@zakodium/nmrium-core-plugins 0.0.1 → 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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Vn={};vr(Vn,{BrukerLoaderPlugin:()=>B,JDFLoaderPlugin:()=>J,JcampLoaderPlugin:()=>W,MolfileLoaderPlugin:()=>V,NMReLoaderPlugin:()=>_,SDFLoaderPlugin:()=>H,SmilesLoaderPlugin:()=>X,VarianLoaderPlugin:()=>Y,brukerLoader:()=>ce,default:()=>xr,init:()=>xr,jcampLoader:()=>ue,jdfLoader:()=>fe,molfileLoader:()=>de,nmreLoader:()=>ye,processJcamp:()=>Ee,readSDF:()=>We,readSMILES:()=>Je,recommended:()=>Mr,sdfLoader:()=>Fe,smilesLoader:()=>Ne,spectrum1DToJcamp:()=>Cr,varianLoader:()=>Pe});module.exports=qr(Vn);var Dr=require("@zakodium/nmrium-core");var nt=require("@zakodium/nmrium-core"),se=require("brukerconverter");function Z(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($r(i,n))}return r}function $r(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}}var 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Ke=require("nmr-processing");function T(e,r=","){if(e&&typeof e=="string")return e.split(r)}function te(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=T(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(Ge(r.experiment[0]))),zr(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=Ge(r.experiment[0])),i.map(Ke.normalizeNucleus)}function zr(e){return 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"use strict";var Tr=Object.create;var Z=Object.defineProperty;var Er=Object.getOwnPropertyDescriptor;var Lr=Object.getOwnPropertyNames;var kr=Object.getPrototypeOf,wr=Object.prototype.hasOwnProperty;var vr=(e,r)=>{for(var t in r)Z(e,t,{get:r[t],enumerable:!0})},_e=(e,r,t,i)=>{if(r&&typeof r=="object"||typeof r=="function")for(let n of Lr(r))!wr.call(e,n)&&n!==t&&Z(e,n,{get:()=>r[n],enumerable:!(i=Er(r,n))||i.enumerable});return e};var Se=(e,r,t)=>(t=e!=null?Tr(kr(e)):{},_e(r||!e||!e.__esModule?Z(t,"default",{value:e,enumerable:!0}):t,e)),qr=e=>_e(Z({},"__esModule",{value:!0}),e);var Jn={};vr(Jn,{AutoPostProcessingPlugin:()=>z,BrukerLoaderPlugin:()=>B,JCAMPDXLoaderPlugin:()=>X,JEOLLoaderPlugin:()=>J,MolfileLoaderPlugin:()=>_,NMReDATALoaderPlugin:()=>V,SDFLoaderPlugin:()=>H,SMILESLoaderPlugin:()=>Y,VarianLoaderPlugin:()=>G,autoPostProcessing:()=>te,brukerLoader:()=>ue,default:()=>Ar,init:()=>Ar,jcampDXLoader:()=>de,jeolLoader:()=>ye,molfileLoader:()=>he,nmreDATALoader:()=>Fe,processJCAMPDX:()=>qe,readSDF:()=>We,readSMILES:()=>Xe,recommended:()=>Mr,sdfLoader:()=>Pe,smilesLoader:()=>Ne,spectrum1DToJCAMPDX:()=>Or,varianLoader:()=>De});module.exports=qr(Jn);var Rr=require("@zakodium/nmrium-core");var ee=require("nmr-processing");var Ve=require("@zakodium/nmrium-core");function Q(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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o.length>0&&o!=="undefined"?o:e.dimension?`${e.dimension}d`:""}var Re=require("@zakodium/nmrium-core"),$r=["no","exponential","modifiedGaussian","sine","qsine","trap","user","sinc","qsinc","traf","trafs"];function jr(e){return e in He}function Me(e,r){let{prefix:t="",index:i=0}=r,n=(0,Re.getOneIfArray)(e[`${t}WDW`],i),o=$r[n?Number(n):0],s={};if(!jr(o))return s;let l=He[o];if(l){let{kind:a,parameters:m}=l,u={};for(let c in m){let g=m[c],{source:y,processor:d}=g;if(y){let p=(0,Re.getOneIfArray)(e[`${t}${y}`],i);if(!p)continue;let f=Number(p);u[c]=d?d(f):f}else g.value!==void 0&&(u[c]=g.value)}s[a]={apply:!0,options:u}}return s}var 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Qe=require("nmr-processing"),xe=["digitalFilter","backwardLinearPrediction","forwardLinearPrediction","apodization","zeroFilling","fft",["shiftX","phaseCorrection","baselineCorrection"]],k={};for(let e=0;e<xe.length;e++){let r=xe[e];for(let t of Array.isArray(r)?r:[r])k[t]=e}for(let e of Object.values(Qe.Filters1D))e.name in k||(k[e.name]=xe.length);var et=require("nmr-processing"),Ce=["digitalFilter2D","blpDimension1","flpDimension1","apodizationDimension1","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","nusDimension2","apodizationDimension2","zeroFillingDimension2","fftDimension2","phaseCorrectionTwoDimensions",["shift2DX","shift2DY","symmetrizeCosyLike"]],w={};for(let e=0;e<Ce.length;e++){let r=Ce[e];for(let t of Array.isArray(r)?r:[r])w[t]=e}for(let e of Object.values(et.Filters2D))e.name in w||(w[e.name]=Ce.length);var Ur=new Set(["backwardLinearPrediction","forwardLinearPrediction","digitalFilter2D","phaseCorrectionTwoDimensions","blpDimension1","flpDimension1","apodizationDimension1","apodizationDimension2","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","zeroFillingDimension2","fftDimension2","nusDimension2","symmetrizeCosyLike"]);function Wr(e,r){let{filter:t,experimentalFeatures:i=!1}=r,{name:n}=t;({...ee.Filters1D,...ee.Filters2D})[n]&&(e.some(s=>s.name===n)||(i||!Ur.has(n))&&e.push({...t,enabled:!0}))}function tt(e,r={}){let{data:t}=e;if(!t)return e;let{autoProcessing:i,experimentalFeatures:n}=r,o=(l,a)=>Wr(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:Xr(m)}}),c.sort((F,h)=>k[F.name]-k[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 N=Ze(u,{experiment:F});o(c,{filter:{name:"apodizationDimension1",value:N.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:N.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((S,D)=>w[S.name]-w[D.name])}}}}function Xr(e){let{phc0:r=0,phc1:t=0}=e;return rt([r,t])?{}:{ph0:r,ph1:t}}function rt(e){return Array.isArray(e)?e.every(r=>!r&&r===0):rt([e])}var z=class{id="@zakodium/nmrium-core-plugins#AutoPostProcessingPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onProcessing:this.onPostProcessing.bind(this)}}onPostProcessing(r,t){tt(r,t)}};function te(){return new z}var pt=require("@zakodium/nmrium-core"),me=require("brukerconverter");function re(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(Jr(i,n))}return r}function Jr(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}}var Oe=require("is-any-array");function I(e){if(_r(e))return Vr(e)?e.map(nt):nt(e);if(typeof e=="object"&&e!