@zakodium/nmrium-core-plugins 0.1.1 → 0.1.2

package/LICENSE

@@ -0,0 +1,438 @@
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package/README.md

@@ -9,11 +9,7 @@
 
 # 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.
+Package containing core plugins to work with NMRium.
 It provides essential loaders:
 
 - bruker
@@ -77,7 +73,7 @@ console.log(result);
 //   molecules: [],
 // }
 
-// readSource function accept a partial FileCollectionItems and a baseURL to generate a 
+// 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(
@@ -105,11 +101,3 @@ It returns an array of plugins, you have to register them in the core.
 © 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.js

@@ -0,0 +1,10 @@
+import{NMRiumCore as ms}from"@zakodium/nmrium-core";import{Filters1D as Or,Filters2D as wr}from"nmr-processing";import{getOneIfArray as xr}from"@zakodium/nmrium-core";function re(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 e.dimension?`${e.dimension}d`:"";if(i=i.toLowerCase(),i.includes("zg")||i.includes("single_pulse_dec")||i.includes("udeft"))return"1d";if(i.includes("hsqct")||i.includes("invi")&&(i.includes("ml")||i.includes("di")))return"hsqctocsy";if(i.includes("hsqc")||i.includes("invi"))return"hsqc";if(i.includes("hmbc")||i.includes("inv4")&&i.includes("lp"))return"hmbc";if(i.includes("hmqc"))return"hmqc";if(i.includes("cosy"))return"cosy";if(i.includes("jres"))return"jres";if(i.includes("dosy"))return"dosy";if(i.includes("tocsy")||i.includes("mlev")||i.includes("dipsi"))return"tocsy";if(i.includes("noesy"))return"noesy";if(i.includes("roesy"))return"roesy";if(i.includes("dept"))return"dept";if(i.includes("jmod")||i.includes("apt"))return"aptjmod";if(i.includes("inad"))return"inadequate";if(i.includes("adeq"))return"adequate";let{prefix:n=""}=t,s=(xr(r[`${n}SPECTYP`])||"").replace(/^<(.*)>$/,"$1").toLowerCase();return s.length>0&&s!=="undefined"?s:e.dimension?`${e.dimension}d`:""}import{getOneIfArray as He}from"@zakodium/nmrium-core";var Mr=["no","exponential","modifiedGaussian","sine","qsine","trap","user","sinc","qsinc","traf","trafs"];function Rr(e){return e in Ze}function Me(e,r){let{prefix:t="",index:i=0}=r,n=He(e[`${t}WDW`],i),s=Mr[n?Number(n):0],o={};if(!Rr(s))return o;let l=Ze[s];if(l){let{kind:a,parameters:m}=l,f={};for(let c in m){let b=m[c],{source:u,processor:y}=b;if(u){let g=He(e[`${t}${u}`],i);if(!g)continue;let p=Number(g);f[c]=y?y(p):p}else b.value!==void 0&&(f[c]=b.value)}o[a]={apply:!0,options:f}}return o}var Ze={exponential:{kind:"exponential",parameters:{lineBroadening:{source:"LB"}}},modifiedGaussian:{kind:"gaussian",parameters:{lineBroadening:{source:"LB"},lineBroadeningCenter:{source:"GB"}}},sine:{kind:"sineBell",parameters:{offset:{source:"SSB",processor:e=>1/e},exponent:{value:1}}},qsine:{kind:"sineSquare",parameters:{offset:{source:"SSB",processor:e=>1/e}}},traf:{kind:"traf",parameters:{lineBroadening:{source:"LB"}}}};var Ke={sineBell:et({offset:0})},Qe={cosy:{...Ke},hmbc:{...Ke},hsqc:{sineBell:et({offset:.5})}},Ir={...Qe};function Re(e="",r=1){let t=Er(e),i={},n=r===1?Qe[t||""]:Ir[t||""];return n&&(i=structuredClone(n)),i}function et(e){return{apply:!0,options:e}}function Er(e){let t=e.toLowerCase().match(/cosy|hsqc|hmbc/);return t?t[0]:null}function tt(e,r={}){let{prefix:t="",experiment:i=re(e)}=r;return e[`${t}WDW`]?