@zakodium/nmrium-core-plugins 0.0.1

package/README.md

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+<h3 align="center">
+  <a href="https://www.zakodium.com">
+    <img src="https://www.zakodium.com/brand/zakodium-logo-white.svg" width="50" alt="Zakodium logo" />
+  </a>
+  <p>
+    Maintained by <a href="https://www.zakodium.com">Zakodium</a>
+  </p>
+</h3>
+
+# nmrium-core-plugins
+
+[![NPM version][npm-image]][npm-url]
+[![npm download][download-image]][download-url]
+[![DOI][doi-image]][doi-url]
+
+Package containing core plugins to work with nmrium.
+It provides essential loaders:
+
+- bruker
+- jcamp
+- jdx
+- molfile
+- nmre
+- sdf
+- smiles
+- varian
+
+And it provides the recommended post-processing plugin.
+
+For 1D spectra:
+
+- digitalFilter
+- backwardLinearPrediction
+- apodization
+- zeroFilling
+- fft
+- phaseCorrection
+
+For 2D spectra:
+
+- blpDimension1
+- apodizationDimension1
+- zeroFillingDimension1
+- fftDimension1
+- nusDimension2
+- apodizationDimension2
+- zeroFillingDimension2
+- symmetrizeCosyLike
+- phaseCorrectionTwoDimensions
+- fftDimension2
+
+These features can change at any time to be sold in dedicated plugins.
+
+## Installation
+
+`$ npm i @zakodium/nmrium-core-plugins`
+
+## Usage
+
+```js
+import { fileCollectionFromPath } from 'filelist-utils';
+import init from '@zakodium/nmrium-core-plugins';
+
+/**
+ * Initialize the core with the recommended plugins
+ */
+const core = init();
+
+const fileCollection = fileCollectionFromPath('path_to_data');
+// we can read a zip, jdx, jdf, nmredata, json, nmrium file extensions
+const result = await core.read(fileCollection, options);
+
+// based on extension we choose the format processor
+console.log(result);
+// return {
+//   spectra: [],
+//   molecules: [],
+// }
+
+// readSource function accept a partial FileCollectionItems and a baseURL to generate a 
+// data structure with a source object inside with { files, filter, baseURL }
+
+const nmriumObject = await core.readFromWebSource(
+  {
+    baseURL: 'https://cheminfo.github.io',
+    files: [
+      {
+        name: 'aspirin-1h.zip',
+        relativePath: 'bruker-data-test/data/zipped/aspirin-1h.zip',
+      },
+    ],
+  },
+  {},
+);
+```
+
+This package exports all plugin classes with their instanciation method helpers.
+Ex: `BrukerLoaderPlugin` class, and `brukerLoader()` method.
+
+And it exports the `recommended(core, plugins)` method to instance all plugins from this package and concate them with your own plugins.
+It returns an array of plugins, you have to register them in the core.
+
+## License
+
+© 2025 Zakodium Sàrl. This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. [CC BY-NC-SA 4.0](./LICENSE)
+
+This package is based on MIT-licensed code that can be found here: https://doi.org/10.5281/zenodo.7100132
+
+[npm-image]: https://img.shields.io/npm/v/@zakodium/nmrium-core-plugins.svg
+[npm-url]: https://www.npmjs.com/package/@zakodium/nmrium-core-plugins
+[download-image]: https://img.shields.io/npm/dm/@zakodium/nmrium-core-plugins.svg
+[download-url]: https://www.npmjs.com/package/@zakodium/nmrium-core-plugins
+[doi-image]: https://zenodo.org/badge/DOI/10.5281/zenodo.7101438.svg
+<!-- TODO: fix doi-url for nmrium-core-plugins package -->
+[doi-url]: https://doi.org/10.5281/zenodo.7101438

package/dist/nmrium-core-plugins.cjs

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Un(e,r){let{filter:t,experimentalFeatures:i=!1}=r,{name:n}=t;({...he.Filters1D,...he.Filters2D})[n]&&(e.some(s=>s.name===n)||(i||!zn.has(n))&&e.push({...t,enabled:!0}))}function cr(e,r={}){let{data:t}=e;if(!t)return e;let{autoProcessing:i,experimentalFeatures:n}=r,o=(l,a)=>Un(l,{...a,experimentalFeatures:n}),{spectra:s}=t;for(let l of s){let{data:a,info:m,meta:u,filters:c}=l,{dimension:g,isFid:y}=m;if(y){if(g===1){let d=a.re.length,{tdOff:p,digitalFilter:f}=m;if(f&&f>0&&o(c,{filter:{name:"digitalFilter",value:{digitalFilterValue:f}}}),!i)continue;p&&Math.abs(p)>0&&o(c,{filter:{name:"backwardLinearPrediction",value:{nbInputs:d/2}}}),o(c,{filter:{name:"apodization",value:{exponential:{apply:!0,options:{lineBroadening:1}}}}}),o(c,{filter:{name:"zeroFilling",value:{nbPoints:2*d}}}),o(c,{filter:{name:"fft",value:{}}}),o(c,{filter:{name:"phaseCorrection",value:Wn(m)}}),c.sort((F,h)=>$[F.name]-$[h.name])}else if(g===2){if(!i||!n)continue;let d=a.re.z.length,p=a.re.z[0].length,{tdOff:f,experiment:F=""}=m,h=m.spectrumSize;Array.isArray(h)&&h.length>1?