Merge branch 'development' of https://github.com/NFDI4Chem/nmrkit into development

Author: NishaSharma14

app/routers/predict.py

@@ -24,7 +24,8 @@
     "mf-parser": "^3.6.0",
     "ml-spectra-processing": "^14.19.0",
     "nmr-processing": "^22.1.0",
-    "playwright": "1.56.1",
+    "openchemlib": "^9.19.0",
+    "playwright": "^1.56.1",
     "yargs": "^18.0.0"
   },
   "devDependencies": {
@@ -34,4 +35,4 @@
     "ts-node": "^10.9.2",
     "typescript": "^5.9.3"
   }
-}
+}

app/scripts/nmr-cli/package-lock.json

@@ -2,8 +2,8 @@
 import yargs, { type Argv, type CommandModule, type Options } from 'yargs'
 import { loadSpectrumFromURL, loadSpectrumFromFilePath } from './parse/prase-spectra'
 import { generateSpectrumFromPublicationString } from './publication-string'
-import { parsePredictionCommand } from './prediction/parsePredictionCommand'
 import { hideBin } from 'yargs/helpers'
+import { parsePredictionCommand } from './prediction'
 
 const usageMessage = `
 Usage: nmr-cli  <command> [options]
@@ -24,19 +24,40 @@ Arguments for 'parse-publication-string' command:
   publicationString   Publication string
  
 Options for 'predict' command:
-  -ps,--peakShape     Peak shape algorithm (default: "lorentzian") choices: ["gaussian", "lorentzian"]
-  -n, --nucleus       Predicted nucleus, choices: ["1H","13C"]    (required)
+
+Common options:
+  -e, --engine        Prediction engine (required)                choices: ["nmrdb.org", "nmrshift"]
+      --spectra       Spectra types to predict (required)         choices: ["proton", "carbon", "cosy", "hsqc", "hmbc"]
+  -s, --structure     MOL file content (structure) (required)
+
+nmrdb.org engine options:
+      --name          Compound name (default: "")
+      --frequency     NMR frequency (MHz) (default: 400)
+      --protonFrom    Proton (1H) from in ppm (default: -1)
+      --protonTo      Proton (1H) to in ppm (default: 12)
+      --carbonFrom    Carbon (13C) from in ppm (default: -5)
+      --carbonTo      Carbon (13C) to in ppm (default: 220)
+      --nbPoints1d    1D number of points (default: 131072)
+      --lineWidth     1D line width (default: 1)
+      --nbPoints2dX   2D spectrum X-axis points (default: 1024)
+      --nbPoints2dY   2D spectrum Y-axis points (default: 1024)
+      --autoExtendRange  Auto extend range (default: true)
+
+nmrshift engine options:
   -i, --id            Input ID (default: 1)
-  -t, --type          NMR type (default: "nmr;1H;1d")
-  -s, --shifts        Chemical shifts (default: "1")
+      --shifts        Chemical shifts (default: "1")
       --solvent       NMR solvent (default: "Dimethylsulphoxide-D6 (DMSO-D6, C2D6SO)")
-  -m, --molText       MOL text (required)
-      --from          From in (ppm)
-      --to            To in (ppm)
+                      choices: ["Any", "Chloroform-D1 (CDCl3)", "Dimethylsulphoxide-D6 (DMSO-D6, C2D6SO)",
+                                "Methanol-D4 (CD3OD)", "Deuteriumoxide (D2O)", "Acetone-D6 ((CD3)2CO)",
+                                "TETRACHLORO-METHANE (CCl4)", "Pyridin-D5 (C5D5N)", "Benzene-D6 (C6D6)",
+                                "neat", "Tetrahydrofuran-D8 (THF-D8, C4D4O)"]
+      --from          From in (ppm) for spectrum generation
+      --to            To in (ppm) for spectrum generation
       --nbPoints      Number of points (default: 1024)
       --lineWidth     Line width (default: 1)
       --frequency     NMR frequency (MHz) (default: 400)
       --tolerance     Tolerance to group peaks with close shift (default: 0.001)
+  -ps,--peakShape     Peak shape algorithm (default: "lorentzian") choices: ["gaussian", "lorentzian"]
 