{f2:Me(e,{...r,index:0}),f1:Me(e,{...r,index:1})}:{f2:Re(i,1),f1:Re(i,2)}}import{Filters1D as Cr}from"nmr-processing";var Ie=["digitalFilter","backwardLinearPrediction","forwardLinearPrediction","apodization","zeroFilling","fft",["shiftX","phaseCorrection","baselineCorrection"]],z={};for(let e=0;e<Ie.length;e++){let r=Ie[e];for(let t of Array.isArray(r)?r:[r])z[t]=e}for(let e of Object.values(Cr))e.name in z||(z[e.name]=Ie.length);import{Filters2D as Tr}from"nmr-processing";var Ee=["digitalFilter2D","blpDimension1","flpDimension1","apodizationDimension1","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","nusDimension2","apodizationDimension2","zeroFillingDimension2","fftDimension2","phaseCorrectionTwoDimensions",["shift2DX","shift2DY","symmetrizeCosyLike"]],W={};for(let e=0;e<Ee.length;e++){let r=Ee[e];for(let t of Array.isArray(r)?r:[r])W[t]=e}for(let e of Object.values(Tr))e.name in W||(W[e.name]=Ee.length);var vr=new Set(["backwardLinearPrediction","forwardLinearPrediction","digitalFilter2D","phaseCorrectionTwoDimensions","blpDimension1","flpDimension1","apodizationDimension1","apodizationDimension2","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","zeroFillingDimension2","fftDimension2","nusDimension2","symmetrizeCosyLike"]);function Lr(e,r){let{filter:t,experimentalFeatures:i=!1}=r,{name:n}=t;({...Or,...wr})[n]&&(e.some(o=>o.name===n)||(i||!vr.has(n))&&e.push({...t,enabled:!0}))}function rt(e,r={}){let{data:t}=e;if(!t)return e;let{autoProcessing:i,experimentalFeatures:n}=r,s=(l,a)=>Lr(l,{...a,experimentalFeatures:n}),{spectra:o}=t;for(let l of o){let{data:a,info:m,meta:f,filters:c}=l,{dimension:b,isFid:u}=m;if(u){if(b===1){let 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t=e[".SHIFTREFERENCE"],i=t.trim().startsWith("(")?/\((?<data>[^)]+)\)/:/(?<data>[^)]+)/,n=t.match(i);if(n.groups.data){let s=n.groups.data.split(",");if(s.length<4)return;let o=Number.parseInt(r.numberOfPoints,10),{spectralWidth:l,baseFrequency:a}=r,m=Number.parseInt(s[2],10),f=Number.parseFloat(s[3]),c;if(r.isFid){if(["baseFrequency","numberOfPoints","spectralWidth"].some(b=>!(b in r)))return;c=f+(o*.5-m)*l/o}else{let b=Number.parseFloat(r.firstX),u=Number.parseFloat(r.lastX),y=(u+b)/2,g=(u-b)/(o+1),p=g<0?b:u+(m-1)*g;c=(y-p)/a+f}c!==void 0&&!Number.isNaN(c)&&(r.frequencyOffset=c*a)}}function me(e){if(Le(e)){let r=[];for(let t of e)r.push(typeof t=="string"?Number.parseFloat(t):t);return r}return typeof e=="string"?Number.parseFloat(e):e}function hn(e){switch(String(Le(e)?e[1]:e).toLowerCase().replaceAll(/\s/g,"")){case"1":case"notphasesensitive":return"notPhaseSensitive";case"2":return"QSEQ";case"3":case"tppi":return"TPPI";case"4":case"states":return"States";case"5":case"tppi-states":return"States-TPPI";case"6":case"echo-antiecho":return"Echo-antiecho";default:return"undefined"}}function yn(e,r,t={}){let{prefix:i="",separator:n=`
+`}=t;D(e,"spectralWidth",r[`${i}SweepWidth`]/e.originFrequency[0]);let s=r[`${i}.PULSESEQUENCE`].split(n),o=[];r[".OBSERVENUCLEUS"]&&o.push(r[".OBSERVENUCLEUS"]),r.INDIRECTNUCLEUS&&o.push(r.INDIRECTNUCLEUS),e.nucleus=k(o),e.pulseSequence=s[0];let l=s.slice(2,-1);if(o.length>1)if(o[0]===o[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,f=Number.parseFloat(a.groups.sw);e.spectralWidth.push(f/m[1])}}return e}function bn(e,r){let{T1NUCLEUS:t,T2NUCLEUS:i,PAGE:n}=r;e.pulseSequence=r.EXPERIMENT||r[".PULSESEQUENCE"];let s=[],{dimension:o,isComplex:l}=e;if(o===2&&e.pulseSequence==="T1"){let f=l?2:1;for(let c=0;c<n.length;c+=f){let b=n[c].replace(/T1=/,"");s.push(Number(b))}r.vdlistValues=s}e.nucleus=o>1?[i,t]:i;let{phc0:a,phc1:m}=e;if(a&&m){let f=le({phc0:a,phc1:m});e={...e,...f}}}var Sn={keepRecordsRegExp:/.