npm - nmr-processing - Versions diffs - 12.4.0 → 12.5.0 - Mend

nmr-processing 12.4.0 → 12.5.0

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package/nmr-processing.cjs CHANGED Viewed

	@@ -1 +1 @@
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new Error(`baselineCorrection: algorithm unknown: ${n}`)}Object.assign(t.data,{re:o})}function ni(t){return!t.info.isFid}function or(t,e){return{once:!0,reduce:e}}var Un={};I(Un,{DOMAIN_UPDATE_RULES:()=>lr,apply:()=>rr,id:()=>ei,isApplicable:()=>si,name:()=>ar,reduce:()=>mr});var ei="digitalFilter",ar="Digital Filter",lr={updateXDomain:!0,updateYDomain:!0};function rr(t,e={}){if(!si(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===ei);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 si(t){return!!(t.info.isComplex&&t.info.isFid)}function mr(){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,ri.xSequentialFillFromStep)({from:n[0],size:o,step:n[1]-n[0]});t.data={...t.data,re:a,im:l,x:c}}var Dr="fft",Or="FFT",xr={updateXDomain:!0,updateYDomain:!0};function br(t){if(!ci(t))throw new Error("fft not applicable on this data");Nr(t);let e=t.filters.some(o=>o.name==="digitalFilter"&&o.flag),{info:{aqMod:n}}=t;n===1&&Pr(t,e),ai(t.data.x.length)\|\|mi(t,e);let{data:s,info:i}=t;if(Object.assign(s,(0,J.reimFFT)({re:s.re,im:i.reverse?(0,J.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?180W:0;Object.assign(s,(0,J.reimPhaseCorrection)(s,l,-a,{reverse:!0}))}t.data.x=Sr(t),t.info={...t.info,isFid:!1,isFt:!0}}function ci(t){return!!(t.info.isComplex&&t.info.isFid)}function vr(){return{once:!0,reduce:void 0}}function Sr(t){let 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Ce(t,e={}){let{re:n,im:s}=t,i=n.length,o=n[0].length,{reverse:a,digitalFilterValue:l=0}=e,r=new ge.Matrix(i,o),m=new ge.Matrix(i,o),{phaseCorrection:c={}}=e,{ph0:g,ph1:C,mode:u="no"}=c;for(let p=0;p<i;p++){let d={re:n[p],im:a?(0,mt.xMultiply)(s[p],-1):s[p]};Object.assign(d,Ri(d,{digitalFilterValue:l})),Object.assign(d,(0,mt.reimFFT)(d,{applyZeroShift:!0}));let f=lMath.PI2;f>0&&Object.assign(d,(0,mt.reimPhaseCorrection)(d,0,-f,{reverse:!0})),u==="pk"&&g!==void 0&&C!==void 0&&Object.assign(d,(0,mt.reimPhaseCorrection)(d,gMath.PI/180,CMath.PI/180,{reverse:!0})),r.setRow(p,d.re),m.setRow(p,d.im)}return{re:r,im:m}}var Q=require("ml-spectra-processing");function Fi(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,Q.xSubtract)((0,Q.xMultiply)(m,-1),l)),s.push((0,Q.xSubtract)(r,a)),i.push((0,Q.xAdd)(r,a)),i.push((0,Q.xSubtract)(m,l))}return{re:s,im:i}}var Om="fftDimension1",xm="FFT Dimension 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roform:[{proton:"CH",coupling:0,multiplicity:"s",shift:8.02}],cyclohexane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:1.43}],"1,2-dichloroethane":[{proton:"CH2",coupling:0,multiplicity:"s",shift:3.87}],dichloromethane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:5.63}],diethyl_ether:[{proton:"CH3",coupling:7,multiplicity:"t",shift:1.11},{proton:"CH2",coupling:7,multiplicity:"q",shift:3.41}],diglyme:[{proton:"CH2",coupling:0,multiplicity:"m",shift:3.56},{proton:"CH2",coupling:0,multiplicity:"m",shift:3.47},{proton:"OCH3",coupling:0,multiplicity:"s",shift:3.28}],"1,2-dimethoxyethane":[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.28},{proton:"CH2",coupling:0,multiplicity:"s",shift:3.46}],dimethylacetamide:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:1.97},{proton:"NCH3",coupling:0,multiplicity:"s",shift:3},{proton:"NCH3",coupling:0,multiplicity:"s",shift:2.83}],dimethylformamide:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.96},{proton:"CH3",coupling:0,multiplicity:"s",shift:2.94},{proton:"CH3",coupling:0,multiplicity:"s",shift:2.78}],dimethyl_sulfoxide:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.52}],dioxane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:3.59}],ethanol:[{proton:"CH3",coupling:7,multiplicity:"t",shift:1.12},{proton:"CH2",coupling:7,multiplicity:"q",shift:3.57},{proton:"OH",coupling:5,multiplicity:"s,t",shift:3.39}],ethyl_acetate:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:1.97},{proton:"CH2CH3",coupling:7,multiplicity:"q",shift:4.05},{proton:"CH2CH3",coupling:7,multiplicity:"t",shift:1.2}],ethyl_methyl_ketone:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:2.07},{proton:"CH2CH3",coupling:7,multiplicity:"q",shift:2.45},{proton:"CH2CH3",coupling:7,multiplicity:"t",shift:.96}],ethylene_glycol:[{proton:"CH",coupling:0,multiplicity:"s",shift:3.28}],"grease^f":[{proton:"CH3",coupling:0,multiplicity:"m",shift:.87},{proton:"CH2",coupling:0,multiplicity:"br_s",shift:1.29}],"n-hexane":[{proton:"CH3",coupling:0,multiplicity:"t",shift:.88},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.28}],hmpag:[{proton:"CH3",coupling:9.5,multiplicity:"d",shift:2.59}],methanol:[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.31},{proton:"OH",coupling:0,multiplicity:"s",shift:3.12}],nitromethane:[{proton:"CH3",coupling:0,multiplicity:"s",shift:4.43}],"n-pentane":[{proton:"CH3",coupling:7,multiplicity:"t",shift:.88},{proton:"CH2",coupling:0,multiplicity:"m",shift:1.27}],"2-propanol":[{proton:"CH3",coupling:6,multiplicity:"d",shift:1.1},{proton:"CH",coupling:6,multiplicity:"sep",shift:3.9}],pyridine:[{proton:"CH(2)",coupling:0,multiplicity:"m",shift:8.58},{proton:"CH(3)",coupling:0,multiplicity:"m",shift:7.35},{proton:"CH(4)",coupling:0,multiplicity:"m",shift:7.76}],silicone_greasei:[{proton:"CH3",coupling:0,multiplicity:"s",shift:.13}],tetrahydrofuran:[{proton:"CH2",coupling:0,multiplicity:"m",shift:1.79},{proton:"CH2O",coupling:0,multiplicity:"m",shift:3.63}],toluene:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.32},{proton:"CH(o/p)",coupling:0,multiplicity:"m",shift:7.5},{proton:"CH(m)",coupling:0,multiplicity:"m",shift:7.5}],triethylamine:[{proton:"CH3",coupling:7,multiplicity:"t",shift:.96},{proton:"CH2",coupling:7,multiplicity:"q",shift:2.45}]},dmso:{tms:[{proton:"X",coupling:0,multiplicity:"",shift:0}],solvent:[{proton:"X",coupling:0,multiplicity:"quint",shift:2.5}],h2o:[{proton:"H2O",coupling:0,multiplicity:"s",shift:3.33}],acetic_acid:[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.91}],acetone:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.09}],acetonitrile:[{proton:"CH3",coupling:0,multiplicity:"s",shift:2.07}],benzene:[{proton:"CH",coupling:0,multiplicity:"s",shift:7.37}],"tert-butyl_alcohol":[{proton:"CH3",coupling:0,multiplicity:"s",shift:1.11},{proton:"OHc",coupling:0,multiplicity:"s",shift:4.19}],"tert-butyl_methyl_ether":[{proton:"CCH3",coupling:0,multiplicity:"s",shift:1.11},{proton:"OCH3",coupling:0,multiplicity:"s",shift:3.08}],bhtb:[{proton:"ArH",coupling:0,multiplicity:"s",shift:6.87},{proton:"OHc",coupling:0,multiplicity:"s",shift:6.65},{proton:"ArCH3",coupling:0,multiplicity:"s",shift:2.18},{proton:"ArC(CH3)3",coupling:0,multiplicity:"s",shift:1.36}],chloroform:[{proton:"CH",coupling:0,multiplicity:"s",shift:8.32}],cyclohexane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:1.4}],"1,2-dichloroethane":[{proton:"CH2",coupling:0,multiplicity:"s",shift:3.9}],dichloromethane:[{proton:"CH2",coupling:0,multiplicity:"s",shift:5.76}],diethyl_ether:[{proton:"CH3",coupling:7,multiplicity:"t",shift