(h[0]<=p&&(h[0]=p*2),h[0]<=d&&(h[0]=d*2)):h=[p*2,2*d];let b=F.toLowerCase().includes("cosy");f&&Math.abs(f[0])>0&&o(c,{filter:{name:"blpDimension1",value:{nbInputs:p/2}}});let P=or(u,{experiment:F});o(c,{filter:{name:"apodizationDimension1",value:P.f2}}),o(c,{filter:{name:"zeroFillingDimension1",value:{nbPoints:h[0]}}}),o(c,{filter:{name:"fftDimension1",value:{}}}),u&&"nuslist"in u&&o(c,{filter:{name:"nusDimension2",value:{}}}),o(c,{filter:{name:"apodizationDimension2",value:P.f1}}),o(c,{filter:{name:"zeroFillingDimension2",value:{nbPoints:h[b?0:1]}}}),b?o(c,{filter:{name:"symmetrizeCosyLike",value:{}}}):o(c,{filter:{name:"phaseCorrectionTwoDimensions",value:{}}}),o(c,{filter:{name:"fftDimension2",value:{}}}),c.sort((R,S)=>j[R.name]-j[S.name])}}}}function Wn(e){let{phc0:r=0,phc1:t=0}=e;return mr([r,t])?{}:{ph0:r,ph1:t}}function mr(e){return Array.isArray(e)?e.every(r=>!r&&r===0):mr([e])}var be=class{id="nmrium-core-plugins#NmriumPostProcessingPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onProcessing:this.onPostProcessing.bind(this)}}onPostProcessing(r,t){cr(r,t)}};function Ue(){return new be}var lr=require("sdf-parser");function We(e,r={}){let{mixedEOL:t}=r,{molecules:i}=(0,lr.parse)(e,{mixedEOL:t}),n=[];for(let{molfile:o}of i){let s=w(o);n.push(...s)}return n}async function ur(e,r={}){let{logger:t,mixedEOL:i}=r,n=await e.text(),o=We(n,{mixedEOL:i}),s={molecules:o,spectra:[]};return t&&t[o.length>0?"info":"debug"](`Loaded ${s.molecules.length} molecules from the ${e.name} file`),s}var H=class{id="nmrium-core-plugins#SDFLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={supportedExtensions:["sdf"],onFile:this.onReadProcessFile.bind(this)}}onReadProcessFile(r,t={}){let{logger:i}=t;return i?.debug(`Reading sdf file: ${r.name}`),ur(r,{logger:i})}};function Fe(){return new H}var pr=require("openchemlib/full");function Je(e){let r=[],t=e.split(/\r?\n/).filter(Boolean);for(let i of t){let o=pr.Molecule.fromSmiles(i).toMolfile();r.push({molfile:o})}return r}async function fr(e,r={}){let t=await e.text(),i=Je(t),n={molecules:i,spectra:[]};return r.logger?.info(`Found ${i.length} molecules from the ${e.name} file`),n}var X=class{id="nmrium-core-plugins#SmilesLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={supportedExtensions:["smi","smiles"],onFile:this.onReadProcessFile.bind(this)}}onReadProcessFile(r,t={}){let{logger:i}=t;return fr(r,{logger:i})}};function Ne(){return new X}var br=require("@zakodium/nmrium-core"),Fr=require("filelist-utils"),Nr=require("is-any-array"),Pr=require("ml-spectra-processing"),Sr=require("varian-converter");var dr=require("nmr-processing");function gr(e,r){let{meta:t,procpar:i}=e,n={};for(let h of i)n[h.name]=h.values;let o={},s={},{np:l,solvent:a,sfrq:m,reffrq:u,temp:c,rp:g,sw:y,rfl:d,rfp:p}=n;N(o,"numberOfPoints",l&&Number(C(l))/2),N(o,"solvent",C(a)),N(o,"originFrequency",C(m)),N(o,"baseFrequency",C(u)),(Number.isNaN(o.originFrequency)||o.originFrequency===0)&&(o.originFrequency=400,r?.warn("The frequency could not be determined and was set to 400MHz")),N(o,"temperature",C(c)),N(o,"phc0",g&&Number(g[0])),N(s,"rfl",d&&Number(C(d))),N(s,"rfp",p&&Number(C(p))),N(s,"sw",y&&Number(C(y)));for(let h in s){let b=s[h];Array.isArray(b)&&b.length===1&&(s[h]=b[0])}if(!("baseFrequency"in o)&&"originFrequency"in o){let h=Number.parseFloat(o.originFrequency);if(["sw","rfl","rfp"].every(b=>b in s)){let{sw:b=1,rfl:P=1,rfp:R=1}=Jn(s,["sw","rfl","rfp"]);N(o,"baseFrequency",h-(b/2-P+R)/1e6)}else N(o,"baseFrequency",h)}let{baseFrequency:f,originFrequency:F}=o;N(o,"frequencyOffset",(F-f)*1e6),N(o,"spectralWidth",y&&Number(y[0])/o.baseFrequency);for(let h in o)o[h].length===1&&(o[h]=o[h][0]);return n.tn&&(o.nucleus=n.tn.map(dr.normalizeNucleus)),o.dimension=1,o.isFid=!t.status.isSpectrum,{info:o,meta:{...s,...yr(t),...n}}}function C(e){return e&&(Array.isArray(e)?e[0]:e)}function Jn(e,r){let t={};for(let i of r){let n=e[i];n&&typeof n=="number"&&(t[i]=n)}return t}function yr(e){let r={};for(let t of Object.keys(e)){let i=e[t];typeof i=="object"&&i!