*/,keepFiles:!0};async function pe(e,r={}){let t={spectra:[],molecules:[]},{converter:i={},selector:n={},logger:s}=r,o=ct(e,{logger:s,...Dn(n)}),l=[];for(let m of o)l.push(gt(m,{...Sn,...i}).then(f=>Nn(f,r)));let a=await Promise.allSettled(l);for(let m=0;m<a.length;m++){let f=a[m];if(f.status==="fulfilled"){let c=le(f.value.info);t.spectra.push({...f.value,info:{...f.value.info,...c}})}else if(f.reason){let c=o[m].name;s?.warn(`Bruker data: ${c}, fails with: ${f.reason}`);continue}}return s&&s[t.spectra.length>0?"info":"debug"](`Loaded ${t.spectra.length} spectra from Bruker files`),Fn(t)}function Nn(e,r={}){let{keepSource:t=!1,logger:i}=r,n={...e.info,...e.meta},s=ue(n,{logger:i}),o={},{isFid:l}=s;if(Pn(e)){let u=e.minMax;for(let y in u){let g=u[y];g&&(g.z=$(g.z))}o.components=e.minMax}else s.dimension===1&&(o.components=e.spectra);let{source:a}=e,{expno:m,name:f,files:c}=a;n.vdlist&&(n.vdlistValues=oe(n.vdlist));let b={dependentVariables:[o],meta:n,info:{...s,experimentNumber:m,name:f}};return c&&t&&(b.sourceSelector={files:c.map(u=>u.relativePath)}),An(b,e),b}function Dn(e){let{general:r={},bruker:t={}}=e,{processingNumbers:i,experimentNumbers:n,...s}=t;return{...r,...s,processingNumbers:Dt(i),experimentNumbers:Dt(n)}}function Dt(e){if(e)return e.split(/[^\d]+/).filter(Boolean).map(r=>Number.parseInt(r,10))}function Pn(e){let{info:r}=e;return r.twoD}function An(e,r){if(!("integrals"in r))return;let{integrals:t=[]}=r;e.integrals={values:t.map(i=>{let{from:n,to:s,integration:o}=i;return{from:n,to:s,integral:o,kind:"signal"}})}}var fe=class{id="@zakodium/nmrium-core-plugins#BrukerLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(r,t)=>{let{sourceSelector:i,converter:n,keepSource:s,logger:o}=t??{};return pe(r,{converter:n?.bruker,selector:i,keepSource:s,logger:o})}};function ke(){return new fe}import{formatSpectra as ii}from"@zakodium/nmrium-core";import{createTree as si}from"jcampconverter";function Pt(e,r,t={}){let{selector:i={},keepSource:n=!1}=t;if(!n)return e;for(let s=0;s<e.spectra.length;s++){let o=e.spectra[s];o.sourceSelector={files:[r.relativePath],jcamp:{index:s,...i}}}return e}import{convert as xn}from"jcampconverter";function qe(e,r,t){let{dataType:i,children:n}=e,s=i==="LINK"&&n?n:[e];for(let o of s){if(o.dataType==="LINK"){qe(o,r,t);continue}let l=xn(o.jcamp,t);r.push(...l.flatten)}}function Mt(e,r={}){let t=[],i=Rt(e,r);for(let o of i?e:[])o.dataType==="LINK"?o.children=Be(o.children,r):o=Be([o],r)[0],t.push(o);let{name:n,logger:s}=r;return e.length===0&&s?.warn(`There is no data ${n?`in ${n}`:"in the JCAMP-DX"}`),t}function Be(e=[],r={}){let{name:t,logger:i,tree:n=[],dataSelection:s="both"}=r,o=[];for(let f of e){let{dataType:c,dataClass:b}=f;if(c==="LINK")f.children=Be(f.children,r);else if(n.some(u=>{let{dataClass:y=b,dataType:g=c}=u;return b===y&&c===g})){i?.warn(`Skipping ${b} and ${c} ${t?`in ${t}`:"in the JCAMP-DX"}, 
+        because it didn't match the import filters`);continue}o.push(f)}let l=[],a=o.some(xt),m=o.some(At);for(let f of o){if(s!=="both"&&f.dataType!=="LINK"){if(xt(f)&&(s==="ft"||s==="preferFT"&&m)){i?.warn(`Skipping raw data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(At(f)&&(s==="fid"||s==="preferFID"&&a)){i?.warn(`Skipping FFT data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}}l.push(f)}return l}function At(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function xt(e){return e.dataType?.toUpperCase().includes("FID")}function Rt(e,r={}){let{logger:t,name:i=""}=r;for(let n of e){if(n.dataType==="LINK"&&Rt(n.children,r))return!0;let{dataType:s=""}=n,o=s.toLowerCase();if(o.length>0){if(o.includes("spectrum")&&!o.includes("nmr"))return t?.warn(`File ${i} was ignored because it is a ${s}`),!1;if(o.includes("nmr"))return!0}}return!1}import{generateID as Ct}from"@zakodium/nmrium-core";import{parseJcampCS as On}from"jcampconverter";import*as wn from"openchemlib";import{isMolfileNotEmpty as Mn}from"nmr-processing";import{Molecule as Rn}from"openchemlib";async function It(e,r={}){let t=await e.text(),i=J(t),n={molecules:i,spectra:[]};return i.length===0&&r.logger?.debug(`${e.name} is an empty molfile`),n}function J(e){let r=[];if(!Mn(e))return[];let i=Rn.fromMolfile(e).toMolfile();return r.push({molfile:i}),r}import{isMolfileNotEmpty as En}from"nmr-processing";import*as Cn from"openchemlib";import{getDiastereotopicAtomIDsFromMolfile as Tn}from"openchemlib-utils";var In=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function de(e){let{dataType:r="",dataClass:t=""}=e,i=r.replaceAll(/\s/g,"").toLowerCase(),n=t.replaceAll(/\s/g,"").toLowerCase();return In.has(i)&&n!