programmatic-tool-calling

programmatic-tool-calling is a skill for Claude Code, Codex from KonghaYao/peri. It costs 33 tokens per session (662 once invoked), scanned A, original, Apache-2.0.

A guide for running Protenix, an open model that predicts the three-dimensional shapes of proteins and protein complexes from sequence data. It is presented as an alternative for AlphaFold3-style structure prediction.

In plain words
What is it for?
Use it to predict protein complexes or check designed binder–target complexes. It also covers FASTA or JSON inputs, seeds, model selection, and running the job through Biomodals.
Why use it?
It gives a documented way to run complex-structure predictions and choose between the general model and the antibody–antigen model. It also identifies the required input format, runner, and GPU setup.

Skill for Claude CodeCodex

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 skills/konghayao/peri/programmatic-tool-calling
Any agent
npx skills add KonghaYao/peri --skill programmatic-tool-calling
Clone the repo
git clone --depth 1 https://github.com/KonghaYao/peri

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 programmatic-tool-calling

README.md
[![agentmods](https://agentmods.dev/badge/skills/konghayao/peri/programmatic-tool-calling.svg)](https://agentmods.dev/skills/konghayao/peri/programmatic-tool-calling)
Your own site
<a href="https://agentmods.dev/skills/konghayao/peri/programmatic-tool-calling"><img src="https://agentmods.dev/badge/skills/konghayao/peri/programmatic-tool-calling.svg" alt="Measured on agentmods" height="20"></a>
Per session 33 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 662 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 $0.00033 $0.00662
Opus 5 $0.00016 $0.00331
Sonnet 5 $0.00007 $0.00132
Haiku 4.5 $0.00003 $0.00066

Measured 4d ago against content hash fef5bfdfdd49, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

programmatic-tool-calling 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 4d 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.

peri-middlewares/src/skills/builtin/skills/programmatic-tool-calling/SKILL.md · 38 lines

How it starts

The opening of the file, as written. The whole thing — 38 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Programmatic Tool Calling

This builtin skill is named programmatic-tool-calling and keeps the generic alias ptc, so users may invoke it as /ptc.

Use this skill when a task benefits from discovering extra tools and orchestrating several dependent or repetitive calls in one bounded program. It is especially useful for filtering, joining, or summarizing structured tool results without copying large intermediate payloads into the conversation.

Do not use it for a single ordinary tool call, when the required tool is already directly available, for interactive workflows that need user input between steps, or to bypass an approval or access-control boundary.

Workflow

  1. Call SearchExtraTools to locate RunPtcCode and every deferred tool the program needs, and inspect their schemas.
  2. Invoke canonical deferred target RunPtcCode through ExecuteExtraTool with a small ESM program that invokes the discovered tools, checks results, and returns only the JSON-compatible data needed by the task.
  3. Use ExecuteExtraTool directly instead when no program is needed, or to validate another discovered tool before composing it.

The PTC entry pattern is SearchExtraTools → ExecuteExtraTool(RunPtcCode). RunPtcCode is not a direct tool; existing direct tools remain unchanged. The old run_code name is only a search migration keyword, not an executable alias. Never guess an extra tool name or input schema.

Code and result constraints

  • Code runs in an ESM-only function body. Load Node modules only with dynamic await import("node:..."); static import statements and CommonJS require/module.exports are unavailable.
  • Inputs, intermediate tool arguments, and the final return value must be JSON-compatible: objects, arrays, strings, numbers, booleans, or null. Do not return functions, classes, cyclic values, streams, or binary handles.
  • Keep programs bounded. Limit tool-call count, loop iterations, concurrency, output size, and retained intermediate data. Prefer projection and aggregation over returning raw bulk responses.
  • Handle missing fields and tool errors explicitly. Return a compact structured error rather than retrying indefinitely.

Read the full file on GitHub · 38 lines

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. 4d ago First seen · 38 lines · 33 tokens per session scan A fef5bfdfdd49

Subscribe to this mod's changes

programmatic-tool-calling is a skill published in the GitHub repository KonghaYao/peri (159 stars, last pushed today), licensed Apache-2.0. It adds 33 tokens to every session and 662 once invoked, about $0.0002 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 2026-08-30.

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