==null&&i.constructor&&i.constructor!==Object?r[t]=yr(i):r[t]=i}return r}function hr(e){let r={},t=new Set(e.files.map(i=>i.relativePath));for(let i of e){let n=i.name.toLowerCase();if(n.match(/^(?:fid|procpar|text|log)$/)){if(n.match(/^(?:fid|text|log)$/)){let l=i.relativePath.replace(/(?:fid|text|log)$/,"procpar");if(!t.has(l))continue}let o=i.relativePath.split("/"),s=o.slice(0,-1).join("/");r[s]||(r[s]={name:o.at(-2),files:[]}),r[s].files.push(i)}}return Object.values(r)}async function Rr(e,r={}){let{keepSource:t,logger:i}=r,n=hr(e);i&&i.debug(`Found ${Object.keys(n).length} varian experiments`);let o=[],s={spectra:[],molecules:[]};for(let a of n){let{name:m,files:u}=a,c=new Fr.FileCollection(u),g=(0,Sr.convert1D)(c).then(y=>{let{info:d,meta:p}=gr(y),f=y.fid.data[0],F=(0,Nr.isAnyArray)(f.im),h={data:{...f,x:y.x},meta:p,info:{isComplex:F,name:m,...d},display:{name:m}};if(d.isFid&&F){let{im:b}=h.data;(0,Pr.xMultiply)(b,-1,{output:b})}u&&t&&(h.sourceSelector={files:u.map(b=>b.relativePath)}),s.spectra.push(h)});o.push(g)}let l=await Promise.allSettled(o);for(let a=0;a<l.length;a++){let m=l[a];if(m.status==="rejected"&&m.reason){let u=n[a].name;i?.warn(`Varian data: ${u}, fails with: ${m.reason}`)}}return s.spectra.length>0&&i?.info(`Loaded ${s.spectra.length}  spectra from Varian files`),(0,br.formatSpectra)(s)}var Y=class{id="nmrium-core-plugins#VarianLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(r,t)=>{let{keepSource:i,logger:n}=t??{};return Rr(r,{keepSource:i,logger:n})}};function Pe(){return new Y}function Mr(e,r=[]){return[ye(e),Pe(),ce(),ue(),de(),Fe(),Ne(),fe(),Ue()].concat(r)}function xr(){let e=new Dr.NMRiumCore;return e.registerPlugins(Mr(e)),e}var Ve=require("@zakodium/nmrium-core"),Or=require("convert-to-jcamp");function Ar(e,r){return e.filters.find(t=>t.name===r)}function Cr(e,r={}){let{info:t,meta:i,data:n}=e,{onlyReal:o=!1}=r,{isFid:s,spectralWidth:l}=t,a=(0,Ve.getOneIfArray)(t.baseFrequency||t.originFrequency),{x:m,re:u,im:c}=n,g=new Float64Array(u),y=!o&&c?new Float64Array(c):void 0,d={};G(d,"SW",l),G(d,"BF1",a);let p=Ar(e,"fft")?.enabled,f={originFrequency:t.originFrequency,dataType:!t.isFid||p?"NMR SPECTRUM":"NMR FID",dataClass:!o&&c?"NTUPLES":"XYDATA"};if(s){let b=e.filters.find(P=>P.name==="digitalFilter");if(b&&!p){let{value:{digitalFilterValue:P},enabled:R}=b;if(R){let S=Math.floor(P);g.set(u.slice(u.length-S)),g.set(u.slice(0,u.length-S),S),c&&y&&(y.set(c.slice(c.length-S)),y.set(c.slice(0,c.length-S),S))}}G(f,"decim",t.decim),G(f,"dspfvs",t.dspfvs),G(f,"digitalFilter",t.digitalFilter)}let F={xyEncoding:"DIFDUP",info:{...t,...f},meta:{...i,...d}},h={x:{data:m,label:t.isFid?"TIME":"FREQUENCY",units:t.isFid?"second":"HZ",symbol:"X"},r:{data:g,label:`${t.isFid?"FID":"SPECTRUM"}/REAL`,units:"ARBITRARY UNITS",symbol:"R"}};return y&&(h.i={data:y,label:`${t.isFid?"FID":"SPECTRUM"}/IMAG`,units:"ARBITRARY UNITS",symbol:"I"}),(0,Or.from1DNMRVariables)(h,F)}function G(e,r,t){t!==void 0&&(e[r]=(0,Ve.getOneIfArray)(t))}

package/dist/nmrium-core-plugins.d.ts

@@ -0,0 +1,165 @@
+import type { DataSelectionOption } from '@zakodium/nmrium-core';
+import type { FileCollection } from 'filelist-utils';
+import type { Logger } from 'cheminfo-types';
+import { NMRiumCore } from '@zakodium/nmrium-core';
+import type { NmriumData } from '@zakodium/nmrium-core';
+import type { NMRiumPlugin } from '@zakodium/nmrium-core';
+import type { NMRiumPluginMigration } from '@zakodium/nmrium-core';
+import type { NMRiumPluginOnReadProcess } from '@zakodium/nmrium-core';
+import type { ParsingOptions } from '@zakodium/nmrium-core';
+import type { Spectrum1D } from '@zakodium/nmrium-core';
+import type { StateMolecule } from '@zakodium/nmrium-core';
+
+export declare function brukerLoader(): NMRiumPlugin;
+
+export declare class BrukerLoaderPlugin implements NMRiumPlugin {
+    id: string;
+    version: number;
+    migrations: NMRiumPluginMigration[];
+    onReadProcess: NMRiumPluginOnReadProcess;
+    constructor();
+    onReadProcessFiles: (files: FileCollection, options?: ParsingOptions) => Promise<NmriumData>;
+}
+
+declare interface FilterTreeByDataTypeDataClass {
+    /**
+     * dataClass to be filter out of the tree, default value is
+     * the same dataClass of the input data.
