matvenus-cli 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +22 -0
- package/LICENSE +201 -0
- package/README.md +408 -0
- package/bin/cli.js +3 -0
- package/dist/client.d.ts +13 -0
- package/dist/client.js +62 -0
- package/dist/commands/alphafold_protein_folding.d.ts +2 -0
- package/dist/commands/alphafold_protein_folding.js +262 -0
- package/dist/commands/cancel_tool_result.d.ts +2 -0
- package/dist/commands/cancel_tool_result.js +388 -0
- package/dist/commands/diffdock_protein_ligand_docking.d.ts +2 -0
- package/dist/commands/diffdock_protein_ligand_docking.js +252 -0
- package/dist/commands/esmfold_protein_folding.d.ts +2 -0
- package/dist/commands/esmfold_protein_folding.js +219 -0
- package/dist/commands/get_tool_result.d.ts +2 -0
- package/dist/commands/get_tool_result.js +388 -0
- package/dist/commands/gromacs_analysis.d.ts +2 -0
- package/dist/commands/gromacs_analysis.js +212 -0
- package/dist/commands/gromacs_md.d.ts +2 -0
- package/dist/commands/gromacs_md.js +236 -0
- package/dist/commands/index.d.ts +2 -0
- package/dist/commands/index.js +39 -0
- package/dist/commands/predict_functional_residue.d.ts +2 -0
- package/dist/commands/predict_functional_residue.js +234 -0
- package/dist/commands/predict_protein_properties.d.ts +2 -0
- package/dist/commands/predict_protein_properties.js +228 -0
- package/dist/commands/proteinmpnn_sequence_design.d.ts +2 -0
- package/dist/commands/proteinmpnn_sequence_design.js +271 -0
- package/dist/commands/rfdiffusion_protein_design.d.ts +2 -0
- package/dist/commands/rfdiffusion_protein_design.js +333 -0
- package/dist/commands/upload_file_base_64.d.ts +2 -0
- package/dist/commands/upload_file_base_64.js +212 -0
- package/dist/commands/venusg_protein_function_prediction.d.ts +2 -0
- package/dist/commands/venusg_protein_function_prediction.js +234 -0
- package/dist/commands/venusmine_protein_mining.d.ts +2 -0
- package/dist/commands/venusmine_protein_mining.js +212 -0
- package/dist/commands/venusprime_multipoint_prediction.d.ts +2 -0
- package/dist/commands/venusprime_multipoint_prediction.js +322 -0
- package/dist/commands/venusrem_mutation_prediction.d.ts +2 -0
- package/dist/commands/venusrem_mutation_prediction.js +260 -0
- package/dist/commands/venusx_functional_residue_prediction.d.ts +2 -0
- package/dist/commands/venusx_functional_residue_prediction.js +234 -0
- package/dist/index.d.ts +2 -0
- package/dist/index.js +125 -0
- package/dist/types.d.ts +12 -0
- package/dist/types.js +6 -0
- package/package.json +41 -0
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.register = register;
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const client_1 = require("../client");
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function register(program, baseUrl) {
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program
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.command('proteinmpnn-sequence-design')
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.description('Proteinmpnn Design')
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.option('--body <json>', 'Request body as JSON string', (value) => value)
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.option('--base-url <url>', 'Override base URL')
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.option('--output <format>', 'Output format: json, table', 'json')
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.option('--schema', 'Show API schema and exit')
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.action(async (options) => {
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if (options.schema) {
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console.log(JSON.stringify({
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"method": "post",
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"operationId": "proteinmpnn_sequence_design",
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"summary": "Proteinmpnn Design",
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"tags": [
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"tools-predict"
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],
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"parameters": [],
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"requestBody": {
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"required": true,
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"contentType": "application/json",
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"schema": {
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"properties": {
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"pdb_path": {
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"type": "string",
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"title": "Pdb Path",
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"description": "OSS URL to input PDB file"
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},
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"designed_chains": {
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"anyOf": [
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{
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"items": {
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"type": "string"
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},
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"type": "array"
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},
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{
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"type": "null"
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}
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],
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"title": "Designed Chains",
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"description": "Chain IDs to design (e.g., ['A', 'B']). If None, designs all chains"
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},
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"fixed_chains": {
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"anyOf": [
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{
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"items": {
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"type": "string"
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},
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"type": "array"
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},
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{