 
 

app/scripts/nmr-cli/package.json

@@ -0,0 +1,64 @@
+import type { Options } from 'yargs'
+import type { Spectrum } from '@zakodium/nmrium-core'
+
+/**
+ * Supported experiment types
+ */
+export type Experiment = 'proton' | 'carbon' | 'cosy' | 'hsqc' | 'hmbc'
+
+/**
+ * Nucleus types used in NMR
+ */
+export type Nucleus = '1H' | '13C'
+
+/**
+ * Map from experiment name to nucleus
+ */
+export const experimentToNucleus: Record<string, Nucleus> = {
+    proton: '1H',
+    carbon: '13C',
+}
+
+/**
+ * Base interface that all engines must implement
+ */
+export interface Engine {
+    /** Unique engine identifier (e.g., 'nmrdb.org') */
+    readonly id: string
+
+    readonly name: string
+    readonly description: string
+    readonly supportedSpectra: readonly Experiment[]
+
+    /** Command-line options specific to this engine */
+    readonly options: Record<string, Options>
+
+    /** List of required option keys */
+    readonly requiredOptions: readonly string[]
+
+    /**
+     * Build the payload options for the API request
+     * @param argv - Command line arguments
+     * @returns Options object to send in the API payload
+     */
+    buildPayloadOptions(argv: Record<string, unknown>): any
+
+    /**
+     * Predict and generate spectra
+     * This is the main entry point for prediction
+     * @param structure - MOL file content
+     * @param options - Command line options
+     * @returns Array of generated spectra
+     */
+    predict(
+        structure: string,
+        options: Record<string, unknown>,
+    ): Promise<Spectrum[]>
+
+    /**
+     * Optional: Custom validation beyond required options
+     * @param argv - Command line arguments
+     * @returns true if valid, error message if invalid
+     */
+    validate?(argv: Record<string, unknown>): true | string
+}

app/scripts/nmr-cli/src/index.ts

@@ -0,0 +1,5 @@
+import './nmrdb/nmrdb.engine'
+import './nmrshift/nmrshift.engine'
+
+export { engineRegistry } from './registry';
+export type { Engine } from './base';

app/scripts/nmr-cli/src/prediction/engines/base.ts

@@ -0,0 +1,91 @@
+import { xMinMaxValues } from "ml-spectra-processing"
+import { Experiment } from "../../base"
+import { isProton } from "../../../../utilities/isProton"
+import { Prediction1D, Prediction2D } from "nmr-processing"
+import { PredictedSpectraResult, PredictionOptions } from "../nmrdb.engine"
+
+export function checkFromTo(
+    predictedSpectra: PredictedSpectraResult,
+    inputOptions: PredictionOptions,
+) {
+    const setFromTo = (inputOptions: any, nucleus: any, fromTo: any) => {
+        inputOptions['1d'][nucleus].to = fromTo.to
+        inputOptions['1d'][nucleus].from = fromTo.from
+        if (fromTo.signalsOutOfRange) {
+            signalsOutOfRange[nucleus] = true
+        }
+    }
+
+    const { autoExtendRange, spectra } = inputOptions
+    const signalsOutOfRange: Record<string, boolean> = {}
+
+    for (const exp in predictedSpectra) {
+        const experiment = exp as Experiment
+        if (!spectra[experiment]) continue
+        if (predictedSpectra[experiment]?.signals.length === 0) continue
+
+        if (['carbon', 'proton'].includes(experiment)) {
+            const spectrum = predictedSpectra[experiment] as Prediction1D
+            const { signals, nucleus } = spectrum
+            const { from, to } = (inputOptions['1d'] as any)[nucleus]
+            const fromTo = getNewFromTo({
+                deltas: signals.map((s) => s.delta),
+                from,
+                to,
+                nucleus,
+                autoExtendRange,
+            })
+            setFromTo(inputOptions, nucleus, fromTo)
+        } else {
+            const { signals, nuclei } = predictedSpectra[experiment] as Prediction2D
+            for (const nucleus of nuclei) {
+                const axis = isProton(nucleus) ? 'x' : 'y'
+                const { from, to } = (inputOptions['1d'] as any)[nucleus]
+                const fromTo = getNewFromTo({
+                    deltas: signals.map((s) => s[axis].delta),
+                    from,
+                    to,
+                    nucleus,
+                    autoExtendRange,
+                })
+                setFromTo(inputOptions, nucleus, fromTo)
+            }
+        }
+    }
+
+    for (const nucleus of ['1H', '13C']) {
+        if (signalsOutOfRange[nucleus]) {
+            const { from, to } = (inputOptions['1d'] as any)[nucleus]
+            if (autoExtendRange) {
+                console.log(
+                    `There are ${nucleus} signals out of the range, it was extended to ${from}-${to}.`,
+                )
+            } else {
+                console.log(`There are ${nucleus} signals out of the range.`)
+            }
+        }
+    }
+}
+
+
+
+function getNewFromTo(params: {
+    deltas: number[]
+    from: number
+    to: number
+    nucleus: string
+    autoExtendRange: boolean
+}) {
+    const { deltas, nucleus, autoExtendRange } = params
+    let { from, to } = params
+    const { min, max } = xMinMaxValues(deltas)
+    const signalsOutOfRange = from > min || to < max
+
+    if (autoExtendRange && signalsOutOfRange) {
+        const spread = isProton(nucleus) ? 0.2 : 2
+        if (from > min) from = min - spread
+        if (to < max) to = max + spread
+    }
+
+    return { from, to, signalsOutOfRange }
+}