+     */
+    dataClass?: string;
+    /**
+     * dataType to be filter out of the tree, default value is
+     * the same dataType of the input data.
+     */
+    dataType?: string;
+}
+
+/**
+ * Init NMRiumCore with recommended plugins.
+ */
+declare function init(): NMRiumCore;
+export default init;
+export { init }
+
+declare interface JcampConverterOptions {
+    keepRecordsRegExp?: RegExp;
+    profiling?: boolean;
+}
+
+export declare function jcampLoader(): NMRiumPlugin;
+
+export declare class JcampLoaderPlugin implements NMRiumPlugin {
+    id: string;
+    version: number;
+    migrations: NMRiumPluginMigration[];
+    onReadProcess: NMRiumPluginOnReadProcess;
+    constructor();
+    private onReadProcessFile;
+    private getJcampSelector;
+}
+
+declare interface JcampParsingOptions {
+    name?: string;
+    converter?: JcampConverterOptions;
+    selector?: JcampSelectorOptions;
+    keepSource?: boolean;
+    logger?: Logger;
+}
+
+declare interface JcampSelectorOptions {
+    index?: number;
+    tree?: FilterTreeByDataTypeDataClass[];
+    dataSelection?: DataSelectionOption;
+}
+
+export declare function jdfLoader(): NMRiumPlugin;
+
+export declare class JDFLoaderPlugin implements NMRiumPlugin {
+    id: string;
+    version: number;
+    migrations: NMRiumPluginMigration[];
+    onReadProcess: NMRiumPluginOnReadProcess;
+    constructor();
+    private onReadProcessFile;
+}
+
+export declare function molfileLoader(): NMRiumPlugin;
+
+export declare class MolfileLoaderPlugin implements NMRiumPlugin {
+    id: string;
+    version: number;
+    migrations: NMRiumPluginMigration[];
+    onReadProcess: NMRiumPluginOnReadProcess;
+    constructor();
+    private onReadProcessFile;
+}
+
+export declare function nmreLoader(core: NMRiumCore): NMRiumPlugin;
+
+export declare class NMReLoaderPlugin implements NMRiumPlugin {
+    private core;
+    id: string;
+    version: number;
+    migrations: NMRiumPluginMigration[];
+    onReadProcess: NMRiumPluginOnReadProcess;
+    constructor(core: NMRiumCore);
+    onReadProcessFiles: (files: FileCollection, options?: ParsingOptions) => Promise<NmriumData>;
+}
+
+declare interface ParseSDFOptions {
+    mixedEOL?: boolean;
+}
+
+export declare function processJcamp(text: string, options?: JcampParsingOptions): NmriumData;
+
+export declare function readSDF(text: string, options?: ParseSDFOptions): StateMolecule[];
+
+export declare function readSMILES(text: string): StateMolecule[];
+
+/**
+ * Recommended plugins for NMRium.
+ * This helper allows passing your own plugins to the recommended ones.
+ * Recommended plugins will have higher priority than the passed ones.
+ * @param core - NMRePlugin depend on core to load webSource.
+ * @param plugins - optional, convenient to pass your own plugins.
