matvenus-cli 0.1.0

package/dist/commands/gromacs_analysis.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.register = register;
+const client_1 = require("../client");
+function register(program, baseUrl) {
+    program
+        .command('gromacs-analysis')
+        .description('Gromacs Analysis')
+        .option('--body <json>', 'Request body as JSON string', (value) => value)
+        .option('--base-url <url>', 'Override base URL')
+        .option('--output <format>', 'Output format: json, table', 'json')
+        .option('--schema', 'Show API schema and exit')
+        .action(async (options) => {
+        if (options.schema) {
+            console.log(JSON.stringify({
+                "method": "post",
+                "operationId": "gromacs_analysis",
+                "summary": "Gromacs Analysis",
+                "tags": [
+                    "tools-predict"
+                ],
+                "parameters": [],
+                "requestBody": {
+                    "required": true,
+                    "contentType": "application/json",
+                    "schema": {
+                        "properties": {
+                            "tpr_file": {
+                                "type": "string",
+                                "title": "Tpr File",
+                                "description": "OSS URL to .tpr file (from gromacs_md output)"
+                            },
+                            "xtc_file": {
+                                "type": "string",
+                                "title": "Xtc File",
+                                "description": "OSS URL to .xtc file (from gromacs_md output)"
+                            }
+                        },
+                        "type": "object",
+                        "required": [
+                            "tpr_file",
+                            "xtc_file"
+                        ],
+                        "title": "GromacsAnalysisInput",
+                        "description": "Input for GROMACS trajectory analysis"
+                    },
+                    "isBinary": false
+                },
+                "responses": [
+                    {
+                        "statusCode": "200",
+                        "description": "Successful Response",
+                        "contentType": "application/json",
+                        "schema": {
+                            "properties": {
+                                "tool_call_id": {
+                                    "type": "string",
+                                    "title": "Tool Call Id",
+                                    "description": "系统生成的调用唯一ID"
+                                },
+                                "status": {
+                                    "description": "调用状态: running, success, error 等",
+                                    "type": "string",
+                                    "enum": [
+                                        "pending",
+                                        "running",
+                                        "success",
+                                        "error"
+                                    ],
+                                    "title": "ToolResultStatus"
+                                },
+                                "result": {
+                                    "anyOf": [
+                                        {},
+                                        {
+                                            "type": "null"
+                                        }
+                                    ],
+                                    "title": "Result",
+                                    "description": "如果即时成功，这里是工具的返回结果字典"
+                                },
+                                "error_message": {
+                                    "anyOf": [
+                                        {
+                                            "type": "string"
+                                        },
+                                        {
+                                            "type": "null"
+                                        }
+                                    ],
+                                    "title": "Error Message",
+                                    "description": "如果有错误，提供错误信息"
+                                },
+                                "credits_cost": {
+                                    "anyOf": [
+                                        {
+                                            "type": "number"
+                                        },
+                                        {
+                                            "type": "null"
+                                        }
+                                    ],
+                                    "title": "Credits Cost",
+                                    "description": "消费积分"
+                                },
+                                "tool_name": {
+                                    "type": "string",
+                                    "title": "Tool Name",
+                                    "description": "执行的工具名"
+                                }
+                            },
+                            "type": "object",
+                            "required": [
+                                "tool_call_id",
+                                "status",
+                                "tool_name"
+                            ],
+                            "title": "ToolInvokeResponse"
+                        },
+                        "isBinary": false
+                    },
+                    {
+                        "statusCode": "422",
+                        "description": "Validation Error",
+                        "contentType": "application/json",
+                        "schema": {
+                            "properties": {
+                                "detail": {
+                                    "items": {
+                                        "properties": {
+                                            "loc": {
+                                                "items": {
+                                                    "anyOf": [
+                                                        {
+                                                            "type": "string"
+                                                        },
+                                                        {
+                                                            "type": "integer"
+                                                        }
+                                                    ]
+                                                },
+                                                "type": "array",
+                                                "title": "Location"
+                                            },
+                                            "msg": {
+                                                "type": "string",
+                                                "title": "Message"
+                                            },
+                                            "type": {
+                                                "type": "string",
+                                                "title": "Error Type"
+                                            }
+                                        },
+                                        "type": "object",
+                                        "required": [
+                                            "loc",
+                                            "msg",
+                                            "type"
+                                        ],
+                                        "title": "ValidationError"
+                                    },
+                                    "type": "array",
+                                    "title": "Detail"
+                                }
+                            },
+                            "type": "object",
+                            "title": "HTTPValidationError"
+                        },
+                        "isBinary": false
+                    }
+                ],
+                "security": [
+                    "HTTPBearer"
+                ]
+            }, null, 2));
+            return;
+        }
+        try {
+            const currentBaseUrl = options.baseUrl || baseUrl;
+            const config = { baseUrl: currentBaseUrl };
+            const path = '/api/tools/predict/gromacs-analysis';
+            const url = path;
+            const body = options.body ? JSON.parse(options.body) : undefined;
+            const response = await (0, client_1.request)(config, {
+                method: 'post',
+                path: url,
+                headers: undefined,
+                body: body,
+                isBinary: false,
+            });
+            const data = response;
+            if (options.output === 'json') {
+                console.log(JSON.stringify(data, null, 2));
+            }
+            else {
+                console.log(data);
+            }
+        }
+        catch (error) {
+            if (error.status) {
+                console.error('API Error:', error.status, error.message);
+                if (error.data) {
+                    console.error(JSON.stringify(error.data, null, 2));
+                }
+            }
+            else {
+                console.error('Error:', error.message);
+            }
+            process.exit(1);
+        }
+    });
+}

