m3triq 0.2.12 → 0.2.13

package/dist/cli.js

@@ -25,7 +25,7 @@ const program = new Command();
 program
     .name('m3t')
     .description('M3TRIQ — protein-ligand analysis from the terminal')
-    .version('0.2.12')
+    .version('0.2.13')
     .option('--json', 'Output as JSON (machine-readable)')
     .hook('preAction', (thisCommand) => {
     const opts = thisCommand.optsWithGlobals();

package/dist/commands/predict.js

@@ -13,19 +13,14 @@ export function registerPredictCommands(program) {
         .action(async (sequence, opts) => {
         await runPredict(sequence, 'esmfold', opts.name);
     });
-    // m3t predict alphafold2 — RETIRED (the alphafold2-nim VM was decommissioned in
-    // favour of ESMFold2). Kept as a signpost so scripts get a clear redirect instead
-    // of a job that silently fails on the deleted backend.
+    // m3t predict alphafold2 — AF2 (ptm) monomer via the self-hosted ColabFold service
+    // (the alphafold2-nim VM was retired; same AF2 weights, deep MSA from m3t_msa_server).
     predict.command('alphafold2')
-        .argument('[sequence]', 'Amino acid sequence (single letter codes)')
+        .argument('<sequence>', 'Amino acid sequence (single letter codes, max 2048aa)')
         .option('--name <name>', 'Name for the prediction')
-        .description('[RETIRED → use `predict esmfold2`] AlphaFold2 single-sequence prediction')
-        .action(async () => {
-        process.stderr.write('AlphaFold2 has been retired (the self-hosted backend was decommissioned).\n' +
-            'Use ESMFold2 instead — higher accuracy and it folds complexes too:\n' +
-            '  m3t predict esmfold2 --sequence <seq>            # monomer\n' +
-            '  m3t predict esmfold2 --chain A:<seq> --chain B:<seq>   # complex\n');
-        process.exit(2);
+        .description('AlphaFold2 (ptm) monomer prediction — deep MSA + ColabFold (~5-15 min, +cold start)')
+        .action(async (sequence, opts) => {
+        await runPredict(sequence, 'alphafold2', opts.name);
     });
     // m3t predict esmfold2 — monomer OR multi-chain (antibody-antigen, PPI)
     predict.command('esmfold2')
@@ -101,7 +96,7 @@ async function runPredict(sequence, method, name) {
     });
     const url = jobUrl(consoleUrl, project.id, result.job_id);
     maybeOpenBrowser(url);
-    const timeEst = method === 'alphafold2' ? '~15-20 minutes (varies with length)' : '~10 seconds';
+    const timeEst = method === 'alphafold2' ? '~5-15 minutes (deep MSA + ColabFold; +cold start)' : '~10 seconds';
     const data = { job_id: result.job_id, method, sequence_length: sequence.length, url };
     output(data, `${method} prediction created\nJob ID: ${result.job_id.substring(0, 8)}\nLength: ${sequence.length} residues\nEstimated: ${timeEst}`);
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "m3triq",
-  "version": "0.2.12",
+  "version": "0.2.13",
   "description": "M3TRIQ \u2014 protein-ligand analysis from the terminal",
   "type": "module",
   "bin": {