+ */
+export declare function recommended(core: NMRiumCore, plugins?: NMRiumPlugin[]): NMRiumPlugin[];
+
+export declare function sdfLoader(): NMRiumPlugin;
+
+export declare class SDFLoaderPlugin implements NMRiumPlugin {
+    id: string;
+    version: number;
+    migrations: NMRiumPluginMigration[];
+    onReadProcess: NMRiumPluginOnReadProcess;
+    constructor();
+    private onReadProcessFile;
+}
+
+export declare function smilesLoader(): NMRiumPlugin;
+
+export declare class SmilesLoaderPlugin implements NMRiumPlugin {
+    id: string;
+    version: number;
+    migrations: NMRiumPluginMigration[];
+    onReadProcess: NMRiumPluginOnReadProcess;
+    constructor();
+    private onReadProcessFile;
+}
+
+export declare function spectrum1DToJcamp(spectrum: Spectrum1D, options?: {
+    onlyReal?: boolean;
+}): string;
+
+export declare function varianLoader(): NMRiumPlugin;
+
+export declare class VarianLoaderPlugin implements NMRiumPlugin {
+    id: string;
+    version: number;
+    migrations: NMRiumPluginMigration[];
+    onReadProcess: NMRiumPluginOnReadProcess;
+    constructor();
+    onReadProcessFiles: (files: FileCollection, options?: ParsingOptions) => Promise<NmriumData>;
+}
+
+export { }

package/dist/nmrium-core-plugins.mjs

@@ -0,0 +1,6 @@
+import{NMRiumCore as wn}from"@zakodium/nmrium-core";import{formatSpectra as Kt}from"@zakodium/nmrium-core";import{convertOneExperiment as Zt,groupByExperiments as Qt}from"brukerconverter";function U(e){let r=[];for(let t of e){if(!t)continue;let{groups:{value:i,unit:n}={}}=t.trim().match(/[$$]*\s*(?<value>[\d.]+)\s*(?<unit>[a-zA-Z]+)/)||{};r.push(jt(i,n))}return r}function jt(e,r){switch(r.toLowerCase()){case"s":return Number.parseFloat(e);case"ms":return Number.parseFloat(e)/1e3;case"m":case"min":return Number.parseFloat(e)*60;default:return Number.NaN}}import{isAnyArray as Oe}from"is-any-array";function I(e){if(Bt(e))return zt(e)?e.map(Ae):Ae(e);if(typeof e=="object"&&e!==null){let r={};for(let t in e)r[t]=I(e[t]);return r}return e}function Bt(e){return Oe(e)}function Ae(e){return Float64Array.from(e)}function zt(e){return Oe(e[0])}import{getOneIfArray as j}from"@zakodium/nmrium-core";import{getGyromagneticRatio as Vt}from"gyromagnetic-ratio";import{isAnyArray as ce}from"is-any-array";import{getFrequency as _t}from"nmr-processing";import{isAnyArray as T}from"is-any-array";function W(e){return typeof e=="number"}function J(e){let{phc0:r,phc1:t}=e;return!T(r)&&!W(r)||!T(t)&&!W(t)||T(r)&&!W(r[0])||T(t)&&!W(t[0])?{}:(T(t)?t[0]*=-1:t*=-1,T(r)?r[0]*=-1:r*=-1,{phc0:r,phc1:t})}function Ie(e,r,t){if(e>0)return Number(e);if(r>14||r===0)return 0;if(Ce[r]){let i=Ce[r];if(!i[t])throw new Error(`decim ${t} not in lookup table for dspfvs ${r}`);return i[t]}else throw new Error(`dspfvs ${r} not in lookup table`)}var Ce={10:{2:44.75,3:33.5,4:66.625,6:59.08333333333333,8:68.5625,12:60.375,16:69.53125,24:61.02083333333333,32:70.015625,48:61.34375,64:70.2578125,96:61.50520833333333,128:70.37890625,192:61.5859375,256:70.439453125,384:61.62630208333333,512:70.4697265625,768:61.646484375,1024:70.48486328125,1536:61.65657552083333,2048:70.492431640625},11:{2:46,3:36.5,4:48,6:50.16666666666667,8:53.25,12:69.5,16:72.25,24:70.16666666666667,32:72.75,48:70.5,64:73,96:70.66666666666667,128:72.5,192:71.33333333333333,256:72.25,384:71.66666666666667,512:72.125,768:71.83333333333333,1024:72.0625,1536:71.91666666666667,2048:72.03125},12:{2:46,3:36.5,4:48,6:50.16666666666667,8:53.25,12:69.5,16:71.625,24:70.16666666666667,32:72.125,48:70.5,64:72.375,96:70.66666666666666,128:72.5,192:71.333333333,256:72.25,384:71.66666666666667,512:72.125,768:71.83333333333333,1024:72.0625,1536:71.91666666666667,2048:72.03125},13:{2:2.75,3:2.833333333333333,4:2.875,6:2.916666666666667,8:2.9375,12:2.958333333333333,16:2.96875,24:2.979166666666667,32:2.984375,48:2.989583333333333,64:2.9921875,96:2.994791666666667}};import{normalizeNucleus as Ut}from"nmr-processing";function E(e,r=","){if(e&&typeof e=="string")return e.split(r)}function V(e,r,t){let i=[];if(e[`${t}AXNUC`]&&(i=e[`${t}AXNUC`],Array.isArray(i)||(i=[i]),i=O(i)),i.length===0&&e[`${t}NUC1`]&&(i=e[`${t}NUC1`],Array.isArray(i)||(i=[i]),i=O(i)),i.length===0&&e[".NUCLEUS"]){let n=E(e[".NUCLEUS"]);if(e[`${t}SYMBOL`]){let o=e[`${t}SYMBOL`].split(","),s=o.findIndex(a=>a.includes("2")),l=o.findIndex(a=>a.includes("1"));s!