package/dist/commands/gromacs_md.d.ts

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+import { Command } from 'commander';
+export declare function register(program: Command, baseUrl: string): void;

package/dist/commands/gromacs_md.js

@@ -0,0 +1,236 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.register = register;
+const client_1 = require("../client");
+function register(program, baseUrl) {
+    program
+        .command('gromacs-md')
+        .description('Gromacs Md')
+        .option('--body <json>', 'Request body as JSON string', (value) => value)
+        .option('--base-url <url>', 'Override base URL')
+        .option('--output <format>', 'Output format: json, table', 'json')
+        .option('--schema', 'Show API schema and exit')
+        .action(async (options) => {
+        if (options.schema) {
+            console.log(JSON.stringify({
+                "method": "post",
+                "operationId": "gromacs_md",
+                "summary": "Gromacs Md",
+                "tags": [
+                    "tools-predict"
+                ],
+                "parameters": [],
+                "requestBody": {
+                    "required": true,
+                    "contentType": "application/json",
+                    "schema": {
+                        "properties": {
+                            "pdb_file": {
+                                "type": "string",
+                                "title": "Pdb File",
+                                "description": "OSS URL to input PDB file"
+                            },
+                            "force_field": {
+                                "type": "string",
+                                "title": "Force Field",
+                                "description": "Force field name (default: amber99sb-ildn)",
+                                "default": "amber99sb-ildn"
+                            },
+                            "water_model": {
+                                "type": "string",
+                                "title": "Water Model",
+                                "description": "Water model (default: tip3p)",
+                                "default": "tip3p"
+                            },
+                            "temp": {
+                                "type": "string",
+                                "title": "Temp",
+                                "description": "Temperature in K (default: 300)",
+                                "default": "300"
+                            },
+                            "pressure": {
+                                "type": "string",
+                                "title": "Pressure",
+                                "description": "Pressure in bar (default: 1.0)",
+                                "default": "1.0"
+                            },
+                            "md_steps": {
+                                "type": "string",
+                                "title": "Md Steps",
+                                "description": "Production MD steps (default: 50000, ~100ns at dt=2fs)",
+                                "default": "50000"
+                            }
+                        },
+                        "type": "object",
+                        "required": [
+                            "pdb_file"
+                        ],
+                        "title": "GromacsMdInput",
+                        "description": "Input for GROMACS MD (build system + production simulation)"
+                    },
+                    "isBinary": false
+                },
+                "responses": [
+                    {
+                        "statusCode": "200",
+                        "description": "Successful Response",
+                        "contentType": "application/json",
+                        "schema": {
+                            "properties": {
+                                "tool_call_id": {
+                                    "type": "string",
+                                    "title": "Tool Call Id",
+                                    "description": "系统生成的调用唯一ID"
+                                },
+                                "status": {
+                                    "description": "调用状态: running, success, error 等",
+                                    "type": "string",
+                                    "enum": [
+                                        "pending",
+                                        "running",
+                                        "success",
+                                        "error"
+                                    ],
+                                    "title": "ToolResultStatus"
+                                },
+                                "result": {
+                                    "anyOf": [
+                                        {},
+                                        {
+                                            "type": "null"
+                                        }
+                                    ],
+                                    "title": "Result",
+                                    "description": "如果即时成功，这里是工具的返回结果字典"
+                                },
+                                "error_message": {
+                                    "anyOf": [
+                                        {
+                                            "type": "string"
+                                        },
+                                        {
+                                            "type": "null"
+                                        }
+                                    ],
+                                    "title": "Error Message",
+                                    "description": "如果有错误，提供错误信息"
+                                },
+                                "credits_cost": {
+                                    "anyOf": [
+                                        {
+                                            "type": "number"
+                                        },
+                                        {
+                                            "type": "null"
+                                        }
+                                    ],
+                                    "title": "Credits Cost",
+                                    "description": "消费积分"
+                                },
+                                "tool_name": {
+                                    "type": "string",
+                                    "title": "Tool Name",
+                                    "description": "执行的工具名"
+                                }
+                            },
+                            "type": "object",
+                            "required": [
+                                "tool_call_id",
+                                "status",
+                                "tool_name"
+                            ],
+                            "title": "ToolInvokeResponse"
+                        },
+                        "isBinary": false
+                    },
+                    {
+                        "statusCode": "422",
+                        "description": "Validation Error",
+                        "contentType": "application/json",
+                        "schema": {
+                            "properties": {
+                                "detail": {
+                                    "items": {
+                                        "properties": {
+                                            "loc": {
+                                                "items": {
+                                                    "anyOf": [
+                                                        {
+                                                            "type": "string"
+                                                        },
+                                                        {
+                                                            "type": "integer"
+                                                        }
+                                                    ]
+                                                },
+                                                "type": "array",
+                                                "title": "Location"
+                                            },
+                                            "msg": {
+                                                "type": "string",
+                                                "title": "Message"
+                                            },
+                                            "type": {
+                                                "type": "string",
+                                                "title": "Error Type"
+                                            }
+                                        },
+                                        "type": "object",
+                                        "required": [
+                                            "loc",
+                                            "msg",
+                                            "type"
+                                        ],
+                                        "title": "ValidationError"
+                                    },
+                                    "type": "array",
+                                    "title": "Detail"
+                                }
+                            },
+                            "type": "object",
+                            "title": "HTTPValidationError"
+                        },
+                        "isBinary": false
+                    }
+                ],
+                "security": [
+                    "HTTPBearer"
+                ]
+            }, null, 2));
+            return;
+        }
+        try {
+            const currentBaseUrl = options.baseUrl || baseUrl;
+            const config = { baseUrl: currentBaseUrl };
+            const path = '/api/tools/predict/gromacs-md';
+            const url = path;
+            const body = options.body ? JSON.parse(options.body) : undefined;
+            const response = await (0, client_1.request)(config, {
+                method: 'post',
+                path: url,
+                headers: undefined,
+                body: body,
+                isBinary: false,
+            });
+            const data = response;
+            if (options.output === 'json') {
+                console.log(JSON.stringify(data, null, 2));
+            }
+            else {
+                console.log(data);
+            }
+        }
+        catch (error) {
+            if (error.status) {
+                console.error('API Error:', error.status, error.message);
+                if (error.data) {
+                    console.error(JSON.stringify(error.data, null, 2));
+                }
+            }
+            else {
+                console.error('Error:', error.message);
+            }
+            process.exit(1);
+        }
+    });
+}