=="peaktable"}function Et(e,r,t={}){let{spectra:i,info:n,meta:s}=e,o=i[0].data,l=[],a={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:m,name:f,spectraData:c}=t,{CROSSREFERENCE:b}=n,u=typeof b!="string"?b:b.split(/\r?\n/).map(S=>S.trim()).filter(Boolean),y=u.find(S=>S?.toLowerCase().includes("structure"));if(y===void 0)return m&&m.warn(`There is not a structure reference for ${f} file, assignment object could not be completed`),null;let g=Number.parseInt(y?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(g)||g<1)return m&&m.warn(`Structure block_id not found for ${f} file, assignment object could not be completed`),null;let d=c?.molecules?.find(S=>S.blockId===g)?.molfile??"";if(d===""){let S=r.find(M=>M.info.BLOCKID===g),{MOLFILE:A=""}=S?.meta||{};d=A}if(!En(d))return m&&m.warn(`Empty molfile for ${f} file with structure block_id = ${g}, assignment object could not be completed`),null;let h=Tn(Cn,d),F=ce({...n,...s},{},"");for(let S=0;S<o.x.length;S++){let A={};for(let M in o){let I=o[M][S];typeof I=="string"&&I.startsWith("<")&&I.endsWith(">")&&(I=I.slice(1,-1)),A[a[M]]=I}if("atom"in A){let M=h.map[A.atom-1];F.includes("1H")?M.nbHydrogens>0?(A.diaIDs=M.hydrogenOCLIDs,A.nbHydrogens=M.nbHydrogens):(A.diaIDs=[M.oclID],A.nbHydrogens=M.nbHydrogens):(A.diaIDs=[M.oclID],A.nbHydrogens=1)}l.push(A)}let N={};for(let S of l){let{delta:A,diaIDs:M}=S,I=`${A}_${M.join("_")}`;if(N[I])N[I].atoms.push(S.atom);else{let{atom:Pe,...P}=S;N[I]={...P,atoms:[S.atom]}}}let x=[];for(let S of u)S.toLowerCase().includes("spectrum")&&x.push(Number(S.toLowerCase().replace(/_/,"").replace(/.*:\s*blockid=(?<blockId>.*)/,"$<blockId>")));if(x.length===0){for(let S of r)if(de(S)){let{BLOCKID:A}=S.info;x.push(Number(A))}x.length>1&&(x=[],m&&m.warn(`There is not a spectral cross-reference for the peak assignment in the ${f} 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Yn}from"ml-spectra-processing";import{xyAutoRangesPicking as Gn}from"nmr-processing";function Y(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function G(e){e.sort((r,t)=>r.from-t.from);for(let r=0;r<e.length-1;r++)e[r].to>e[r+1].from&&(e[r].to=Math.max(e[r+1].to,e[r].to),e[r].signals=e[r].signals.concat(e[r+1].signals),e[r].integration+=e[r+1].integration,e.splice(r+1,1),r--);return e}import{splitPatterns as jn}from"nmr-processing";import{xMaxValue as Bn}from"ml-spectra-processing";function ee(e){return e.trim().slice(1,-1).split(/,\s*/).map(r=>r.trim())}var _n={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},Ot=["I","X","Y","Hs","An","H","C","N","(J)"];function wt(e){let r={headersFromParenthesis:[],headersFromComments:[],comments:[],data:[],multiplets:[]},t=e.split(/\r?\n/).filter(i=>i.trim()!=="");if(t.length===0)return r;if(t[0].startsWith("(")&&!t[0].match(/\d/)){let i=t.shift();r.headersFromParenthesis=ee(i)}return r.comments=t.filter(i=>i.startsWith("$$")).map(i=>i.replace(/^\$\$\s*/,"")),r.headersFromComments=$n(r.comments),r.data=t.filter(i=>!i.startsWith("$$")).map(ee),r.multiplets=Un(r),r}function Un(e,r={}){let{logger:t}=r,i=e.data[0].map((a,m)=>m).filter(a=>e.data.every(m=>Number.isNaN(m[a])||Number.isNaN(Number(m[a]))));if(t?.trace(`Parsing JCAMP-DX assignment: stringColumnIndexes: ${i.join(",")}`),i.length===0)return t?.warn("Parsing JCAMP-DX assignment: No string columns found. 