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"type": "null"
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}
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],
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"title": "Fixed Chains",
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"description": "Chain IDs to keep fixed (e.g., ['C', 'D'])"
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},
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"num_sequences": {
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"type": "integer",
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"title": "Num Sequences",
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"description": "Number of sequences to generate (default: 4)",
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"default": 4
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},
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"temperatures": {
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"items": {
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"type": "number"
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},
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"type": "array",
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"title": "Temperatures",
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"description": "Sampling temperatures for sequence generation (default: [0.1])",
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"default": [
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0.1
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]
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},
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"omit_aas": {
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"type": "string",
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"title": "Omit Aas",
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"description": "Amino acids to omit from design (default: 'X')",
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"default": "X"
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},
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"homomer": {
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"type": "boolean",
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"title": "Homomer",
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"description": "Enable homomer symmetric design for multi-chain proteins (default: False)",
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"default": false
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},
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"ca_only": {
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"type": "boolean",
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"title": "Ca Only",
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"description": "Use Cα-only mode for backbone representation (default: False)",
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"default": false
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}
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},
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"type": "object",
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"required": [
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"pdb_path"
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],
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"title": "ProteinMPNNInput",
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"description": "Input for ProteinMPNN sequence design"
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},
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"isBinary": false
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},
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"responses": [
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{
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"statusCode": "200",
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"description": "Successful Response",
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"contentType": "application/json",
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"schema": {
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"properties": {
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"tool_call_id": {
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"type": "string",
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"title": "Tool Call Id",
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"description": "系统生成的调用唯一ID"
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},
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"status": {
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"description": "调用状态: running, success, error 等",
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"type": "string",
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"enum": [
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"pending",
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"running",
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"success",
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"error"
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],
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"title": "ToolResultStatus"
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},
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"result": {
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"anyOf": [
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{},
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{
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"type": "null"
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}
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],
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"title": "Result",
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"description": "如果即时成功，这里是工具的返回结果字典"
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},
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"error_message": {
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"anyOf": [
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{
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"type": "string"
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},
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{
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"type": "null"
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}
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],
