m3triq 0.1.0 → 0.2.1

package/dist/commands/zinc.js

@@ -0,0 +1,122 @@
+import { output, formatTable } from '../output.js';
+import { createAgentsClient } from '../cli.js';
+import { requireApiKey } from '../config.js';
+export function registerZincCommands(program) {
+    const zinc = program
+        .command('zinc')
+        .description('Query ZINC purchasable compounds (self-hosted, 14M drug-like)')
+        .hook('preAction', () => { requireApiKey(); });
+    // ── m3t zinc search ───────────────���───────────────────────────
+    zinc
+        .command('search')
+        .option('--mw-min <n>', 'Min molecular weight')
+        .option('--mw-max <n>', 'Max molecular weight')
+        .option('--logp-min <n>', 'Min LogP')
+        .option('--logp-max <n>', 'Max LogP')
+        .option('--subset <s>', 'Subset: drug-like, lead-like, fragment-like, fda, in-stock')
+        .option('--limit <n>', 'Max results', '20')
+        .description('Search purchasable compounds by properties')
+        .action(async (opts) => {
+        const agents = createAgentsClient();
+        const params = {
+            limit: parseInt(opts.limit),
+        };
+        if (opts.mwMin)
+            params.mw_min = parseFloat(opts.mwMin);
+        if (opts.mwMax)
+            params.mw_max = parseFloat(opts.mwMax);
+        if (opts.logpMin)
+            params.logp_min = parseFloat(opts.logpMin);
+        if (opts.logpMax)
+            params.logp_max = parseFloat(opts.logpMax);
+        if (opts.subset)
+            params.subset = opts.subset;
+        const data = await agents.callMcpTool('zinc', 'search_purchasable', params);
+        if (typeof data.result === 'string') {
+            output(data, data.result);
+            return;
+        }
+        const compounds = extractArray(data, ['compounds', 'results', 'data']);
+        if (compounds.length === 0) {
+            output([], 'No compounds found.');
+            return;
+        }
+        const rows = compounds.map(c => [
+            str(c.zinc_id),
+            str(c.smiles || c.canonical_smiles, 45),
+            str(c.mw || c.molecular_weight),
+            str(c.logp),
+            str(c.subset || c.sub_set),
+        ]);
+        output(compounds, formatTable(['ZINC ID', 'SMILES', 'MW', 'LogP', 'Subset'], rows));
+    });
+    // ── m3t zinc info <zinc_id> ───────────────────────────────────
+    zinc
+        .command('info')
+        .argument('<id>', 'ZINC compound ID (e.g., ZINC000000000001)')
+        .description('Get details for a ZINC compound')
+        .action(async (id) => {
+        const agents = createAgentsClient();
+        const data = await agents.callMcpTool('zinc', 'get_compound', { zinc_id: id });
+        if (typeof data.result === 'string') {
+            output(data, data.result);
+        }
+        else {
+            output(data, JSON.stringify(data, null, 2));
+        }
+    });
+    // ── m3t zinc random ───────��──────────────────────────────���────
+    zinc
+        .command('random')
+        .option('--count <n>', 'Number of compounds', '20')
+        .option('--subset <s>', 'Subset: drug-like, lead-like, fragment-like')
+        .description('Get random purchasable compounds')
+        .action(async (opts) => {
+        const agents = createAgentsClient();
+        const params = {
+            count: parseInt(opts.count),
+        };
+        if (opts.subset)
+            params.subset = opts.subset;
+        const data = await agents.callMcpTool('zinc', 'get_random_compounds', params);
+        if (typeof data.result === 'string') {
+            output(data, data.result);
+            return;
+        }
+        const compounds = extractArray(data, ['compounds', 'results', 'data']);
+        if (compounds.length === 0) {
+            output([], 'No compounds found.');
+            return;
+        }
+        const rows = compounds.map(c => [
+            str(c.zinc_id),
+            str(c.smiles || c.canonical_smiles, 45),
+            str(c.mw || c.molecular_weight),
+            str(c.logp),
+        ]);
+        output(compounds, formatTable(['ZINC ID', 'SMILES', 'MW', 'LogP'], rows));
+    });
+}
+// ── Helpers ────���──────────────────────��───────────────────────────
+function str(val, maxLen) {
+    const s = val != null ? String(val) : '-';
+    return maxLen ? s.substring(0, maxLen) : s;
+}
+function extractArray(data, keys) {
+    if (Array.isArray(data))
+        return data;
+    for (const key of keys) {
+        if (Array.isArray(data[key]))
+            return data[key];
+    }
+    if (typeof data.result === 'string') {
+        try {
+            return extractArray(JSON.parse(data.result), keys);
+        }
+        catch { /* not JSON */ }
+    }
+    if (typeof data.result === 'object' && data.result !== null) {
+        return extractArray(data.result, keys);
+    }
+    return [];
+}

