matvenus-cli 0.1.0

package/CHANGELOG.md

@@ -0,0 +1,22 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0] - 2026-03-30
+
+### Added
+- Initial project release.
+- Support for protein folding prediction (AlphaFold2, AlphaFold3, ESMFold).
+- Support for functional residue prediction (ESM2, VenusX).
+- Support for protein function prediction (VenusG).
+- Support for mutation prediction (VenusREM, VenusPrime).
+- Support for molecular dynamics simulations (GROMACS).
+- Support for de novo protein design (RFdiffusion, ProteinMPNN).
+- Support for protein mining (VenusMine).
+- Standardized CLI interface with `commander.js`.
+
+### Changed
+- Preparation for NPM publication.

package/LICENSE

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package/README.md

@@ -0,0 +1,408 @@
+# matvenus-cli
+
+Command-line interface for the VenusFactory Protein Tools API. Provides access to protein structure prediction, mutation analysis, molecular dynamics, and de novo protein design via the VenusFactory MCP server.
+
+## Installation
+
+```bash
+npm install
+npm run build
+npm link   # optional: install globally as `matvenus-cli`
+```
+
+## Authentication
+
+Set the Bearer token via environment variable before running any command:
+
+```bash
+export API_BEARER_TOKEN="your-api-key-here"
+```
+
+## Base URL
+
+The default base URL is `https://venus.matwings.com`. Override per-command with `--base-url <url>`.
+
+## Async Execution Pattern
+
+**All compute-heavy commands are asynchronous.** They return immediately with:
+
+```json
+{
+  "tool_call_id": "abc-123",
+  "status": "pending",
+  "tool_name": "alphafold_protein_folding"
+}
+```
+
+You must poll `get-tool-result` until `status` is `success` or `error`:
+
+```bash
+# Submit job
+matvenus-cli alphafold-protein-folding --body '{"sequence": "MKTAYIAKQ..."}'
+
+# Poll for result (repeat until status = success)
+matvenus-cli get-tool-result --tool-call-id abc-123
+```
+
+Status values: `pending` → `running` → `success` | `error`
+
+## Uploading Local Files
+
+Many commands accept `fasta_file`, `pdb_file`, etc. as OSS URLs. To use a local file:
+
+```bash
+# 1. Base64-encode the file
+CONTENT=$(base64 -w 0 my_protein.fasta)
+
+# 2. Upload and get OSS URL
+matvenus-cli upload-file-base-64 \
+  --body "{\"filename\": \"my_protein.fasta\", \"content_base64\": \"$CONTENT\"}"
+# Returns: result.url = "oss://bucket/..."
+
+# 3. Use the URL in prediction commands
+matvenus-cli alphafold-protein-folding \
+  --body '{"fasta_file": "oss://bucket/..."}'
+```
+
+## Commands
+
+### Functional Residue Prediction
+
+#### `predict-functional-residue`
+Predict functional residues (activity/binding/conserved sites, motifs).
+
+```bash
+matvenus-cli predict-functional-residue --body '{
+  "sequence": "MKTAYIAKQRQISFVKSHFSRQ...",
+  "model_name": "ESM2-650M",
+  "task": "Activity Site"
+}'
+```
+
+| Parameter | Type | Default | Options |
+|-----------|------|---------|---------|
+| sequence | string \| null | — | Inline amino acid sequence |
+| fasta_file | string \| null | — | OSS URL to FASTA file |
+| model_name | string | `ESM2-650M` | `ESM2-650M`, `Ankh-large`, `ProtT5-xl-uniref50` |
+| task | string | `Activity Site` | `Activity Site`, `Binding Site`, `Conserved Site`, `Motif` |
+
+#### `venusx-functional-residue-prediction`
+VenusX model for functional site prediction (higher accuracy than base model).
+
+```bash
+matvenus-cli venusx-functional-residue-prediction --body '{
+  "sequence": "MKTAYIAKQ...",