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"title": "Error Message",
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"description": "如果有错误，提供错误信息"
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},
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"credits_cost": {
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"anyOf": [
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{
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"type": "number"
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},
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{
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"type": "null"
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}
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],
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"title": "Credits Cost",
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"description": "消费积分"
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},
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"tool_name": {
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"type": "string",
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"title": "Tool Name",
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"description": "执行的工具名"
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}
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},
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"type": "object",
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"required": [
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"tool_call_id",
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"status",
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"tool_name"
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],
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"title": "ToolInvokeResponse"
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},
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"isBinary": false
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},
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{
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"statusCode": "422",
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"description": "Validation Error",
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"contentType": "application/json",
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"schema": {
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"properties": {
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"detail": {
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"items": {
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"properties": {
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"loc": {
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"items": {
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"anyOf": [
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{
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"type": "string"
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},
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{
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"type": "integer"
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}
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]
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},
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"type": "array",
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"title": "Location"
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},
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"msg": {
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"type": "string",
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"title": "Message"
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},
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"type": {
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"type": "string",
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"title": "Error Type"
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}
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},
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"type": "object",
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"required": [
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"loc",
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"msg",
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"type"
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],
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"title": "ValidationError"
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},
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"type": "array",
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"title": "Detail"
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}
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},
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"type": "object",
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"title": "HTTPValidationError"
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},
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"isBinary": false
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}
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],
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"security": [
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"HTTPBearer"
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]
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}, null, 2));
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return;
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}
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try {
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const currentBaseUrl = options.baseUrl || baseUrl;
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const config = { baseUrl: currentBaseUrl };
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const path = '/api/tools/predict/proteinmpnn-design';
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const url = path;
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const body = options.body ? JSON.parse(options.body) : undefined;
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const response = await (0, client_1.request)(config, {
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method: 'post',
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path: url,
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headers: undefined,
