npm - nmr-processing - Versions diffs - 12.0.1 → 12.1.0 - Mend

nmr-processing 12.0.1 → 12.1.0

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package/nmr-processing.cjs CHANGED Viewed

	@@ -1 +1 @@
1	- "use strict";var Ol=Object.create;var Kt=Object.defineProperty;var xl=Object.getOwnPropertyDescriptor;var bl=Object.getOwnPropertyNames;var vl=Object.getPrototypeOf,Sl=Object.prototype.hasOwnProperty;var I=(t,e)=>{for(var n in e)Kt(t,n,{get:e[n],enumerable:!0})},$t=(t,e,n,s)=>{if(e&&typeof e=="object"\|\|typeof e=="function")for(let i of bl(e))!Sl.call(t,i)&&i!==n&&Kt(t,i,{get:()=>e[i],enumerable:!(s=xl(e,i))\|\|s.enumerable});return t},j=(t,e,n)=>($t(t,e,"default"),n&&$t(n,e,"default")),z=(t,e,n)=>(n=t!=null?Ol(vl(t)):{},$t(e\|\|!t\|\|!t.__esModule?Kt(n,"default",{value:t,enumerable:!0}):n,t)),Pl=t=>$t(Kt({},"__esModule",{value:!0}),t);var N={};I(N,{DatumKind:()=>gt,Filters:()=>Y,Filters1D:()=>It,Filters2D:()=>xe,FiltersManager:()=>qe,MultiplicityPatterns:()=>W,RangeUtilities:()=>Re,SignalKinds:()=>tc,SignalKindsToInclude:()=>Tt,XYAutoPeaksPickingWindowSizeError:()=>Pn,apodization:()=>U,apodizationFilter:()=>Qt,carbonImpurities:()=>QC,checkIntegralKind:()=>kt,checkMultiplet:()=>ds,checkMultiplicity:()=>lu,couplingACSPatterns:()=>zt,couplingPatterns:()=>St,fftDirectDimension:()=>ie,fftIndirectDimension:()=>le,findMultiplet:()=>Vt,get13CAssignments:()=>lg,get1DErrorFactor:()=>Et,get1HAssignments:()=>ig,get2DErrorFactor:()=>we,getAssignments:()=>Sg,getBaselineZones:()=>mu,getDatabase:()=>GC,getFrequency:()=>yn,getPeakDelta:()=>on,getShiftX:()=>ct,impurities:()=>Xe,isEmptyMolecule:()=>is,isMolfileNotEmpty:()=>aC,isRangeExists:()=>Ne,isZoneExists:()=>Ie,mapIntegrals:()=>be,mapPeaks:()=>Se,mapRanges:()=>je,mapZones:()=>Te,markSolventPeaks:()=>ou,normalizeNucleus:()=>gC,optimizeSignals:()=>sC,peakToXY:()=>vc,peaksFilterImpurities:()=>Be,peaksToXY:()=>Ye,predict:()=>J,predictSpectra:()=>Jc,protonImpurities:()=>tu,rangeFromSignal:()=>Bt,rangesToACS:()=>Fg,rangesToXY:()=>Zg,resurrect:()=>lC,signalJoinCouplings:()=>ss,signalMultiplicityPattern:()=>qt,signals2DToZ:()=>_e,signalsToFID:()=>oC,signalsToRanges:()=>Le,signalsToXY:()=>Wt,simulate1D:()=>Je,solventSuppression:()=>fs,splitPatterns:()=>_t,translateMultiplet:()=>ru,updateIntegralsRelativeValues:()=>ve,updateRanges:()=>Ae,updateRangesRelativeValues:()=>Fe,xBackwardLinearPrediction:()=>kn,xForwardLinearPrediction:()=>Wn,xyAutoPeaksPicking:()=>rs,xyAutoRangesPicking:()=>PC,xyCalculateT1:()=>MC,xyPeaksOptimization:()=>NC,xyzAutoSignalsPicking:()=>Cs,xyzAutoZonesPicking:()=>FC,xyzJResAnalyzer:()=>ZC,xyzPhaseCorrection:()=>pe});module.exports=Pl(N);var 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new Error(`baselineCorrection: algorithm unknown: ${n}`)}Object.assign(t.data,{re:o})}function Ls(t){return!t.info.isFid}function Xl(t,e){return{once:!0,reduce:e}}var qn={};I(qn,{DOMAIN_UPDATE_RULES:()=>Yl,apply:()=>Wl,id:()=>Us,isApplicable:()=>_s,name:()=>Bl,reduce:()=>Ll});var Us="digitalFilter",Bl="Digital Filter",Yl={updateXDomain:!0,updateYDomain:!0};function Wl(t,e={}){if(!_s(t))throw new Error("Digital Filter is not applicable on this data");let{digitalFilterValue:n}=e;if(!n){n=t.info.digitalFilter\|\|0;let m=t.filters.find(c=>c.name===Us);m&&(m.value={digitalFilterValue:n})}let s=new Float64Array(t.data.re),i=new Float64Array(t.data.im),o=Math.floor(n),a=0;o+=0;let l=new Float64Array(s.length),r=new Float64Array(i.length);l.set(s.slice(o)),l.set(s.slice(a,o),s.length-o),r.set(i.slice(o)),r.set(i.slice(a,o),i.length-o),t.data.re=l,t.data.im=r}function _s(t){return!!(t.info.isComplex&&t.info.isFid)}function Ll(){return{once:!0,reduce:void 0}}var 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Float64Array(o),r=t.info?.digitalFilter\|\|0,m=r>0?Math.floor(r):0;a.set(s.slice(0,o-m)),l.set(i.slice(0,o-m)),m>0&&e&&(a.set(s.slice(s.length-m),o-m),l.set(i.slice(s.length-m),o-m));let c=(0,$s.xSequentialFillFromStep)({from:n[0],size:o,step:n[1]-n[0]});t.data={...t.data,re:a,im:l,x:c}}var nr="fft",er="FFT",sr={updateXDomain:!0,updateYDomain:!0};function ir(t){if(!Qs(t))throw new Error("fft not applicable on this data");rr(t);let e=t.filters.some(o=>o.name==="digitalFilter"&&o.flag),{info:{aqMod:n}}=t;n===1&&lr(t,e),Vs(t.data.x.length)\|\|Ks(t,e);let{data:s,info:i}=t;if(Object.assign(s,(0,_.reimFFT)({re:s.re,im:i.reverse?(0,_.xMultiply)(s.im,-1):s.im},{applyZeroShift:!0})),e){let{digitalFilter:o=0}=i,a=(o-Math.floor(o))Math.PI2,l=Math.floor(o)%2?180$:0;Object.assign(s,(0,_.reimPhaseCorrection)(s,l,-a,{reverse:!0}))}t.data.x=ar(t),t.info={...t.info,isFid:!1,isFt:!0}}function Qs(t){return!!(t.info.isComplex&&t.info.isFid)}function or(){return{once:!0,reduce:void 0}}function ar(t){let e=t.info,n=Number(e.baseFrequency),s=Number(e.frequencyOffset),i=Number(e.spectralWidth),o=s/n,a=.5i,l=t.data.x.length,r=o-a,m=i/(l-1),c=new Float64Array(l);for(let g=0;g<l;g++)c[g]=r,r+=m;return c}function lr(t,e){let{digitalFilter:n=0}=e&&t.info?t.info:{},s=t.data,i=s.re.length,o=new Float64Array(s.re),a=new Float64Array(s.im),l=(0,_.xMean)(s.re.slice(i.75>>0,i-n)),r=(0,_.xMean)(s.im.slice(i.75>>0,i-n));for(let m=e?0:n;m<i-n;m++)o[m]-=l,a[m]-=r;return Object.assign(t.data,{re:o,im:a}),t}function rr(t){let{data:e}=t;if(e.x.length!==e.re.length\|\|e.x.length!==e.im.length)throw new Error("The length of data should be equal")}var Ln={};I(Ln,{DOMAIN_UPDATE_RULES:()=>cr,apply:()=>gr,id:()=>ni,isApplicable:()=>ei,name:()=>mr,reduce:()=>Cr});var ti=require("ml-spectra-processing");var nn=require("ml-matrix");function Wn(t,e){let{nbCoefficients:n,nbInputs:s,nbPoints:i}=e;if(t.length<s+n+i)throw new RangeError("data length should be bigger than nbInputs + nbCoefficients + nbPoints");let 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ft:3.41}],"grease^f":[{proton:"CH3",coupling:0,multiplicity:"m",shift:.92},{proton:"CH2",coupling:0,multiplicity:"br_s",shift:1.36}],"n-hexane":[{proton:"CH3",coupling:0,multiplicity:"t",shift:.89},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.24}],hmpag:[{proton:"CH3",coupling:9.5,multiplicity:"d",shift:2.4}],methanol:[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.07}],nitromethane:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.94}],"n-pentane":[{proton:"CH3",coupling:7,multiplicity:"t",shift:.86},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.23}],"2-propanol":[{proton:"CH3",coupling:6,multiplicity:"d",shift:.95},{proton:"CH",coupling:6,multiplicity:"sep",shift:3.67}],pyridine:[{proton:"CH(2)",coupling:0,multiplicity:"m",shift:8.53},{proton:"CH(3)",coupling:0,multiplicity:"m",shift:6.66},{proton:"CH(4)",coupling:0,multiplicity:"m",shift:6.98}],silicone_greasei:[{proton:"CH3",coupling:0,multiplicity:"s",shift:.29}],tetrahydrofuran:[{proton:"CH2",coupling:0,multiplicity:"m",shift:1.4},{proton:"CH2O",coupling:0,multiplicity:"m",shift:3.57}],toluene:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.11},{proton:"CH(o/p)",coupling:0,multiplicity:"m",shift:7.02},{proton:"CH(m)",coupling:0,multiplicity:"m",shift:7.13}],triethylamine:[{proton:"CH3",coupling:7,multiplicity:"t",shift:.96},{proton:"CH2",coupling:7,multiplicity:"q",shift:2.4}]},cd3cn:{tms:[{proton:"X",coupling:0,multiplicity:"",shift:0}],solvent:[{proton:"X",coupling:0,multiplicity:"",shift:1.94}],h2o:[{proton:"H2O",coupling:0,multiplicity:"s",shift:2.13}],acetic_acid:[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.96}],acetone:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.08}],acetonitrile:[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.96}],benzene:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.37}],"tert-butyl_alcohol":[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.16},{proton:"OHc",coupling:0,multiplicity:"s",shift:2.18}],"tert-butyl_methyl_ether":[{proton:"CCH3",coupling:0,multiplicity:"s",shift:1.14},{proton:"OCH3",coupling:0,multiplicity:"s",shift:3.13}],bhtb:[{proton:"ArH",coupling:0,multiplicity:"s",shift:6.97},{proton:"OHc",coupling:0,multiplicity:"s",shift:5.2},{proton:"ArCH3",coupling:0,multiplicity:"s",shift:2.22},{proton:"ArC(CH3)3",coupling:0,multiplicity:"s",shift:1.39}],chloroform:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.58}],cyclohexane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:1.44}],"1,2-dichloroethane":[{proton:"CH2",coupling:0,multiplicity:"s",shift:3.81}],dichloromethane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:5.44}],diethyl_ether:[{proton:"CH3",coupling:7,multiplicity:"t",shift:1.12},{proton:"CH2",coupling:7,multiplicity:"q",shift:3.42}],diglyme:[{proton:"CH2",coupling:0,multiplicity:"m",shift:3.53},{proton:"CH2",coupling:0,multiplicity:"m",shift:3.45},{proton:"OCH3",coupling:0,multiplicity:"s",shift:3.29}],"1,2-dimethoxyethane":[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.28},{proton:"CH2",coupling:0,multiplicity:"s",shift:3.45}],dimethylacetamide:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:1.97},{proton:"NCH3",coupling:0,multiplicity:"s",shift:2.96},{proton:"NCH3",coupling:0,multiplicity:"s",shift:2.83}],dimethylformamide:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.92},{proton:"CH3",coupling:0,multiplicity:"s",shift:2.89},{proton:"CH3",coupling:0,multiplicity:"s",shift:2.77}],dimethyl_sulfoxide:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.5}],dioxane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:3.6}],ethanol:[{proton:"CH3",coupling:7,multiplicity:"t",shift:1.12},{proton:"CH2",coupling:7,multiplicity:"q",shift:3.54},{proton:"OH",coupling:5,multiplicity:"s,t",shift:2.47}],ethyl_acetate:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:1.97},{proton:"CH2CH3",coupling:7,multiplicity:"q",shift:4.06},{proton:"CH2CH3",coupling:7,multiplicity:"t",shift:1.2}],ethyl_methyl_ketone:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:2.06},{proton:"CH2CH3",coupling:7,multiplicity:"q",shift:2.43},{proton:"CH2CH3",coupling:7,multiplicity:"t",shift:.96}],ethylene_glycol:[{proton:"CH",coupling:0,multiplicity:"s",shift:3.51}],"grease^f":[{proton:"CH3",coupling:0,multiplicity:"m",shift:.86},{proton:"CH2",coupling:0,multiplicity:"br_s",shift:1.27}],"n-hexane":[{proton:"CH3",coupling:0,multiplicity:"t",shift:.89},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.28}],hmpag:[{proton:"CH3",coupling:9.5,multiplicity:"d",shift:2.57}],methanol:[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.28},{proton:"OH",coupling:0,multiplicity:"s",shift:2.16}],nitromethane:[{proton:"CH3",coupling:0,multiplicity:"s",shift:4.31}],"n-pentane":[{proton:"CH3",coupling:7,multiplicity:"t",shift:.87},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.29}],"2-propanol":[{proton:"CH3",coupling:6,multiplicity:"d",shift:1.09},{proton:"CH",coupling:6,multiplicity:"sep",shift:3.87}],pyridine:[{proton:"CH(2)",coupling:0,multiplicity:"m",shift:8.57},{proton:"CH(3)",coupling:0,multiplicity:"m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Nc={h:"1H",c:"13C"};function po(t){return Object.values(t).map(e=>Nc[e.toLowerCase()])}function jc(t){if(!t.from\|\|!t.to)throw new Error("options from and to are mandatory")}async function Pt(t,e){jc(e);let{from:n,to:s,minLength:i=0,maxLength:o,predictions:a,joinDistance:l={H:.05,C:.5},includeDiagonal:r=!1}=e,m=Mc(t,{fromLabel:n,toLabel:s,minLength:i,maxLength:o}),c=t.getGroupedDiastereotopicAtomIDs(),g=[];for(let x of c)g.push({...x,pathInfo:JSON.parse(JSON.stringify(m[x.atoms[0]]))});let C=a[s],u=a[n];if(!u\|\|!C)throw new Error("predictions are not availaible");let p={x:u,y:C},f={x:{},y:{}};for(let x in f)for(let h of p[x].joinedSignals){if(!h.diaIDs)throw new Error("Signal has not diaIDs");f[x][h.diaIDs[0]]=h}let d={};for(let x of g){let h=x.pathInfo;if(h.paths.length<1\|\|!f.x[h.oclID])continue;let D=h.paths;for(let S of D){if(!f.y[m[S.to].oclID])continue;let H={x:h,y:m[S.to]},b=`${H.x.oclID}-${H.y.oclID}`;if(b===`${h.oclID}-${h.oclID}`\|\|d[b])continue;let v={id:(0,gn.v4)(),z:100},P={id:(0,gn.v4)(),x:{},y:{}};for(let R in H){let M=H[R].oclID;v[R]=f[R][M].delta,P[R].delta=f[R][M].delta,P[R].diaIDs=[M],P[R].atoms=f[R][M].atoms}P.peaks=[v],d[b]=P}}r&&Fc(d,{paths:m,signalsByDiaID:f});let y=Object.values(d),O=Ac(y,{joinDistance:l,from:n,to:s});return{nuclei:po({from:n,to:s}),joinedSignals:y,signals:Rc(y),zones:O}}function Mc(t,e){let{fromLabel:n,toLabel:s,minLength:i,maxLength:o}=e,a=t.diaIDs,l=t.moleculeWithH,r=t.distanceMatrix,m=We.Molecule.getAtomicNoFromLabel(n),c=We.Molecule.getAtomicNoFromLabel(s),g=[];for(let C=0;C<l.getAllAtoms();C++){let u={oclID:a[C],paths:[]};for(let p=0;p<l.getAllAtoms();p++){if(C===p\|\|l.getAtomicNo(p)!==c\|\|l.getAtomicNo(C)!