+  "task": "VenusX-Activity",
+  "mode": "pro"
+}'
+```
+
+| Parameter | Type | Default | Options |
+|-----------|------|---------|---------|
+| sequence | string \| null | — | |
+| fasta_file | string \| null | — | OSS URL |
+| task | string | `VenusX-Activity` | `VenusX-Activity`, `VenusX-Binding`, `VenusX-Evo` |
+| mode | string | `pro` | `pro` (Ankh-large), `light` (ESM2-650M) |
+
+### Protein Function Prediction
+
+#### `venusg-protein-function-prediction`
+Predict protein-level properties: solubility, localization, stability, kinetics, etc.
+
+```bash
+matvenus-cli venusg-protein-function-prediction --body '{
+  "sequence": "MKTAYIAKQ...",
+  "task": "VenusG-Solubility",
+  "mode": "light"
+}'
+```
+
+| Parameter | Type | Default | Options |
+|-----------|------|---------|---------|
+| sequence | string \| null | — | |
+| fasta_file | string \| null | — | OSS URL |
+| task | string | `VenusG-Solubility` | `VenusG-Solubility`, `VenusG-SubcellularLocalization`, `VenusG-MembraneProtein`, `VenusG-Metalionbinding`, `VenusG-Stability`, `VenusG-Sortingsignal`, `VenusG-OptimumTemperature`, `VenusG-Kcat`, `VenusG-OptimalPH` |
+| mode | string | `light` | `pro` (ESM2-650M), `light` (ProtBert) |
+
+#### `predict-protein-properties`
+Calculate physicochemical properties and structural features.
+
+```bash
+matvenus-cli predict-protein-properties --body '{
+  "sequence": "MKTAYIAKQ...",
+  "task_name": "Physical and chemical properties"
+}'
+```
+
+| Parameter | Type | Default | Options |
+|-----------|------|---------|---------|
+| sequence | string \| null | — | |
+| fasta_file | string \| null | — | OSS URL to FASTA or PDB |
+| task_name | string | `Physical and chemical properties` | `Physical and chemical properties`, `Relative solvent accessible surface area (PDB only)`, `SASA value (PDB only)`, `Secondary structure (PDB only)` |
+
+### Structure Prediction
+
+#### `esmfold-protein-folding`
+Fast protein structure prediction using ESMFold (sequence only, no MSA).
+
+```bash
+matvenus-cli esmfold-protein-folding --body '{
+  "sequence": "MKTAYIAKQRQISFVKSHFSRQ"
+}'
+```
+
+| Parameter | Required | Default |
+|-----------|----------|---------|
+| sequence | yes | — |
+| verbose | no | `true` |
+
+#### `alphafold-protein-folding`
+High-accuracy structure prediction with AlphaFold2 or AlphaFold3.
+
+```bash
+# Single chain (AF2)
+matvenus-cli alphafold-protein-folding --body '{
+  "model_version": "alphafold2",
+  "sequence": "MKTAYIAKQ..."
+}'
+
+# Multi-chain complex with ligand (AF3)
+matvenus-cli alphafold-protein-folding --body '{
+  "model_version": "alphafold3",
+  "sequences": [
+    {"protein": {"id": "A", "sequence": "MKTAYIAKQ..."}},
+    {"ligand": {"id": "Z", "ccdCodes": ["ATP"]}}
+  ],
+  "model_seeds": [42]
+}'
+```
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| model_version | string | `alphafold2` | `alphafold2` or `alphafold3` |
+| sequence | string \| null | — | Single-chain sequence (AF2/AF3 simple) |
+| fasta_file | string \| null | — | OSS URL to FASTA |
+| sequences | array \| null | — | Multi-chain/ligand entities (see schema) |
+| model_seeds | int[] \| null | `[42]` | Random seeds (AF3 only) |
+
+### Mutation Prediction
+
+#### `venusrem-mutation-prediction`
+Single-point mutation effect prediction using multi-model ensemble.
+
+```bash
+# Light mode (sequence-based)
+matvenus-cli venusrem-mutation-prediction --body '{
+  "task": "stability",
+  "mode": "light",
+  "sequence": "MKTAYIAKQ..."
+}'
+