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p){if(F.js.every(N=>N===F.js[0])){h.push(F);continue}if(F.multiplicity!==F.js.length+1){h.push(F);continue}for(let N=0;N<F.multiplicity-1;N++)h.push({value:"d",multiplicity:2,js:[F.js[N]]})}h.sort((F,N)=>N.js[0]-F.js[0]),u.js=h.map(F=>({coupling:F.js[0],multiplicity:F.value}))}typeof s.assignment=="string"&&(u.assignment=Xn(s.assignment)),typeof s.multiplicity=="string"&&(u.multiplicity=s.multiplicity),n.multiplets.push(u)}return n}function zn(e){let r={};for(let t in e){let i=e[t],n=typeof i=="number"?i:Number.parseFloat(i);Number.isNaN(n)||(r[t]=n)}return r}var Wn={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function Xn(e){return e.replaceAll(/&(\w+);/gi,(r,t)=>Wn[t.toLowerCase()]||r)}function Lt(e){let r=e.split(/\r?\n/).filter(i=>i.trim()!==""),t=[];for(let i of r)if(i.startsWith("(")){let[n,s,o]=ee(i).map(Number.parseFloat);t.push({id:n,x:s,y:o})}return t}function kt(e,r={}){let t={};if(!e["OBSERVED MULTIPLETS"])return[];let i=vt(e["OBSERVED MULTIPLETS"],r);if(!i)return[];let{multiplets:n}=i;for(let s of n){let{id:o,from:l,to:a,integration:m=0,...f}=s;t[o]={from:l,to:a,integration:m,signals:[{id:o,...f}]}}if(e["OBSERVED MULTIPLETS PEAKS"]){let s=Lt(e["OBSERVED MULTIPLETS PEAKS"]),o={};for(let l of s){let{id:a,x:m,y:f}=l;o[a]||(o[a]=[]),o[a].push({x:m,y:f,width:.05})}for(let l in t)o[l]&&(t[l].signals[0].peaks=o[l])}return G(Object.values(t))}function qt(e,r){let i=[...e.getMolecularFormula().formula.matchAll(/(?<element>[A-Z][a-z]?)(?<count>\d*)/g)].map(s=>({element:s?.groups?.element,count:s?.groups?.count?Number(s.groups.count):1})),n=[...r.nucleus[0].matchAll(/[0-9]*(?<element>[A-Z][a-z]?)/g,"$element")][0].groups.element;return i.find(s=>s.element===n)?.count||100}function Bt(e){let r={};return".PHASE0"in e&&(r.ph0=Number.parseFloat(e[".PHASE0"]),r.ph1=Number.parseFloat(e[".PHASE1"])),r}function _e(e){let{ph0:r,ph1:t}=e;return Number.isFinite(r)&&Number.isFinite(t)}import{generateID as 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o)){let{sw:F=1,rfl:N=1,rfp:x=1}=ss(o,["sw","rfl","rfp"]);D(s,"baseFrequency",h-(F/2-N+x)/1e6)}else D(s,"baseFrequency",h)}let{baseFrequency:p,originFrequency:d}=s;D(s,"frequencyOffset",(d-p)*1e6),D(s,"spectralWidth",u&&Number(u[0])/s.baseFrequency);for(let h in s)s[h].length===1&&(s[h]=s[h][0]);return n.tn&&(s.nucleus=n.tn.map(is)),s.dimension=1,s.isFid=!t.status.isSpectrum,{info:s,meta:{...o,...Sr(t),...n}}}function _(e){return e&&(Array.isArray(e)?e[0]:e)}function ss(e,r){let t={};for(let i of r){let n=e[i];n&&typeof n=="number"&&(t[i]=n)}return t}function Sr(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]=Sr(i):r[t]=i}return r}function Nr(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 s=i.relativePath.split("/"),o=s.slice(0,-1).join("/");r[o]||(r[o]={name:s.at(-2),files:[]}),r[o].files.push(i)}}return Object.values(r)}async function Dr(e,r={}){let{keepSource:t,logger:i}=r,n=Nr(e);i&&i.debug(`Found ${Object.keys(n).length} varian experiments`);let s=[],o={spectra:[],molecules:[]};for(let a of n){let{name:m,files:f}=a,c=new as(f),b=br(c).then(u=>{let{info:y,meta:g}=Fr(u),p=u.fid.data[0],d=ls(p.im),h={data:{...p,x:u.x},meta:g,info:{isComplex:d,name:m,...y},display:{name:m}};if(y.isFid&&d){let{im:F}=h.data;cs(F,-1,{output:F})}f&&t&&(h.sourceSelector={files:f.map(F=>F.relativePath)}),o.spectra.push(h)});s.push(b)}let l=await Promise.allSettled(s);for(let a=0;a<l.length;a++){let m=l[a];if(m.status==="rejected"&&m.reason){let f=n[a].name;i?.warn(`Varian data: ${f}, fails with: ${m.reason}`)}}return o.spectra.length>0&&i?.info(`Loaded ${o.spectra.length}  spectra from Varian files`),os(o)}var De=class{id="@zakodium/nmrium-core-plugins#VarianLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(r,t)=>{let{keepSource:i,logger:n}=t??