==-1&&l!==-1&&n?i=O([n[s],n[l]]):i=O(n).reverse()}else i=O(n)}return i.length===0&&e[".OBSERVENUCLEUS"]&&(i=O([e[".OBSERVENUCLEUS"]])),i.length===0&&r.experiment&&(i=O(Ee(r.experiment[0]))),Wt(e)&&(i=[e["2D_X_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,""),e["2D_Y_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,"")]),r.experiment&&(r.experiment[0].match("jres")||r.experiment[0].match("dosy"))&&(i=Ee(r.experiment[0])),i.map(Ut)}function Wt(e){return e["2D_X_NUCLEUS"]&&!e["2D_X_NUCLEUS"].includes("off")&&e["2D_Y_NUCLEUS"]&&!e["2D_Y_NUCLEUS"].includes("off")}function Ee(e){return typeof e!="string"?[]:(e=e.toLowerCase(),e.includes("jres")?["1H","Hz"]:e.includes("dosy")?["1H","D"]:e.includes("hmbc")||e.includes("hsqc")?["1H","13C"]:e.includes("cosy")||e.includes("tocsy")?["1H","1H"]:[])}function O(e){if(!e)return[];let r=e.map(i=>String(i).replaceAll(/[^A-Za-z0-9]/g,"").replace("NA","").replace("off","")),t=0;for(let i of r)i||t++;return t===0?r:[]}import{getOneIfArray as Jt}from"@zakodium/nmrium-core";function _(e={},r={},t={}){e===null&&(e={}),typeof e=="string"&&(e={pulseSequence:e});let i=Array.isArray(e.pulseSequence)?e.pulseSequence[0]:e.pulseSequence||"";if(typeof i!="string")return 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+`}=t;N(e,"spectralWidth",r[`${i}SweepWidth`]/e.originFrequency[0]);let o=r[`${i}.PULSESEQUENCE`].split(n),s=[];r[".OBSERVENUCLEUS"]&&s.push(r[".OBSERVENUCLEUS"]),r.INDIRECTNUCLEUS&&s.push(r.INDIRECTNUCLEUS),e.nucleus=O(s),e.pulseSequence=o[0];let l=o.slice(2,-1);if(s.length>1)if(s[0]===s[1])e.spectralWidth.push(e.spectralWidth[0]);else{let a=JSON.stringify(l).match(/\$\$SW1=\s*(?<sw>[+-]?(?:[0-9]*[.])?[0-9]+)/);if(a?.groups){let{originFrequency:m}=e,u=Number.parseFloat(a.groups.sw);e.spectralWidth.push(u/m[1])}}return e}function Gt(e,r){let{T1NUCLEUS:t,T2NUCLEUS:i,PAGE:n}=r;e.pulseSequence=r.EXPERIMENT||r[".PULSESEQUENCE"];let o=[],{dimension:s,isComplex:l}=e;if(s===2&&e.pulseSequence==="T1"){let u=l?2:1;for(let c=0;c<n.length;c+=u){let g=n[c].replace(/T1=/,"");o.push(Number(g))}r.vdlistValues=o}e.nucleus=s>1?[i,t]:i;let{phc0:a,phc1:m}=e;if(a&&m){let u=J({phc0:a,phc1:m});e={...e,...u}}}var er={keepRecordsRegExp:/.*/,keepFiles:!0};async function Y(e,r={}){let t={spectra:[],molecules:[]},{converter:i={},selector:n={},logger:o}=r,s=Qt(e,{logger:o,...rr(n)}),l=[];for(let m of s)l.push(Zt(m,{...er,...i}).then(u=>tr(u,r)));let a=await Promise.allSettled(l);for(let m=0;m<a.length;m++){let u=a[m];if(u.status==="fulfilled"){let c=J(u.value.info);t.spectra.push({...u.value,info:{...u.value.info,...c}})}else if(u.reason){let c=s[m].name;o?.warn(`Bruker data: ${c}, fails with: ${u.reason}`);continue}}return o&&o[t.spectra.length>0?"info":"debug"](`Loaded ${t.spectra.length} spectra from Bruker files`),Kt(t)}function tr(e,r={}){let{keepSource:t=!1,logger:i}=r,n={...e.info,...e.meta},o=X(n,{logger:i}),s={},{isFid:l}=o;if(nr(e)){let y=e.minMax;for(let d in y){let p=y[d];p&&(p.z=I(p.z))}s.components=e.minMax}else o.dimension===1&&(s.components=e.spectra);let{source:a}=e,{expno:m,name:u,files:c}=a;n.vdlist&&(n.vdlistValues=U(n.vdlist));let g={dependentVariables:[s],meta:n,info:{...o,experimentNumber:m,name:u}};return c&&t&&(g.sourceSelector={files:c.map(y=>y.relativePath)}),ir(g,e),g}function rr(e){let{general:r={},bruker:t={}}=e,{processingNumbers:i,experimentNumbers:n,...o}=t;return{...r,...o,processingNumbers:Le(i),experimentNumbers:Le(n)}}function Le(e){if(e)return e.split(/[^\d]+/).filter(Boolean).map(r=>Number.parseInt(r,10))}function nr(e){let{info:r}=e;return r.twoD}function ir(e,r){if(!("integrals"in r))return;let{integrals:t=[]}=r;e.integrals={values:t.map(i=>{let{from:n,to:o,integration:s}=i;return{from:n,to:o,integral:s,kind:"signal"}})}}var G=class{id="nmrium-core-plugins#BrukerLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(r,t)=>{let{sourceSelector:i,converter:n,keepSource:o,logger:s}=t??