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body: body,
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isBinary: false,
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});
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const data = response;
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if (options.output === 'json') {
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console.log(JSON.stringify(data, null, 2));
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}
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else {
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console.log(data);
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}
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}
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catch (error) {
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if (error.status) {
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console.error('API Error:', error.status, error.message);
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if (error.data) {
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console.error(JSON.stringify(error.data, null, 2));
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}
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}
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else {
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console.error('Error:', error.message);
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}
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process.exit(1);
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}
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});
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}
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@@ -0,0 +1,333 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.register = register;
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const client_1 = require("../client");
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function register(program, baseUrl) {
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program
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.command('rfdiffusion-protein-design')
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.description('Rfdiffusion Design')
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.option('--body <json>', 'Request body as JSON string', (value) => value)
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.option('--base-url <url>', 'Override base URL')
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.option('--output <format>', 'Output format: json, table', 'json')
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.option('--schema', 'Show API schema and exit')
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.action(async (options) => {
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if (options.schema) {
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console.log(JSON.stringify({
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"method": "post",
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"operationId": "rfdiffusion_protein_design",
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"summary": "Rfdiffusion Design",
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"tags": [
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"tools-predict"
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],
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"parameters": [],
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"requestBody": {
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"required": true,
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"contentType": "application/json",
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"schema": {
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"properties": {
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"input_pdb": {
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"anyOf": [
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{
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"type": "string"
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},
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{
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"type": "null"
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}
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],
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"title": "Input Pdb",
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"description": "OSS URL to input PDB file (optional for unconditional generation)"
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},
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"contig": {
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"anyOf": [
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{
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|
43
|
+
"type": "string"
|
|
44
|
+
},
|
|
45
|
+
{
|
|
46
|
+
"type": "null"
|
|
47
|
+
}
|
|
48
|
+
],
|
|
49
|
+
"title": "Contig",
|
|
50
|
+
"description": "Contig specification string (e.g., 'A10-20,80' for motif scaffolding)"
|
|
51
|
+
},
|
|
52
|
+
"num_designs": {
|
|
53
|
+
"type": "integer",
|
|
54
|
+
"title": "Num Designs",
|
|
55
|
+
"description": "Number of designs to generate (default: 1)",
|
|
56
|
+
"default": 1
|
|
57
|
+
},
|
|
58
|
+
"length": {
|
|
59
|
+
"anyOf": [
|
|
60
|
+
{
|
|
61
|
+
"type": "string"
|
|
62
|
+
},
|
|
63
|
+
{
|
|
64
|
+
"type": "null"
|
|
65
|
+
}
|
|
66
|
+
],
|
|
67
|
+
"title": "Length",
|
|
68
|
+
"description": "Total design length constraint (e.g., '100' or '80-120')"
|
|
69
|
+
},
|
|
70
|
+
"hotspots": {
|
|
71
|
+
"anyOf": [
|
|
72
|
+
{
|
|
73
|
+
"type": "string"
|
|
74
|
+
},
|
|
75
|
+
{
|
|
76
|
+
"type": "null"
|
|
77
|
+
}
|
|
78
|
+
],
|
|
79
|
+
"title": "Hotspots",
|
|
80
|
+
"description": "Hotspot residues specification for binder design (e.g., 'A10,A15,A20')"
|
|
81
|
+
},
|
|
82
|
+
"partial_t": {
|
|
83
|
+
"anyOf": [
|
|
84
|
+
{
|
|
85
|
+
"type": "number"
|
|
86
|
+
},
|
|
87
|
+
{
|
|
88
|
+
"type": "null"
|
|
89
|
+
}
|
|
90
|
+
],
|
|
91
|
+
"title": "Partial T",
|
|
92
|
+
"description": "Noise level for partial diffusion in Angstroms (e.g., 5.0-15.0)"
|
|
93
|
+
},
|
|
94
|
+
"T": {
|
|
95
|
+
"type": "integer",
|
|
96
|
+
"title": "T",
|
|
97
|
+
"description": "Number of diffusion steps (default: 50)",
|
|
98
|
+
"default": 50
|
|
99
|
+
},
|
|
100
|
+
"seed_offset": {
|
|
101
|
+
"type": "integer",
|