==m)continue;let f=r[C][p];f>=i&&f<=o&&u.paths.push({from:C,to:p})}g.push(u)}return g}function Rc(t){let e=[];for(let n of t)for(let s of n.x.atoms\|\|[])for(let i of n.y.atoms\|\|[]){let o=JSON.parse(JSON.stringify(n));o.x.atoms=[s],o.y.atoms=[i],e.push(o)}return cn(e)}function Fc(t,e){let{paths:n=[],signalsByDiaID:s}=e;for(let i of n){if(i.paths.length<1)continue;let o=i.oclID;if(!s.x[o]\|\|t[`${o}-${o}`])continue;let a={x:{},y:{}},l={z:1};for(let r of["x","y"])l[r]=s[r][o].delta,a[r].delta=s[r][o].delta,a[r].diaIDs=[o],a[r].atoms=s[r][o].atoms;a.peaks=[l],t[`${i.oclID}-${i.oclID}`]=a}}function Ac(t,e){if(t.length<1)return[];let{joinDistance:n,from:s,to:i}=e,o=new yo.Matrix(t.map(p=>[p.x.delta,p.y.delta])),a=o.minColumn(0),l=o.maxColumn(0),r=o.minColumn(1),m=o.maxColumn(1);o.mulColumn(0,1/(l-a)),o.mulColumn(1,1/(m-r));let c=Math.sqrt((n[s]/(l-a))2+(n[i]/(m-r))2),g=(0,fo.agnes)(o.to2DArray(),{method:"centroid"}),C=ho([g],c),u=[];for(let p of C){let f=[];p.isLeaf&&f.push(t[p.index]);for(let d of p.children)for(let y of d.indices())f.push(t[y]);u.push({id:(0,gn.v4)(),...wc(f,{joinDistance:n,from:s,to:i}),signals:f})}return u}function wc(t,e){let{joinDistance:n,from:s,to:i}=e,o=Number.MAX_SAFE_INTEGER,a=Number.MAX_SAFE_INTEGER,l=Number.MIN_SAFE_INTEGER,r=Number.MIN_SAFE_INTEGER;for(let m of t)m.x.delta<o&&(o=m.x.delta),m.x.delta>l&&(l=m.x.delta),m.y.delta<a&&(a=m.y.delta),m.y.delta>r&&(r=m.y.delta);return{x:{from:o-n[s],to:l+n[s]},y:{from:a-n[i],to:r+n[i]}}}function ho(t,e){let n=t.length;for(let s=0;s<t.length;s++){let i=t[s];i.height>e&&(t.push(...i.children),t.splice(s--,1))}return t.length<n?ho(t,e):t}async function Ho(t,e){let{minLength:n=2,maxLength:s=3,joinDistance:i={H:.05,C:.5},includeDiagonal:o=!0}=e;return Pt(t,{...e,from:"H",to:"H",minLength:n,maxLength:s,joinDistance:i,includeDiagonal:o})}var So=require("@lukeed/uuid");var Do=require("@lukeed/uuid");function Bt(t,e={}){let{nucleus:n="1H",frequency:s=400}=e,{tolerance:i=Ic(n)/s}=e,o=0,{js:a=[],multiplicity:l}=t;if(a.length>0)for(let r of a){let{coupling:m,multiplicity:c="d"}=r;o+=tt[c]m/s}else l==="m"?o=16/s:(l==="b"\|\|l==="br s")&&(o=7/s);return 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No(t,e){let{minLength:n=2,maxLength:s=3,joinDistance:i={H:.05,C:.5}}=e;return Pt(t,{...e,from:"H",to:"C",minLength:n,maxLength:s,joinDistance:i})}async function jo(t,e){let{minLength:n=1,maxLength:s=1,joinDistance:i={H:.05,C:.5}}=e;return Pt(t,{...e,from:"H",to:"C",minLength:n,maxLength:s,joinDistance:i})}async function Mo(t,e={}){if(t.molecule.getAllAtoms()===0)return{nucleus:"1H",joinedSignals:[],signals:[],ranges:[]};let{predictor:n=xo,cache:s}=e;return Cn(t,n,s)}function Ue(t,e){if(t in e)return!0;let n="hsqc"in e\|\|"hmbc"in e;return t==="C"?n:t==="H"?n\|\|"cosy"in e:!1}var qc={cosy:{predictor:Ho,required:["H"],message:"Proton prediction is missing so COSY could not be generated."},hsqc:{predictor:jo,required:["H","C"],message:"Carbon and / or proton prediction is missing so HSQC could not be generated."},hmbc:{predictor:No,required:["H","C"],message:"Carbon and / or proton prediction is missing so HMBC could not be generated."}};async function J(t,e={}){let{logger:n,joinDistance:s={H:.05,C:.5},predictOptions:i={H:{},C:{},hsqc:{},hmbc:{},cosy:{}}}=e,o=new Fo.TopicMolecule(t),a=Ue("H",i)?await Mo(o,{...i?.H}):void 0,l=Ue("C",i)?await Po(o,i?.C):void 0,r={},m=o.diaIDs,c={};Ro(a,m)&&(c.H=a,"H"in i&&(r.proton=a)),Ro(l,m)&&(c.C=l,"C"in i&&(r.carbon=l));for(let g in i){if(g==="H"\|\|g==="C")continue;let{predictor:C,required:u,message:p}=qc[g];u.every(f=>f in c)?r[g]=await C(o,{predictions:c,joinDistance:s,...i[g]}):n&&n.warn(p)}return{diaIDs:o.diaIDs,hoses:o.hoseCodes,distanceMatrix:o.distanceMatrix,moleculeWithHydrogens:o.moleculeWithH,groupedDiaIDs:o.getGroupedDiastereotopicAtomIDs(),molfile:o.toMolfile(),molfileWithH:o.toMolfileWithH(),spectra:r}}function Ro(t,e=[]){if(!t\|\|t.ranges.length===0)return!1;let{signals:n}=t;for(let s of n)if(!s.diaIDs?.every(o=>e.includes(o)))return!1;return!0}var Ao=require("spectrum-generator");function _e(t,e={}){let{from:n=-1,to:s=12,nbPoints:i=512,factor:o=3}=e,{width:a=.02}=e,l=t.reduce((r,{x:m,y:c})=>(r.x.push(m.delta),r.y.push(c.delta),r.z.push(1e6),r),{x:[],y:[],z:[]});return a=un(a),(0,Ao.generateSpectrum2D)(Xc(l),{generator:{from:un(n),to:un(s),nbPoints:un(i)},peaks:{width:a,factor:o}})}function un(t){return typeof t!="object"?{x:t,y:t}:{...t}}function Xc(t){let e=JSON.parse(JSON.stringify(t));for(let n=0;n<e.x.length;n++)for(let s=n+1;s<e.x.length;s++)e.x[n]===e.x[s]&&e.y[n]===e.y[s]&&(e.z[n]+=e.z[s],e.x.splice(s,1),e.y.splice(s,1),e.z.splice(s,1),s--);return e}var Nt=require("ml-spectra-processing");var Io=require("ml-matrix");var pn=require("ml-matrix"),wo=z(require("ml-simple-clustering"));function nt(t){let{couplingConstants:e,connectivity:n}=t,s=pn.Matrix.checkMatrix(e),i=n?pn.Matrix.checkMatrix(n):Bc(s),{levels:o=new 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To=require("ml-sparse-matrix");function ko(t){let e=(t-1)/2,n=new Array(t),s=new Array(t);for(let m=0;m<t;m++)n[m]=t-1-m-e,s[m]=Math.sqrt(e(e+1)-n[m](n[m]+1));let i=Ze(s,1,t,t);for(let m=0;m<t;m++)s[m]=Math.sqrt(e(e+1)-n[m](n[m]-1));let o=Ze(s,-1,t,t),a=i.clone().add(o).mul(.5),l=o.clone().mul(-1).add(i).mul(-.5),r=Ze(n,0,t,t);return{x:a,y:l,z:r,m:o,p:i}}function Ze(t,e,n,s){let i=new To.SparseMatrix(n,s,{initialCapacity:20});for(let o=0;o<t.length;o++)o-e>=0&&o-e<n&&o<s&&i.set(o-e,o,t[o]);return i}var Wc=ko(2);function Yt(t){return t===2?Wc:ko(t)}var fn=.01;function st(t,e={}){let{lineWidth:n=1,maxClusterSize:s=8,frequency:i=400}=e,o=nt(t),a=o.chemicalShifts.slice();for(let m=0;m<a.length;m++)a[m]=a[m]i;let l=o.levels,r=[];for(let m of o.clusters){let c=m.map(d=>d<0?-d-1:d),g=1,C=0,u=[],p=[];if(m.length>s){let d=0;for(;m[d++]<0;);d=m[d-1],u.push(-a[d]);for(let y=0;y<m.length;y++)if(m[y]<0){let O=o.couplingConstants.get(d,c[y])/2,x=u.length;for(let h=0;h<x;h++)u.push(u[h]+O),u[h]-=O}u.sort((y,O)=>y-O),C=u.length,g=1;for(let y=0;y<C;y++)p.push(1)}else{let d=Lc(a,o.couplingConstants,l,o.connectivity,c),y=d.rows,O=new dn.EVD(d),x=O.eigenvectorMatrix,h=O.realEigenvalues,D=new L.SparseMatrix(y,y),S=m.length;g=0;for(let M=0;M<S;M++){let A=Yt(l[c[M]]),w=1;for(let E=0;E<M;E++)w=l[c[E]];let F=L.SparseMatrix.eye(w);w=1;for(let E=M+1;E<S;E++)w=l[c[E]];let T=L.SparseMatrix.eye(w),k=F.kroneckerProduct(A.m).kroneckerProduct(T);m[M]>=0?(D.add(k.mul(m[M]+1)),g++):D.add(k.mul(m[M]))}let H=dn.Matrix.zeros(y,y);D.forEachNonZero((M,A,w)=>{if(w>0)for(let F=0;F<x.columns;F++){let T=x.get(A,F);T!==0&&H.set(M,F,H.get(M,F)+T)}return w});let b=H.clone();D.forEachNonZero((M,A,w)=>{if(w<0)for(let F=0;F<x.columns;F++){let T=x.get(A,F);T!==0&&b.set(M,F,b.get(M,F)+T)}return w});let v=x.transpose();H=v.mmul(H);let P=new L.SparseMatrix(H.to2DArray(),{threshold:fn});Eo(P,fn),b=v.mmul(b);let R=new L.SparseMatrix(b.to2DArray(),{threshold:fn});R.forEachNonZero((M,A,w)=>w),Eo(R,fn),R.forEachNonZero((M,A,w)=>{let F=H.get(M,A);F=Math.min(Math.abs(F),Math.abs(w)),F=F,C+=F;let T=h[M]-h[A],k=(0,zo.default)(u,T,(E,G)=>E-G);k<0?(u.splice(-1-k,0,T),p.splice(-1-k,0,F)):p[k]+=F})}let f=u.length;if(f>0){g/=C;let d=n/64,y=u[0],O=p[0],x=1;for(let h=1;h<f;h++)Math.abs(u[h]-y/x)<d?(O+=p[h],y+=u[h],x++):(r.push({x:-y/x/i,y:Og}),y=u[h],O=p[h],x=1);r.push({x:-y/x/i,y:Og})}}return r.filter(m=>m.x<1e3)}function Eo(t,e){t.forEachNonZero((n,s,i)=>Math.abs(i)<=e?0:i)}function Lc(t,e,n,s,i){let o=1;for(let l of i)o=n[l];let a=new L.SparseMatrix(o,o);for(let l=0;l<i.length;l++){let r=i[l],m=Yt(n[r]),c=1;for(let f=0;f<l;f++)c=n[i[f]];let g=L.SparseMatrix.eye(c);c=1;for(let f=l+1;f<i.length;f++)c=n[i[f]];let C=L.SparseMatrix.eye(c),u=t[r],p=g.kroneckerProduct(m.z).kroneckerProduct(C);a.add(p.mul(u));for(let f=0;f<i.length;f++){let d=i[f];if(s.get(r,d)===1){let y=Yt(n[d]),O=1;for(let S=0;S<f;S++)O=n[i[S]];let 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t=="string"?yn(t,{nucleus:"1H",frequency:e}):t[0]===t[1]?`${e},${e}`:`${e},${yn(t[1],{nucleus:t[0],frequency:e})}`}var Ke=z(require("ml-tree-set"));function Lo(t){let{restrictionByCS:e,predictions:n,targets:s,useIntegrationRestriction:i}=t,{tolerance:o,chemicalShiftRestriction:a}=e,l=Math.abs(o),r={};for(let m in n){let c=n[m];if(c.error&&(c.error=Math.abs(c.error)),r[m]=[],s)for(let g in s){let C=s[g],{nbAtoms:u}=c,{integration:p}=C;if(i&&p>0?u-p<1:!0)if(!a\|\|typeof c.delta>"u")r[m].push(g);else{let d=l;c.error&&(d=Math.max(d,c.error));let y=C.signals&&C.signals.length>0?C.signals[0].delta:(C.to+C.from)/2;Math.abs(c.delta-y-l)<4l&&r[m].push(g)}}r[m].push("")}return r}function Uo(t,e){let{useIntegrationRestriction:n,diaIDPeerPossibleAssignment:s,nbAllowedUnAssigned:i,restrictionByCS:o,predictions:a,targets:l}=e,{useChemicalShiftScore:r}=o,m=0,c=t.length,g={},C=[];for(let d=0;d<t.length;d++){let y=t[d];y&&y!==""&&(C.push(d),g[y]\|\|(g[y]=[]),g[y].push(s[d])),y===""&&m++}if(m>i)return 0;let u=Object.keys(g);if(u.length===0)return 0;if(n)for(let d of u){let y=g[d],O=0;for(let h of y){let D=a[h];O+=D.allHydrogens}let{integration:x}=l[d];if(O-x>=.5)return 0}let p=r?Kc(t,e):1,f=m/c;return p-f}function Kc(t,e){let{tolerance:n}=e.restrictionByCS,{diaIDPeerPossibleAssignment:s,predictions:i,targets:o}=e,a=0,l=0;for(let r=0;r<t.length;r++){let m=t[r];if(m&&m!==""){l++;let c=s[r],g=i[c],C=o[m],u=n;if(g.error&&(u=Math.max(g.error,n)),typeof g.delta>"u")a+=1;else{let p=C.signals&&C.signals.length>0?C.signals[0].delta:(C.to+C.from)/2,f=Math.abs(g.delta-p);f<u?a+=1:(f=Math.abs(f-u),a+=-.25/uf+1)}}}return l>0&&(a/=l),a}function $e(t,e,n,s){let{nSources:i,restrictionByCS:o,timeout:a,timeStart:l,maxSolutions:r,targets:m,predictions:c,lowerBoundScore:g,nbAllowedUnAssigned:C,possibleAssignmentMap:u,useIntegrationRestriction:p,diaIDPeerPossibleAssignment:f}=t;if(Date.now()-l>a)return s;let d=f[e],y=u[d];for(let O of y){n[e]=O;let x=Uo(n,{useIntegrationRestriction:p,diaIDPeerPossibleAssignment:f,nbAllowedUnAssigned:C,restrictionByCS:o,predictions:c,targets:m});if(x===0){O===""&&(n[e]=null);continue}e===i-1&&x>=g?Qc(s,{predictions:c,partial:n,score:x,maxSolutions:r}):e<i-1&&$e({nSources:i,restrictionByCS:o,timeout:a,timeStart:l,maxSolutions:r,targets:m,predictions:c,lowerBoundScore:g,nbAllowedUnAssigned:C,possibleAssignmentMap:u,useIntegrationRestriction:p,diaIDPeerPossibleAssignment:f},e+1,JSON.parse(JSON.stringify(n)),s)}}function Qc(t,e){let{score:n,maxSolutions:s,partial:i,predictions:o}=e;t.nSolutions++;let a={assignment:JSON.parse(JSON.stringify(i)),score:n/tg(i,o)};t.nSolutions>=s?a.score>t.solutions.last().score&&(t.solutions.pollLast(),t.solutions.add(a)):(t.solutions.add(a),t.nSolutions++)}function tg(t,e){let n=Object.keys(e).length,s=new Set(t),i=n-s.size;return i>0?2i:1}var _o=(t,e)=>e.score-t.score;async function hn(t){let{restrictionByCS:e={},useIntegrationRestriction:n,timeout:s,minScore:i,nbAllowedUnAssigned:o,maxSolutions:a,targets:l,joinedSignals:r}=t,{tolerance:m=1,useChemicalShiftScore:c=!1,chemicalShiftRestriction:g=!0}=e,C={solutions:new Ke.default(_o),nSolutions:0},u=r.length,p={};for(let h of r){let D=h.diaIDs[0],S=h.atoms[0];p[D]={...h,diaIDIndex:S,allHydrogens:h.nbAtoms}}let f=Lo({restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:g},useIntegrationRestriction:n,predictions:p,targets:l}),d=Object.keys(f),y=ng(u);C={solutions:new Ke.default(_o),nSolutions:0};let O=Date.now();$e({nSources:u,restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:g},timeout:s,timeStart:O,targets:l,predictions:p,maxSolutions:a,lowerBoundScore:i,nbAllowedUnAssigned:o,possibleAssignmentMap:f,diaIDPeerPossibleAssignment:d,useIntegrationRestriction:n},0,y,C);let x=[];for(let h of C.solutions.elements){let{assignment:D,score:S}=h,H=JSON.parse(JSON.stringify(l));for(let b=0;b<D.length;b++){let v=H[D[b]];v.diaIDs\|\|(v.diaIDs=[]),D[b]&&v.diaIDs.push(d[b])}x.push({score:S,assignment:Object.values(H)})}return x}function ng(t,e=null){let n=new Array(t);for(let s=0;s<t;s++)n[s]=e;return n}function eg(t){for(let e of t){if(!e.atoms)throw new Error("signal has not atoms property");if(!e.diaIDs)throw new Error("signal has not diaIDs property");if(!e.nbAtoms)throw new Error("signal has not nbAtoms property")}}function sg(t){for(let e of t)if(e.integration===void 0)throw new Error("ranges has not integration property")}async function ig(t,e,n={}){let{restrictionByCS:s,minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:l=6e3,predictionOptions:r={}}=n;if(!e)throw new Error("It is needed a OCL molecule instance to assign");let{spectra:m}=await J(e,{predictOptions:{H:r}}),c=m.proton?.joinedSignals\|\|[];sg(t),eg(c);let g={};for(let C of t){let{id:u=(0,Zo.v4)()}=C;g[u]=JSON.parse(JSON.stringify(C))}return