==null){let r={};for(let t in e)r[t]=I(e[t]);return r}return e}function _r(e){return(0,Oe.isAnyArray)(e)}function nt(e){return Float64Array.from(e)}function Vr(e){return(0,Oe.isAnyArray)(e[0])}var v=require("@zakodium/nmrium-core"),mt=require("gyromagnetic-ratio"),ae=require("is-any-array"),lt=require("nmr-processing");var T=require("is-any-array");function ne(e){return typeof e=="number"}function ie(e){let{phc0:r,phc1:t}=e;return!(0,T.isAnyArray)(r)&&!ne(r)||!(0,T.isAnyArray)(t)&&!ne(t)||(0,T.isAnyArray)(r)&&!ne(r[0])||(0,T.isAnyArray)(t)&&!ne(t[0])?{}:((0,T.isAnyArray)(t)?t[0]*=-1:t*=-1,(0,T.isAnyArray)(r)?r[0]*=-1:r*=-1,{phc0:r,phc1:t})}function ot(e,r,t){if(e>0)return Number(e);if(r>14||r===0)return 0;if(it[r]){let i=it[r];if(!i[t])throw new Error(`decim ${t} not in lookup table for dspfvs ${r}`);return i[t]}else throw new Error(`dspfvs ${r} not in lookup table`)}var it={10:{2:44.75,3:33.5,4:66.625,6:59.08333333333333,8:68.5625,12:60.375,16:69.53125,24:61.02083333333333,32:70.015625,48:61.34375,64:70.2578125,96:61.50520833333333,128:70.37890625,192:61.5859375,256:70.439453125,384:61.62630208333333,512:70.4697265625,768:61.646484375,1024:70.48486328125,1536:61.65657552083333,2048:70.492431640625},11:{2:46,3:36.5,4:48,6:50.16666666666667,8:53.25,12:69.5,16:72.25,24:70.16666666666667,32:72.75,48:70.5,64:73,96:70.66666666666667,128:72.5,192:71.33333333333333,256:72.25,384:71.66666666666667,512:72.125,768:71.83333333333333,1024:72.0625,1536:71.91666666666667,2048:72.03125},12:{2:46,3:36.5,4:48,6:50.16666666666667,8:53.25,12:69.5,16:71.625,24:70.16666666666667,32:72.125,48:70.5,64:72.375,96:70.66666666666666,128:72.5,192:71.333333333,256:72.25,384:71.66666666666667,512:72.125,768:71.83333333333333,1024:72.0625,1536:71.91666666666667,2048:72.03125},13:{2:2.75,3:2.833333333333333,4:2.875,6:2.916666666666667,8:2.9375,12:2.958333333333333,16:2.96875,24:2.979166666666667,32:2.984375,48:2.989583333333333,64:2.9921875,96:2.994791666666667}};var at=require("nmr-processing");function E(e,r=","){if(e&&typeof e=="string")return e.split(r)}function oe(e,r,t){let i=[];if(e[`${t}AXNUC`]&&(i=e[`${t}AXNUC`],Array.isArray(i)||(i=[i]),i=C(i)),i.length===0&&e[`${t}NUC1`]&&(i=e[`${t}NUC1`],Array.isArray(i)||(i=[i]),i=C(i)),i.length===0&&e[".NUCLEUS"]){let n=E(e[".NUCLEUS"]);if(e[`${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=C([n[s],n[l]]):i=C(n).reverse()}else i=C(n)}return i.length===0&&e[".OBSERVENUCLEUS"]&&(i=C([e[".OBSERVENUCLEUS"]])),i.length===0&&r.experiment&&(i=C(st(r.experiment[0]))),Hr(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=st(r.experiment[0])),i.map(at.normalizeNucleus)}function Hr(e){return e["2D_X_NUCLEUS"]&&!e["2D_X_NUCLEUS"].includes("off")&&e["2D_Y_NUCLEUS"]&&!e["2D_Y_NUCLEUS"].includes("off")}function st(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 C(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:[]}function P(e,r,t,i=!1){t===void 0||r in e&&!i||(Array.isArray(t)?e[r]=t.map(ct):e[r]=[ct(t)])}function ct(e){return typeof e=="string"&&(e.startsWith("<")&&e.endsWith(">")&&(e=e.slice(1,-1)),e=e.replace(/\$.*/,"").trim()),e}function ce(e,r={}){let{prefix:t="",logger:i}=r,n={dimension:0,nucleus:[],isFid:!1,isFt:!1},o=JSON.stringify(e),s=/\r\n/.exec(o)?`\r
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2
2
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`:`
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3
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-
`,{JCAMPDX:l="",ORIGIN:a=""}=e,m=String(l).toLowerCase()+String(a).toLowerCase();"SPECTROMETER/DATASYSTEM"in e&&(m=e["SPECTROMETER/DATASYSTEM"]);let u=(d=[])=>{for(let p of d)if(!(p in n))return!1;return!0};(m.includes("mestre")||m.includes("nova"))&&(m="mnova"),n.creator=m,e.LONGDATE&&
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4
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-
`}=t;
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5
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-
because it didn't match the import filters`);continue}s.push(u)}let l=[],a=s.some(at),m=s.some(st);for(let u of s){if(o!=="both"&&u.dataType!=="LINK"){if(at(u)&&(o==="ft"||o==="preferFT"&&m)){i?.warn(`Skipping raw data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(st(u)&&(o==="fid"||o==="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(u)}return l}function st(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function at(e){return e.dataType?.toUpperCase().includes("FID")}function mt(e,r={}){let{logger:t,name:i=""}=r;for(let n of e){if(n.dataType==="LINK"&&mt(n.children,r))return!0;let{dataType:o=""}=n,s=o.toLowerCase();if(s.length>0){if(s.includes("spectrum")&&!s.includes("nmr"))return t?.warn(`File ${i} was ignored because it is a ${o}`),!1;if(s.includes("nmr"))return!0}}return!1}var Ae=require("@zakodium/nmrium-core"),yt=require("jcampconverter"),Qr=Se(require("openchemlib/full"),1);var lt=require("nmr-processing"),ut=require("openchemlib/full");async function pt(e,r={}){let t=await e.text(),i=w(t),n={molecules:i,spectra:[]};return i.length===0&&r.logger?.debug(`${e.name} is an empty molfile`),n}function w(e){let r=[];if(!(0,lt.isMolfileNotEmpty)(e))return[];let i=ut.Molecule.fromMolfile(e).toMolfile();return r.push({molfile:i}),r}var ft=require("nmr-processing"),Zr=Se(require("openchemlib/full"),1),dt=require("openchemlib-utils");var Kr=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function me(e){let{dataType:r="",dataClass:t=""}=e,i=r.replaceAll(/\s/g,"").toLowerCase(),n=t.replaceAll(/\s/g,"").toLowerCase();return Kr.has(i)&&n!