|
102
|
+
"title": "Seed Offset",
|
|
103
|
+
"description": "Random seed offset (default: 0)",
|
|
104
|
+
"default": 0
|
|
105
|
+
},
|
|
106
|
+
"recenter": {
|
|
107
|
+
"type": "boolean",
|
|
108
|
+
"title": "Recenter",
|
|
109
|
+
"description": "Recenter structure (default: True)",
|
|
110
|
+
"default": true
|
|
111
|
+
},
|
|
112
|
+
"radius": {
|
|
113
|
+
"type": "number",
|
|
114
|
+
"title": "Radius",
|
|
115
|
+
"description": "Radius for neighbor calculation (default: 10.0)",
|
|
116
|
+
"default": 10
|
|
117
|
+
},
|
|
118
|
+
"num_recycles": {
|
|
119
|
+
"type": "integer",
|
|
120
|
+
"title": "Num Recycles",
|
|
121
|
+
"description": "Number of recycles (default: 1)",
|
|
122
|
+
"default": 1
|
|
123
|
+
},
|
|
124
|
+
"softmax_T": {
|
|
125
|
+
"type": "number",
|
|
126
|
+
"title": "Softmax T",
|
|
127
|
+
"description": "Softmax temperature (default: 1e-5)",
|
|
128
|
+
"default": 0.00001
|
|
129
|
+
},
|
|
130
|
+
"write_trb": {
|
|
131
|
+
"type": "boolean",
|
|
132
|
+
"title": "Write Trb",
|
|
133
|
+
"description": "Write .trb files (default: True)",
|
|
134
|
+
"default": true
|
|
135
|
+
},
|
|
136
|
+
"cautious": {
|
|
137
|
+
"type": "boolean",
|
|
138
|
+
"title": "Cautious",
|
|
139
|
+
"description": "Use cautious mode (default: True)",
|
|
140
|
+
"default": true
|
|
141
|
+
},
|
|
142
|
+
"align_motif": {
|
|
143
|
+
"type": "boolean",
|
|
144
|
+
"title": "Align Motif",
|
|
145
|
+
"description": "Align motif (default: True)",
|
|
146
|
+
"default": true
|
|
147
|
+
},
|
|
148
|
+
"final_step": {
|
|
149
|
+
"type": "integer",
|
|
150
|
+
"title": "Final Step",
|
|
151
|
+
"description": "Final diffusion step (default: 1)",
|
|
152
|
+
"default": 1
|
|
153
|
+
},
|
|
154
|
+
"guide_scale": {
|
|
155
|
+
"type": "number",
|
|
156
|
+
"title": "Guide Scale",
|
|
157
|
+
"description": "Guidance scale (default: 10.0)",
|
|
158
|
+
"default": 10
|
|
159
|
+
}
|
|
160
|
+
},
|
|
161
|
+
"type": "object",
|
|
162
|
+
"required": [
|
|
163
|
+
"input_pdb"
|
|
164
|
+
],
|
|
165
|
+
"title": "RFdiffusionInput",
|
|
166
|
+
"description": "Input for RFdiffusion protein design"
|
|
167
|
+
},
|
|
168
|
+
"isBinary": false
|
|
169
|
+
},
|
|
170
|
+
"responses": [
|
|
171
|
+
{
|
|
172
|
+
"statusCode": "200",
|
|
173
|
+
"description": "Successful Response",
|
|
174
|
+
"contentType": "application/json",
|
|
175
|
+
"schema": {
|
|
176
|
+
"properties": {
|
|
177
|
+
"tool_call_id": {
|
|
178
|
+
"type": "string",
|
|
179
|
+
"title": "Tool Call Id",
|
|
180
|
+
"description": "系统生成的调用唯一ID"
|
|
181
|
+
},
|
|
182
|
+
"status": {
|
|
183
|
+
"description": "调用状态: running, success, error 等",
|
|
184
|
+
"type": "string",
|
|
185
|
+
"enum": [
|
|
186
|
+
"pending",
|
|
187
|
+
"running",
|
|
188
|
+
"success",
|
|
189
|
+
"error"
|
|
190
|
+
],
|
|
191
|
+
"title": "ToolResultStatus"
|
|
192
|
+
},
|
|
193
|
+
"result": {
|
|
194
|
+
"anyOf": [
|
|
195
|
+
{},
|
|
196
|
+
{
|
|
197
|
+
"type": "null"
|
|
198
|
+
}
|
|
199
|
+
],
|
|
200
|
+
"title": "Result",
|
|
201
|
+
"description": "如果即时成功，这里是工具的返回结果字典"
|
|
202
|
+
},
|
|
203
|
+
"error_message": {
|
|
204
|
+
"anyOf": [
|
|
205
|
+
{
|
|
206
|
+
"type": "string"
|
|
207
|
+
},
|
|
208
|
+
{
|
|
209
|
+
"type": "null"
|
|
210
|
+
}
|
|
211
|
+
],
|
|
212
|
+
"title": "Error Message",
|
|
213
|
+
"description": "如果有错误，提供错误信息"
|
|
214
|
+
},
|
|
215
|
+
"credits_cost": {
|
|
216
|
+
"anyOf": [
|
|
217
|
+
{
|
|
218
|
+
"type": "number"
|
|
219
|
+
},
|
|
220
|
+
{
|
|
221
|
+
"type": "null"
|
|
222
|
+
}
|
|
223
|
+
],
|
|
224
|
+
"title": "Credits Cost",
|
|
225
|
+
"description": "消费积分"
|
|
226
|
+
},
|
|
227
|
+
"tool_name": {
|
|
228
|
+
"type": "string",
|
|
229
|
+
"title": "Tool Name",
|
|
230
|
+
"description": "执行的工具名"
|
|
231
|
+
}
|
|
232
|
+
},
|
|
233
|
+
"type": "object",
|
|
234
|
+
"required": [
|
|
235
|
+
"tool_call_id",
|
|
236
|
+
"status",
|
|
237
|
+
"tool_name"
|
|
238
|
+
],
|
|
239
|
+
"title": "ToolInvokeResponse"
|
|
240
|
+
},
|
|
241
|
+
"isBinary": false
|
|
242
|
+
},
|
|
243
|
+
{
|
|
244
|
+
"statusCode": "422",
|
|
245
|
+
"description": "Validation Error",
|
|
246
|
+
"contentType": "application/json",
|
|
247
|
+
"schema": {
|
|
248
|
+
"properties": {
|
|
249
|
+
"detail": {
|
|
250
|
+
"items": {
|
|
251
|
+
"properties": {
|
|
252
|
+
"loc": {
|
|
253
|
+
"items": {
|
|
254
|
+
"anyOf": [
|
|
255
|
+
{
|
|
256
|
+
"type": "string"
|
|
257
|
+
},
|
|
258
|
+
{
|
|
259
|
+
"type": "integer"
|
|
260
|
+
}
|
|
261
|
+
]
|
|
262
|
+
},
|
|
263
|
+
"type": "array",
|
|
264
|
+
"title": "Location"
|
|
265
|
+
},
|
|
266
|
+
"msg": {
|
|
267
|
+
"type": "string",
|
|
268
|
+
"title": "Message"
|
|
269
|
+
},
|
|
270
|
+
"type": {
|
|
271
|
+
"type": "string",
|
|
272
|
+
"title": "Error Type"
|
|
273
|
+
}
|
|
274
|
+
},
|
|
275
|
+
"type": "object",
|
|
276
|
+
"required": [
|
|
277
|
+
"loc",
|
|
278
|
+
"msg",
|
|
279
|
+
"type"
|
|
280
|
+
],
|
|
281
|
+
"title": "ValidationError"
|
|
282
|
+
},
|
|
283
|
+
"type": "array",
|
|
284
|
+
"title": "Detail"
|
|
285
|
+
}
|
|
286
|
+
},
|
|
287
|
+
"type": "object",
|
|
288
|
+
"title": "HTTPValidationError"
|
|
289
|
+
},
|
|
290
|
+
"isBinary": false
|
|
291
|
+
}
|
|
292
|
+
],
|
|
293
|
+
"security": [
|
|
294
|
+
"HTTPBearer"
|
|
295
|
+
]
|
|
296
|
+
}, null, 2));
|
|
297
|
+
return;
|
|
298
|
+
}
|
|
299
|
+
try {
|
|
300
|
+
const currentBaseUrl = options.baseUrl || baseUrl;
|
|
301
|
+
const config = { baseUrl: currentBaseUrl };
|
|
302
|
+
const path = '/api/tools/predict/rfdiffusion-design';
|
|
303
|
+
const url = path;
|
|
304
|
+
const body = options.body ? JSON.parse(options.body) : undefined;
|
|
305
|
+
const response = await (0, client_1.request)(config, {
|
|
306
|
+
method: 'post',
|
|
307
|
+
path: url,
|
|
308
|
+
headers: undefined,
|
|
309
|
+
body: body,
|
|
310
|
+
isBinary: false,
|
|
311
|
+
});
|
|
312
|
+
const data = response;
|
|
313
|
+
if (options.output === 'json') {
|
|
314
|
+
console.log(JSON.stringify(data, null, 2));
|
|
315
|
+
}
|
|
316
|
+
else {
|
|
317
|
+
console.log(data);
|
|
318
|
+
}
|
|
319
|
+
}
|
|
320
|
+
catch (error) {
|
|
321
|
+
if (error.status) {
|
|
322
|
+
console.error('API Error:', error.status, error.message);
|
|
323
|
+
if (error.data) {
|
|
324
|
+
console.error(JSON.stringify(error.data, null, 2));
|
|
325
|
+
}
|
|
326
|
+
}
|
|
327
|
+
else {
|
|
328
|
+
console.error('Error:', error.message);
|
|
329
|
+
}
|
|
330
|
+
process.exit(1);
|
|
331
|
+
}
|
|
332
|
+
});
|
|
333
|
+
}
|