{};return Dr(r,{keepSource:i,logger:n})}};function Ge(){return new De}function us(e,r=[]){return[Xe(e),Ge(),ke(),Ue(),We(),Ve(),Je(),ze(),Ce()].concat(r)}function ps(){let e=new ms;return e.registerPlugins(us(e)),e}import{getOneIfArray as Ar}from"@zakodium/nmrium-core";import{from1DNMRVariables as fs}from"convert-to-jcamp";function Pr(e,r){return e.filters.find(t=>t.name===r)}function ds(e,r={}){let{info:t,meta:i,data:n}=e,{onlyReal:s=!1}=r,{isFid:o,spectralWidth:l}=t,a=Ar(t.baseFrequency||t.originFrequency),{x:m,re:f,im:c}=n,b=new Float64Array(f),u=!s&&c?new Float64Array(c):void 0,y={};te(y,"SW",l),te(y,"BF1",a);let g=Pr(e,"fft")?.enabled,p={originFrequency:t.originFrequency,dataType:!t.isFid||g?"NMR SPECTRUM":"NMR FID",dataClass:!s&&c?"NTUPLES":"XYDATA"};if(o){let F=e.filters.find(N=>N.name==="digitalFilter");if(F&&!g){let{value:{digitalFilterValue:N},enabled:x}=F;if(x){let S=Math.floor(N);b.set(f.slice(f.length-S)),b.set(f.slice(0,f.length-S),S),c&&u&&(u.set(c.slice(c.length-S)),u.set(c.slice(0,c.length-S),S))}}te(p,"decim",t.decim),te(p,"dspfvs",t.dspfvs),te(p,"digitalFilter",t.digitalFilter)}let d={xyEncoding:"DIFDUP",info:{...t,...p},meta:{...i,...y}},h={x:{data:m,label:t.isFid?"TIME":"FREQUENCY",units:t.isFid?"second":"HZ",symbol:"X"},r:{data:b,label:`${t.isFid?"FID":"SPECTRUM"}/REAL`,units:"ARBITRARY UNITS",symbol:"R"}};return u&&(h.i={data:u,label:`${t.isFid?"FID":"SPECTRUM"}/IMAG`,units:"ARBITRARY UNITS",symbol:"I"}),fs(h,d)}function te(e,r,t){t!==void 0&&(e[r]=Ar(t))}export{ne as AutoPostProcessingPlugin,fe as BrukerLoaderPlugin,he as JCAMPDXLoaderPlugin,ye as JEOLLoaderPlugin,be as MolfileLoaderPlugin,Fe as NMReDATALoaderPlugin,Se as SDFLoaderPlugin,Ne as SMILESLoaderPlugin,De as VarianLoaderPlugin,Ce as autoPostProcessing,ke as brukerLoader,ps as default,ps as init,Ue as jcampDXLoader,ze as jeolLoader,We as molfileLoader,Xe as nmreDATALoader,Yt as processJCAMPDX,fr as readSDF,gr as readSMILES,us as recommended,Ve as sdfLoader,Je as smilesLoader,ds as spectrum1DToJCAMPDX,Ge as varianLoader};

package/package.json

@@ -1,83 +1,62 @@
 {
   "name": "@zakodium/nmrium-core-plugins",
-  "version": "0.1.1",
+  "version": "0.1.2",
   "description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
-  "author": "",
+  "author": "Zakodium Sàrl",
   "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"
-    }
-  },
+  "exports": "./dist/nmrium-core-plugins.js",
   "files": [
-    "dist/nmrium-core-plugins.d.ts",
-    "dist/nmrium-core-plugins.cjs",
-    "dist/nmrium-core-plugins.mjs"
+    "dist"
   ],
   "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": "node scripts/esbuild.js && npm run bundle-types",
     "bundle-types": "npm run tsc && npm run api-extractor",
-    "check-types": "tsc --noEmit",
     "clean": "rimraf types dist coverage",
-    "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",
-    "prettier": "prettier --check src",
-    "prettier-write": "prettier --write src",
+    "prepack": "npm run clean && npm run bundle",
     "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",
+    "test": "yarn g:test-only && yarn g:check-types && yarn g:eslint && yarn g:prettier",
     "tsc": "tsc --project tsconfig.types.json"
   },
   "devDependencies": {
-    "@microsoft/api-extractor": "^7.52.1",
+    "@microsoft/api-extractor": "^7.52.7",
     "@types/lodash.merge": "^4.6.9",
-    "@types/node": "^22.13.11",
-    "@vitest/coverage-istanbul": "^3.0.9",
+    "@types/node": "^22.15.16",
+    "@zakodium/bruker-parser": "^0.0.0",
+    "@zakodium/jeol-parser": "^0.0.0",
+    "@zakodium/varian-parser": "^0.0.0",