=="peaktable"}function gt(e,r,t={}){let{spectra:i,info:n,meta:o}=e,s=i[0].data,l=[],a={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:m,name:u,spectraData:c}=t,{CROSSREFERENCE:g}=n,y=typeof 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h=[];for(let b of f){if(b.js.every(P=>P===b.js[0])){h.push(b);continue}if(b.multiplicity!==b.js.length+1){h.push(b);continue}for(let P=0;P<b.multiplicity-1;P++)h.push({value:"d",multiplicity:2,js:[b.js[P]]})}h.sort((b,P)=>P.js[0]-b.js[0]),y.js=h.map(b=>({coupling:b.js[0],multiplicity:b.value}))}typeof o.assignment=="string"&&(y.assignment=ln(o.assignment)),typeof o.multiplicity=="string"&&(y.multiplicity=o.multiplicity),n.multiplets.push(y)}return n}function cn(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 mn={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function ln(e){return e.replaceAll(/&(\w+);/gi,(r,t)=>mn[t.toLowerCase()]||r)}function Rt(e){let r=e.split(/\r?\n/).filter(i=>i.trim()!==""),t=[];for(let i of r)if(i.startsWith("(")){let[n,o,s]=z(i).map(Number.parseFloat);t.push({id:n,x:o,y:s})}return t}function Dt(e,r={}){let t={};if(!e["OBSERVED 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Ce=require("@zakodium/nmrium-core");function At(e,r,t){for(let i=0;i<e.length;i++){if(r.includes(i))continue;let{delta:n,multiplicity:o="",diaIDs:s}=e[i],l=Number(n)-.01,a=Number(n)+.01;t.push({from:l,to:a,integration:1,id:(0,Ce.generateID)(),signals:[{id:(0,Ce.generateID)(),delta:n,multiplicity:o,diaIDs:s}]})}}var Ot=require("linear-sum-assignment"),Ct=require("ml-spectra-processing");function It(e,r){let t=e.map(s=>s.delta),i=r.map(s=>s.delta),n=(0,Ct.xCostMatrix)(i,t,{fct:(s,l)=>Math.abs(s-l)}),{rowAssignments:o}=(0,Ot.linearSumAssignment)(n,{maximaze:!1});return Array.from(o)}function Et(e,r){let{assignments:t,ranges:i}=r;t?.sort((s,l)=>l.delta-s.delta);let n=[],o=[];for(let s of i){let l=0,{from:a,to:m}=s,u=[];for(let c=l;c<t.length;c++){let{delta:g}=t[c];g<=m&&g>=a?(u.push(t[c]),o.push(c)):g>m&&(l=c)}if(u.length>0){let c=s.signals,g=[],y=u.length>1&&c.length>1?It(c,u):[0];for(let d=0;d<u.length;d++){let 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hn(e,r){let{ph0:t,ph1:i}=r,{re:n,im:o}=(0,U.reimPhaseCorrection)({re:e.spectra[0].data.y,im:e.spectra[1].data.y},t*Math.PI/180,i*Math.PI/180);return{re:n,im:o}}function wt(e,r,t){let{logger:i}=t,n=[];for(let o of e)if(o.spectra&&o.spectra.length>0||o.minMax){bn(o);let s={...o.info,...o.meta},l=oe(s,{logger:i});if(l.experiment==="wobble_curve")continue;n.push(Lt(o,s,l,r,t))}return n}function bn(e){let r=e.meta["BRUKER FILE EXP"];if(!r)return;let i=(Array.isArray(r)?r:[r]).find(o=>o.slice(0,10).includes("vdlist"));if(!i)return;let n=i.split(`
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6
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3
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4
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+
`}=t;P(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=C(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 Zr(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=ie({phc0:a,phc1:m});e={...e,...u}}}var Qr={keepRecordsRegExp:/.*/,keepFiles:!0};async function le(e,r={}){let t={spectra:[],molecules:[]},{converter:i={},selector:n={},logger:o}=r,s=(0,me.groupByExperiments)(e,{logger:o,...tn(n)}),l=[];for(let m of s)l.push((0,me.convertOneExperiment)(m,{...Qr,...i}).then(u=>en(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=ie(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`),(0,pt.formatSpectra)(t)}function en(e,r={}){let{keepSource:t=!1,logger:i}=r,n={...e.info,...e.meta},o=ce(n,{logger:i}),s={},{isFid:l}=o;if(rn(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=re(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)}),nn(g,e),g}function tn(e){let{general:r={},bruker:t={}}=e,{processingNumbers:i,experimentNumbers:n,...o}=t;return{...r,...o,processingNumbers:ut(i),experimentNumbers:ut(n)}}function ut(e){if(e)return e.split(/[^\d]+/).filter(Boolean).map(r=>Number.parseInt(r,10))}function rn(e){let{info:r}=e;return r.twoD}function nn(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 B=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:o,logger:s}=t??{};return le(r,{converter:n?.bruker,selector:i,keepSource:o,logger:s})}};function ue(){return new B}var Jt=require("@zakodium/nmrium-core"),_t=require("jcampconverter");function ft(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}var dt=require("jcampconverter");function Te(e,r,t){let{dataType:i,children:n}=e,o=i==="LINK"&&n?n:[e];for(let s of o){if(s.dataType==="LINK"){Te(s,r,t);continue}let l=(0,dt.convert)(s.jcamp,t);r.push(...l.flatten)}}function ht(e,r={}){let t=[],i=bt(e,r);for(let s of i?e:[])s.dataType==="LINK"?s.children=Ee(s.children,r):s=Ee([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 Ee(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=Ee(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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5
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+
because it didn't match the import filters`);continue}s.push(u)}let l=[],a=s.some(yt),m=s.some(gt);for(let u of s){if(o!=="both"&&u.dataType!=="LINK"){if(yt(u)&&(o==="ft"||o==="preferFT"&&m)){i?.warn(`Skipping raw data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(gt(u)&&(o==="fid"||o==="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(u)}return l}function gt(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function yt(e){return e.dataType?.toUpperCase().includes("FID")}function bt(e,r={}){let{logger:t,name:i=""}=r;for(let n of e){if(n.dataType==="LINK"&&bt(n.children,r))return!0;let{dataType:o=""}=n,s=o.toLowerCase();if(s.length>0){if(s.includes("spectrum")&&!s.includes("nmr"))return t?.warn(`File ${i} was ignored because it is a ${o}`),!1;if(s.includes("nmr"))return!0}}return!1}var Le=require("@zakodium/nmrium-core"),Mt=require("jcampconverter"),an=Se(require("openchemlib"),1);var Ft=require("nmr-processing"),Pt=require("openchemlib");async function Nt(e,r={}){let t=await e.text(),i=q(t),n={molecules:i,spectra:[]};return i.length===0&&r.logger?.debug(`${e.name} is an empty molfile`),n}function q(e){let r=[];if(!