+# Pro mode (structure-based, higher accuracy)
+matvenus-cli venusrem-mutation-prediction --body '{
+  "task": "activity",
+  "mode": "pro",
+  "structure_file": "oss://bucket/protein.pdb"
+}'
+```
+
+| Parameter | Required | Options |
+|-----------|----------|---------|
+| task | yes | `activity`, `binding`, `stability`, `expression`, `general` |
+| mode | yes | `pro` (structure-based), `light` (sequence-based) |
+| structure_file | pro mode | OSS URL to PDB |
+| sequence | light mode | Inline sequence |
+| fasta_file | light mode | OSS URL to FASTA |
+
+#### `venusprime-multipoint-prediction`
+Multi-point combination mutation prediction using trained ensemble models.
+
+Two-step workflow: **train** → **inference**
+
+```bash
+# Step 1: Train models from experimental data
+matvenus-cli venusprime-multipoint-prediction --body '{
+  "mode": "train",
+  "sequence": "MKTAYIAKQ...",
+  "experiment_file": "oss://bucket/mutations.csv",
+  "score_col_name": "fitness",
+  "model_num": 5
+}'
+# Returns tool_call_id; poll until success; result contains model_path_list
+
+# Step 2: Inference on combination mutations
+matvenus-cli venusprime-multipoint-prediction --body '{
+  "mode": "inference",
+  "model_path_list": ["oss://bucket/model_0.pkl", "..."],
+  "site": [10, 25, 42]
+}'
+```
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| mode | string | `inference` | `train` or `inference` |
+| venus_mode | string | `light` | `light` (ridge regression) |
+| sequence | string \| null | — | Wild-type sequence (train) |
+| fasta_file | string \| null | — | OSS URL to FASTA (train) |
+| experiment_file | string \| null | — | OSS URL to CSV with `mutant`+`score` cols (train) |
+| score_col_name | string | — | Score column name in experiment_file |
+| model_path_list | string[] \| null | — | Trained model OSS URLs (inference) |
+| site | int[] \| null | `[2,3,4]` | Mutation site positions (inference) |
+| model_num | int | `5` | Ensemble model count (train) |
+| target_server | string | `slurm` | `slurm` or `paracloud` |
+
+### Molecular Dynamics
+
+#### `gromacs-md`
+Run GROMACS MD simulation (system build + production run).
+
+```bash
+matvenus-cli gromacs-md --body '{
+  "pdb_file": "oss://bucket/protein.pdb",
+  "force_field": "amber99sb-ildn",
+  "water_model": "tip3p",
+  "temp": "300",
+  "md_steps": "50000"
+}'
+```
+
+| Parameter | Required | Default |
+|-----------|----------|---------|
+| pdb_file | yes | OSS URL to PDB |
+| force_field | no | `amber99sb-ildn` |
+| water_model | no | `tip3p` |
+| temp | no | `300` (K) |
+| pressure | no | `1.0` (bar) |
+| md_steps | no | `50000` (~100ps at dt=2fs) |
+
+#### `gromacs-analysis`
+Analyze GROMACS MD trajectory (RMSD, RMSF, Rg, etc.).
+
+Requires output from a completed `gromacs-md` run.
+
+```bash
+matvenus-cli gromacs-analysis --body '{
+  "tpr_file": "oss://bucket/md.tpr",
+  "xtc_file": "oss://bucket/md.xtc"
+}'
+```
+
+### Protein Mining & Design
+
+#### `venusmine-protein-mining`
+Mine novel protein variants from structure-based screening.
+
+```bash
+matvenus-cli venusmine-protein-mining --body '{
+  "pdb_file": "oss://bucket/protein.pdb",
+  "target_server": "slurm"
+}'
+```
+
+#### `proteinmpnn-sequence-design`
+Design sequences for a given protein backbone using ProteinMPNN.
+
+```bash
+matvenus-cli proteinmpnn-sequence-design --body '{
+  "pdb_path": "oss://bucket/backbone.pdb",
+  "designed_chains": ["A"],
+  "fixed_chains": ["B"],
+  "num_sequences": 4,
+  "temperatures": [0.1]
+}'
+```