     "bruker-data-test": "^0.5.4",
-    "esbuild": "^0.25.1",
-    "eslint": "^9.22.0",
-    "eslint-config-cheminfo-typescript": "^18.0.0",
+    "esbuild": "^0.25.4",
     "fifo-logger": "^1.0.0",
     "jcamp-data-test": "^0.8.3",
     "jeol-data-test": "^0.5.2",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "msw": "^2.7.5",
+    "msw": "^2.7.6",
     "nmredata-data-test": "^0.4.0",
-    "prettier": "^3.5.3",
     "rimraf": "^6.0.1",
-    "typescript": "^5.8.2",
-    "vitest": "^3.0.9"
+    "vitest": "^3.1.3"
   },
   "dependencies": {
-    "@zakodium/nmrium-core": "^0.1.0",
-    "brukerconverter": "^8.0.3",
+    "@zakodium/nmrium-core": "^0.1.1",
+    "cheminfo-types": "^1.8.1",
     "convert-to-jcamp": "^5.4.11",
     "filelist-utils": "^1.11.3",
-    "gyromagnetic-ratio": "^1.2.1",
+    "gyromagnetic-ratio": "^2.0.0",
     "is-any-array": "^2.0.1",
     "jcampconverter": "^11.0.1",
-    "jeolconverter": "^1.0.4",
     "linear-sum-assignment": "^1.0.7",
     "lodash.merge": "^4.6.2",
-    "ml-spectra-processing": "^14.11.0",
-    "nmr-processing": "^18.0.1",
+    "ml-spectra-processing": "^14.12.0",
+    "nmr-processing": "^18.0.2",
     "nmredata": "^1.0.0",
-    "openchemlib": "^9.0.1",
-    "openchemlib-utils": "^8.1.0",
-    "sdf-parser": "^7.0.4",
-    "varian-converter": "^2.0.1"
+    "openchemlib": "^9.1.1",
+    "openchemlib-utils": "^8.1.1",
+    "sdf-parser": "^7.0.4"
   },
   "volta": {
     "extends": "../../../package.json"

package/dist/nmrium-core-plugins.cjs

@@ -1,6 +0,0 @@
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e){let a={x:{},y:{},id:Rt(),kind:"signal"},m={id:Rt(),kind:"signal",peaks:[]},u={x:10,y:10};for(let c of yn){let{coupling:g=[],delta:y,diaIDs:d=[]}=l[c];for(let p of g)u[c]+=p.coupling;if(l.activeCoupling){let{activeCoupling:p=[]}=l;for(let f of p)u[c]+=f.coupling}u[c]/=s[c],a[c]={from:y-u[c],to:y+u[c]},m[c]={delta:y,diaIDs:d,originalDelta:y-n[c]}}i.push({...a,signals:[m]})}r.zones.values=i}function At(e){return bn(e.data)}function bn(e){return"rr"in e||!("x"in e)&&"re"in e}async function xt(e,r,t={}){let i={spectra:[],molecules:[]},n=await Nn(e,r,t);if(n.spectra.length>0){let{spectra:o,molecules:s,usedFiles:l}=n;i.spectra.push(...o),i.molecules.push(...s);let a=e.files.length;for(let m=a-1;m>=0;m--){let u=e.files[m].relativePath;!u.match(/acqu.*/s)&&l.includes(u)&&e.files.splice(m,1)}}return i}async function Nn(e,r,t){let i=[],n=await Fn(e),o={spectra:[],molecules:[]};if(n.length===0)return{...o,usedFiles:i};let s=[];for(let a of n){let 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a.value;a.reason&&t?.logger?.error(a.reason)}return{spectra:[],molecules:[],files:[]}}async function Rn(e,r,t={}){let i={entries:[{relativePath:e}]},n={name:v(e||""),xy:!0,noContours:!0,...t},{data:o}=await r.readFromWebSource(i,n);return o}async function Mn(e,r={}){let{converter:t,sourceSelector:i}=r;switch(e.type){case"jcamp":return Q(e.fileCollection.files[0],{name:e?.fileCollection.files[0].name||"",converter:t?.jcamp,selector:i?.jcamp,logger:r.logger,keepSource:r.keepSource});case"brukerFiles":return G(e.fileCollection,{converter:t?.bruker,selector:i});default:throw new Error("There is not a supported source")}}var ne=class{constructor(r){this.core=r;this.onReadProcess={onFiles:this.onReadProcessFiles}}id="@zakodium/nmrium-core-plugins#NMReDATALoaderPlugin";version=1;migrations=[];onReadProcess;onReadProcessFiles=(r,t)=>xt(r,this.core,t)};function Se(e){return new ne(e)}import{parse as An}from"sdf-parser";function 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molecules from the ${e.name} file`),n}var oe=class{id="@zakodium/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 Tt(r,{logger:i})}};function