(0,Ft.isMolfileNotEmpty)(e))return[];let i=Pt.Molecule.fromMolfile(e).toMolfile();return r.push({molfile:i}),r}var Dt=require("nmr-processing"),sn=Se(require("openchemlib"),1),St=require("openchemlib-utils");var on=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function pe(e){let{dataType:r="",dataClass:t=""}=e,i=r.replaceAll(/\s/g,"").toLowerCase(),n=t.replaceAll(/\s/g,"").toLowerCase();return on.has(i)&&n!=="peaktable"}function Rt(e,r,t={}){let{spectra:i,info:n,meta:o}=e,s=i[0].data,l=[],a={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:m,name:u,spectraData:c}=t,{CROSSREFERENCE:g}=n,y=typeof 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e){let{meta:o,dataClass:s="",dataType:l="",info:a}=n,m=Number.parseInt(String(a.BLOCKID),10);o.MOLFILE?un(String(o.MOLFILE),r,m):n.jcampCS&&ln(n,r,m),cn(s,l)&&mn(r,n,e,i),pe(n)&&t.push(n)}}function cn(e,r){return e?.toLowerCase().includes("assignments")&&r?.toLowerCase().includes("assignments")}function mn(e,r,t,i){let n=Rt(r,t,{spectraData:e,logger:i.logger,name:i.name});if(e.assignmentsByBlocks||(e.assignmentsByBlocks={}),n){let{spectraBlockIDs:o}=n;for(let s of o)e.assignmentsByBlocks[s]=n}}function ln(e,r,t){r.molecules||(r.molecules=[]);let i=(0,Mt.parseJcampCS)(e,{OCL:an}),n=q(i?.molfile||"");n.length>0&&r.molecules.push({id:(0,Le.generateID)(),blockId:t,...n[0]})}function un(e,r,t){r.molecules||(r.molecules=[]);let i=q(String(e));r.molecules.push({id:(0,Le.generateID)(),blockId:t,...i[0]})}var ve=require("@zakodium/nmrium-core"),W=require("ml-spectra-processing"),Bt=require("nmr-processing");function $(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function j(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}var It=require("nmr-processing");var Ct=require("ml-spectra-processing");function U(e){return e.trim().slice(1,-1).split(/,\s*/).map(r=>r.trim())}var pn={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},xt=["I","X","Y","Hs","An","H","C","N","(J)"];function Ot(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=U(i)}return r.comments=t.filter(i=>i.startsWith("$$")).map(i=>i.replace(/^\$\$\s*/,"")),r.headersFromComments=dn(r.comments),r.data=t.filter(i=>!i.startsWith("$$")).map(U),r.multiplets=fn(r),r}function fn(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: ${i.join(",")}`),i.length===0)return t?.warn("Parsing JCAMP-DX assignment: No string columns found. 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h=[];for(let b of f){if(b.js.every(N=>N===b.js[0])){h.push(b);continue}if(b.multiplicity!==b.js.length+1){h.push(b);continue}for(let N=0;N<b.multiplicity-1;N++)h.push({value:"d",multiplicity:2,js:[b.js[N]]})}h.sort((b,N)=>N.js[0]-b.js[0]),y.js=h.map(b=>({coupling:b.js[0],multiplicity:b.value}))}typeof o.assignment=="string"&&(y.assignment=hn(o.assignment)),typeof o.multiplicity=="string"&&(y.multiplicity=o.multiplicity),n.multiplets.push(y)}return n}function gn(e){let r={};for(let t in e){let i=e[t],n=typeof i=="number"?i:Number.parseFloat(i);Number.isNaN(n)||(r[t]=n)}return r}var yn={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function hn(e){return e.replaceAll(/&(\w+);/gi,(r,t)=>yn[t.toLowerCase()]||r)}function Et(e){let r=e.split(/\r?\n/).filter(i=>i.trim()!==""),t=[];for(let i of r)if(i.startsWith("(")){let[n,o,s]=U(i).map(Number.parseFloat);t.push({id:n,x:o,y:s})}return t}function Lt(e,r={}){let t={};if(!e["OBSERVED 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we=require("@zakodium/nmrium-core");function vt(e,r,t){for(let i=0;i<e.length;i++){if(r.includes(i))continue;let{delta:n,multiplicity:o="",diaIDs:s}=e[i],l=Number(n)-.01,a=Number(n)+.01;t.push({from:l,to:a,integration:1,id:(0,we.generateID)(),signals:[{id:(0,we.generateID)(),delta:n,multiplicity:o,diaIDs:s}]})}}var qt=require("linear-sum-assignment"),$t=require("ml-spectra-processing");function jt(e,r){let t=e.map(s=>s.delta),i=r.map(s=>s.delta),n=(0,$t.xCostMatrix)(i,t,{fct:(s,l)=>Math.abs(s-l)}),{rowAssignments:o}=(0,qt.linearSumAssignment)(n,{maximaze:!1});return Array.from(o)}function zt(e,r){let{assignments:t,ranges:i}=r;t?.sort((s,l)=>l.delta-s.delta);let n=[],o=[];for(let s of i){let l=0,{from:a,to:m}=s,u=[];for(let c=l;c<t.length;c++){let{delta:g}=t[c];g<=m&&g>=a?(u.push(t[c]),o.push(c)):g>m&&(l=c)}if(u.length>0){let c=s.signals,g=[],y=u.length>1&&c.length>1?jt(c,u):[0];for(let d=0;d<u.length;d++){let p=y[d],{delta:f,multiplicity:F,diaIDs:h}=u[d];p>-1?g.push({...c[p],diaIDs:h}):g.push({delta:f,multiplicity:F,diaIDs:h})}s.signals=g,n.push(s)}}vt(t,o,n),n.sort((s,l)=>s.from-l.from),e.ranges={values:j(n).map(s=>{let{integration:l,...a}=s;return a}),options:{sum:r.integrationSum,isSumConstant:!0,sumAuto:!0}},e.ranges.options.moleculeId=String(r.moleculeId)}function Ut(e,r,t,i,n){let{logger:o}=n,s={components:Wt(e)?Pn(e,t.isFid):Fn(e)},{name:l=t.title||`jcamp_${(0,ve.generateID)()}`}=n,a={dependentVariables:[s],meta:r,info:{...t,name:$(l)}};return bn(e)&&Nn(a,i,r,e,t,{logger:o}),a}function Wt(e){return"minMax"in e}function bn(e){return!Wt(e)}function Fn(e){return e.spectra.map(r=>{let t=I(r.data);return{...r,data:t}})}function Pn(e,r){let t={...e.minMax,z:I(e.minMax?.z)};return r?Dn(t):{rr:t}}function Nn(e,r,t,i,n,o){let{assignmentsByBlocks:s}=r,l=wt(t);ke(l)&&Sn(e,l);let a=String(i.info.BLOCKID);if(s?.[a]){let{molecule:m,assignments:u,moleculeBlockID:c}=s[a],g=kt(m,n),y=I(i.spectra[0].data);if(y.x[0]>y.x[1])for(let F of i.spectra)F.data.x.reverse(),F.data.y.reverse();if(ke(l)&&i.spectra.length>1){let{re:F}=Rn(i,l);y.y=F}let{x:d,y:p}=y,f=Lt(t,o)??