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| pdb_path | string | — | OSS URL to PDB (required) |
+| designed_chains | string[] \| null | — | Chains to redesign |
+| fixed_chains | string[] \| null | — | Chains to keep fixed |
+| num_sequences | int | `4` | Sequences to generate |
+| temperatures | float[] | `[0.1]` | Sampling temperatures |
+| omit_aas | string | `X` | Amino acids to exclude |
+| homomer | bool | `false` | Symmetric homomer design |
+| ca_only | bool | `false` | Cα-only backbone |
+
+#### `rfdiffusion-protein-design`
+De novo protein structure generation using RFdiffusion.
+
+```bash
+# Unconditional generation
+matvenus-cli rfdiffusion-protein-design --body '{
+  "length": "100",
+  "num_designs": 3
+}'
+
+# Motif scaffolding
+matvenus-cli rfdiffusion-protein-design --body '{
+  "input_pdb": "oss://bucket/motif.pdb",
+  "contig": "A10-20,80",
+  "num_designs": 5
+}'
+
+# Binder design
+matvenus-cli rfdiffusion-protein-design --body '{
+  "input_pdb": "oss://bucket/target.pdb",
+  "hotspots": "A10,A15,A20",
+  "length": "80-120"
+}'
+```
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| input_pdb | string \| null | — | OSS URL (optional for unconditional) |
+| contig | string \| null | — | Contig string, e.g. `A10-20,80` |
+| num_designs | int | `1` | Designs to generate |
+| length | string \| null | — | Length constraint, e.g. `100` or `80-120` |
+| hotspots | string \| null | — | Hotspot residues, e.g. `A10,A15` |
+| partial_t | float \| null | — | Noise level for partial diffusion (Å) |
+| T | int | `50` | Diffusion steps |
+
+### File Upload
+
+#### `upload-file-base-64`
+Upload a local file to OSS storage and get a URL for use in other commands.
+
+```bash
+CONTENT=$(base64 -w 0 protein.fasta)
+matvenus-cli upload-file-base-64 --body "{
+  \"filename\": \"protein.fasta\",
+  \"content_base64\": \"$CONTENT\"
+}"
+# Response: result.url = OSS URL to use in other commands
+```
+
+### Result Management
+
+#### `get-tool-result`
+Poll for the result of an async job.
+
+```bash
+matvenus-cli get-tool-result --tool-call-id <tool_call_id>
+```
+
+Response includes `status` (`pending`/`running`/`success`/`error`), `tool_result` (on success), and `slurm_tasks` with per-job details.
+
+#### `cancel-tool-result`
+Cancel a pending or running job.
+
+```bash
+matvenus-cli cancel-tool-result --tool-call-id <tool_call_id>
+```
+
+## Global Options
+
+All commands support:
+
+| Option | Description |
+|--------|-------------|
+| `--base-url <url>` | Override default base URL |
+| `--output json\|table` | Output format (default: `json`) |
+| `--schema` | Print the API schema for this command and exit |
+
+## Inspect Command Schema
+
+```bash
+matvenus-cli alphafold-protein-folding --schema
+matvenus-cli venusrem-mutation-prediction --schema
+```

package/bin/cli.js

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+const path = require('path');
+require(path.join(__dirname, '../dist/index.js'));

package/dist/client.d.ts

@@ -0,0 +1,13 @@
+export interface ApiClientConfig {
+    baseUrl: string;
+}
+export interface RequestOptions {
+    method: string;
+    path: string;
+    headers?: Record<string, string>;
+    body?: any;
+    isBinary?: boolean;
+}
+export declare function request(config: ApiClientConfig, options: RequestOptions): Promise<any>;
+export declare function buildPath(template: string, params: Record<string, any>): string;
+export declare function buildQuery(params: Record<string, any>): string;