hn({restrictionByCS:s,timeout:l,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:g,joinedSignals:c,useIntegrationRestriction:!0})}var Jo=require("@lukeed/uuid");function og(t){for(let e of t){if(!e.atoms)throw new Error("signal has not atoms property");if(!e.diaIDs)throw new Error("signal has not diaIDs property");if(!e.nbAtoms)throw new Error("signal has not nbAtoms property")}}function ag(t){for(let e of t)e.integration===void 0&&(e.integration=0);return t}async function lg(t,e,n={}){let{restrictionByCS:s={},minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:l=6e3,predictionOptions:r={}}=n,{spectra:m}=await J(e,{predictOptions:{C:r}}),c=m.carbon?.joinedSignals\|\|[];og(c);let g=ag(t),C={};for(let u of g){let{id:p=(0,Jo.v4)()}=u;C[p]=JSON.parse(JSON.stringify(u))}return hn({restrictionByCS:s,timeout:l,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:C,joinedSignals:c,useIntegrationRestriction:!1})}var ga=require("openchemlib-utils");var ts=z(require("ml-tree-set")),ea=require("openchemlib-utils");var Vo=require("nmr-correlation");function Go(t,e){let{restrictionByCS:n,predictions:s,targets:i}=e,{tolerance:o,chemicalShiftRestriction:a}=n,l=Object.keys(s);for(let r of l){let m=o[r],c=s[r],g=i[r];t[r]\|\|(t[r]={});for(let C in c){let u=c[C];if(t[r][C]=[],g)for(let p in g){let f=g[p],{nbAtoms:d,protonsCount:y}=u,{integration:O,protonsCount:x}=f;if(O?r==="H"?d-O<1:x.length>0?x.some(D=>y===D):!0:!0)if(!a\|\|typeof u.delta>"u")t[r][C].push(p);else{let D=(0,Vo.getCorrelationDelta)(f);if(D===void 0)throw new Error("Correlation has not delta");Math.abs(u.delta-D-m)<4m&&t[r][C].push(p)}}t[r][C].push("")}}return t}var Ko=require("nmr-correlation");function rg(t,e,n){let s=t[0],{H:i=[]}=e[s].attachment,o=[{targetIDs:[s],attachments:new Set(i)}];for(let a=1;a<t.length;a++){let l=t[a],r=e[l],{H:m=[]}=r.attachment,c=!0;for(let g of o)if(m.some(u=>g.attachments.has(u))){c=!1,g.targetIDs.push(l);for(let u of m)g.attachments.add(u);break}c&&o.push({targetIDs:[l],attachments:new Set(m)})}return o.map(a=>({atomType:"C",targetIDs:a.targetIDs,integration:n?Array.from(a.attachments).reduce((l,r)=>n[r].integration+l,0):0}))}var $o=rg;function Qo(t,e){let{diaIDPeerPossibleAssignment:n,infoByAtomTypes:s,restrictionByCS:i,predictions:o,targets:a,correlations:l}=e,{tolerance:r,useChemicalShiftScore:m}=i,c=0,g=0,C={},u={},p=Object.keys(t);for(let H of p){let b=0,{nbAllowedUnAssigned:v}=s[H],P={},R=t[H]\|\|[];C[H]=P,u[H]=[],g+=R.length;for(let M=0;M<R.length;M++){let A=R[M];A&&A!==""&&(u[H].push(M),P[A]\|\|(P[A]=[]),P[A].push(n[H][M])),A===""&&b++}if(b>v)return 0;c+=b}let f={};for(let H in C)f[H]=Object.keys(C[H]);let d=Object.values(f);if(d.reduce((H,b)=>b.length===0?H+1:H,0)===d.length)return 0;let y=cg.bind({},o),O=[];for(let H in t)if(H==="C"&&f[H].length>0)O.push(...$o(f[H],a[H],l));else for(let b of f[H])O.push({atomType:H,targetIDs:[b],integration:a.H[b].integration});for(let H of O){let{integration:b,atomType:v}=H;if(b===void 0\|\|isNaN(b))continue;let P=0;for(let R of H.targetIDs){let M=C[v][R];for(let A of M){let{prediction:w,atomType:F}=y(A);v===F&&(P+=w.allHydrogens)}}if(P-b>=5)return 0}let x=1,h=1;if(m){h=0,x=0;for(let H of Object.keys(t)){let b=t[H],v=a[H];for(let P=0;P<b.length;P++){let R=b[P];if(R&&R!==""){x++;let M=n[H][P],A=o[H][M],w=v[R],F=r[H];if(typeof A.delta>"u")h+=1;else{let T=(0,Ko.getCorrelationDelta)(w);if(T===void 0)throw new Error("correlation has not delta");let k=Math.abs(A.delta-T);k<F?h+=1:(k=Math.abs(k-F),h+=-.25/Fk+1)}}}}x>0&&(h/=x)}let D=0;if(gg(f)>1){let H={},b=[];for(let P of Object.keys(u))b=b.concat(u[P].map(R=>({index:R,atomType:P})));for(let P=0;P<b.length;P++){let{atomType:R,index:M}=b[P],A=o[R][n[R][M]];for(let 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Kg(t){let{signals:e,data:n,frequency:s,shiftValue:i,range:o}=t,a=l=>{let r=Mt([l],{frequency:s,maxClusterSize:1}),m=r.reduce((g,C)=>C.y>g.y?C:g,r[0]),{y:c}=(0,Na.xyFindClosestPoint)(n,m.x);return c};return e.map(l=>{let{intensity:r=a(l)}=l;return{...l,js:l.js\|\|[],intensity:(r-i)/o}})}function Qg(t){let{signal:e,frequency:n,parameter:s,property:i,minMaxY:o,shapeFct:a}=t,l=e?.parameters?.[s]?.[i];if(l)return Ut(l,s,i,o,n,t.baseline);let r=t?.parameters?.[s]?.[i];if(r){if(typeof r=="number")return Ut(r,s,i,o,n,t.baseline);{let c=r(e);return Ut(c,s,i,o,n,t.baseline)}}if(!Lt[s])throw new Error(`No default parameter for ${s}`);let m=Lt[s][i];return m({signal:e,shape:a})}function Ut(t,e,n,s,i,o){return e==="intensity"?n==="gradientDifference"?t:o!==void 0?(t-o)/s.range:(t-s.min)/s.range:e==="fwhm"?t/i:t}var tC={maxClusterSize:1};function Ma(t,e){let n={...tC,...e};return function(i){let o=[];for(let a of t){let l=i[a.fromIndex],r=i[a.fromIndex+1];for(let 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t?.match(/V[23]0/)?!is(Ta.Molecule.fromMolfile(t)):!1}var xn=[];for(let{label:t,value:e,names:n}of W)xn.push(t,e,...n);xn=xn.sort((t,e)=>e.length-t.length);function _t(t){if(t=t.replace(/broad/g,""),t=t.replace(/br\.?/g,""),/^\s$/.exec(t))return[];let e=new RegExp(xn.join("\|"),"g"),n=t.match(e);return n?n.map(s=>s.trim()):[t]}function bn(t){let e=/ (?<before>[^(]?) $ (?<inside>.?) $ (?<after>.?) /.exec(t);return e?e.groups:{before:t,inside:"",after:""}}function vn(t,e={}){let{nucleus:n,frequency:s,logger:i}=e,o=bn(t);if(!o.before)return;let a=/.?(?<from>-?[0-9.]+)-?(?<to>-?[0-9.])./.exec(o.before);if(!a?.groups)return;let l=a.groups.to!=="",r=Number(a.groups.from),m=l?Number(a.groups.to):r,c=o.inside.split(/ , /),g={delta:NaN,js:[]},C={from:r,to:m,signals:[g]},u=c.filter(y=>y.match(/^[0-9]+\sH$/));u.length===1&&(C.integration=Number(u[0].replace("H","")));let p=c.filter(y=>y.match(/^([br ])\.\s[a-zA-Z]+\.$/));if(p.length===1){let 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t.parts)if(s.toLowerCase().includes("nmr"))mC(t,s);else{t.info.frequency\|\|(t.info.frequency=400,n?.warn("Frequency not defined, assuming 400 MHz")),t.info.nucleus\|\|(t.info.nucleus="1H",n?.warn("Nucleus not defined, assuming 1H"));let i=vn(s,{...t.info,logger:n});i&&t.ranges.push(i)}}function mC(t,e){let n=bn(e),s=n.before.replace(/[ -]nmr[ -]/i,"").replace(/[ -]/g,"");if(/^[0-9]+[A-Z][a-z]?$/.exec(s)&&(t.info.nucleus=s),/^[A-Z][a-z]?[0-9]+$/.exec(s)&&(t.info.nucleus=s.replace(/^([A-Z][a-z]?)([0-9]+)$/,"$2$1")),n.inside){let i=n.inside.split(/[,]/),o=i.filter(l=>/[0-9]{2}/.exec(l));if(o.length){let l=o[0].replace(/[^0-9]/g,"");l.length>1&&(t.info.frequency=Number(l))}let a=i.filter(l=>!l.match(/[0-9]{2}/));a.length&&(t.info.solvent=a[0])}}function cC(t){let e=[],n=0;for(let a=0;a<t.normalized.length;a++)",;)".includes(t.normalized[a])&&(e.push(t.normalized.slice(n,a+1)),n=a+1);e.push(t.normalized.slice(n));let s=[],i="",o=0;for(let a of e)i+=a,o+=(a.match(/$/g)\|\|[]).length,o-=(a.match(/$/g)\|\|[]).length,o===0&&(s.push(i),i="");i&&s.push(i),s=s.filter(a=>!a.match(/^[,; ]$/));for(let a=0;a<s.length;a++)s[a]=s[a].replace(/ [,;]+$/,"").replace(/ +/g," ").trim();t.parts=s}var os=require("gyromagnetic-ratio");function gC(t){if(os.gyromagneticRatio[t])return t;if(t.toLowerCase()==="proton")return"1H";let e=t.replace(/[^0-9]/g,"");if(!e)return t;for(let n in os.gyromagneticRatio)if(n.includes(e))return n;return t}var at=require("ml-gsd"),Ea=require("ml-signal-processing"),V=require("ml-spectra-processing");function Sn(t,e){return rn(t,{...e,convertTo:"hz"})}function rs(t,e){let{from:n,to:s,frequency:i,noiseLevel:o,thresholdFactor:a=3,minMaxRatio:l=.05,broadRatio:r=25e-5,useSanPlot:m=!1,smoothY:c=!0,optimize:g=!1,factorLimits:C=4,realTopDetection:u=!0,shape:p={kind:"gaussian"},optimization:f={kind:"lm"},broadWidth:d=.25,sgOptions:y={},direction:O="positive"}=e,x=1/i/(t.x[1]-t.x[0]),h=Math.max(Math.round(x/2),5),{windowSize:D=h-h%2+1,polynomial:S=3}=y;if(!D)throw new Pn({windowSize:D,ws:h,pointsPerHz:x,frequency:i,x:t.x.slice(0,2),sgOptions:y,autoWindowSizeFormula:"ws - (ws % 2) + 1",pointsPerHzFormula:"1 / frequency / (x[1] - x[0])"});if(t.x.length<D)return[];let H,{maxAbsDdY:b}=e;if(n!==void 0&&s!==void 0){if(!("maxAbsDdY"in e)){let R=(0,Ea.savitzkyGolay)(t,{windowSize:D,polynomial:S,derivative:2});b=(0,V.xMaxAbsoluteValue)(R.data.y)}H=(0,V.xyExtract)(t,{zones:[{from:n,to:s}]})}else H=t;let v=uC(H.y,{noiseLevel:o,useSanPlot:m,thresholdFactor:a}),P={shape:p,maxAbsDdY:b,frequency:i,broadWidth:d,optimize:g,factorLimits:C,maxCriteria:!0,sgOptions:{windowSize:D,polynomial:S},minMaxRatio:l,broadRatio:r,noiseLevel:v.positive,smoothY:c,optimization:f,realTopDetection:u};switch(O){case"positive":return ls(H,P);case"negative":return ka(H,v,P);case"both":return[...ls(H,P),...ka(H,v,P)];default:throw Error(`Unknown distribution ${O}`)}}function ka(t,e,n){return n.noiseLevel=e.negative,n.maxCriteria=!1,ls(t,n)}function ls(t,e){let{shape:n,maxAbsDdY:s,frequency:i,broadWidth:o,optimize:a,maxCriteria:l,factorLimits:r,sgOptions:m,minMaxRatio:c,broadRatio:g,noiseLevel:C,smoothY:u,optimization:p,realTopDetection:f}=e,d=(0,at.gsd)(t,{sgOptions:m,maxCriteria:l,minMaxRatio:c,noiseLevel:C,smoothY:u,realTopDetection:f}),y=(0,at.setShape)(d,{output:d,shape:n}),O=o?(0,at.joinBroadPeaks)(y,{shape:n,broadWidth:o,optimization:p,broadRatio:CC(d,{maxAbsDdY:s,broadRatio:g})}).map(as):y.map(as);return Sn(a?(0,at.optimizePeaks)(t,O,{shape:n,factorLimits:r,optimization:p}).map(as):O,{frequency:i})}function CC(t,e={}){let{maxAbsDdY:n,broadRatio:s=.0025}=e;if(n&&t.length>0){let i=(0,V.xMaxAbsoluteValue)(t.map(o=>o.ddY));return sn/i}return s}function uC(t,e){let{noiseLevel:n,useSanPlot:s,thresholdFactor:i}=e,o=a=>typeof a=="number"?{positive:a,negative:-a}:a;return n?o(n):s?(0,V.xNoiseSanPlot)(t,{factorStd:i}):o((0,V.xAbsoluteMedian)(t)i)}function as(t){let{id:e,shape:n,x:s,y:i,width:o}=t;return{id:e,x:s,y:i,width:o,shape:n}}var Pn=class extends Error{constructor(e){super("windowSize must be an odd integer >= 5, check data property of this error for contextual information"),this.data=e}};var gs=require("@lukeed/uuid"),La=require("ml-spectra-processing");var za=require("@lukeed/uuid");function qa(t){t.sort((e,n)=>e.from-n.from);for(let e=0;e<t.length-1;e++){let n=t[e],s=t[e+1];n.to>s.from&&(n.id=(0,za.v4)(),n.to=Math.max(s.to,n.to),n.signals&&s.signals&&(n.signals=n.signals.concat(s.signals)),n.integration!==void 0&&(n.integration+=s.integration\|\|0),t.splice(e+1,1),e--)}return t}var Nn=["s","d","t","q","quint","h","sept","o","n"],pC=2.5,fC=1,dC={jAxis:"x",intensity:"intensity"};function yC(t){if(!("symRank"in t))throw new Error("Internal error, symRank was not calculated");if(!("mask"in t))throw new Error("Internal Error, mask was not added")}var jn={compilePattern:(t,e={})=>{let{jAxisKey:n=dC,symRatio:s=2.5}=e,i=bC(t,{...e,symRatio:s,maxError:pC,iteration:1,jAxisKey:n});if(i.multiplicity="m",i.asymmetric=!0,yC(i),i.symRank>=.95&&i.peaksComp.length<32){i.asymmetric=!1;let o,a,l,r=1,m=[];for(let c=0;c<9;c++){let g=vC(i,c),C=!1;if(g.length===1&&c===0)C=!0;else if(g.length<=1)continue;let u=xC(g);a=2c;let p=null,f=1;for(;!C&&(p=OC(u,a))!==null&&f<400;){let d=new Array(p.length);r=1;for(let h=0;h<p.length;h++){d[h]=new Array(p[h]);for(let D=0;D<p[h];D++)d[h][D]=r++}m=[];let y=1;m.push(g[1].x-g[0].x),o=g[0].x,d[0].splice(0,1),d[1].splice(0,1),r=1;let O=2;for(l=2c-1;m.length<c&&O<l&&r<g.length;){for(f+=1,y++;r<g.length&&d[r].length===0;)r++;if(r<g.length){m.push(g[r].x-g[0].x),d[r].splice(0,1),O++;for(let h=2;h<=y;h++){let D=0;for(let S=0;S<h;S++)D+=m[S];for(let S=1;S<d.length;S++)if(Math.abs(g[S].x-(o+D))<.25){d[S].splice(0,1),O++;break}}}}let x=DC(m);C=!0;for(let h=0;h<x.length;h++)x[h].intensity!==p[h]&&(C=!1)}C&&hC(i,m)}}for(let o of i.peaksComp)o.x/=i.observe,o.width=i.observe;return i}};function hC(t,e){let n=t.peaksComp,s=n.length;t.startX=n[0].x/t.observe-n[0].width,t.stopX=n[s-1].x/t.observe+n[s-1].width,t.integralData.from=n[0].x/t.observe-n[0].width3,t.integralData.to=n[s-1].x/t.observe+n[s-1].width3,t.maskPattern=t.mask2,t.multiplicity=HC(t,e),t.pattern=t.multiplicity}function HC(t,e){let s="",i=1,o=[];if(e&&e.length>0){e.sort((l,r)=>r-l);for(let l=0;l<e.length-1;l++)Math.abs(e[l]-e[l+1])<.05?i++:(o.push({coupling:Math.abs(e[l]),multiplicity:Nn[i]}),s+=Nn[i],i=1);let a=e.length-1;o.push({coupling:Math.abs(e[a]),multiplicity:Nn[i]}),s+=Nn[i],t.nmrJs=o}else s="s",Math.abs(t.startX-t.stopX)t.observe>16&&(s="br s");return s}function DC(t){let n=[{x:0,intensity:2*t.length}];for(let s of t)for(let i=n.length-1;i>=0;i--)n.push({x:n[i].x+s/2,intensity:n[i].intensity/2}),n[i].x=n[i].x-s/2,n[i].intensity=n[i].intensity/2;n.sort((s,i)=>s.x-i.x);for(let s=n.length-2;s>=0;s--)Math.abs(n[s].x-n[s+1].x)<.1&&(n[s].intensity+=n[s+1].intensity,n.splice(s+1,1));return n}function OC(t,e){let n=Math.ceil(t.values.length.5),s=t.values.length,i=0,o;for(;i!