(0,Bt.xyAutoRangesPicking)({x:d,y:p},{peakPicking:{frequency:n.originFrequency},ranges:{frequency:n.originFrequency,integrationSum:g}});zt(e,{moleculeId:c,ranges:f,assignments:u,integrationSum:g})}}function Dn(e){let{z:r,...t}=e,i=[],n=[];for(let l=0;l<r.length;l+=2)i.push(r[l].slice()),n.push(r[l+1].slice());let o=(0,W.matrixMinMaxZ)(i),s=(0,W.matrixMinMaxZ)(n);return{re:{...t,z:i,minZ:o.min,maxZ:o.max},im:{...t,z:n,minZ:s.min,maxZ:s.max}}}function Sn(e,r){let{ph0:t,ph1:i}=r;e.filters||(e.filters=[]),e.filters.push({id:(0,ve.generateID)(),name:"phaseCorrection",value:{ph0:t,ph1:i,absolute:!1},enabled:!0})}function Rn(e,r){let{ph0:t,ph1:i}=r,{re:n,im:o}=(0,W.reimPhaseCorrection)({re:e.spectra[0].data.y,im:e.spectra[1].data.y},t*Math.PI/180,i*Math.PI/180);return{re:n,im:o}}function Xt(e,r,t){let{logger:i}=t,n=[];for(let o of e)if(o.spectra&&o.spectra.length>0||o.minMax){Mn(o);let s={...o.info,...o.meta},l=ce(s,{logger:i});if(l.experiment==="wobble_curve")continue;n.push(Ut(o,s,l,r,t))}return n}function Mn(e){let r=e.meta["BRUKER FILE EXP"];if(!r)return;let i=(Array.isArray(r)?r:[r]).find(o=>o.slice(0,10).includes("vdlist"));if(!i)return;let n=i.split(`
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6
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Mr(e,r=[]){return[Fe(e),De(),ue(),de(),he(),Pe(),Ne(),ye(),te()].concat(r)}function Ar(){let e=new Rr.NMRiumCore;return e.registerPlugins(Mr(e)),e}var Je=require("@zakodium/nmrium-core"),Cr=require("convert-to-jcamp");function xr(e,r){return e.filters.find(t=>t.name===r)}function Or(e,r={}){let{info:t,meta:i,data:n}=e,{onlyReal:o=!1}=r,{isFid:s,spectralWidth:l}=t,a=(0,Je.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={};K(d,"SW",l),K(d,"BF1",a);let p=xr(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 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1
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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 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,o=(Jt(r[`${n}SPECTYP`])||"").replace(/^<(.*)>$/,"$1").toLowerCase();return o.length>0&&o!=="undefined"?o:e.dimension?`${e.dimension}d`:""}function N(e,r,t,i=!1){t===void 0||r in e&&!i||(Array.isArray(t)?e[r]=t.map(Te):e[r]=[Te(t)])}function Te(e){return typeof e=="string"&&(e.startsWith("<")&&e.endsWith(">")&&(e=e.slice(1,-1)),e=e.replace(/\$.*/,"").trim()),e}function X(e,r={}){let{prefix:t="",logger:i}=r,n={dimension:0,nucleus:[],isFid:!1,isFt:!1},o=JSON.stringify(e),s=/\r\n/.exec(o)?`\r
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import{NMRiumCore as wn}from"@zakodium/nmrium-core";import{Filters1D as _t,Filters2D as Vt}from"nmr-processing";import{getOneIfArray as jt}from"@zakodium/nmrium-core";function U(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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k}from"is-any-array";function J(e){return typeof e=="number"}function _(e){let{phc0:r,phc1:t}=e;return!k(r)&&!J(r)||!k(t)&&!J(t)||k(r)&&!J(r[0])||k(t)&&!J(t[0])?{}:(k(t)?t[0]*=-1:t*=-1,k(r)?r[0]*=-1:r*=-1,{phc0:r,phc1:t})}function $e(e,r,t){if(e>0)return Number(e);if(r>14||r===0)return 0;if(qe[r]){let i=qe[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 qe={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 er}from"nmr-processing";function T(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=C(i)),i.length===0&&e[`${t}NUC1`]&&(i=e[`${t}NUC1`],Array.isArray(i)||(i=[i]),i=C(i)),i.length===0&&e[".NUCLEUS"]){let n=T(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=C([n[s],n[l]]):i=C(n).reverse()}else i=C(n)}return i.length===0&&e[".OBSERVENUCLEUS"]&&(i=C([e[".OBSERVENUCLEUS"]])),i.length===0&&r.experiment&&(i=C(je(r.experiment[0]))),tr(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=je(r.experiment[0])),i.map(er)}function tr(e){return e["2D_X_NUCLEUS"]&&!e["2D_X_NUCLEUS"].includes("off")&&e["2D_Y_NUCLEUS"]&&!e["2D_Y_NUCLEUS"].includes("off")}function je(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 C(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:[]}function P(e,r,t,i=!1){t===void 0||r in e&&!i||(Array.isArray(t)?e[r]=t.map(ze):e[r]=[ze(t)])}function ze(e){return typeof e=="string"&&(e.startsWith("<")&&e.endsWith(">")&&(e=e.slice(1,-1)),e=e.replace(/\$.*/,"").trim()),e}function Y(e,r={}){let{prefix:t="",logger:i}=r,n={dimension:0,nucleus:[],isFid:!1,isFt:!1},o=JSON.stringify(e),s=/\r\n/.exec(o)?`\r
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2
2
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`:`
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3
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-
`,{JCAMPDX:l="",ORIGIN:a=""}=e,m=String(l).toLowerCase()+String(a).toLowerCase();"SPECTROMETER/DATASYSTEM"in e&&(m=e["SPECTROMETER/DATASYSTEM"]);let u=(d=[])=>{for(let p of d)if(!(p in n))return!1;return!0};(m.includes("mestre")||m.includes("nova"))&&(m="mnova"),n.creator=m,e.LONGDATE&&
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4
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-
`}=t;
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5
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-
because it didn't match the import filters`);continue}s.push(u)}let l=[],a=s.some(ve),m=s.some(we);for(let u of s){if(o!=="both"&&u.dataType!=="LINK"){if(ve(u)&&(o==="ft"||o==="preferFT"&&m)){i?.warn(`Skipping raw data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(we(u)&&(o==="fid"||o==="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(u)}return l}function we(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function ve(e){return e.dataType?.toUpperCase().includes("FID")}function $e(e,r={}){let{logger:t,name:i=""}=r;for(let n of e){if(n.dataType==="LINK"&&$e(n.children,r))return!0;let{dataType:o=""}=n,s=o.toLowerCase();if(s.length>0){if(s.includes("spectrum")&&!s.includes("nmr"))return t?.warn(`File ${i} was ignored because it is a ${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 Be(e,r,t={}){let{spectra:i,info:n,meta:o}=e,s=i[0].data,l=[],a={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:m,name:u,spectraData:c}=t,{CROSSREFERENCE:g}=n,y=typeof g!="string"?g:g.split(/\r?\n/).map(S=>S.trim()).filter(Boolean),d=y.find(S=>S?.toLowerCase().includes("structure"));if(d===void 0)return m&&m.warn(`There is not a structure reference for ${u} file, assignment object could not be completed`),null;let p=Number.parseInt(d?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(p)||p<1)return m&&m.warn(`Structure block_id not found for ${u} file, assignment object could not be completed`),null;let F=c?.molecules?.find(S=>S.blockId===p)?.molfile??"";if(F===""){let S=r.find(x=>x.info.BLOCKID===p),{MOLFILE:D=""}=S?.meta||{};F=D}if(!mr(F))return m&&m.warn(`Empty molfile for ${u} file with structure block_id = ${p}, assignment object could not be completed`),null;let 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} file`))}return{moleculeBlockID:p,spectraBlockIDs:R,assignments:Object.values(P),molecule:h.molecule}}function Ue(e,r,t,i){for(let n of e){let{meta:o,dataClass:s="",dataType:l="",info:a}=n,m=Number.parseInt(String(a.BLOCKID),10);o.MOLFILE?hr(String(o.MOLFILE),r,m):n.jcampCS&&yr(n,r,m),dr(s,l)&&gr(r,n,e,i),K(n)&&t.push(n)}}function dr(e,r){return e?.toLowerCase().includes("assignments")&&r?.toLowerCase().includes("assignments")}function gr(e,r,t,i){let n=Be(r,t,{spectraData:e,logger:i.logger,name:i.name});if(e.assignmentsByBlocks||(e.assignmentsByBlocks={}),n){let{spectraBlockIDs:o}=n;for(let s of o)e.assignmentsByBlocks[s]=n}}function yr(e,r,t){r.molecules||(r.molecules=[]);let i=pr(e,{OCL:fr}),n=L(i?.molfile||"");n.length>0&&r.molecules.push({id:ze(),blockId:t,...n[0]})}function hr(e,r,t){r.molecules||(r.molecules=[]);let i=L(String(e));r.molecules.push({id:ze(),blockId:t,...i[0]})}import{generateID as tt}from"@zakodium/nmrium-core";import{matrixMinMaxZ as et,reimPhaseCorrection as Or}from"ml-spectra-processing";import{xyAutoRangesPicking as Cr}from"nmr-processing";function k(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function w(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 Sr}from"nmr-processing";import{xMaxValue as br}from"ml-spectra-processing";function B(e){return e.trim().slice(1,-1).split(/,\s*/).map(r=>r.trim())}var Fr={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},We=["I","X","Y","Hs","An","H","C","N","(J)"];function Je(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=B(i)}return r.comments=t.filter(i=>i.startsWith("$$")).map(i=>i.replace(/^\$\$\s*/,"")),r.headersFromComments=Pr(r.comments),r.data=t.filter(i=>!i.startsWith("$$")).map(B),r.multiplets=Nr(r),r}function Nr(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: ${i.join(",")}`),i.length===0)return t?.warn("Parsing JCAMP-DX assignment: No string columns found. Skipping parsing of assignment."),[];let n=i[0],o;if(e.headersFromParenthesis.length>0&&e.headersFromParenthesis[n]==="C")o=e.headersFromParenthesis;else if(e.headersFromComments.length>0&&e.headersFromComments[n]==="C")o=e.headersFromComments;else if(We[n]==="C")o=We;else return t?.warn("No header found for multiplicity. Skipping parsing of assignment."),[];return br(e.data.map(a=>a.length))>o.length&&t?.warn("Some assignments are containing more values than headers"),e.data.map(a=>{let m={};for(let u=0;u<o.length;u++){let c=o[u];m[Fr[c]||c]=a[u]}return m})}function Pr(e){return e.map(r=>r.split(":")[0].trim()).filter(r=>r.length>0)}function Ve(e,r={}){let{logger:t}=r,i=Je(e),n={multiplets:[],comments:i.comments};for(let o of i.multiplets){let{id:s,from:l,to:a,delta:m,integration:u,nbAtoms:c,multiplicity:g}=o,y={id:s,js:[],multiplicity:"",...Rr({from:l,to:a,delta:m,integration:u,nbAtoms:c})};if(typeof o.js=="string"){let d=o.js.split(/\s+/).map(Number.parseFloat),p=0,f=Sr(g).map(b=>{let P=(b?.multiplicity||1)-1;return p+=P,{value:b.value,multiplicity:b?.multiplicity,js:d.slice(p-P,p)}}),F=f.reduce((b,P)=>b+(P.multiplicity?P.multiplicity-1:0),0);d.length!==F&&t?.warn(`The number of j values (${d.length}) is not equal to the sum of the multiplicities - 1 (${F})`);let h=[];for(let b of f){if(b.js.every(P=>P===b.js[0])){h.push(b);continue}if(b.multiplicity!==b.js.length+1){h.push(b);continue}for(let P=0;P<b.multiplicity-1;P++)h.push({value:"d",multiplicity:2,js:[b.js[P]]})}h.sort((b,P)=>P.js[0]-b.js[0]),y.js=h.map(b=>({coupling:b.js[0],multiplicity:b.value}))}typeof o.assignment=="string"&&(y.assignment=Mr(o.assignment)),typeof o.multiplicity=="string"&&(y.multiplicity=o.multiplicity),n.multiplets.push(y)}return n}function Rr(e){let r={};for(let t in e){let i=e[t],n=typeof i=="number"?i:Number.parseFloat(i);Number.isNaN(n)||(r[t]=n)}return r}var Dr={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function Mr(e){return e.replaceAll(/&(\w+);/gi,(r,t)=>Dr[t.toLowerCase()]||r)}function _e(e){let r=e.split(/\r?\n/).filter(i=>i.trim()!==""),t=[];for(let i of r)if(i.startsWith("(")){let[n,o,s]=B(i).map(Number.parseFloat);t.push({id:n,x:o,y:s})}return t}function He(e,r={}){let t={};if(!e["OBSERVED MULTIPLETS"])return[];let i=Ve(e["OBSERVED MULTIPLETS"],r);if(!i)return[];let{multiplets:n}=i;for(let o of n){let{id:s,from:l,to:a,integration:m=0,...u}=o;t[s]={from:l,to:a,integration:m,signals:[{id:s,...u}]}}if(e["OBSERVED MULTIPLETS PEAKS"]){let o=_e(e["OBSERVED MULTIPLETS PEAKS"]),s={};for(let l of o){let{id:a,x:m,y:u}=l;s[a]||(s[a]=[]),s[a].push({x:m,y:u,width:.05})}for(let l in t)s[l]&&(t[l].signals[0].peaks=s[l])}return w(Object.values(t))}function Xe(e,r){let i=[...e.getMolecularFormula().formula.matchAll(/(?<element>[A-Z][a-z]?)(?<count>\d*)/g)].map(o=>({element:o?.groups?.element,count:o?.groups?.count?Number(o.groups.count):1})),n=[...r.nucleus[0].matchAll(/[0-9]*(?