Me(){return new oe}import{formatSpectra as In}from"@zakodium/nmrium-core";import{FileCollection as Tn}from"filelist-utils";import{isAnyArray as En}from"is-any-array";import{xMultiply as Ln}from"ml-spectra-processing";import{convert1D as kn}from"varian-converter";import{normalizeNucleus as Cn}from"nmr-processing";function Et(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;P(o,"numberOfPoints",l&&Number(O(l))/2),P(o,"solvent",O(a)),P(o,"originFrequency",O(m)),P(o,"baseFrequency",O(u)),(Number.isNaN(o.originFrequency)||o.originFrequency===0)&&(o.originFrequency=400,r?.warn("The frequency could not be determined and was set to 400MHz")),P(o,"temperature",O(c)),P(o,"phc0",g&&Number(g[0])),P(s,"rfl",d&&Number(O(d))),P(s,"rfp",p&&Number(O(p))),P(s,"sw",y&&Number(O(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:N=1,rfp:S=1}=On(s,["sw","rfl","rfp"]);P(o,"baseFrequency",h-(b/2-N+S)/1e6)}else P(o,"baseFrequency",h)}let{baseFrequency:f,originFrequency:F}=o;P(o,"frequencyOffset",(F-f)*1e6),P(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(Cn)),o.dimension=1,o.isFid=!t.status.isSpectrum,{info:o,meta:{...s,...Lt(t),...n}}}function O(e){return e&&(Array.isArray(e)?e[0]:e)}function On(e,r){let t={};for(let i of r){let n=e[i];n&&typeof n=="number"&&(t[i]=n)}return t}function Lt(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]=Lt(i):r[t]=i}return r}function kt(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 wt(e,r={}){let{keepSource:t,logger:i}=r,n=kt(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 Tn(u),g=kn(c).then(y=>{let{info:d,meta:p}=Et(y),f=y.fid.data[0],F=En(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="@zakodium/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 Ae(){return new se}function vn(e,r=[]){return[Se(e),Ae(),de(),be(),De(),Re(),Me(),Ne(),ue()].concat(r)}function qn(){let e=new wn;return e.registerPlugins(vn(e)),e}import{getOneIfArray as qt}from"@zakodium/nmrium-core";import{from1DNMRVariables as $n}from"convert-to-jcamp";function vt(e,r){return e.filters.find(t=>t.name===r)}function jn(e,r={}){let{info:t,meta:i,data:n}=e,{onlyReal:o=!1}=r,{isFid:s,spectralWidth:l}=t,a=qt(t.baseFrequency||t.originFrequency),{x:m,re:u,im:c}=n,g=new Float64Array(u),y=!o&&c?new Float64Array(c):void 0,d={};B(d,"SW",l),B(d,"BF1",a);let p=vt(e,"fft")?.enabled,f={originFrequency:t.originFrequency,dataType:!t.isFid||p?"NMR SPECTRUM":"NMR FID",dataClass:!o&&c?"NTUPLES":"XYDATA"};if(s){let b=e.filters.find(N=>N.name==="digitalFilter");if(b&&!p){let{value:{digitalFilterValue:N},enabled:S}=b;if(S){let D=Math.floor(N);g.set(u.slice(u.length-D)),g.set(u.slice(0,u.length-D),D),c&&y&&(y.set(c.slice(c.length-D)),y.set(c.slice(0,c.length-D),D))}}B(f,"decim",t.decim),B(f,"dspfvs",t.dspfvs),B(f,"digitalFilter",t.digitalFilter)}let F={xyEncoding:"DIFDUP",info:{...t,...f},meta:{...i,...d}},h={x:{data:m,label:t.isFid?"TIME":"FREQUENCY",units:t.isFid?"second":"HZ",symbol:"X"},r:{data:g,label:`${t.isFid?"FID":"SPECTRUM"}/REAL`,units:"ARBITRARY UNITS",symbol:"R"}};return y&&(h.i={data:y,label:`${t.isFid?"FID":"SPECTRUM"}/IMAG`,units:"ARBITRARY UNITS",symbol:"I"}),$n(h,F)}function B(e,r,t){t!==void 0&&(e[r]=qt(t))}export{W as AutoPostProcessingPlugin,K as BrukerLoaderPlugin,ee as JCAMPDXLoaderPlugin,te as JEOLLoaderPlugin,re as MolfileLoaderPlugin,ne as NMReDATALoaderPlugin,ie as SDFLoaderPlugin,oe as SMILESLoaderPlugin,se as VarianLoaderPlugin,ue as autoPostProcessing,de as brukerLoader,qn as default,qn as init,be as jcampDXLoader,Ne as jeolLoader,De as molfileLoader,Se as nmreDATALoader,ft as processJCAMPDX,Ct as readSDF,It as readSMILES,vn as recommended,Re as sdfLoader,Me as smilesLoader,jn as spectrum1DToJCAMPDX,Ae as varianLoader};