==e;){for(o=!1;!o;)if(o=!0,t.currentIndex[t.active]++,t.currentIndex[t.active]>=t.values[t.active].length){if(t.active+1===n)return null;t.currentIndex[t.active]=0,o=!1,t.active++}else t.active=0;i=0;for(let a=0;a<n;a++)i+=t.values[a][t.currentIndex[a]]2;t.values.length%2!==0&&(i-=t.values[n-1][t.currentIndex[n-1]])}if(i===e){let a=new Array(s);for(let l=0;l<n;l++)a[l]=t.values[l][t.currentIndex[l]],a[s-l-1]=t.values[l][t.currentIndex[l]];return a}return null}function xC(t){let e=new Array(t.length),n=new Array(t.length),s,i;e[0]=[1],e[t.length-1]=[1],n[0]=-1,n[t.length-1]=0;for(let o=1;o<t.length-1;o++){s=Math.round(t[o].intensity.85),i=Math.round(t[o].intensity1.15),e[o]=[];for(let a=s;a<=i;a++)e[o].push(a);n[o]=0}return{values:e,currentIndex:n,active:0}}function bC(t,e){let n=ms(t,e);if(!n.peaksComp)throw new Error("internal peaksComp was not created");let s=n.peaksComp,i=n.mask,o=t.delta;t.delta=(t.peaks[0].x+t.peaks[t.peaks.length-1].x)/2;let a=ms(t,e);if(!a.peaksComp)throw new Error("internal peaksComp was not created");return a.peaksComp.length>s.length?a:(t.delta=o,t.peaksComp=s,t.mask=i,n)}function 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y=0;y<l;y++)f[d+p].set(t.z[d],u);return{...t,z:f,minX:n-uc,maxX:s+uc,minY:i-pm,maxY:o+pm}}var WC=[[0,0,1,2,2,2,1,0,0],[0,1,4,7,7,7,4,1,0],[1,4,5,3,0,3,5,4,1],[2,7,3,-12,-23,-12,3,7,2],[2,7,0,-23,-40,-23,0,7,2],[2,7,3,-12,-23,-12,3,7,2],[1,4,5,3,0,3,5,4,1],[0,1,3,7,7,7,3,1,0],[0,0,1,2,2,2,1,0,0]];function Cs(t,e){let{sizeToPad:n=14,realTopDetection:s=!0,nuclei:i=["1H","1H"],observedFrequencies:o,enhanceSymmetry:a=!1,clean:l=!0,maxPercentCutOff:r=.03,tolerances:m=[24,24],convolutionByFFT:c=!0,kernel:g}=e,{thresholdFactor:C=.5}=e;if(!(0,rl.isAnyArray)(o))throw new Error("observedFrequencies is mandatory");C=C===0?1:Math.abs(C);let u=t.z[0].length,p=t.z.length;p<n&&(t=al(t,{width:n}),u=t.z[0].length,p=t.z.length);let f=new Float64Array(up),d=new Float64Array(up);for(let D=0;D<p;D++){let S=t.z[D];for(let H=0;H<u;H++){let b=Du+H;f[b]=Math.abs(S[H]),d[b]=S[H]}}let y=g?el(g):WC,O=c?An.fft(f,y,{rows:p,cols:u}):An.direct(f,y,{rows:p,cols:u}),x=ml.findPeaks2DRegion(f,{originalData:d,filteredData:O,rows:p,cols:u,nStdDev:C});l&&(x=sl(x,r));let h=LC(Rn(x),{nRows:p,nCols:u,minX:t.minX,maxX:t.maxX,minY:t.minY,maxY:t.maxY,absoluteData:f,originalData:d,tolerances:m,nuclei:i,observedFrequencies:o,realTopDetection:s});return a&&(h=il(h)),h}function LC(t,e){let{nCols:n,nRows:s,absoluteData:i,originalData:o,observedFrequencies:a,tolerances:l,nuclei:r,realTopDetection:m,minY:c,maxY:g,minX:C,maxX:u}=e,[p,f]=r,[d,y]=l,[O,x]=a,h=(g-c)/(s-1),D=(u-C)/(n-1);m&&(t=tl(t,{nCols:n,absoluteData:i,originalData:o,minX:C,maxX:u,minY:c,maxY:g}));for(let v=t.length-1;v>=0;v--){let{x:P,y:R}=t[v];t[v].x=C+DP,t[v].y=c+hR,t[v].minX=C+Dt[v].minX,t[v].minY=c+ht[v].minY,t[v].maxX=C+Dt[v].maxX,t[v].maxY=c+ht[v].maxY}let S=[];for(let v=0;v<t.length;v++)for(let P=v;P<t.length;P++)Math.abs(t[v].x-t[P].x)O<d&&Math.abs(t[v].y-t[P].y)x<y?S.push(1):S.push(0);let H=(0,cl.default)(S),b=[];if(H)for(let v of H){let P={id:(0,ll.v4)(),x:{delta:0,nucleus:p,resolution:D},y:{delta:0,nucleus:f,resolution:h}},R=[],M=0;for(let A=0;A<v.length;A++)v[A]===1&&(R.push(t[A]),P.x.delta+=t[A].xt[A].z,P.y.delta+=t[A].yt[A].z,M+=t[A].z);P.x.delta/=M,P.y.delta/=M,P.peaks=R,b.push(P)}return b}var gl=require("@lukeed/uuid"),Cl=z(require("ml-simple-clustering"));var{parse:UC,stringify:_C}=JSON;function ZC(t,e={}){let{reference:n=0,getZones:s=!1,referenceMaxShiftError:i=.08,tolerances:o=[10,100],nuclei:a=["1H","1H"],observedFrequencies:l=[400,400],jAnalyzer:r={jAxisKey:{jAxis:"y",intensity:"z"}}}=e,m=JC(t,{observedFrequencies:l,tolerances:o,nuclei:a,jAnalyzer:r}),c=[];for(let g of m){let C=g.y.delta;Math.abs(C-n)>i\|\|c.push(g)}return c=Rn(c),s?Mn(c):c}function JC(t,e){let{observedFrequencies:n,tolerances:s,nuclei:i,jAnalyzer:o}=e,a={observedFrequencies:n,tolerances:s,nuclei:i,dx:t[0].x.resolution,dy:t[0].y.resolution},l=.02n[0],r=[];for(let m of t){let c=[];for(let g of m.peaks\|\|[])c.push({...g,width:l});c.sort((g,C)=>g.y-C.y),r.push({nbPeaks:c.length,multiplicity:"",pattern:"",startX:c[0].y-l,stopX:c[c.length-1].y+l,delta:m.y.delta,observe:n[1],integralData:{value:-1,from:Number.MAX_SAFE_INTEGER,to:Number.MIN_SAFE_INTEGER},peaks:c})}for(let m=0;m<t.length;m++){let c=jn.compilePattern(r[m],o);if(c.maskPattern&&c.multiplicity!=="m"&&c.multiplicity!==""){let g=[];for(let C=c.maskPattern.length-1;C>=0;C--)if(!c.maskPattern[C]){let u=c.peaks.splice(C,1)[0];g.push(u),c.mask.splice(C,1),c.mask2?.splice(C,1),c.maskPattern.splice(C,1),c.nbPeaks--}if(g.length>0){g.reverse();let C=VC(g,a);for(let u of C)r.push(u)}}}return t.sort((m,c)=>c.x.delta-m.x.delta),t}function VC(t,e){let{observedFrequencies:n,tolerances:s,nuclei:i,dx:o,dy:a}=e,l=UC(_C(t)),[r,m]=i,[c,g]=s,[C,u]=n,p=[];for(let y=0;y<l.length;y++)for(let O=y;O<l.length;O++)Math.abs(l[y].x-l[O].x)C<c&&Math.abs(l[y].y-l[O].y)u<g?p.push(1):p.push(0);let f=(0,Cl.default)(p),d=[];if(f)for(let y of f){let O={id:(0,gl.v4)(),nucleusX:r,nucleusY:m,integralData:{from:Number.MAX_SAFE_INTEGER,to:Number.MIN_SAFE_INTEGER},nbPeaks:0,multiplicity:"",pattern:"",observe:u,resolutionX:o,resolutionY:a,shiftX:0,shiftY:0},x=[],h=[Number.MAX_VALUE,0],D=[Number.MAX_VALUE,0],S=0;for(let H=y.length-1;H>=0;H--)y[H]===1&&(O.nbPeaks++,l[H].width\|\|(l[H].width=.02),x.push(l[H]),O.shiftX+=l[H].xl[H].z,O.shiftY+=l[H].yl[H].z,S+=l[H].z,l[H].minX<h[0]&&(h[0]=l[H].minX),l[H].maxX>h[1]&&(h[1]=l[H].maxX),l[H].minY<D[0]&&(D[0]=l[H].minY),l[H].maxY>D[1]&&(D[1]=l[H].maxY));O.fromTo=[{from:h[0],to:h[1]},{from:D[0],to:D[1]}],O.shiftX/=S,O.shiftY/=S,O.delta1=O.shiftY,O.peaks=x,d.push(O)}return d}async function GC(t="https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing",e={}){let{format:n="tsv"}=e;t.includes("google.com")&&(t=`https://googledocs.cheminfo.org/spreadsheets/d/${$C(t)}/export?format=tsv`);let s,i=await fetch(t);switch(n){case"tsv":s=KC(await i.text());break;case"json":s=await i.json();break;default:throw new Error("unknown database format")}let o=[];for(let a of s.data){let l={smiles:"",solvent:"",nucleus:"",jcampURL:"",names:[],meta:{},ranges:[]};for(let r=0;r<a.length;r++)switch(s.kinds[r]){case"smiles":l.smiles=a[r];break;case"solvent":l.solvent=a[r];break;case"nucleus":l.nucleus=a[r];break;case"jcampURL":l.jcampURL=a[r];break;case"name":l.names&&l.names.push(a[r]);break;case"meta":l.meta&&(l.meta[s.labels[r]]=a[r]);break;case"signal":{let m=vn(a[r]);m&&l.ranges.push(m);break}default:throw new Error(`Unknown column kind: ${s.kinds[r]}`)}o.push(l)}return o}function $C(t){return t.replace(/.\/(?<uuid>[^/]{20,50})./,"$<uuid>")}function KC(t){let e=t.split(/\r?\n/).filter(o=>!/^\s$/.exec(o)).map(o=>o.split(" ").map(a=>a.trim())),n=e[0],s=e[1],i=e.slice(2);return{labels:n,kinds:s,data:i}}var QC=[{names:["acetic acid"],smiles:"CC(=O)O",ranges:[{signals:[{delta:171.69,assignment:"CO"}],from:171.685,to:171.695},{signals:[{delta:20.13,assignment:"CH\u2083"}],from:20.125,to:20.134999999999998}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["acetone"],smiles:"CC(=O)C",ranges:[{signals:[{delta:204.19,assignment:"CO"}],from:204.185,to:204.195},{signals:[{delta:30.17,assignment:"CH\u2083"}],from:30.165000000000003,to:30.175}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["acetonitrile"],smiles:"CC#N",ranges:[{signals:[{delta:116.79,assignment:"CN"}],from:116.78500000000001,to:116.795},{signals:[{delta:.45,assignment:"CH\u2083"}],from:.445,to:.455}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["benzene"],smiles:"c1ccccc1",ranges:[{signals:[{delta:128.84,assignment:"CH"}],from:128.835,to:128.845}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["tert -butyl alcohol"],smiles:"CC(C)(C)O",ranges:[{signals:[{delta:67.5,assignment:"(CH\u2083)\u2083C"}],from:67.495,to:67.505},{signals:[{delta:30.57,assignment:"(CH\u2083)\u2083C"}],from:30.565,to:30.575}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["carbon dioxide"],smiles:"O=C=O",ranges:[{signals:[{delta:125.69,assignment:"CO\u2082"}],from:125.685,to:125.695}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["carbon disulfide"],smiles:"S=C=S",ranges:[{signals:[{delta:193.37,assignment:"CS\u2082"}],from:193.365,to:193.375}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["carbon tetrachloride"],smiles:"ClC(Cl)(Cl)Cl",ranges:[{signals:[{delta:96.89,assignment:"CCl\u2084"}],from:96.885,to:96.895}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["chloroform"],smiles:"ClC(Cl)Cl",ranges:[{signals:[{delta:79.24,assignment:"CH"}],from:79.235,to:79.24499999999999}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["18-crown-6"],smiles:"C1COCCOCCOCCOCCOCCO1",ranges:[{signals:[{delta:71.34,assignment:"CH\u2082"}],from:71.33500000000001,to:71.345}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["cyclohexane"],smiles:"C1CCCCC1",ranges:[{signals:[{delta:27.58,assignment:"CH\u2082"}],from:27.575,to:27.584999999999997}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["1,2-dichloroethane"],smiles:"ClCCCl",ranges:[{signals:[{delta:44.64,assignment:"CH\u2082"}],from:44.635,to:44.645}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["dichloromethane"],smiles:"ClCCl",ranges:[{signals:[{delta:54.67,assignment:"CH\u2082"}],from:54.665,to:54.675000000000004}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["diethyl ether"],smiles:"CCOCC",ranges:[{signals:[{delta:15.49,assignment:"CH\u2083"}],from:15.485,to:15.495000000000001},{signals:[{delta:66.14,assignment:"CH\u2082"}],from:66.135,to:66.145}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["diglyme"],smiles:"COCCOCCOC",ranges:[{signals:[{delta:58.72,assignment:"CH\u2083"}],from:58.714999999999996,to:58.725},{signals:[{delta:71.17,assignment:"CH\u2082"}],from:71.165,to:71.175},{signals:[{delta:72.72,assignment:"CH\u2082"}],from:72.715,to:72.725}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["dimethylformamide"],smiles:"C(=O)N(C)C",ranges:[{signals:[{delta:161.96,assignment:"CH"}],from:161.955,to:161.965},{signals:[{delta:35.65,assignment:"CH\u2083"}],from:35.644999999999996,to:35.655},{signals:[{delta:30.7,assignment:"CH\u2083"}],from:30.695,to:30.705}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["1,4-dioxane"],smiles:"C1COCCOC1",ranges:[{signals:[{delta:67.65,assignment:"CH\u2082"}],from:67.64500000000001,to:67.655}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["DME","diethyl ether"],smiles:"CCOCC",ranges:[{signals:[{delta:58.72,assignment:"CH\u2083"}],from:58.714999999999996,to:58.725},{signals:[{delta:72.58,assignment:"CH\u2082"}],from:72.575,to:72.585}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["ethane"],smiles:"CC",ranges:[{signals:[{delta:6.79,assignment:"CH\u2083"}],from:6.785,to:6.795}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["ethanol"],smiles:"CCO",ranges:[{signals:[{delta:18.9,assignment:"CH\u2083"}],from:18.895,to:18.904999999999998},{signals:[{delta:57.6,assignment:"CH\u2082"}],from:57.595,to:57.605000000000004}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["ethyl acetate"],smiles:"CC(=O)CC",ranges:[{signals:[{delta:20.45,assignment:"CH\u2083CO"}],from:20.445,to:20.455},{signals:[{delta:170.32,assignment:"CO"}],from:170.315,to:170.325},{signals:[{delta:60.3,assignment:"CH\u2082"}],from:60.294999999999995,to:60.305},{signals:[{delta:14.37,assignment:"CH\u2083"}],from:14.364999999999998,to:14.375}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["ethylene"],smiles:"C=C",ranges:[{signals:[{delta:123.09,assignment:"CH\u2082"}],from:123.08500000000001,to:123.095}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["ethylene glycol"],smiles:"OCCO",ranges:[{signals:[{delta:64.35,assignment:"CH\u2082"}],from:64.345,to:64.35499999999999}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["H 