package/dist/types.d.ts

@@ -3,6 +3,40 @@ export interface Project {
     name: string;
     description: string;
     created_at: string;
+    updated_at?: string;
+    last_activity_at?: string;
+    context?: string;
+    session_count?: number;
+    user_role?: string;
+    owner_email?: string;
+    owner_name?: string;
+    member_count?: number;
+    is_shared?: boolean;
+}
+export interface ChatSession {
+    id: string;
+    title: string;
+    created_at: string;
+    updated_at: string;
+    message_count?: number;
+    has_notes?: boolean;
+    context_notes?: string;
+    project?: string;
+    project_name?: string;
+    user_name?: string;
+    selected_tab?: number;
+    model?: string;
+    messages?: ChatMessage[];
+}
+export interface ChatMessage {
+    id: number;
+    role: 'user' | 'assistant';
+    content: string;
+    order: number;
+    created_at: string;
+    elapsed_time?: number | null;
+    total_tokens?: number | null;
+    thinking_steps?: unknown[];
 }
 export interface Job {
     id: string;
@@ -55,6 +89,46 @@ export interface DiffDockParams {
     protein_pdb: string;
     num_samples?: number;
 }
+export type Boltz2MoleculeType = 'protein' | 'dna' | 'rna';
+export interface Boltz2Polymer {
+    molecule_type: Boltz2MoleculeType;
+    sequence: string;
+    id?: string;
+}
+export interface Boltz2Ligand {
+    smiles?: string;
+    ccd_code?: string;
+}
+export interface Boltz2McpParams {
+    polymers: Boltz2Polymer[];
+    ligands?: Boltz2Ligand[];
+    recycling_steps?: number;
+    sampling_steps?: number;
+    diffusion_samples?: number;
+    step_scale?: number;
+}
+export interface Boltz2McpResult {
+    success?: boolean;
+    model?: string;
+    complex?: string;
+    output_format?: string;
+    diffusion_samples?: number;
+    num_structures_returned?: number;
+    structure_data?: string;
+    confidence_scores?: number[];
+    best_confidence?: number | null;
+    affinities?: Record<string, unknown> | null;
+    metrics?: Record<string, unknown> | null;
+    quality?: string;
+    message?: string;
+    error?: string;
+}
+export interface Boltz2JobParams {
+    project_id: string;
+    title: string;
+    result_data: Record<string, unknown>;
+    description?: string;
+}
 export interface SandboxParams {
     project_id: string;
     script: string;
@@ -69,3 +143,48 @@ export interface McpCallResult {
     result?: unknown;
     [key: string]: unknown;
 }
+export interface CreditUsageLogEntry {
+    event: string;
+    credits: number;
+    job_id?: string | null;
+    note?: string;
+    metadata?: Record<string, unknown>;
+    created_at: string;
+}
+export interface CreditQuota {
+    tier: string;
+    monthly_credits: number;
+    credits_used: number;
+    topup_credits: number;
+    credits_remaining: number;
+    usage_percentage: number;
+    period_start?: string;
+    period_end?: string;
+    is_quota_exceeded: boolean;
+    last_used?: string | null;
+    recent_events?: CreditUsageLogEntry[];
+}
+export interface CreditLogResponse {
+    count: number;
+    next: string | null;
+    previous: string | null;
+    results: CreditUsageLogEntry[];
+}
+export interface PricingItem {
+    label: string;
+    unit: string;
+    credits: number;
+    note?: string;
+}
+export interface PricingCatalog {
+    credit_usd: number;
+    note: string;
+    jobs: PricingItem[];
+    md_simulation: PricingItem[];
+    sandbox: PricingItem;
+    ai: {
+        label: string;
+        unit: string;
+        range: string;
+    };
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "m3triq",
-  "version": "0.1.0",
+  "version": "0.2.1",
   "description": "M3TRIQ — protein-ligand analysis from the terminal",
   "type": "module",
   "bin": {
@@ -10,8 +10,11 @@
   "keywords": ["bioinformatics", "chembl", "docking", "protein", "ligand", "drug-discovery", "cli"],
   "repository": {
     "type": "git",
-    "url": "https://github.com/khai-m3triq/m3t_mono.git",
-    "directory": "m3triq_cli"
+    "url": "https://github.com/M3TRIQ/m3t.git"
+  },
+  "homepage": "https://github.com/M3TRIQ/m3t#readme",
+  "bugs": {
+    "url": "https://github.com/M3TRIQ/m3t/issues"
   },
   "scripts": {
     "build": "tsc",