{};return Y(r,{converter:n?.bruker,selector:i,keepSource:o,logger:s})}};function me(){return new G}import{formatSpectra as $r}from"@zakodium/nmrium-core";import{createTree as jr}from"jcampconverter";function ke(e,r,t={}){let{selector:i={},keepSource:n=!1}=t;if(!n)return e;for(let o=0;o<e.spectra.length;o++){let s=e.spectra[o];s.sourceSelector={files:[r.relativePath],jcamp:{index:o,...i}}}return e}import{convert as or}from"jcampconverter";function le(e,r,t){let{dataType:i,children:n}=e,o=i==="LINK"&&n?n:[e];for(let s of o){if(s.dataType==="LINK"){le(s,r,t);continue}let l=or(s.jcamp,t);r.push(...l.flatten)}}function qe(e,r={}){let t=[],i=$e(e,r);for(let s of i?e:[])s.dataType==="LINK"?s.children=ue(s.children,r):s=ue([s],r)[0],t.push(s);let{name:n,logger:o}=r;return e.length===0&&o?.warn(`There is no data ${n?`in ${n}`:"in the JCAMP-DX"}`),t}function ue(e=[],r={}){let{name:t,logger:i,tree:n=[],dataSelection:o="both"}=r,s=[];for(let u of e){let{dataType:c,dataClass:g}=u;if(c==="LINK")u.children=ue(u.children,r);else if(n.some(y=>{let{dataClass:d=g,dataType:p=c}=y;return g===d&&c===p})){i?.warn(`Skipping ${g} and ${c} ${t?`in ${t}`:"in the JCAMP-DX"}, 
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${o}`),!1;if(s.includes("nmr"))return!0}}return!1}import{generateID as ze}from"@zakodium/nmrium-core";import{parseJcampCS as pr}from"jcampconverter";import*as fr from"openchemlib/full";import{isMolfileNotEmpty as sr}from"nmr-processing";import{Molecule as ar}from"openchemlib/full";async function je(e,r={}){let t=await e.text(),i=L(t),n={molecules:i,spectra:[]};return i.length===0&&r.logger?.debug(`${e.name} is an empty molfile`),n}function L(e){let r=[];if(!sr(e))return[];let i=ar.fromMolfile(e).toMolfile();return r.push({molfile:i}),r}import{isMolfileNotEmpty as mr}from"nmr-processing";import*as lr from"openchemlib/full";import{getDiastereotopicAtomIDsFromMolfile as ur}from"openchemlib-utils";var cr=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function K(e){let{dataType:r="",dataClass:t=""}=e,i=r.replaceAll(/\s/g,"").toLowerCase(),n=t.replaceAll(/\s/g,"").toLowerCase();return cr.has(i)&&n!=="peaktable"}function 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h=ur(lr,F),b=V({...n,...o},{},"");for(let S=0;S<s.x.length;S++){let D={};for(let x in s){let A=s[x][S];typeof A=="string"&&A.startsWith("<")&&A.endsWith(">")&&(A=A.slice(1,-1)),D[a[x]]=A}if("atom"in D){let x=h.map[D.atom-1];b.includes("1H")?x.nbHydrogens>0?(D.diaIDs=x.hydrogenOCLIDs,D.nbHydrogens=x.nbHydrogens):(D.diaIDs=[x.oclID],D.nbHydrogens=x.nbHydrogens):(D.diaIDs=[x.oclID],D.nbHydrogens=1)}l.push(D)}let P={};for(let S of l){let{delta:D,diaIDs:x}=S,A=`${D}_${x.join("_")}`;if(P[A])P[A].atoms.push(S.atom);else{let{atom:Bn,...$t}=S;P[A]={...$t,atoms:[S.atom]}}}let R=[];for(let S of y)S.toLowerCase().includes("spectrum")&&R.push(Number(S.toLowerCase().replace(/_/,"").replace(/.*:\s*blockid=(?<blockId>.*)/,"$<blockId>")));if(R.length===0){for(let S of r)if(K(S)){let{BLOCKID:D}=S.info;R.push(Number(D))}R.length>1&&(R=[],m&&m.warn(`There is not a spectral cross-reference for the peak assignment in the ${u} 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n){let{name:m,files:u}=a,c=new En(u),g=kn(c).then(y=>{let{info:d,meta:p}=Tt(y),f=y.fid.data[0],F=Tn(f.im),h={data:{...f,x:y.x},meta:p,info:{isComplex:F,name:m,...d},display:{name:m}};if(d.isFid&&F){let{im:b}=h.data;Ln(b,-1,{output:b})}u&&t&&(h.sourceSelector={files:u.map(b=>b.relativePath)}),s.spectra.push(h)});o.push(g)}let l=await Promise.allSettled(o);for(let a=0;a<l.length;a++){let m=l[a];if(m.status==="rejected"&&m.reason){let u=n[a].name;i?.warn(`Varian data: ${u}, fails with: ${m.reason}`)}}return s.spectra.length>0&&i?.info(`Loaded ${s.spectra.length}  spectra from Varian files`),In(s)}var se=class{id="nmrium-core-plugins#VarianLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(r,t)=>{let{keepSource:i,logger:n}=t??