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N={};I(N,{DatumKind:()=>gt,Filters:()=>W,Filters1D:()=>It,Filters2D:()=>be,FiltersManager:()=>Xe,MultiplicityPatterns:()=>Y,RangeUtilities:()=>Fe,SignalKinds:()=>Qm,SignalKindsToInclude:()=>Tt,XYAutoPeaksPickingWindowSizeError:()=>Pn,apodization:()=>_,apodizationFilter:()=>Qt,carbonImpurities:()=>KC,checkIntegralKind:()=>kt,checkMultiplet:()=>ys,checkMultiplicity:()=>au,couplingACSPatterns:()=>zt,couplingPatterns:()=>St,fftDirectDimension:()=>ie,fftIndirectDimension:()=>le,findMultiplet:()=>Vt,get13CAssignments:()=>ag,get1DErrorFactor:()=>Et,get1HAssignments:()=>sg,get2DErrorFactor:()=>Ie,getAssignments:()=>vg,getBaselineZones:()=>ru,getDatabase:()=>VC,getFrequency:()=>yn,getPeakDelta:()=>on,getShiftX:()=>ct,impurities:()=>Be,isEmptyMolecule:()=>os,isMolfileNotEmpty:()=>oC,isRangeExists:()=>je,isZoneExists:()=>Te,mapIntegrals:()=>ve,mapPeaks:()=>Pe,mapRanges:()=>Me,mapZones:()=>ke,markSolventPeaks:()=>iu,normalizeNucleus:()=>cC,optimizeSignals:()=>eC,peakToXY:()=>bc,peaksFilterImpurities:()=>We,peaksToXY:()=>Ye,predict:()=>J,predictSpectra:()=>Uc,protonImpurities:()=>QC,rangeFromSignal:()=>Bt,rangesToACS:()=>Rg,rangesToXY:()=>Zg,resurrect:()=>aC,signalJoinCouplings:()=>is,signalMultiplicityPattern:()=>qt,signals2DToZ:()=>Ue,signalsToFID:()=>iC,signalsToRanges:()=>_e,signalsToXY:()=>Yt,simulate1D:()=>Ve,solventSuppression:()=>ds,splitPatterns:()=>Zt,translateMultiplet:()=>lu,updateIntegralsRelativeValues:()=>Se,updateRanges:()=>we,updateRangesRelativeValues:()=>Ae,xBackwardLinearPrediction:()=>kn,xForwardLinearPrediction:()=>Yn,xyAutoPeaksPicking:()=>ms,xyAutoRangesPicking:()=>SC,xyCalculateT1:()=>jC,xyPeaksOptimization:()=>PC,xyzAutoSignalsPicking:()=>us,xyzAutoZonesPicking:()=>RC,xyzJResAnalyzer:()=>ZC,xyzPhaseCorrection:()=>fe});module.exports=Sl(N);var Xe={};I(Xe,{addFilter:()=>ze,applyFilter:()=>Cc,deleteFilter:()=>pc,enableFilter:()=>ro,lookupForFilter:()=>lo,reapplyFilters:()=>Ee});var oo=require("@lukeed/uuid");function Ds(t){let{x:e,re:n,im:s}=t\|\|{x:[],re:[],im:[]};return{x:e.slice(),re:n.slice(),im:s?.slice()\|\|null}}function xs(t){let e={};if(Pl(t))for(let n in t)Os(e,n,t[n]);else for(let n in t)Os(e,n,t[n]);return e}function Pl(t){return"re"in t}function Os(t,e,n){if(n){let{z:s,...i}=n;t[e]={z:s.slice(),...i}}}var Tn={};I(Tn,{DOMAIN_UPDATE_RULES:()=>jl,apply:()=>Ml,id:()=>Es,isApplicable:()=>zs,name:()=>Nl,reduce:()=>Rl});function At(t,e){let n=t.length,{windowData:s,start:i=0,length:o=n,pointsToShift:a=0,output:l=new Float64Array(t)}=e,r=Math.min(i+o,n-a);for(let m=i,c=0;m<r;m++)l[m]=s[c++];for(let m=n-1,c=0;m>n-a-1;m--)l[m]=s[c++];return l}function bs(t,e){let n=new Float64Array(e),s=Number.MIN_SAFE_INTEGER;for(let i=0;i<e;i++){let o=t(i);n[i]=o,o>s&&(s=o)}for(let i=0;i<e;i++)n[i]/=s;return n}function 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defined");return{kind:"modifiedGaussian",options:{dwellTime:s,length:n,...e}}}function Rs(t){let{exponent:e=1,offset:n=0,end:s=1,length:i}=t;if(i===void 0)throw new Error("length options should exists for sineBell shape");if(s<0\|\|s>1)throw new Error("the end parameter should be [0-1]");let o=Math.PIn,a=Math.PI(s-n)/(i-1);return l=>Math.sin(o+al)*e}function Fs(t,e){let{length:n=t.re.length}=e;return{kind:"sineBell",options:{length:n,...e}}}function As(t){let{length:e,lb:n=1,dw:s}=t,i=-s/n;return o=>{let a=Math.exp(io);return a/(a*2+Math.exp(-i(o-e))*2)}}function ws(t,e){let{dw:n}=e,{length:s=t.re.length}=e;if(n===void 0)if("x"in t){let{x:i}=t;n=i[1]-i[0]}else throw new Error("dw should be defined");return{kind:"traf",options:{dw:n,length:s,...e}}}function Is(t){let{kind:e,options:n}=t;switch(e){case"exponential":return vs(n);case"modifiedGaussian":return js(n);case"lorentzToGauss":return Ps(n);case"sineBell":return Rs(n);case"traf":return As(n);default:throw Error(`Unknown 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Qt(t,e){let{lineBroadening:n,gaussBroadening:s,lineBroadeningCenter:i}=e,o=t.filters?.find(C=>C.name==="digitalFilter"&&C.flag),a=o?Math.floor(o.value.digitalFilterValue):0,l=t.data.re,r=t.data.im,m=t.data.x,c=l.length,g=(m[c-1]-m[0])/(c-1);return _({re:l,im:r},{pointsToShift:a,compose:{length:c,shapes:[{start:0,shape:{kind:"lorentzToGauss",options:{length:c,dw:g,exponentialHz:s>0?n:-n,gaussianHz:s,center:i}}}]}})}var Es="apodization",Nl="Apodization",jl={updateXDomain:!0,updateYDomain:!1};function Ml(t,e){if(!zs(t))throw new Error("apodization not applicable on this data");let{lineBroadening:n=1,gaussBroadening:s=0,lineBroadeningCenter:i=0}=e;if(Object.keys(e).length===0){let a=t.filters?.find(l=>l.name===Es);a&&(a.value={lineBroadening:n,gaussBroadening:s,lineBroadeningCenter:i})}let o=Qt(t,{lineBroadening:n,gaussBroadening:s,lineBroadeningCenter:i});t.data={...t.data,re:o.re,im:o.im}}function zs(t){return!!(t.info.isComplex&&t.info.isFid)}function 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ie(t,e={}){let{re:n,im:s}=t,i=n.length,o=n[0].length,{reverse:a,digitalFilterValue:l=0}=e,r=new se.Matrix(i,o),m=new se.Matrix(i,o),{phaseCorrection:c={}}=e,{ph0:g,ph1:C,mode:u="no"}=c;for(let p=0;p<i;p++){let f={re:n[p],im:a?(0,rt.xMultiply)(s[p],-1):s[p]};Object.assign(f,Di(f,{digitalFilterValue:l})),Object.assign(f,(0,rt.reimFFT)(f,{applyZeroShift:!0}));let d=lMath.PI2;d>0&&Object.assign(f,(0,rt.reimPhaseCorrection)(f,0,-d,{reverse:!0})),u==="pk"&&g!==void 0&&C!==void 0&&Object.assign(f,(0,rt.reimPhaseCorrection)(f,gMath.PI/180,CMath.PI/180,{reverse:!0})),r.setRow(p,f.re),m.setRow(p,f.im)}return{re:r,im:m}}var K=require("ml-spectra-processing");function Oi(t){let{re:{z:e},im:{z:n}}=t,s=[],i=[];for(let o=0;o<e.length;o+=2){let a=e[o],l=n[o],r=e[o+1],m=n[o+1];s.push((0,K.xSubtract)((0,K.xMultiply)(m,-1),l)),s.push((0,K.xSubtract)(r,a)),i.push((0,K.xAdd)(r,a)),i.push((0,K.xSubtract)(m,l))}return{re:s,im:i}}var nm="fftDimension1",em="FFT Dimension 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n={re:mt.Matrix.checkMatrix(t.re),im:mt.Matrix.checkMatrix(t.im)},s=n.re.rows,i=n.re.columns,{acquisitionScheme:o,reverse:a}=e,l={...e},r={};if(o==="notPhaseSensitive"){let m=new mt.Matrix(s,i),c=new mt.Matrix(s,i);for(let g=0;g<i;g++){let C={re:n.re.getColumn(g),im:a\|\|o==="notPhaseSensitive"?(0,Q.xMultiply)(n.im.getColumn(g),-1):n.im.getColumn(g)};C.re[0]=.5,C.im[0]=.5;let{re:u,im:p}=bi(C,l);m.setColumn(g,u),c.setColumn(g,p)}r.rr=m,r.ir=c}else for(let m in n){let c=o==="SEQ"?s:s/2,g=new mt.Matrix(c,i),C=new mt.Matrix(c,i);for(let u=0;u<i;u++){let p=am(n[m],{acquisitionScheme:o,index:u,reverse:a});p.re[0]=.5,p.im[0]=.5;let{re:f,im:d}=bi(p,l);g.setColumn(u,f),C.setColumn(u,d)}m==="re"?(r.rr=g,r.ri=C):(r.ir=g,r.ii=C)}return r}function bi(t,e){let{acquisitionScheme:n,phaseCorrection:s={}}=e;t.re[0]=.5,t.im[0]=.5;let i=(0,Q.reimFFT)(t,{applyZeroShift:n!=="SEQ"}),{mode:o,ph0:a,ph1:l}=s;return(o&&o==="mc"\|\|n==="notPhaseSensitive")&&Object.assign(i,{re:(0,Q.reimAbsolute)(i),im:new 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ft:3.41}],"grease^f":[{proton:"CH3",coupling:0,multiplicity:"m",shift:.92},{proton:"CH2",coupling:0,multiplicity:"br_s",shift:1.36}],"n-hexane":[{proton:"CH3",coupling:0,multiplicity:"t",shift:.89},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.24}],hmpag:[{proton:"CH3",coupling:9.5,multiplicity:"d",shift:2.4}],methanol:[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.07}],nitromethane:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.94}],"n-pentane":[{proton:"CH3",coupling:7,multiplicity:"t",shift:.86},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.23}],"2-propanol":[{proton:"CH3",coupling:6,multiplicity:"d",shift:.95},{proton:"CH",coupling:6,multiplicity:"sep",shift:3.67}],pyridine:[{proton:"CH(2)",coupling:0,multiplicity:"m",shift:8.53},{proton:"CH(3)",coupling:0,multiplicity:"m",shift:6.66},{proton:"CH(4)",coupling:0,multiplicity:"m",shift:6.98}],silicone_greasei:[{proton:"CH3",coupling:0,multiplicity:"s",shift:.29}],tetrahydrofuran:[{proton:"CH2",coupling:0,multiplicity:"m",shift:1.4},{proton:"CH2O",coupling:0,multiplicity:"m",shift:3.57}],toluene:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.11},{proton:"CH(o/p)",coupling:0,multiplicity:"m",shift:7.02},{proton:"CH(m)",coupling:0,multiplicity:"m",shift:7.13}],triethylamine:[{proton:"CH3",coupling:7,multiplicity:"t",shift:.96},{proton:"CH2",coupling:7,multiplicity:"q",shift:2.4}]},cd3cn:{tms:[{proton:"X",coupling:0,multiplicity:"",shift:0}],solvent:[{proton:"X",coupling:0,multiplicity:"",shift:1.94}],h2o:[{proton:"H2O",coupling:0,multiplicity:"s",shift:2.13}],acetic_acid:[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.96}],acetone:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.08}],acetonitrile:[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.96}],benzene:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.37}],"tert-butyl_alcohol":[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.16},{proton:"OHc",coupling:0,multiplicity:"s",shift:2.18}],"tert-butyl_methyl_ether":[{proton:"CCH3",coupling:0,multiplicity:"s",shift:1.14},{proton:"OCH3",coupling:0,multiplicity:"s",shift:3.13}],bhtb:[{proton:"ArH",coupling:0,multiplicity:"s",shift:6.97},{proton:"OHc",coupling:0,multiplicity:"s",shift:5.2},{proton:"ArCH3",coupling:0,multiplicity:"s",shift:2.22},{proton:"ArC(CH3)3",coupling:0,multiplicity:"s",shift:1.39}],chloroform:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.58}],cyclohexane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:1.44}],"1,2-dichloroethane":[{proton:"CH2",coupling:0,multiplicity:"s",shift:3.81}],dichloromethane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:5.44}],diethyl_ether:[{proton:"CH3",coupling:7,multiplicity:"t",shift:1.12},{proton:"CH2",coupling:7,multiplicity:"q",shift:3.42}],diglyme:[{proton:"CH2",coupling:0,multiplicity:"m",shift:3.53},{proton:"CH2",coupling:0,multiplicity:"m",shift:3.45},{proton:"OCH3",coupling:0,multiplicity:"s",shift:3.29}],"1,2-dimethoxyethane":[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.28},{proton:"CH2",coupling:0,multiplicity:"s",shift:3.45}],dimethylacetamide:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:1.97},{proton:"NCH3",coupling:0,multiplicity:"s",shift:2.96},{proton:"NCH3",coupling:0,multiplicity:"s",shift:2.83}],dimethylformamide:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.92},{proton:"CH3",coupling:0,multiplicity:"s",shift:2.89},{proton:"CH3",coupling:0,multiplicity:"s",shift:2.77}],dimethyl_sulfoxide:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.5}],dioxane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:3.6}],ethanol:[{proton:"CH3",coupling:7,multiplicity:"t",shift:1.12},{proton:"CH2",coupling:7,multiplicity:"q",shift:3.54},{proton:"OH",coupling:5,multiplicity:"s,t",shift:2.47}],ethyl_acetate:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:1.97},{proton:"CH2CH3",coupling:7,multiplicity:"q",shift:4.06},{proton:"CH2CH3",coupling:7,multiplicity:"t",shift:1.2}],ethyl_methyl_ketone:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:2.06},{proton:"CH2CH3",coupling:7,multiplicity:"q",shift:2.43},{proton:"CH2CH3",coupling:7,multiplicity:"t",shift:.96}],ethylene_glycol:[{proton:"CH",coupling:0,multiplicity:"s",shift:3.51}],"grease^f":[{proton:"CH3",coupling:0,multiplicity:"m",shift:.86},{proton:"CH2",coupling:0,multiplicity:"br_s",shift:1.27}],"n-hexane":[{proton:"CH3",coupling:0,multiplicity:"t",shift:.89},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.28}],hmpag:[{proton:"CH3",coupling:9.5,multiplicity:"d",shift:2.57}],methanol:[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.28},{proton:"OH",coupling:0,multiplicity:"s",shift:2.16}],nitromethane:[{proton:"CH3",coupling:0,multiplicity:"s",shift:4.31}],"n-pentane":[{proton:"CH3",coupling:7,multiplicity:"t",shift:.87},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.29}],"2-propanol":[{proton:"CH3",coupling:6,multiplicity:"d",shift:1.09},{proton:"CH",coupling:6,multiplicity:"sep",shift:3.87}],pyridine:[{proton:"CH(2)",coupling:0,multiplicity:"m",shift:8.57},{proton:"CH(3)",coupling:0,multiplicity:"m",shift:7.33},{proton:"CH(4)",coupling:0,multiplicity:"m",shift:7.73}],silicone_greasei:[{proton:"CH3",coupling:0,multiplicity:"s",shift:.08}],tetrahydrofuran:[{proton:"CH2",coupling:0,multiplicity:"m",shift:1.8},{proton:"CH2O",coupling:0,multiplicity:"m",shift:3.64}],toluene:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.33},{proton:"CH(o/p)",coupling:0,multiplicity:"m",shift:7.2},{proton:"CH(m)",coupling:0,multiplicity:"m",shift:7.2}],triethylamine:[{proton:"CH3",coupling:7,multiplicity:"t",shift:.96},{proton:"CH2",coupling:7,multiplicity:"q",shift:2.45}]},cd3od:{tms:[{proton:"X",coupling:0,multiplicity:"",shift:0}],solvent:[{proton:"X",coupling:0,multiplicity:"",shift:3.31}],h2o:[{proton:"H2O",coupling:0,multiplicity:"s",shift:4.87}],acetic_acid:[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.99}],acetone:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.15}],acetonitrile:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.03}],benzene:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.33}],"tert-butyl_alcohol":[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.4}],"tert-butyl_methyl_ether":[{proton:"CCH3",coupling:0,multiplicity:"s",shift:1.15},{proton:"OCH3",coupling:0,multiplicity:"s",shift:3.2}],bhtb:[{proton:"ArH",coupling:0,multiplicity:"s",shift:6.92},{proton:"ArCH3",coupling