From 8aef07202858d79a5a0d39fb2d9e2116a45d7310 Mon Sep 17 00:00:00 2001
From: Venkata Nainala <mailcs76@gmail.com>
Date: Tue, 29 Sep 2026 08:55:43 +0100
Subject: [PATCH 1/2] feat: include atom shifts in nmrshift predictions

The spectrum response dropped the atom-to-shift map, so clients could not label atoms or mark the matching peaks.
---
 .../engines/nmrshift/nmrshift.engine.ts       | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/app/scripts/nmr-cli/src/prediction/engines/nmrshift/nmrshift.engine.ts b/app/scripts/nmr-cli/src/prediction/engines/nmrshift/nmrshift.engine.ts
index 8e22e8e..2e906b2 100644
--- a/app/scripts/nmr-cli/src/prediction/engines/nmrshift/nmrshift.engine.ts
+++ b/app/scripts/nmr-cli/src/prediction/engines/nmrshift/nmrshift.engine.ts
@@ -176,6 +176,52 @@ async function predictNMR(
     }
   }
 
+  for (let i = 0; i < results.length; i++) {
+    const response: PredictionResponse = results[i].data
+    const experimentInfo = experiments[i]
+
+    for (const item of response.result) {
+      const data = generatePredictedSpectrumData(item.shifts, {
+        from,
+        to,
+        nbPoints,
+        lineWidth,
+        frequency,
+        tolerance,
+        peakShape,
+      })
+
+      if (!data) continue
+
+      const name = crypto.randomUUID()
+
+      outputSpectra.push({
+        id: crypto.randomUUID(),
+        data,
+        info: {
+          isFid: false,
+          isComplex: false,
+          dimension: 1,
+          originFrequency: frequency,
+          baseFrequency: frequency,
+          pulseSequence: '',
+          solvent,
+          isFt: true,
+          name,
+          nucleus: experimentInfo.nucleus,
+          // Kept so clients can label atoms and mark the matching peaks.
+          // NMRShiftDB atom numbers are 1-based and follow openchemlib's
+          // addImplicitHydrogens order.
+          predictionShifts: item.shifts.map(shift => ({
+            atom: shift.atom,
+            prediction: shift.prediction,
+            status: shift.status,
+          })),
+        },
+      } as unknown as Spectrum)
+    }
+  }
+
   return outputSpectra
 }
 

From 332c1770e33c0994e777988018e68f5d49083885 Mon Sep 17 00:00:00 2001
From: hamed musallam <hamed.musallam@gmail.com>
Date: Fri, 2 Oct 2026 11:51:20 +0200
Subject: [PATCH 2/2] refactor(nmrshift): extract prediction shifts helper

---
 .../engines/nmrshift/nmrshift.engine.ts       | 57 ++++---------------
 1 file changed, 12 insertions(+), 45 deletions(-)

diff --git a/app/scripts/nmr-cli/src/prediction/engines/nmrshift/nmrshift.engine.ts b/app/scripts/nmr-cli/src/prediction/engines/nmrshift/nmrshift.engine.ts
index 2e906b2..9386b4b 100644
--- a/app/scripts/nmr-cli/src/prediction/engines/nmrshift/nmrshift.engine.ts
+++ b/app/scripts/nmr-cli/src/prediction/engines/nmrshift/nmrshift.engine.ts
@@ -1,6 +1,6 @@
 import type { Options } from 'yargs'
 import type { Spectrum } from '@zakodium/nmrium-core'
-import https from 'https'
+import https from 'node:https'
 import axios, { type AxiosResponse } from 'axios'
 
 import { defineEngine } from '../registry.js'
@@ -63,6 +63,15 @@ function getBaseUrl(): string {
   return url
 }
 
+function getPredictionShifts(shifts: ShiftsItem[]) {
+  // NMRShiftDB atom numbers are 1-based and follow openchemlib's addImplicitHydrogens order.
+  return shifts.map(({ atom, prediction, status }) => ({
+    atom,
+    prediction,
+    status,
+  }))
+}
+
 async function callPredict(
   structure: string,
   options: {
@@ -155,43 +164,7 @@ async function predictNMR(
 
       if (!data) continue
 
-      const name = crypto.randomUUID()
-
-      outputSpectra.push({
-        id: crypto.randomUUID(),
-        data,
-        info: {
-          isFid: false,
-          isComplex: false,
-          dimension: 1,
-          originFrequency: frequency,
-          baseFrequency: frequency,
-          pulseSequence: '',
-          solvent,
-          isFt: true,
-          name,
-          nucleus: experimentInfo.nucleus,
-        },
-      } as unknown as Spectrum)
-    }
-  }
-
-  for (let i = 0; i < results.length; i++) {
-    const response: PredictionResponse = results[i].data
-    const experimentInfo = experiments[i]
-
-    for (const item of response.result) {
-      const data = generatePredictedSpectrumData(item.shifts, {
-        from,
-        to,
-        nbPoints,
-        lineWidth,
-        frequency,
-        tolerance,
-        peakShape,
-      })
-
-      if (!data) continue
+      const predictionShifts = getPredictionShifts(item.shifts)
 
       const name = crypto.randomUUID()
 
@@ -210,13 +183,7 @@ async function predictNMR(
           name,
           nucleus: experimentInfo.nucleus,
           // Kept so clients can label atoms and mark the matching peaks.
-          // NMRShiftDB atom numbers are 1-based and follow openchemlib's
-          // addImplicitHydrogens order.
-          predictionShifts: item.shifts.map(shift => ({
-            atom: shift.atom,
-            prediction: shift.prediction,
-            status: shift.status,
-          })),
+          predictionShifts,
         },
       } as unknown as Spectrum)
     }