<element>[A-Z][a-z]?)/g,"$element")][0].groups.element;return i.find(o=>o.element===n)?.count||100}function Ye(e){let r={};return".PHASE0"in e&&(r.ph0=Number.parseFloat(e[".PHASE0"]),r.ph1=Number.parseFloat(e[".PHASE1"])),r}function pe(e){let{ph0:r,ph1:t}=e;return Number.isFinite(r)&&Number.isFinite(t)}import{generateID as Ge}from"@zakodium/nmrium-core";function Ke(e,r,t){for(let i=0;i<e.length;i++){if(r.includes(i))continue;let{delta:n,multiplicity:o="",diaIDs:s}=e[i],l=Number(n)-.01,a=Number(n)+.01;t.push({from:l,to:a,integration:1,id:Ge(),signals:[{id:Ge(),delta:n,multiplicity:o,diaIDs:s}]})}}import{linearSumAssignment as xr}from"linear-sum-assignment";import{xCostMatrix as Ar}from"ml-spectra-processing";function Ze(e,r){let t=e.map(s=>s.delta),i=r.map(s=>s.delta),n=Ar(i,t,{fct:(s,l)=>Math.abs(s-l)}),{rowAssignments:o}=xr(n,{maximaze:!1});return Array.from(o)}function Qe(e,r){let{assignments:t,ranges:i}=r;t?.sort((s,l)=>l.delta-s.delta);let n=[],o=[];for(let s of i){let l=0,{from:a,to:m}=s,u=[];for(let c=l;c<t.length;c++){let{delta:g}=t[c];g<=m&&g>=a?(u.push(t[c]),o.push(c)):g>m&&(l=c)}if(u.length>0){let c=s.signals,g=[],y=u.length>1&&c.length>1?Ze(c,u):[0];for(let d=0;d<u.length;d++){let p=y[d],{delta:f,multiplicity:F,diaIDs:h}=u[d];p>-1?g.push({...c[p],diaIDs:h}):g.push({delta:f,multiplicity:F,diaIDs:h})}s.signals=g,n.push(s)}}Ke(t,o,n),n.sort((s,l)=>s.from-l.from),e.ranges={values:w(n).map(s=>{let{integration:l,...a}=s;return a}),options:{sum:r.integrationSum,isSumConstant:!0,sumAuto:!0}},e.ranges.options.moleculeId=String(r.moleculeId)}function rt(e,r,t,i,n){let{logger:o}=n,s={components:nt(e)?Tr(e,t.isFid):Er(e)},{name:l=t.title||`jcamp_${tt()}`}=n,a={dependentVariables:[s],meta:r,info:{...t,name:k(l)}};return Ir(e)&&Lr(a,i,r,e,t,{logger:o}),a}function nt(e){return"minMax"in e}function Ir(e){return!nt(e)}function Er(e){return e.spectra.map(r=>{let t=I(r.data);return{...r,data:t}})}function Tr(e,r){let t={...e.minMax,z:I(e.minMax?.z)};return r?kr(t):{rr:t}}function Lr(e,r,t,i,n,o){let{assignmentsByBlocks:s}=r,l=Ye(t);pe(l)&&wr(e,l);let a=String(i.info.BLOCKID);if(s?.[a]){let{molecule:m,assignments:u,moleculeBlockID:c}=s[a],g=Xe(m,n),y=I(i.spectra[0].data);if(y.x[0]>y.x[1])for(let F of i.spectra)F.data.x.reverse(),F.data.y.reverse();if(pe(l)&&i.spectra.length>1){let{re:F}=vr(i,l);y.y=F}let{x:d,y:p}=y,f=He(t,o)??Cr({x:d,y:p},{peakPicking:{frequency:n.originFrequency},ranges:{frequency:n.originFrequency,integrationSum:g}});Qe(e,{moleculeId:c,ranges:f,assignments:u,integrationSum:g})}}function kr(e){let{z:r,...t}=e,i=[],n=[];for(let l=0;l<r.length;l+=2)i.push(r[l].slice()),n.push(r[l+1].slice());let o=et(i),s=et(n);return{re:{...t,z:i,minZ:o.min,maxZ:o.max},im:{...t,z:n,minZ:s.min,maxZ:s.max}}}function wr(e,r){let{ph0:t,ph1:i}=r;e.filters||(e.filters=[]),e.filters.push({id:tt(),name:"phaseCorrection",value:{ph0:t,ph1:i,absolute:!1},enabled:!0})}function vr(e,r){let{ph0:t,ph1:i}=r,{re:n,im:o}=Or({re:e.spectra[0].data.y,im:e.spectra[1].data.y},t*Math.PI/180,i*Math.PI/180);return{re:n,im:o}}function it(e,r,t){let{logger:i}=t,n=[];for(let o of e)if(o.spectra&&o.spectra.length>0||o.minMax){qr(o);let s={...o.info,...o.meta},l=X(s,{logger:i});if(l.experiment==="wobble_curve")continue;n.push(rt(o,s,l,r,t))}return n}function qr(e){let r=e.meta["BRUKER FILE EXP"];if(!r)return;let i=(Array.isArray(r)?r:[r]).find(o=>o.slice(0,10).includes("vdlist"));if(!i)return;let n=i.split(`
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6
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3
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4
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`}=t;P(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=C(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 ar(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=_({phc0:a,phc1:m});e={...e,...u}}}var ur={keepRecordsRegExp:/.*/,keepFiles:!0};async function G(e,r={}){let t={spectra:[],molecules:[]},{converter:i={},selector:n={},logger:o}=r,s=lr(e,{logger:o,...fr(n)}),l=[];for(let m of s)l.push(mr(m,{...ur,...i}).then(u=>pr(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=_(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`),cr(t)}function pr(e,r={}){let{keepSource:t=!1,logger:i}=r,n={...e.info,...e.meta},o=Y(n,{logger:i}),s={},{isFid:l}=o;if(dr(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=X(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)}),gr(g,e),g}function fr(e){let{general:r={},bruker:t={}}=e,{processingNumbers:i,experimentNumbers:n,...o}=t;return{...r,...o,processingNumbers:Be(i),experimentNumbers:Be(n)}}function Be(e){if(e)return e.split(/[^\d]+/).filter(Boolean).map(r=>Number.parseInt(r,10))}function dr(e){let{info:r}=e;return r.twoD}function gr(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 K=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:o,logger:s}=t??{};return G(r,{converter:n?.bruker,selector:i,keepSource:o,logger:s})}};function de(){return new K}import{formatSpectra as Yr}from"@zakodium/nmrium-core";import{createTree as Gr}from"jcampconverter";function Ue(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 yr}from"jcampconverter";function ge(e,r,t){let{dataType:i,children:n}=e,o=i==="LINK"&&n?n:[e];for(let s of o){if(s.dataType==="LINK"){ge(s,r,t);continue}let l=yr(s.jcamp,t);r.push(...l.flatten)}}function Je(e,r={}){let t=[],i=_e(e,r);for(let s of i?e:[])s.dataType==="LINK"?s.children=ye(s.children,r):s=ye([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 ye(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=ye(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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because it didn't match the import filters`);continue}s.push(u)}let l=[],a=s.some(Xe),m=s.some(We);for(let u of s){if(o!=="both"&&u.dataType!