Command line

M3TRIQ from your terminal

The m3t CLI brings docking, structure prediction, generative design, and millions of compounds to your shell — scriptable, pipeable, and CI-ready. Everything you run syncs back to your Console project.

terminal
# 1 · Install
$ npm install -g m3triq
# 2 · Connect (create an API key in the Console)
$ m3t config --key <YOUR_API_KEY>
# 3 · Pick a project to work in
$ m3t use <project-id>
# 4 · Run — results sync to your Console project
$ m3t dock gnina "CC(=O)Oc1ccccc1C(=O)O" 5NJ8 --cx 10 --cy 12 --cz 8
$ m3t chembl search "imatinib"
$ m3t predict esmfold "MKFLILLFNILCLF..."

What you can do

Every major workflow has a command — here's a taste.

Molecular docking

$ m3t dock gnina "<smiles>" 5NJ8 --cx 10 --cy 12 --cz 8$ m3t batch vina compounds.csv 5NJ8 --cx ...

Structure prediction

$ m3t predict esmfold "<sequence>"$ m3t predict alphafold2 "<sequence>"

AI design

$ m3t design rfantibody 7XYZ --hotspots A100,A105

Databases

$ m3t chembl search "imatinib"$ m3t chembl binders PPARG --max-value 10000$ m3t zinc search --mw-min 200 --mw-max 500

ADMET & simulation

$ m3t admet predict "<smiles>"$ m3t md run --protein 5NJ8 --ligand-smiles "<smi>"

Jobs, data & scripts

$ m3t jobs --status completed$ m3t dataset <id> --limit 20$ m3t run analysis.py --packages pandas
Agent-ready

Use it from your AI coding agent

The m3t CLI is just a shell command — so any agentic coding tool that can run your terminal can drive M3TRIQ. Ask your agent to dock a library, predict a structure, or screen ChEMBL, and it runs m3t for you.

Claude CodeClaude Code
CodexCodex
Gemini CLIGemini CLI
GitHub CopilotGitHub Copilot
CursorCursor
AntigravityAntigravity
KiroKiro
ClineCline
WindsurfWindsurf
# you → your coding agent
“Screen these 12 compounds against 5NJ8 and rank them by binding affinity.”
# your agent runs
$ m3t batch gnina compounds.csv 5NJ8 --cx 10 --cy 12 --cz 8 --json

Logos are trademarks of their respective owners, shown for compatibility reference only.

Built for automation

Batch jobs from CSVJSON output for piping (--json)Run inside CI pipelinesResults sync to your projectSame credits as the Console

Pipe results into your own scripts, run large batches overnight, or wire M3TRIQ into a CI pipeline — all billed from the same credit balance as the Console.

Get started in seconds

Create a free account, grab an API key, and run npm install -g m3triq.