:0,multiplicity:"s",shift:2.21},{proton:"ArC(CH3)3",coupling:0,multiplicity:"s",shift:1.4}],chloroform:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.9}],cyclohexane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:1.45}],"1,2-dichloroethane":[{proton:"CH2",coupling:0,multiplicity:"s",shift:3.78}],dichloromethane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:5.49}],diethyl_ether:[{proton:"CH3",coupling:7,multiplicity:"t",shift:1.18},{proton:"CH2",coupling:7,multiplicity:"q",shift:3.49}],diglyme:[{proton:"CH2",coupling:0,multiplicity:"m",shift:3.61},{proton:"CH2",coupling:0,multiplicity:"m",shift:3.58},{proton:"OCH3",coupling:0,multiplicity:"s",shift:3.35}],"1,2-dimethoxyethane":[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.35},{proton:"CH2",coupling:0,multiplicity:"s",shift:3.52}],dimethylacetamide:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:2.07},{proton:"NCH3",coupling:0,multiplicity:"s",shift:3.31},{proton:"NCH3",coupling:0,multiplicity:"s",shift:2.92}],dimethylformamide:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.97},{proton:"CH3",coupling:0,multiplicity:"s",shift:2.99},{proton:"CH3",coupling:0,multiplicity:"s",shift:2.86}],dimethyl_sulfoxide:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.65}],dioxane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:3.66}],ethanol:[{proton:"CH3",coupling:7,multiplicity:"t",shift:1.19},{proton:"CH2",coupling:7,multiplicity:"q",shift:3.6}],ethyl_acetate:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:2.01},{proton:"CH2CH3",coupling:7,multiplicity:"q",shift:4.09},{proton:"CH2CH3",coupling:7,multiplicity:"t",shift:1.24}],ethyl_methyl_ketone:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:2.12},{proton:"CH2CH3",coupling:7,multiplicity:"q",shift:2.5},{proton:"CH2CH3",coupling:7,multiplicity:"t",shift:1.01}],ethylene_glycol:[{proton:"CH",coupling:0,multiplicity:"s",shift:3.59}],"grease^f":[{proton:"CH3",coupling:0,multiplicity:"m",shift:.88},{proton:"CH2",coupling:0,multiplicity:"br_s",shift:1.29}],"n-hexane":[{proton:"CH3",coupling:0,multiplicity:"t",shift:.9},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.29}],hmpag:[{proton:"CH3",coupling:9.5,multiplicity:"d",shift:2.64}],methanol:[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.34}],nitromethane:[{proton:"CH3",coupling:0,multiplicity:"s",shift:4.34}],"n-pentane":[{proton:"CH3",coupling:7,multiplicity:"t",shift:.89},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.29}],"2-propanol":[{proton:"CH3",coupling:6,multiplicity:"d",shift:1.5},{proton:"CH",coupling:6,multiplicity:"sep",shift:3.92}],pyridine:[{proton:"CH(2)",coupling:0,multiplicity:"m",shift:8.53},{proton:"CH(3)",coupling:0,multiplicity:"m",shift:7.44},{proton:"CH(4)",coupling:0,multiplicity:"m",shift:7.85}],silicone_greasei:[{proton:"CH3",coupling:0,multiplicity:"s",shift:.1}],tetrahydrofuran:[{proton:"CH2",coupling:0,multiplicity:"m",shift:1.87},{proton:"CH2O",coupling:0,multiplicity:"m",shift:3.71}],toluene:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.32},{proton:"CH(o/p)",coupling:0,multiplicity:"m",shift:7.16},{proton:"CH(m)",coupling:0,multiplicity:"m",shift:7.16}],triethylamine:[{proton:"CH3",coupling:7,multiplicity:"t",shift:1.05},{proton:"CH2",coupling:7,multiplicity:"q",shift:2.58}]},d2o:{tms:[{proton:"X",coupling:0,multiplicity:"",shift:0}],solvent:[{proton:"X",coupling:0,multiplicity:"",shift:4.79}],h2o:[],acetic_acid:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.08}],acetone:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.22}],acetonitrile:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.06}],benzene:[],"tert-butyl_alcohol":[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.24}],"tert-butyl_methyl_ether":[{proton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Rc(t,e){let{paths:n=[],signalsByDiaID:s}=e;for(let i of n){if(i.paths.length<1)continue;let o=i.oclID;if(!s.x[o]\|\|t[`${o}-${o}`])continue;let a={x:{},y:{}},l={z:1};for(let r of["x","y"])l[r]=s[r][o].delta,a[r].delta=s[r][o].delta,a[r].diaIDs=[o],a[r].atoms=s[r][o].atoms;a.peaks=[l],t[`${i.oclID}-${i.oclID}`]=a}}function Fc(t,e){if(t.length<1)return[];let{joinDistance:n,from:s,to:i}=e,o=new yo.Matrix(t.map(p=>[p.x.delta,p.y.delta])),a=o.minColumn(0),l=o.maxColumn(0),r=o.minColumn(1),m=o.maxColumn(1);o.mulColumn(0,1/(l-a)),o.mulColumn(1,1/(m-r));let c=Math.sqrt((n[s]/(l-a))2+(n[i]/(m-r))2),g=(0,fo.agnes)(o.to2DArray(),{method:"centroid"}),C=ho([g],c),u=[];for(let p of C){let f=[];p.isLeaf&&f.push(t[p.index]);for(let d of p.children)for(let y of d.indices())f.push(t[y]);u.push({id:(0,gn.v4)(),...Ac(f,{joinDistance:n,from:s,to:i}),signals:f})}return u}function Ac(t,e){let{joinDistance:n,from:s,to:i}=e,o=Number.MAX_SAFE_INTEGER,a=Number.MAX_SAFE_INTEGER,l=Number.MIN_SAFE_INTEGER,r=Number.MIN_SAFE_INTEGER;for(let m of t)m.x.delta<o&&(o=m.x.delta),m.x.delta>l&&(l=m.x.delta),m.y.delta<a&&(a=m.y.delta),m.y.delta>r&&(r=m.y.delta);return{x:{from:o-n[s],to:l+n[s]},y:{from:a-n[i],to:r+n[i]}}}function ho(t,e){let n=t.length;for(let s=0;s<t.length;s++){let i=t[s];i.height>e&&(t.push(...i.children),t.splice(s--,1))}return t.length<n?ho(t,e):t}async function Ho(t,e){let{minLength:n=2,maxLength:s=3,joinDistance:i={H:.05,C:.5},includeDiagonal:o=!0}=e;return Pt(t,{...e,from:"H",to:"H",minLength:n,maxLength:s,joinDistance:i,includeDiagonal:o})}var So=require("@lukeed/uuid");var Do=require("@lukeed/uuid");function Bt(t,e={}){let{nucleus:n="1H",frequency:s=400}=e,{tolerance:i=wc(n)/s}=e,o=0,{js:a=[],multiplicity:l}=t;if(a.length>0)for(let r of a){let{coupling:m,multiplicity:c="d"}=r;o+=tt[c]m/s}else l==="m"?o=16/s:(l==="b"\|\|l==="br s")&&(o=7/s);return o=i+o/2,{from:t.delta-o,to:t.delta+o}}function wc(t){switch(t.toUpperCase()){case"1H":return 1.5;case"13C":return 3;default:return 2}}function Ic(t){for(let e of t)if(!e.nbAtoms)throw new Error("nbAtoms is mandatory")}function _e(t,e={}){Ic(t);let{tolerance:n=.05,frequency:s=400}=e,i=t.map(l=>({original:l}));i.forEach(l=>{let r=Bt(l.original,{frequency:s,tolerance:n});l.from=r.from,l.to=r.to}),i=i.sort((l,r)=>l.from-r.from);let o=[],a={};for(let l of i)a.from===void 0\|\|l.from>a.to?(a={id:(0,Do.v4)(),from:l.from,to:l.to,integration:l.original.nbAtoms,signals:[l.original]},o.push(a)):(a.integration+=l.original.nbAtoms,l.to>a.to&&(a.to=l.to),a.signals.push(l.original));return o}function Oo(t,e){async function n(s){let i=await fetch(e,{headers:{accept:"application/json","content-type":"application/json"},method:"POST",body:JSON.stringify({molfile:s.toMolfile({version:3})})});if(i.status!==200){let a=await i.text();throw new Error(`${i.statusText}: ${a}`)}let o=(await i.json()).data;return{nucleus:o.nucleus,joinedSignals:o.joinedSignals??[],signals:o.signals??[],ranges:o.ranges??[]}}return Object.defineProperty(n,"name",{value:`default${t[0].toUpperCase()}${t.slice(1)}Predictor`}),n}var xo=Oo("proton","https://nmr-prediction.service.zakodium.com/v1/predict/proton"),bo=Oo("carbon","https://nmr-prediction.service.zakodium.com/v1/predict/carbon");async function Cn(t,e,n){if(typeof n=="function"){let i=await n(t.idCode);if(i)return i}let s=await e(t);return typeof n=="function"&&await n(t.idCode,s),s}function vo(t,e,n){let{maxSphereSize:s,atomLabel:i}=n,o=[];for(let a=0;a<t.length;a++){let l=t[a];if(i&&l.atomLabel!==i)continue;let r,m=null;for(let g=s;g>=0;g--)if(e[g]?.[l.hoses[g]]){r=e[g][l.hoses[g]],m=g;break}let c={diaIDs:[l.idCode],delta:r?r[0]:null,atoms:[a],nbAtoms:1,level:m,statistic:r&&r.length>1?{mean:r[1],sd:r[2],min:r[3],max:r[4],nb:r[5]}:void 0};o.push(c)}return o}function Tc(t){if(!t.atoms)throw new Error("There is not atoms");if(!t.diaIDs)throw new Error("There is not diaIDs");if(!t.nbAtoms)throw new Error("There is not nbAtoms")}async function Po(t,e={}){let{database:n,predictor:s=bo,cache:i}=e;if(t.molecule.getAllAtoms()===0)return{nucleus:"13C",joinedSignals:[],signals:[],ranges:[]};if(!n)return Cn(t,s,i);let o=n.length-1,{maxSphereSize:a=o}=e;a>o&&(a=o);let l=t.hoseCodes,r=t.diaIDsAndInfo.map((C,u)=>({...C,hoses:l[u]})),m=vo(r,n,{maxSphereSize:a,atomLabel:"C"}),c=kc(m),g=Ec(c);return{nucleus:"13C",joinedSignals:g,signals:c,ranges:_e(g)}}function kc(t){let e=[];for(let n of t){let{nbAtoms:s,atoms:i,delta:o,diaIDs:a,statistic:l}=n,r={id:(0,So.v4)(),delta:o??NaN,atoms:i,diaIDs:a,multiplicity:"s",nbAtoms:s,statistic:l,js:[]};e.push(r)}return e}function Ec(t){let e={};for(let n of t){Tc(n);let s=n.diaIDs[0];e[s]?(e[s].nbAtoms+=n.nbAtoms,e[s].atoms.push(...n.atoms)):e[s]=JSON.parse(JSON.stringify(n))}return cn(Object.values(e))}async function No(t,e){let{minLength:n=2,maxLength:s=3,joinDistance:i={H:.05,C:.5}}=e;return Pt(t,{...e,from:"H",to:"C",minLength:n,maxLength:s,joinDistance:i})}async function jo(t,e){let{minLength:n=1,maxLength:s=1,joinDistance:i={H:.05,C:.5}}=e;return Pt(t,{...e,from:"H",to:"C",minLength:n,maxLength:s,joinDistance:i})}async function Mo(t,e={}){if(t.molecule.getAllAtoms()===0)return{nucleus:"1H",joinedSignals:[],signals:[],ranges:[]};let{predictor:n=xo,cache:s}=e;return Cn(t,n,s)}function Ze(t,e){if(t in e)return!0;let n="hsqc"in e\|\|"hmbc"in e;return t==="C"?n:t==="H"?n\|\|"cosy"in e:!1}var zc={cosy:{predictor:Ho,required:["H"],message:"Proton prediction is missing so COSY could not be generated."},hsqc:{predictor:jo,required:["H","C"],message:"Carbon and / or proton prediction is missing so HSQC could not be generated."},hmbc:{predictor:No,required:["H","C"],message:"Carbon and / or proton prediction is missing so HMBC could not be generated."}};async function J(t,e={}){let{logger:n,joinDistance:s={H:.05,C:.5},predictOptions:i={H:{},C:{},hsqc:{},hmbc:{},cosy:{}}}=e,o=new Fo.TopicMolecule(t),a=Ze("H",i)?await Mo(o,{...i?.H}):void 0,l=Ze("C",i)?await Po(o,i?.C):void 0,r={},m=o.diaIDs,c={};Ro(a,m)&&(c.H=a,"H"in i&&(r.proton=a)),Ro(l,m)&&(c.C=l,"C"in i&&(r.carbon=l));for(let g in i){if(g==="H"\|\|g==="C")continue;let{predictor:C,required:u,message:p}=zc[g];u.every(f=>f in c)?r[g]=await C(o,{predictions:c,joinDistance:s,...i[g]}):n&&n.warn(p)}return{diaIDs:o.diaIDs,hoses:o.hoseCodes,distanceMatrix:o.distanceMatrix,moleculeWithHydrogens:o.moleculeWithH,groupedDiaIDs:o.getGroupedDiastereotopicAtomIDs(),molfile:o.toMolfile(),molfileWithH:o.toMolfileWithH(),spectra:r}}function Ro(t,e=[]){if(!t\|\|t.ranges.length===0)return!1;let{signals:n}=t;for(let s of n)if(!s.diaIDs?.every(o=>e.includes(o)))return!1;return!0}var Ao=require("spectrum-generator");function Ue(t,e={}){let{from:n=-1,to:s=12,nbPoints:i=512,factor:o=3}=e,{width:a=.02}=e,l=t.reduce((r,{x:m,y:c})=>(r.x.push(m.delta),r.y.push(c.delta),r.z.push(1e6),r),{x:[],y:[],z:[]});return a=un(a),(0,Ao.generateSpectrum2D)(qc(l),{generator:{from:un(n),to:un(s),nbPoints:un(i)},peaks:{width:a,factor:o}})}function un(t){return typeof t!="object"?{x:t,y:t}:{...t}}function qc(t){let e=JSON.parse(JSON.stringify(t));for(let n=0;n<e.x.length;n++)for(let s=n+1;s<e.x.length;s++)e.x[n]===e.x[s]&&e.y[n]===e.y[s]&&(e.z[n]+=e.z[s],e.x.splice(s,1),e.y.splice(s,1),e.z.splice(s,1),s--);return e}var Nt=require("ml-spectra-processing");var Io=require("ml-matrix");var pn=require("ml-matrix"),wo=q(require("ml-simple-clustering"));function nt(t){let{couplingConstants:e,connectivity:n}=t,s=pn.Matrix.checkMatrix(e),i=n?pn.Matrix.checkMatrix(n):Xc(s),{levels:o=new Array(i.rows).fill(2),clusters:a=(0,wo.default)(i.to2DArray(),{out:"indexes"})}=t;return{...t,levels:o,clusters:a,connectivity:i,couplingConstants:s}}function Xc(t){let e=pn.Matrix.ones(t.rows,t.rows);for(let n=0;n<t.rows;n++)for(let s=n;s<t.columns;s++)t.get(n,s)===0&&(e.set(n,s,0),e.set(s,n,0));return e}function Bc(t){for(let e of t){if(!e.js)throw new Error("there is not js");if(!e.atoms)throw new Error("there is not atoms");for(let n of e.js)if(!n.atoms)throw new Error("there is not atoms")}}function et(t){Bc(t);let e=t.length,n=new Array(e),s=Io.Matrix.zeros(e,e),i={};for(let o=0;o<e;o++){n[o]=t[o].delta;let a=t[o].atoms[0];i[a]=o}for(let o=0;o<e;o++){let{atoms:a,js:l}=t[o],r=a[0];for(let m of l){let{coupling:c,atoms:g}=m,C=g[0];s.set(i[r],i[C],c),s.set(i[C],i[r],c)}}return nt({couplingConstants:s,chemicalShifts:n})}var qo=require("spectrum-generator");var zo=q(require("binary-search")),dn=require("ml-matrix"),L=require("ml-sparse-matrix");var To=require("ml-sparse-matrix");function ko(t){let e=(t-1)/2,n=new Array(t),s=new Array(t);for(let m=0;m<t;m++)n[m]=t-1-m-e,s[m]=Math.sqrt(e(e+1)-n[m](n[m]+1));let i=Je(s,1,t,t);for(let m=0;m<t;m++)s[m]=Math.sqrt(e(e+1)-n[m](n[m]-1));let o=Je(s,-1,t,t),a=i.clone().add(o).mul(.5),l=o.clone().mul(-1).add(i).mul(-.5),r=Je(n,0,t,t);return{x:a,y:l,z:r,m:o,p:i}}function Je(t,e,n,s){let i=new To.SparseMatrix(n,s,{initialCapacity:20});for(let o=0;o<t.length;o++)o-e>=0&&o-e<n&&o<s&&i.set(o-e,o,t[o]);return i}var Wc=ko(2);function Wt(t){return t===2?Wc:ko(t)}var fn=.01;function st(t,e={}){let{lineWidth:n=1,maxClusterSize:s=8,frequency:i=400}=e,o=nt(t),a=o.chemicalShifts.slice();for(let m=0;m<a.length;m++)a[m]=a[m]i;let l=o.levels,r=[];for(let m of o.clusters){let c=m.map(d=>d<0?