:1.09},{proton:"CH2",coupling:7,multiplicity:"q",shift:3.38}],diglyme:[{proton:"CH2",coupling:0,multiplicity:"m",shift:3.51},{proton:"CH2",coupling:0,multiplicity:"m",shift:3.38},{proton:"OCH3",coupling:0,multiplicity:"s",shift:3.24}],"1,2-dimethoxyethane":[{proton:"CH3",coupling:0,multiplicity:"s",shift:3.24},{proton:"CH2",coupling:0,multiplicity:"s",shift:3.43}],dimethylacetamide:[{proton:"CH3CO",coupling:0,multiplicity:"s",shift:1.96},{proton:"NCH3",coupl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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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Vc={h:"1H",c:"13C"};function Po(t){return Object.values(t).map(e=>Vc[e.toLowerCase()])}function Gc(t){if(!t.from\|\|!t.to)throw new Error("options from and to are mandatory")}async function Mt(t,e){Gc(e);let{from:n,to:s,minLength:i=0,maxLength:o,predictions:a,joinDistance:l={H:.05,C:.5},includeDiagonal:r=!1}=e,m=$c(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},d={x:{},y:{}};for(let x in d)for(let h of p[x].joinedSignals){if(!h.diaIDs)throw new Error("Signal has not diaIDs");d[x][h.diaIDs[0]]=h}let f={};for(let x of g){let h=x.pathInfo;if(h.paths.length<1\|\|!d.x[h.oclID])continue;let D=h.paths;for(let S of D){if(!d.y[m[S.to].oclID])continue;let O={x:h,y:m[S.to]},H=`${O.x.oclID}-${O.y.oclID}`;if(H===`${h.oclID}-${h.oclID}`\|\|f[H])continue;let b={id:(0,yn.v4)(),z:100},P={id:(0,yn.v4)(),x:{},y:{}};for(let R in O){let j=O[R].oclID;b[R]=d[R][j].delta,P[R].delta=d[R][j].delta,P[R].diaIDs=[j],P[R].atoms=d[R][j].atoms}P.peaks=[b],f[H]=P}}r&&Qc(f,{paths:m,signalsByDiaID:d});let y=Object.values(f),v=tg(y,{joinDistance:l,from:n,to:s});return{nuclei:Po({from:n,to:s}),joinedSignals:y,signals:Kc(y),zones:v}}function $c(t,e){let{fromLabel:n,toLabel:s,minLength:i,maxLength:o}=e,a=t.diaIDs,l=t.moleculeWithH,r=t.distanceMatrix,m=Ke.Molecule.getAtomicNoFromLabel(n),c=Ke.Molecule.getAtomicNoFromLabel(s),g=[];for(let C=0;C<l.getAllAtoms();C++){let u={oclID:a[C],paths:[]};for(let p=0;p<l.getAllAtoms();p++){if(C===p\|\|l.getAtomicNo(p)!==c\|\|l.getAtomicNo(C)!==m)continue;let d=r[C][p];d>=i&&d<=o&&u.paths.push({from:C,to:p})}g.push(u)}return g}function Kc(t){let e=[];for(let n of t)for(let s of n.x.atoms\|\|[])for(let i of n.y.atoms\|\|[]){let o=JSON.parse(JSON.stringify(n));o.x.atoms=[s],o.y.atoms=[i],e.push(o)}return dn(e)}function Qc(t,e){let{paths:n=[],signalsByDiaID:s}=e;for(let i of n){if(i.paths.length<1)continue;let o=i.oclID;if(!s.x[o]\|\|t[`${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 tg(t,e){if(t.length<1)return[];let{joinDistance:n,from:s,to:i}=e,o=new Mo.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,No.agnes)(o.to2DArray(),{method:"centroid"}),C=jo([g],c),u=[];for(let p of C){let d=[];p.isLeaf&&d.push(t[p.index]);for(let f of p.children)for(let y of f.indices())d.push(t[y]);u.push({id:(0,yn.v4)(),...ng(d,{joinDistance:n,from:s,to:i}),signals:d})}return u}function ng(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 jo(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?jo(t,e):t}async function Ro(t,e){let{minLength:n=2,maxLength:s=3,joinDistance:i={H:.05,C:.5},includeDiagonal:o=!0}=e;return Mt(t,{...e,from:"H",to:"H",minLength:n,maxLength:s,joinDistance:i,includeDiagonal:o})}var ko=require("@lukeed/uuid");var Fo=require("@lukeed/uuid");function Lt(t,e={}){let{nucleus:n="1H",frequency:s=400}=e,{tolerance:i=eg(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+=nt[c]m/s}else l==="m"?o=16/s:(l==="b"\|\|l==="br s")&&(o=7/s);return 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zo(t,e){let{minLength:n=2,maxLength:s=3,joinDistance:i={H:.05,C:.5}}=e;return