{};return wt(r,{keepSource:i,logger:n})}};function xe(){return new se}function vn(e,r=[]){return[be(e),xe(),me(),fe(),he(),De(),Me(),ye(),Re()].concat(r)}function qn(){let e=new 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F={xyEncoding:"DIFDUP",info:{...t,...f},meta:{...i,...d}},h={x:{data:m,label:t.isFid?"TIME":"FREQUENCY",units:t.isFid?"second":"HZ",symbol:"X"},r:{data:g,label:`${t.isFid?"FID":"SPECTRUM"}/REAL`,units:"ARBITRARY UNITS",symbol:"R"}};return y&&(h.i={data:y,label:`${t.isFid?"FID":"SPECTRUM"}/IMAG`,units:"ARBITRARY UNITS",symbol:"I"}),$n(h,F)}function z(e,r,t){t!==void 0&&(e[r]=qt(t))}export{G as BrukerLoaderPlugin,ee as JDFLoaderPlugin,Q as JcampLoaderPlugin,te as MolfileLoaderPlugin,re as NMReLoaderPlugin,ie as SDFLoaderPlugin,oe as SmilesLoaderPlugin,se as VarianLoaderPlugin,me as brukerLoader,qn as default,qn as init,fe as jcampLoader,ye as jdfLoader,he as molfileLoader,be as nmreLoader,ot as processJcamp,Ot as readSDF,It as readSMILES,vn as recommended,De as sdfLoader,Me as smilesLoader,jn as spectrum1DToJcamp,xe as varianLoader};

package/package.json

@@ -0,0 +1,85 @@
+{
+  "name": "@zakodium/nmrium-core-plugins",
+  "version": "0.0.1",
+  "description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
+  "author": "",
+  "license": "CC-BY-NC-SA-4.0",
+  "type": "module",
+  "exports": {
+    ".": {
+      "types": "./dist/nmrium-core-plugins.d.ts",
+      "require": "./dist/nmrium-core-plugins.cjs",
+      "default": "./dist/nmrium-core-plugins.mjs"
+    }
+  },
+  "files": [
+    "dist/nmrium-core-plugins.d.ts",
+    "dist/nmrium-core-plugins.cjs",
+    "dist/nmrium-core-plugins.mjs"
+  ],
+  "imports": {
+    "#assets": "./src/assets.js"
+  },
+  "scripts": {
+    "api-extractor": "api-extractor run --local",
+    "bundle": "npm run bundle-cjs && npm run bundle-esm && npm run bundle-types",
+    "bundle-common": "esbuild src/index.ts --bundle --packages=external --minify",
+    "bundle-cjs": "npm run bundle-common -- --format=cjs --outfile=./dist/nmrium-core-plugins.cjs",
+    "bundle-esm": "npm run bundle-common -- --format=esm --outfile=./dist/nmrium-core-plugins.mjs",
+    "bundle-types": "npm run tsc && npm run api-extractor",
+    "check-types": "tsc --noEmit",
+    "clean": "rimraf types",
+    "eslint": "eslint src --cache",
+    "eslint-fix": "npm run eslint -- --fix",
+    "dev:eslint-fix": "eslint --cache --fix $(git diff --name-only --relative) --quiet",
+    "prepack": "npm run bundle && npm run bundle-types",
+    "prettier": "prettier --check src",
+    "prettier-write": "prettier --write src",
+    "dev:prettier-write": "prettier --write $(git diff --name-only --relative)",
+    "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
+    "test-only": "vitest run --coverage",
+    "tsc": "tsc --project tsconfig.types.json"
+  },
+  "devDependencies": {
+    "@microsoft/api-extractor": "^7.52.1",
+    "@types/lodash.merge": "^4.6.9",
+    "@types/node": "^22.13.11",
+    "@vitest/coverage-istanbul": "^3.0.9",
+    "bruker-data-test": "^0.5.4",
+    "esbuild": "^0.25.1",
+    "eslint": "^9.22.0",
+    "eslint-config-cheminfo-typescript": "^18.0.0",
+    "fifo-logger": "^1.0.0",
+    "jcamp-data-test": "^0.8.3",
+    "jest-matcher-deep-close-to": "^3.0.2",
+    "msw": "^2.7.5",
+    "nmredata-data-test": "^0.4.0",
+    "prettier": "^3.5.3",
+    "rimraf": "^6.0.1",
+    "typescript": "^5.8.2",
+    "vitest": "^3.0.9"
+  },
+  "dependencies": {
+    "@zakodium/nmrium-core": "^0.0.1",
+    "brukerconverter": "^8.0.3",
+    "convert-to-jcamp": "^5.4.11",
+    "filelist-utils": "^1.11.3",
+    "gyromagnetic-ratio": "^1.2.1",
+    "is-any-array": "^2.0.1",
+    "jcampconverter": "^11.0.1",
+    "jeol-data-test": "^0.5.2",
+    "jeolconverter": "^1.0.4",
+    "linear-sum-assignment": "^1.0.7",
+    "lodash.merge": "^4.6.2",
+    "ml-spectra-processing": "^14.11.0",
+    "nmr-processing": "^18.0.0",
+    "nmredata": "^1.0.0",
+    "openchemlib": "^8.19.0",
+    "openchemlib-utils": "^6.6.0",
+    "sdf-parser": "^7.0.4",
+    "varian-converter": "^2.0.1"
+  },
+  "volta": {
+    "extends": "../../../package.json"
+  }
+}