=="LINK"){if(Xe(u)&&(o==="ft"||o==="preferFT"&&m)){i?.warn(`Skipping raw data ${t?`in ${t}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(We(u)&&(o==="fid"||o==="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(u)}return l}function We(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function Xe(e){return e.dataType?.toUpperCase().includes("FID")}function _e(e,r={}){let{logger:t,name:i=""}=r;for(let n of e){if(n.dataType==="LINK"&&_e(n.children,r))return!0;let{dataType:o=""}=n,s=o.toLowerCase();if(s.length>0){if(s.includes("spectrum")&&!s.includes("nmr"))return t?.warn(`File ${i} was ignored because it is a ${o}`),!1;if(s.includes("nmr"))return!0}}return!1}import{generateID as Ye}from"@zakodium/nmrium-core";import{parseJcampCS as Sr}from"jcampconverter";import*as Rr from"openchemlib";import{isMolfileNotEmpty as hr}from"nmr-processing";import{Molecule as br}from"openchemlib";async function Ve(e,r={}){let t=await e.text(),i=w(t),n={molecules:i,spectra:[]};return i.length===0&&r.logger?.debug(`${e.name} is an empty molfile`),n}function w(e){let r=[];if(!hr(e))return[];let i=br.fromMolfile(e).toMolfile();return r.push({molfile:i}),r}import{isMolfileNotEmpty as Pr}from"nmr-processing";import*as Nr from"openchemlib";import{getDiastereotopicAtomIDsFromMolfile as Dr}from"openchemlib-utils";var Fr=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function Z(e){let{dataType:r="",dataClass:t=""}=e,i=r.replaceAll(/\s/g,"").toLowerCase(),n=t.replaceAll(/\s/g,"").toLowerCase();return Fr.has(i)&&n!=="peaktable"}function He(e,r,t={}){let{spectra:i,info:n,meta:o}=e,s=i[0].data,l=[],a={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:m,name:u,spectraData:c}=t,{CROSSREFERENCE:g}=n,y=typeof g!="string"?g:g.split(/\r?\n/).map(D=>D.trim()).filter(Boolean),d=y.find(D=>D?.toLowerCase().includes("structure"));if(d===void 0)return m&&m.warn(`There is not a structure reference for ${u} file, assignment object could not be completed`),null;let p=Number.parseInt(d?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(p)||p<1)return m&&m.warn(`Structure block_id not found for ${u} file, assignment object could not be completed`),null;let F=c?.molecules?.find(D=>D.blockId===p)?.molfile??"";if(F===""){let D=r.find(A=>A.info.BLOCKID===p),{MOLFILE:R=""}=D?.meta||{};F=R}if(!Pr(F))return m&&m.warn(`Empty molfile for ${u} file with structure block_id = ${p}, assignment object could not be completed`),null;let 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jr}from"ml-spectra-processing";import{xyAutoRangesPicking as zr}from"nmr-processing";function v(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function q(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 Lr}from"nmr-processing";import{xMaxValue as Or}from"ml-spectra-processing";function z(e){return e.trim().slice(1,-1).split(/,\s*/).map(r=>r.trim())}var Ir={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},Ke=["I","X","Y","Hs","An","H","C","N","(J)"];function Ze(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=z(i)}return 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pt(e,r,t){let{logger:i}=t,n=[];for(let o of e)if(o.spectra&&o.spectra.length>0||o.minMax){Hr(o);let s={...o.info,...o.meta},l=Y(s,{logger:i});if(l.experiment==="wobble_curve")continue;n.push(lt(o,s,l,r,t))}return n}function Hr(e){let r=e.meta["BRUKER FILE EXP"];if(!r)return;let i=(Array.isArray(r)?r:[r]).find(o=>o.slice(0,10).includes("vdlist"));if(!i)return;let n=i.split(`
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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};
|
package/package.json
CHANGED
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@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@zakodium/nmrium-core-plugins",
|
|
3
|
-
"version": "0.0
|
|
3
|
+
"version": "0.1.0",
|
|
4
4
|
"description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
|
|
5
5
|
"author": "",
|
|
6
6
|
"license": "CC-BY-NC-SA-4.0",
|
|
@@ -32,7 +32,7 @@
|
|
|
32
32
|
"eslint": "eslint src --cache",
|
|
33
33
|
"eslint-fix": "npm run eslint -- --fix",
|
|
34
34
|
"dev:eslint-fix": "eslint --cache --fix $(git diff --name-only --relative) --quiet",
|
|
35
|
-
"prepack": "npm run bundle
|
|
35
|
+
"prepack": "npm run bundle",
|
|
36
36
|
"prettier": "prettier --check src",
|
|
37
37
|
"prettier-write": "prettier --write src",
|
|
38
38
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"dev:prettier-write": "prettier --write $(git diff --name-only --relative)",
|
|
@@ -51,6 +51,7 @@
|
|
|
51
51
|
"eslint-config-cheminfo-typescript": "^18.0.0",
|
|
52
52
|
"fifo-logger": "^1.0.0",
|
|
53
53
|
"jcamp-data-test": "^0.8.3",
|
|
54
|
+
"jeol-data-test": "^0.5.2",
|
|
54
55
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
55
56
|
"msw": "^2.7.5",
|
|
56
57
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"nmredata-data-test": "^0.4.0",
|
|
@@ -60,22 +61,21 @@
|
|
|
60
61
|
"vitest": "^3.0.9"
|
|
61
62
|
},
|
|
62
63
|
"dependencies": {
|
|
63
|
-
"@zakodium/nmrium-core": "^0.0
|
|
64
|
+
"@zakodium/nmrium-core": "^0.1.0",
|
|
64
65
|
"brukerconverter": "^8.0.3",
|
|
65
66
|
"convert-to-jcamp": "^5.4.11",
|
|
66
67
|
"filelist-utils": "^1.11.3",
|
|
67
68
|
"gyromagnetic-ratio": "^1.2.1",
|
|
68
69
|
"is-any-array": "^2.0.1",
|
|
69
70
|
"jcampconverter": "^11.0.1",
|
|
70
|
-
"jeol-data-test": "^0.5.2",
|
|
71
71
|
"jeolconverter": "^1.0.4",
|
|
72
72
|
"linear-sum-assignment": "^1.0.7",
|
|
73
73
|
"lodash.merge": "^4.6.2",
|
|
74
74
|
"ml-spectra-processing": "^14.11.0",
|
|
75
|
-
"nmr-processing": "^18.0.
|
|
75
|
+
"nmr-processing": "^18.0.1",
|
|
76
76
|
"nmredata": "^1.0.0",
|
|
77
|
-
"openchemlib": "^
|
|
78
|
-
"openchemlib-utils": "^
|
|
77
|
+
"openchemlib": "^9.0.1",
|
|
78
|
+
"openchemlib-utils": "^8.1.0",
|
|
79
79
|
"sdf-parser": "^7.0.4",
|
|
80
80
|
"varian-converter": "^2.0.1"
|
|
81
81
|
},
|