-d-1:d),g=1,C=0,u=[],p=[];if(m.length>s){let d=0;for(;m[d++]<0;);d=m[d-1],u.push(-a[d]);for(let y=0;y<m.length;y++)if(m[y]<0){let b=o.couplingConstants.get(d,c[y])/2,x=u.length;for(let h=0;h<x;h++)u.push(u[h]+b),u[h]-=b}u.sort((y,b)=>y-b),C=u.length,g=1;for(let y=0;y<C;y++)p.push(1)}else{let d=Yc(a,o.couplingConstants,l,o.connectivity,c),y=d.rows,b=new dn.EVD(d),x=b.eigenvectorMatrix,h=b.realEigenvalues,H=new L.SparseMatrix(y,y),S=m.length;g=0;for(let M=0;M<S;M++){let A=Wt(l[c[M]]),w=1;for(let E=0;E<M;E++)w=l[c[E]];let F=L.SparseMatrix.eye(w);w=1;for(let E=M+1;E<S;E++)w=l[c[E]];let T=L.SparseMatrix.eye(w),k=F.kroneckerProduct(A.m).kroneckerProduct(T);m[M]>=0?(H.add(k.mul(m[M]+1)),g++):H.add(k.mul(m[M]))}let D=dn.Matrix.zeros(y,y);H.forEachNonZero((M,A,w)=>{if(w>0)for(let F=0;F<x.columns;F++){let T=x.get(A,F);T!==0&&D.set(M,F,D.get(M,F)+T)}return w});let O=D.clone();H.forEachNonZero((M,A,w)=>{if(w<0)for(let F=0;F<x.columns;F++){let T=x.get(A,F);T!==0&&O.set(M,F,O.get(M,F)+T)}return w});let v=x.transpose();D=v.mmul(D);let P=new L.SparseMatrix(D.to2DArray(),{threshold:fn});Eo(P,fn),O=v.mmul(O);let R=new L.SparseMatrix(O.to2DArray(),{threshold:fn});R.forEachNonZero((M,A,w)=>w),Eo(R,fn),R.forEachNonZero((M,A,w)=>{let F=D.get(M,A);F=Math.min(Math.abs(F),Math.abs(w)),F=F,C+=F;let T=h[M]-h[A],k=(0,zo.default)(u,T,(E,G)=>E-G);k<0?(u.splice(-1-k,0,T),p.splice(-1-k,0,F)):p[k]+=F})}let f=u.length;if(f>0){g/=C;let d=n/64,y=u[0],b=p[0],x=1;for(let h=1;h<f;h++)Math.abs(u[h]-y/x)<d?(b+=p[h],y+=u[h],x++):(r.push({x:-y/x/i,y:bg}),y=u[h],b=p[h],x=1);r.push({x:-y/x/i,y:bg})}}return r.filter(m=>m.x<1e3)}function Eo(t,e){t.forEachNonZero((n,s,i)=>Math.abs(i)<=e?0:i)}function Yc(t,e,n,s,i){let o=1;for(let l of i)o=n[l];let a=new L.SparseMatrix(o,o);for(let l=0;l<i.length;l++){let r=i[l],m=Wt(n[r]),c=1;for(let f=0;f<l;f++)c=n[i[f]];let g=L.SparseMatrix.eye(c);c=1;for(let f=l+1;f<i.length;f++)c=n[i[f]];let C=L.SparseMatrix.eye(c),u=t[r],p=g.kroneckerProduct(m.z).kroneckerProduct(C);a.add(p.mul(u));for(let f=0;f<i.length;f++){let d=i[f];if(s.get(r,d)===1){let y=Wt(n[d]),b=1;for(let S=0;S<f;S++)b=n[i[S]];let x=L.SparseMatrix.eye(b);b=1;for(let S=f+1;S<i.length;S++)b=n[i[S]];let h=L.SparseMatrix.eye(b),H=g.kroneckerProduct(m.x).kroneckerProduct(C).mmul(x.kroneckerProduct(y.x).kroneckerProduct(h));H.add(g.kroneckerProduct(m.y).kroneckerProduct(C).mul(-1).mmul(x.kroneckerProduct(y.y).kroneckerProduct(h))),H.add(g.kroneckerProduct(m.z).kroneckerProduct(C).mmul(x.kroneckerProduct(y.z).kroneckerProduct(h))),a.add(H.mul(e.get(r,d)/2))}}}return a}function Ve(t,e={}){let{lineWidth:n=1,frequency:s=400,from:i=0,to:o=10,nbPoints:a=1024,shape:l={kind:"gaussian"}}=e,r=nt(t),m=n/s,c=st(r,e);return(0,qo.generateSpectrum)(c,{generator:{from:i,to:o,nbPoints:a},peakOptions:{shape:l,width:m}})}var Bo=require("ml-hclust"),Wo=require("ml-matrix");function it(t,e={}){let n=nt(t),{chemicalShifts:s,couplingConstants:i,connectivity:o}=n,{frequency:a=400,maxClusterSize:l=8}=e,r=Lc(s,i,a),m=(0,Bo.agnes)(r,{method:"single",isDistanceMatrix:!0}),c=[],g=s.length;Ge(m,c,{maxClusterSize:l,force:!1,nSpins:g,connectivity:o});let C=_c(c,l),u=C.length,p=new Array(u);for(let f=0;f<u;f++){p[f]=[];for(let d=0;d<g;d++){let y=C[f][d];y!==0&&p[f].push(y<0?-(d+1):d)}}return p}function Ge(t,e,n){let{maxClusterSize:s,force:i,nSpins:o,connectivity:a}=n;if(!i&&t.size<=s)e.push(Xo(t.indices(),o));else for(let l of t.children)if(l.size<=s){let r=Xo(l.indices(),o),m=0;for(let c=0;c<o;c++)if(r[c]===1){for(let g=0;g<o;g++)a.get(c,g)===1&&r[g]===0&&(r[g]=-1,m++);m++}m<=s?e.push(r):l.index<0?Ge(l,e,{maxClusterSize:s,force:!0,nSpins:o,connectivity:a}):(r[l.index]=2,e.push(r))}else Ge(l,e,{maxClusterSize:s,force:!1,nSpins:o,connectivity:a})}function Lc(t,e,n){let s=e.rows,i=e.columns,o=Wo.Matrix.zeros(s,s);for(let a=0;a<s;a++)for(let l=a;l<i;l++){let r=e.get(a,l);if(t[a]-t[l]!==0){let m=1-Math.abs(r/((t[a]-t[l])n));o.set(a,l,m),o.set(l,a,m)}else a===l\|\|r!==0\|\|(o.set(a,l,1),o.set(l,a,1))}return o.to2DArray()}function _c(t,e){for(let n=t.length-1;n>=0;n--){let s=t[n],i=s.length,o=0;for(;o<i&&s[o++]!==-1;);if(!(o>=i))for(let a=t.length-1;a>=n+1;a--){let l=t[a],r=0,m=0;for(let c=0;c<i;c++)s[c]l[c]===-1&&m++,(s[c]!==0\|\|l[c]!==0)&&r++;if(m>0&&r<=e){for(let c=0;c<i;c++)l[c]===1?s[c]=1:l[c]===-1&&s[c]!==1&&(s[c]=-1);t.splice(a,1)}}}return t}function Xo(t,e){let n=new Int16Array(e);for(let s of t)n[s]=1;return n}function Zc(t){for(let e of t){if(!e.js)throw new Error("There is not js");if(!e.atoms)throw new Error("There is not atoms");for(let n of e.js)if(!n.atoms)throw new Error("There is not atoms")}}function Yt(t,e={}){Zc(t);let{frequency:n=400,shape:s={kind:"gaussian"},from:i=0,to:o=10,lineWidth:a=1,nbPoints:l=161024,maxValue:r=1e8,maxClusterSize:m=8}=e;if(t.length===0)return{x:(0,Nt.xSequentialFillFromTo)({from:i,to:o,size:l}),y:new Float64Array(l)};let c=et(t);c.clusters=it(c,{frequency:n,maxClusterSize:m});let g=Ve(c,{frequency:n,from:i,to:o,nbPoints:l,lineWidth:a,maxClusterSize:m,shape:s});return r&&(0,Nt.xIsMonotonic)(g.y)===0&&(g.y=(0,Nt.xRescale)(g.y,{max:r})),g}var $e=require("gyromagnetic-ratio");function yn(t,e){let{nucleus:n,frequency:s}=e,i=(0,$e.getGyromagneticRatio)(t),o=(0,$e.getGyromagneticRatio)(n);if(!o\|\|!i)throw new Error(`${t} or ${n} is not supported`);return si/o}async function Uc(t,e={}){let{logger:n,simulation:s={oneD:{},twoD:{}},prediction:i={}}=e,{spectra:o}=await J(t,{logger:n,...i}),a={proton:{from:0,to:14},carbon:{from:0,to:200},nbPoints:65536,frequency:400,lineWidth:1,...s.oneD\|\|{}},l={from:{x:a.proton.from,y:a.carbon.from},to:{x:a.proton.to,y:a.carbon.to},nbPoints:{x:1024,y:1024},...s.twoD\|\|{}};!("frequency"in s)&&n&&n.warn("Frequency is settled to 400 MHz");let{frequency:r=400}=s,m=[];for(let c in o)switch(c){case"carbon":case"proton":{m.push(Gc(o[c],{nbPoints:a.nbPoints,lineWidth:a.lineWidth,...a[c],experiment:c,frequency:r}));break}case"cosy":case"hsqc":case"hmbc":{m.push(Jc(o[c],{...l,experiment:c,frequency:r}));break}default:break}return{spectra:m,molecules:[{molfile:t.toMolfile()}]}}function Jc(t,e){let{signals:n,zones:s,nuclei:i}=t,{frequency:o,experiment:a}=e,l=Vc(i),r=Yo(i,o);return{data:{rr:{...Ue(n,{...e,width:l,factor:3}),noise:.01}},info:{nucleus:i,originFrequency:r,baseFrequency:r,pulseSequence:a,experiment:"2d"},zones:{values:s}}}function Vc(t){return t[0]===t[1]?.02:{x:.02,y:.2133}}function Gc(t,e){let{frequency:n=400,experiment:s}=e,{signals:i,nucleus:o}=t,a=Yo(o,n),{x:l,y:r}=Yt(i,{...e,frequency:a});return{data:{x:Array.from(l),re:Array.from(r),im:null},info:{nucleus:t.nucleus,dimension:1,isComplex:!1,originFrequency:a,baseFrequency:a,pulseSequence:"prediction",experiment:s,isFt:!0},ranges:{values:t.ranges}}}function Yo(t,e){return typeof t=="string"?yn(t,{nucleus:"1H",frequency:e}):t[0]===t[1]?`${e},${e}`:`${e},${yn(t[1],{nucleus:t[0],frequency:e})}`}var Qe=q(require("ml-tree-set"));function Lo(t){let{restrictionByCS:e,predictions:n,targets:s,useIntegrationRestriction:i}=t,{tolerance:o,chemicalShiftRestriction:a}=e,l=Math.abs(o),r={};for(let m in n){let c=n[m];if(c.error&&(c.error=Math.abs(c.error)),r[m]=[],s)for(let g in s){let C=s[g],{nbAtoms:u}=c,{integration:p}=C;if(i&&p>0?u-p<1:!0)if(!a\|\|typeof c.delta>"u")r[m].push(g);else{let d=l;c.error&&(d=Math.max(d,c.error));let y=C.signals&&C.signals.length>0?C.signals[0].delta:(C.to+C.from)/2;Math.abs(c.delta-y-l)<4l&&r[m].push(g)}}r[m].push("")}return r}function _o(t,e){let{useIntegrationRestriction:n,diaIDPeerPossibleAssignment:s,nbAllowedUnAssigned:i,restrictionByCS:o,predictions:a,targets:l}=e,{useChemicalShiftScore:r}=o,m=0,c=t.length,g={},C=[];for(let d=0;d<t.length;d++){let y=t[d];y&&y!==""&&(C.push(d),g[y]\|\|(g[y]=[]),g[y].push(s[d])),y===""&&m++}if(m>i)return 0;let u=Object.keys(g);if(u.length===0)return 0;if(n)for(let d of u){let y=g[d],b=0;for(let h of y){let H=a[h];b+=H.allHydrogens}let{integration:x}=l[d];if(b-x>=.5)return 0}let p=r?$c(t,e):1,f=m/c;return p-f}function $c(t,e){let{tolerance:n}=e.restrictionByCS,{diaIDPeerPossibleAssignment:s,predictions:i,targets:o}=e,a=0,l=0;for(let r=0;r<t.length;r++){let m=t[r];if(m&&m!==""){l++;let c=s[r],g=i[c],C=o[m],u=n;if(g.error&&(u=Math.max(g.error,n)),typeof g.delta>"u")a+=1;else{let p=C.signals&&C.signals.length>0?C.signals[0].delta:(C.to+C.from)/2,f=Math.abs(g.delta-p);f<u?a+=1:(f=Math.abs(f-u),a+=-.25/uf+1)}}}return l>0&&(a/=l),a}function Ke(t,e,n,s){let{nSources:i,restrictionByCS:o,timeout:a,timeStart:l,maxSolutions:r,targets:m,predictions:c,lowerBoundScore:g,nbAllowedUnAssigned:C,possibleAssignmentMap:u,useIntegrationRestriction:p,diaIDPeerPossibleAssignment:f}=t;if(Date.now()-l>a)return s;let d=f[e],y=u[d];for(let b of y){n[e]=b;let x=_o(n,{useIntegrationRestriction:p,diaIDPeerPossibleAssignment:f,nbAllowedUnAssigned:C,restrictionByCS:o,predictions:c,targets:m});if(x===0){b===""&&(n[e]=null);continue}e===i-1&&x>=g?Kc(s,{predictions:c,partial:n,score:x,maxSolutions:r}):e<i-1&&Ke({nSources:i,restrictionByCS:o,timeout:a,timeStart:l,maxSolutions:r,targets:m,predictions:c,lowerBoundScore:g,nbAllowedUnAssigned:C,possibleAssignmentMap:u,useIntegrationRestriction:p,diaIDPeerPossibleAssignment:f},e+1,JSON.parse(JSON.stringify(n)),s)}}function Kc(t,e){let{score:n,maxSolutions:s,partial:i,predictions:o}=e;t.nSolutions++;let a={assignment:JSON.parse(JSON.stringify(i)),score:n/Qc(i,o)};t.nSolutions>=s?a.score>t.solutions.last().score&&(t.solutions.pollLast(),t.solutions.add(a)):(t.solutions.add(a),t.nSolutions++)}function Qc(t,e){let n=Object.keys(e).length,s=new Set(t),i=n-s.size;return i>0?2i:1}var Zo=(t,e)=>e.score-t.score;async function hn(t){let{restrictionByCS:e={},useIntegrationRestriction:n,timeout:s,minScore:i,nbAllowedUnAssigned:o,maxSolutions:a,targets:l,joinedSignals:r}=t,{tolerance:m=1,useChemicalShiftScore:c=!1,chemicalShiftRestriction:g=!0}=e,C={solutions:new Qe.default(Zo),nSolutions:0},u=r.length,p={};for(let h of r){let H=h.diaIDs[0],S=h.atoms[0];p[H]={...h,diaIDIndex:S,allHydrogens:h.nbAtoms}}let f=Lo({restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:g},useIntegrationRestriction:n,predictions:p,targets:l}),d=Object.keys(f),y=tg(u);C={solutions:new Qe.default(Zo),nSolutions:0};let b=Date.now();Ke({nSources:u,restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:g},timeout:s,timeStart:b,targets:l,predictions:p,maxSolutions:a,lowerBoundScore:i,nbAllowedUnAssigned:o,possibleAssignmentMap:f,diaIDPeerPossibleAssignment:d,useIntegrationRestriction:n},0,y,C);let x=[];for(let h of C.solutions.elements){let{assignment:H,score:S}=h,D=JSON.parse(JSON.stringify(l));for(let O=0;O<H.length;O++){let v=D[H[O]];v.diaIDs\|\|(v.diaIDs=[]),H[O]&&v.diaIDs.push(d[O])}x.push({score:S,assignment:Object.values(D)})}return x}function tg(t,e=null){let n=new Array(t);for(let s=0;s<t;s++)n[s]=e;return n}function ng(t){for(let e of t){if(!e.atoms)throw new Error("signal has not atoms property");if(!e.diaIDs)throw new Error("signal has not diaIDs property");if(!e.nbAtoms)throw new Error("signal has not nbAtoms property")}}function eg(t){for(let e of t)if(e.integration===void 0)throw new Error("ranges has not integration property")}async function sg(t,e,n={}){let{restrictionByCS:s,minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:l=6e3,predictionOptions:r={}}=n;if(!e)throw new Error("It is needed a OCL molecule instance to assign");let{spectra:m}=await J(e,{predictOptions:{H:r}}),c=m.proton?.joinedSignals\|\|[];eg(t),ng(c);let g={};for(let C of t){let{id:u=(0,Uo.v4)()}=C;g[u]=JSON.parse(JSON.stringify(C))}return hn({restrictionByCS:s,timeout:l,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:g,joinedSignals:c,useIntegrationRestriction:!0})}var Jo=require("@lukeed/uuid");function ig(t){for(let e of t){if(!e.atoms)throw new Error("signal has not atoms property");if(!e.diaIDs)throw new Error("signal has not diaIDs property");if(!e.nbAtoms)throw new Error("signal has not nbAtoms property")}}function og(t){for(let e of t)e.integration===void 0&&(e.integration=0);return t}async function ag(t,e,n={}){let{restrictionByCS:s={},minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:l=6e3,predictionOptions:r={}}=n,{spectra:m}=await J(e,{predictOptions:{C:r}}),c=m.carbon?.joinedSignals\|\|[];ig(c);let g=og(t),C={};for(let u of g){let{id:p=(0,Jo.v4)()}=u;C[p]=JSON.parse(JSON.stringify(u))}return 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a=1;a<t.length;a++){let l=t[a],r=e[l],{H:m=[]}=r.attachment,c=!0;for(let g of o)if(m.some(u=>g.attachments.has(u))){c=!1,g.targetIDs.push(l);for(let u of m)g.attachments.add(u);break}c&&o.push({targetIDs:[l],attachments:new Set(m)})}return o.map(a=>({atomType:"C",targetIDs:a.targetIDs,integration:n?Array.from(a.attachments).reduce((l,r)=>n[r].integration+l,0):0}))}var $o=lg;function Qo(t,e){let{diaIDPeerPossibleAssignment:n,infoByAtomTypes:s,restrictionByCS:i,predictions:o,targets:a,correlations:l}=e,{tolerance:r,useChemicalShiftScore:m}=i,c=0,g=0,C={},u={},p=Object.keys(t);for(let D of p){let O=0,{nbAllowedUnAssigned:v}=s[D],P={},R=t[D]\|\|[];C[D]=P,u[D]=[],g+=R.length;for(let M=0;M<R.length;M++){let A=R[M];A&&A!