app/scripts/nmr-cli/src/prediction/engines/index.ts

@@ -0,0 +1,8 @@
+export function generateName(
+    name: string,
+    options: { frequency: number | number[]; experiment: string },
+) {
+    const { frequency, experiment } = options
+    const freq = Array.isArray(frequency) ? frequency[0] : frequency
+    return name || `${experiment.toUpperCase()}_${freq}MHz`
+}

app/scripts/nmr-cli/src/prediction/engines/nmrdb/core/checkFromTo.ts

@@ -0,0 +1,71 @@
+import { getRelativeFrequency, mapRanges, signalsToRanges, signalsToXY, updateIntegralsRelativeValues } from "nmr-processing"
+import { generateName } from "./generateName"
+import { initiateDatum1D } from "../../../../parse/data/data1D/initiateDatum1D"
+import { PredictionOptions } from "../nmrdb.engine"
+
+export function generated1DSpectrum(params: {
+    options: PredictionOptions
+    spectrum: any
+    experiment: string
+    color: string
+}) {
+    const { spectrum, options, experiment, color } = params
+    const { signals, joinedSignals, nucleus } = spectrum
+
+    const {
+        name,
+        '1d': { nbPoints, lineWidth },
+        frequency: freq,
+    } = options
+
+    const SpectrumName = generateName(name, { frequency: freq, experiment })
+    const frequency = getRelativeFrequency(nucleus, {
+        frequency: freq,
+        nucleus,
+    })
+
+    const { x, y } = signalsToXY(signals, {
+        ...(options['1d'] as any)[nucleus],
+        frequency,
+        nbPoints,
+        lineWidth,
+    })
+
+    const first = x[0] ?? 0
+    const last = x.at(-1) ?? 0
+    const getFreqOffset = (freq: any) => {
+        return (first + last) * freq * 0.5
+    }
+
+    const datum = initiateDatum1D(
+        {
+            data: { x, im: null, re: y },
+            display: { color },
+            info: {
+                nucleus,
+                originFrequency: frequency,
+                baseFrequency: frequency,
+                frequencyOffset: Array.isArray(frequency)
+                    ? frequency.map(getFreqOffset)
+                    : getFreqOffset(frequency),
+                pulseSequence: 'prediction',
+                spectralWidth: Math.abs(first - last),
+                solvent: '',
+                experiment,
+                isFt: true,
+                name: SpectrumName,
+                title: SpectrumName,
+            },
+        },
+        {},
+    )
+
+    datum.ranges.values = mapRanges(
+        signalsToRanges(joinedSignals, { frequency }),
+        datum,
+    )
+    updateIntegralsRelativeValues(datum)
+
+    return datum
+}
+