validate_molecules.py <output_dir>

Report: SMILES found/valid, sequences found/valid, other identifiers found. If RDKit or Biopython not installed, suggest installation commands.

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. 2d ago First seen · 37 lines · 18 tokens per session scan A 27822c641e93

Subscribe to this mod's changes

epistract-validate is a command published in the GitHub repository usathyan/epistract (8 stars, last pushed 17d ago), licensed MIT. It adds 18 tokens to every session and 259 once invoked, about $0.0001 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 2026-08-31.