==""&&(u[D].push(M),P[A]\|\|(P[A]=[]),P[A].push(n[D][M])),A===""&&O++}if(O>v)return 0;c+=O}let f={};for(let D in C)f[D]=Object.keys(C[D]);let d=Object.values(f);if(d.reduce((D,O)=>O.length===0?D+1:D,0)===d.length)return 0;let y=mg.bind({},o),b=[];for(let D in 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ts(t,e,n,s){let{currentAtomTypes:i,restrictionByCS:o,timeout:a,timeStart:l,maxSolutions:r,targets:m,predictions:c,correlations:g,lowerBoundScore:C,possibleAssignmentMap:u,diaIDPeerPossibleAssignment:p}=t;if(Date.now()-l>a)return s;for(let f of i){let{currentIndex:d,nSources:y}=e[f];if(d>=y-1&&n[f][d]!==null)continue;let b=p[f][d],x=u[f][b];for(let h of x){n[f][d]=h;let H=Qo(n,{diaIDPeerPossibleAssignment:p,infoByAtomTypes:e,restrictionByCS:o,predictions:c,correlations:g,targets:m});if(H!==0)if(Cg(i,e)&&H>=C)gg(s,{predictions:c,partial:n,score:H,maxSolutions:r});else{let S=JSON.parse(JSON.stringify(e));S[f].currentIndex+=1,ts({currentAtomTypes:i,restrictionByCS:o,timeout:a,timeStart:l,maxSolutions:r,targets:m,predictions:c,correlations:g,lowerBoundScore:C,possibleAssignmentMap:u,diaIDPeerPossibleAssignment:p},S,JSON.parse(JSON.stringify(n)),s)}}}}function gg(t,e){let{score:n,maxSolutions:s,partial:i,predictions:o}=e,a={assignment:JSON.parse(JSON.stringify(i)),score:n/ug(i,o)};t.nSolutions>=s?a.score>t.solutions.last().score&&(t.solutions.pollLast(),t.solutions.add(a)):(t.solutions.add(a),t.nSolutions++)}function Cg(t,e){let n=!0;for(let s of t){let{currentIndex:i,nSources:o}=e[s];n=n&&i>=o-1}return n}function ug(t,e){let n=0;for(let s in e){let i=Object.keys(e[s]).length,o=new Set(t[s]);n+=i-o.size}return n>0?2n:1}function ot(t){return"ranges"in t}function ta(t,e){for(let n=0;n<e.length;n++){let s=e[n],i=ot(s)?s.ranges:s.zones;for(let o=0;o<i.length;o++){let a=i[o].signals\|\|[];for(let l=0;l<a.length;l++)if(t===a[l].id)return{spectrumIndex:n,signalIndex:l,elementIndex:o}}}throw new Error(`There is not a signal with ${t} ID`)}var na=(t,e)=>e.score-t.score;function pg(t){let e=["nbAtoms","diaIDs","atoms"];for(let n of t)for(let s of e)if(!n[s])throw new Error(`property ${s} does not exist`)}var fg={C:(t,e)=>t.getAllHydrogens(e),H:()=>1};async function sa(t){let{spectra:e,molecule:n,restrictionByCS:s,timeout:i,minScore:o,nbAllowedUnAssigned:a={},maxSolutions:l,correlations:r,assignmentOrder:m,predictionOptions:c,predictions:g={},targets:C}=t,u=o,p={solutions:new ns.default(na),nSolutions:0},f=(0,ea.getConnectivityMatrix)(n,{pathLength:!0}),d={},y={},b={},x={};for(let h of m){for(let D of h){let O={};O[D]=c[D];let v=g[D],P=await Hg({molecule:n,predictedSignals:v,options:O,atomType:D});pg(P),y[D]\|\|(y[D]={});let R=0;for(let M of P){let A=M.diaIDs[0],w=M.atoms[0],F=fg[D](n,w);R+=M.nbAtomsF,y[D][A]={...M,diaIDIndex:w,allHydrogens:M.nbAtomsF,protonsCount:F,pathLength:f[w]}}for(let M in y[D])y[D][M].allHydrogens=100/R;d[D]={nSources:P.length,currentIndex:0,nbAllowedUnAssigned:a[D]\|\|0}}b=Go(b,{restrictionByCS:s,predictions:y,targets:C}),x={};for(let D in b)x[D]=Object.keys(b[D]);let H=yg(p,d,h);p={solutions:new ns.default(na),nSolutions:0};let S=Date.now();for(let D of 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t?.match(/V[23]0/)?!os(Ta.Molecule.fromMolfile(t)):!1}var xn=[];for(let{label:t,value:e,names:n}of Y)xn.push(t,e,...n);xn=xn.sort((t,e)=>e.length-t.length);function Zt(t){if(t=t.replace(/broad/g,""),t=t.replace(/br\.?/g,""),/^\s$/.exec(t))return[];let e=new RegExp(xn.join("\|"),"g"),n=t.match(e);return n?n.map(s=>s.trim()):[t]}function bn(t){let e=/ (?<before>[^(]?) $ (?<inside>.?) $ (?<after>.?) /.exec(t);return e?e.groups:{before:t,inside:"",after:""}}function vn(t,e={}){let{nucleus:n,frequency:s,logger:i}=e,o=bn(t);if(!o.before)return;let a=/.?(?<from>-?[0-9.]+)-?(?<to>-?[0-9.])./.exec(o.before);if(!a?.groups)return;let l=a.groups.to!=="",r=Number(a.groups.from),m=l?Number(a.groups.to):r,c=o.inside.split(/ , /),g={delta:NaN,js:[]},C={from:r,to:m,signals:[g]},u=c.filter(y=>y.match(/^[0-9]+\sH$/));u.length===1&&(C.integration=Number(u[0].replace("H","")));let p=c.filter(y=>y.match(/^([br ])\.\s[a-zA-Z]+\.$/));if(p.length===1){let y=p[0];y==="m"?l?(g.delta=(r+m)/2,g.multiplicity=y):(g.delta=r,g.multiplicity=y):l\|\|(g.delta=r,g.multiplicity=y)}else l?(g.delta=(r+m)/2,g.multiplicity="s"):(g.delta=r,g.multiplicity="s");let f=c.filter(y=>y.match(/(Hz\|J\|^[0-9.]+$)/)).map(y=>Number(y.replace(/J[0-9.]\s=/,"J =").replace(/[^0-9.]/g,""))),d=Zt(g.multiplicity\|\|"");if(d.length===f.length)for(let y=0;y<d.length;y++)g.js?g.js.push({coupling:f[y],multiplicity:d[y]}):i.error(`A range has not couplings: ${t}`);if(C.from===C.to&&(C={...C,...Bt(g,{nucleus:n,frequency:s})}),isNaN(C.from)\|\|isNaN(C.to)){i.error(`A range could not be parsed: ${t}`);return}return C}function aC(t,e={}){let{logger:n}=e,s={info:{dimension:1},ranges:[],acsString:t,normalized:t.replace(/\.\s$/,"").replace(/[\r\n\t]/g," ").replace(/[;:]/g,",").replace(/\}/g,")").replace(/\{/g,"(").replace(/[\u2011\u2012\u2013\u2014\u2015\u2212]/g,"-")};return mC(s),lC(s,e),n?.info(`Found: ${s.ranges.length} ranges`),s}function lC(t,e={}){let{logger:n}=e;for(let s of 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ms(t,e){let{from:n,to:s,frequency:i,noiseLevel:o,thresholdFactor:a=3,minMaxRatio:l=.05,broadRatio:r=25e-5,useSanPlot:m=!1,smoothY:c=!0,optimize:g=!1,factorLimits:C=4,realTopDetection:u=!0,shape:p={kind:"gaussian"},optimization:f={kind:"lm"},broadWidth:d=.25,sgOptions:y={},direction:b="positive"}=e,x=1/i/(t.x[1]-t.x[0]),h=Math.max(Math.round(x/2),5),{windowSize:H=h-h%2+1,polynomial:S=3}=y;if(!H)throw new Pn({windowSize:H,ws:h,pointsPerHz:x,frequency:i,x:t.x.slice(0,2),sgOptions:y,autoWindowSizeFormula:"ws - (ws % 2) + 1",pointsPerHzFormula:"1 / frequency / (x[1] - x[0])"});if(t.x.length<H)return[];let D,{maxAbsDdY:O}=e;if(n!==void 0&&s!==void 0){if(!("maxAbsDdY"in e)){let R=(0,Ea.savitzkyGolay)(t,{windowSize:H,polynomial:S,derivative:2});O=(0,V.xMaxAbsoluteValue)(R.data.y)}D=(0,V.xyExtract)(t,{zones:[{from:n,to:s}]})}else D=t;let v=CC(D.y,{noiseLevel:o,useSanPlot:m,thresholdFactor:a}),P={shape:p,maxAbsDdY:O,frequency:i,broadWidth:d,optimize:g,factorLimits:C,maxCriteria:!0,sgOptions:{windowSize:H,polynomial:S},minMaxRatio:l,broadRatio:r,noiseLevel:v.positive,smoothY:c,optimization:f,realTopDetection:u};switch(b){case"positive":return rs(D,P);case"negative":return ka(D,v,P);case"both":return[...rs(D,P),...ka(D,v,P)];default:throw Error(`Unknown distribution ${b}`)}}function ka(t,e,n){return n.noiseLevel=e.negative,n.maxCriteria=!1,rs(t,n)}function rs(t,e){let{shape:n,maxAbsDdY:s,frequency:i,broadWidth:o,optimize:a,maxCriteria:l,factorLimits:r,sgOptions:m,minMaxRatio:c,broadRatio:g,noiseLevel:C,smoothY:u,optimization:p,realTopDetection:f}=e,d=(0,at.gsd)(t,{sgOptions:m,maxCriteria:l,minMaxRatio:c,noiseLevel:C,smoothY:u,realTopDetection:f}),y=(0,at.setShape)(d,{output:d,shape:n}),b=o?(0,at.joinBroadPeaks)(y,{shape:n,broadWidth:o,optimization:p,broadRatio:gC(d,{maxAbsDdY:s,broadRatio:g})}).map(ls):y.map(ls);return Sn(a?(0,at.optimizePeaks)(t,b,{shape:n,factorLimits:r,optimization:p}).map(ls):b,{frequency:i})}function gC(t,e={}){let{maxAbsDdY:n,broadRatio:s=.0025}=e;if(n&&t.length>0){let i=(0,V.xMaxAbsoluteValue)(t.map(o=>o.ddY));return sn/i}return s}function CC(t,e){let{noiseLevel:n,useSanPlot:s,thresholdFactor:i}=e,o=a=>typeof a=="number"?{positive:a,negative:-a}:a;return n?o(n):s?(0,V.xNoiseSanPlot)(t,{factorStd:i}):o((0,V.xAbsoluteMedian)(t)i)}function ls(t){let{id:e,shape:n,x:s,y:i,width:o}=t;return{id:e,x:s,y:i,width:o,shape:n}}var Pn=class extends Error{constructor(e){super("windowSize must be an odd integer >= 5, check data property of this error for contextual information"),this.data=e}};var Cs=require("@lukeed/uuid"),La=require("ml-spectra-processing");var za=require("@lukeed/uuid");function qa(t){t.sort((e,n)=>e.from-n.from);for(let e=0;e<t.length-1;e++){let n=t[e],s=t[e+1];n.to>s.from&&(n.id=(0,za.v4)(),n.to=Math.max(s.to,n.to),n.signals&&s.signals&&(n.signals=n.signals.concat(s.signals)),n.integration!==void 0&&(n.integration+=s.integration\|\|0),t.splice(e+1,1),e--)}return t}var Nn=["s","d","t","q","quint","h","sept","o","n"],uC=2.5,pC=1,fC={jAxis:"x",intensity:"intensity"};function dC(t){if(!("symRank"in t))throw new Error("Internal error, symRank was not calculated");if(!("mask"in t))throw new Error("Internal Error, mask was not added")}var jn={compilePattern:(t,e={})=>{let{jAxisKey:n=fC,symRatio:s=2.5}=e,i=xC(t,{...e,symRatio:s,maxError:uC,iteration:1,jAxisKey:n});if(i.multiplicity="m",i.asymmetric=!0,dC(i),i.symRank>=.95&&i.peaksComp.length<32){i.asymmetric=!1;let o,a,l,r=1,m=[];for(let c=0;c<9;c++){let g=bC(i,c),C=!1;if(g.length===1&&c===0)C=!0;else if(g.length<=1)continue;let u=OC(g);a=2c;let p=null,f=1;for(;!C&&(p=DC(u,a))!==null&&f<400;){let d=new Array(p.length);r=1;for(let h=0;h<p.length;h++){d[h]=new Array(p[h]);for(let 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cs(t,e){let{symRatio:n,iteration:s,jAxisKey:{jAxis:i,intensity:o}}=e,a=JSON.parse(JSON.stringify(t)),l,r,m,c,g,C=new Array(a.peaks.length);for(let O=0;O<C.length;O++){let v=a.peaks[O];C[O]={x:v[i]a.observe,intensity:v[o],width:v.width/a.observe}}for(let O=C.length-2;O>=0;O--)Math.abs(C[O].x-C[O+1].x)<.25&&(C[O].x=C[O].xC[O].intensity+C[O+1].xC[O+1].intensity,C[O].intensity=C[O].intensity+C[O+1].intensity,C[O].x/=C[O].intensity,C[O].intensity/=2,C[O].width+=C[O+1].width,C.splice(O+1,1));a.peaksComp=C;let u=C.length,p=new Array(u);a.mask=p;let f=0,d=C.length-1,y=a.deltaa.observe,b=[(C[0].x+C[u-1].x)/2,1],x=Math.min(Xa(Math.abs(y-b[0])),e.maxError),h=0;for(let O=0;O<u;O++)p[O]=!0,h+=C[O].intensity;for(;f<=d;){if(p[f]=!0,p[d]=!0,f===d)u>2&&Math.abs(C[f].x-y)>x&&(p[f]=!1);else if(l=Math.max(C[f].intensity,C[d].intensity),r=Math.min(C[f].intensity,C[d].intensity),c=l/r,c>n)C[f].intensity===r?(p[f]=!1,d++):(p[d]=!1,f--);else{let 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acetate"],smiles:"CC(=O)CC",ranges:[{signals:[{delta:20.45,assignment:"CH\u2083CO"}],from:20.445,to:20.455},{signals:[{delta:170.32,assignment:"CO"}],from:170.315,to:170.325},{signals:[{delta:60.3,assignment:"CH\u2082"}],from:60.294999999999995,to:60.305},{signals:[{delta:14.37,assignment:"CH\u2083"}],from:14.364999999999998,to:14.375}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["ethylene"],smiles:"C=C",ranges:[{signals:[{delta:123.09,assignment:"CH\u2082"}],from:123.08500000000001,to:123.095}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["ethylene glycol"],smiles:"OCCO",ranges:[{signals:[{delta:64.35,assignment:"CH\u2082"}],from:64.345,to:64.35499999999999}],nucleus:"13C",solvent:"THF-d\u2088"},{names:["H 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ether"],smiles:"CCOCC",ranges:[{signals:[{delta:15.44,assignment:"CH\u2083"}],from:15.434999999999999,to:15.445},{signals:[{delta:66.11,assignment:"CH\u2082"}],from:66.105,to:66.115}],nucleus:"13C",solvent:"CD\u2082Cl\u2082"},{names:["diglyme"],smiles:"COCCOCCOC",ranges:[{signals:[{delta:58.95,assignment:"CH\u2083"}],from:58.945,to:58.955000000000005},{signals:[{delta:70.7,assignment:"CH\u2082"}],from:70.69500000000001,to:70.705},{signals:[{delta:72.25,assignment:"CH\u2082"}],from:72.245,to:72.255}],nucleus:"13C",solvent:"CD\u2082Cl\u2082"},{names:["dimethylformamide"],smiles:"C(=O)N(C)C",ranges:[{signals:[{delta:162.57,assignment:"CH"}],from:162.565,to:162.575},{signals:[{delta:36.56,assignment:"CH\u2083"}],from:36.555,to:36.565000000000005},{signals:[{delta:31.39,assignment:"CH\u2083"}],from:31.385,to:31.395}],nucleus:"13C",solvent:"CD\u2082Cl\u2082"},{names:["1,4-dioxane"],smiles:"C1COCCOC1",ranges:[{signals:[{delta:67.47,assignment:"CH\u2082"}],from:67.465,to:67.475}],nucleus:"13C",solvent:"CD\u2082Cl\u2082"},{names:["DME","diethyl 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