package/dist/commands/index.d.ts

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+import { Command } from 'commander';
+export declare function registerCommands(program: Command, baseUrl: string): void;

package/dist/commands/index.js

@@ -0,0 +1,39 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.registerCommands = registerCommands;
+const predict_functional_residue_1 = require("./predict_functional_residue");
+const venusx_functional_residue_prediction_1 = require("./venusx_functional_residue_prediction");
+const venusg_protein_function_prediction_1 = require("./venusg_protein_function_prediction");
+const predict_protein_properties_1 = require("./predict_protein_properties");
+const esmfold_protein_folding_1 = require("./esmfold_protein_folding");
+const alphafold_protein_folding_1 = require("./alphafold_protein_folding");
+const diffdock_protein_ligand_docking_1 = require("./diffdock_protein_ligand_docking");
+const venusrem_mutation_prediction_1 = require("./venusrem_mutation_prediction");
+const venusprime_multipoint_prediction_1 = require("./venusprime_multipoint_prediction");
+const gromacs_md_1 = require("./gromacs_md");
+const gromacs_analysis_1 = require("./gromacs_analysis");
+const venusmine_protein_mining_1 = require("./venusmine_protein_mining");
+const proteinmpnn_sequence_design_1 = require("./proteinmpnn_sequence_design");
+const rfdiffusion_protein_design_1 = require("./rfdiffusion_protein_design");
+const get_tool_result_1 = require("./get_tool_result");
+const cancel_tool_result_1 = require("./cancel_tool_result");
+const upload_file_base_64_1 = require("./upload_file_base_64");
+function registerCommands(program, baseUrl) {
+    (0, predict_functional_residue_1.register)(program, baseUrl);
+    (0, venusx_functional_residue_prediction_1.register)(program, baseUrl);
+    (0, venusg_protein_function_prediction_1.register)(program, baseUrl);
+    (0, predict_protein_properties_1.register)(program, baseUrl);
+    (0, esmfold_protein_folding_1.register)(program, baseUrl);
+    (0, alphafold_protein_folding_1.register)(program, baseUrl);
+    (0, diffdock_protein_ligand_docking_1.register)(program, baseUrl);
+    (0, venusrem_mutation_prediction_1.register)(program, baseUrl);
+    (0, venusprime_multipoint_prediction_1.register)(program, baseUrl);
+    (0, gromacs_md_1.register)(program, baseUrl);
+    (0, gromacs_analysis_1.register)(program, baseUrl);
+    (0, venusmine_protein_mining_1.register)(program, baseUrl);
+    (0, proteinmpnn_sequence_design_1.register)(program, baseUrl);
+    (0, rfdiffusion_protein_design_1.register)(program, baseUrl);
+    (0, get_tool_result_1.register)(program, baseUrl);
+    (0, cancel_tool_result_1.register)(program, baseUrl);
+    (0, upload_file_base_64_1.register)(program, baseUrl);
+}

package/dist/commands/predict_functional_residue.d.ts

@@ -0,0 +1,2 @@
+import { Command } from 'commander';
+export declare function register(program: Command, baseUrl: string): void;