Mt(t,{...e,from:"H",to:"C",minLength:n,maxLength:s,joinDistance:i})}async function qo(t,e){let{minLength:n=1,maxLength:s=1,joinDistance:i={H:.05,C:.5}}=e;return Mt(t,{...e,from:"H",to:"C",minLength:n,maxLength:s,joinDistance:i})}async function Xo(t,e={}){if(t.molecule.getAllAtoms()===0)return{nucleus:"1H",joinedSignals:[],signals:[],ranges:[]};let{predictor:n=wo,cache:s}=e;return hn(t,n,s)}function ts(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 lg={cosy:{predictor:Ro,required:["H"],message:"Proton prediction is missing so COSY could not be generated."},hsqc:{predictor:qo,required:["H","C"],message:"Carbon and / or proton prediction is missing so HSQC could not be generated."},hmbc:{predictor:zo,required:["H","C"],message:"Carbon and / or proton prediction is missing so HMBC could not be generated."}};async function 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ns(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=Hn(a),(0,Yo.generateSpectrum2D)(rg(l),{generator:{from:Hn(n),to:Hn(s),nbPoints:Hn(i)},peaks:{width:a,factor:o}})}function Hn(t){return typeof t!="object"?{x:t,y:t}:{...t}}function rg(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 jt=require("ml-spectra-processing");var _o=require("ml-matrix");var Dn=require("ml-matrix"),Lo=z(require("ml-simple-clustering"));function et(t){let{couplingConstants:e,connectivity:n}=t,s=Dn.Matrix.checkMatrix(e),i=n?Dn.Matrix.checkMatrix(n):mg(s),{levels:o=new 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Zo=require("ml-sparse-matrix");function Uo(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=es(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=es(s,-1,t,t),a=i.clone().add(o).mul(.5),l=o.clone().mul(-1).add(i).mul(-.5),r=es(n,0,t,t);return{x:a,y:l,z:r,m:o,p:i}}function es(t,e,n,s){let i=new Zo.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 gg=Uo(2);function _t(t){return t===2?gg:Uo(t)}var On=.01;function it(t,e={}){let{lineWidth:n=1,maxClusterSize:s=8,frequency:i=400}=e,o=et(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(f=>f<0?-f-1:f),g=1,C=0,u=[],p=[];if(m.length>s){let f=0;for(;m[f++]<0;);f=m[f-1],u.push(-a[f]);for(let y=0;y<m.length;y++)if(m[y]<0){let v=o.couplingConstants.get(f,c[y])/2,x=u.length;for(let h=0;h<x;h++)u.push(u[h]+v),u[h]-=v}u.sort((y,v)=>y-v),C=u.length,g=1;for(let y=0;y<C;y++)p.push(1)}else{let f=Cg(a,o.couplingConstants,l,o.connectivity,c),y=f.rows,v=new xn.EVD(f),x=v.eigenvectorMatrix,h=v.realEigenvalues,D=new _.SparseMatrix(y,y),S=m.length;g=0;for(let j=0;j<S;j++){let A=_t(l[c[j]]),w=1;for(let E=0;E<j;E++)w=l[c[E]];let F=_.SparseMatrix.eye(w);w=1;for(let E=j+1;E<S;E++)w=l[c[E]];let T=_.SparseMatrix.eye(w),k=F.kroneckerProduct(A.m).kroneckerProduct(T);m[j]>=0?(D.add(k.mul(m[j]+1)),g++):D.add(k.mul(m[j]))}let O=xn.Matrix.zeros(y,y);D.forEachNonZero((j,A,w)=>{if(w>0)for(let F=0;F<x.columns;F++){let T=x.get(A,F);T!==0&&O.set(j,F,O.get(j,F)+T)}return w});let H=O.clone();D.forEachNonZero((j,A,w)=>{if(w<0)for(let F=0;F<x.columns;F++){let T=x.get(A,F);T!==0&&H.set(j,F,H.get(j,F)+T)}return w});let b=x.transpose();O=b.mmul(O);let P=new _.SparseMatrix(O.to2DArray(),{threshold:On});Jo(P,On),H=b.mmul(H);let R=new _.SparseMatrix(H.to2DArray(),{threshold:On});R.forEachNonZero((j,A,w)=>w),Jo(R,On),R.forEachNonZero((j,A,w)=>{let F=O.get(j,A);F=Math.min(Math.abs(F),Math.abs(w)),F=F,C+=F;let T=h[j]-h[A],k=(0,Vo.default)(u,T,(E,K)=>E-K);k<0?(u.splice(-1-k,0,T),p.splice(-1-k,0,F)):p[k]+=F})}let d=u.length;if(d>0){g/=C;let f=n/64,y=u[0],v=p[0],x=1;for(let h=1;h<d;h++)Math.abs(u[h]-y/x)<f?(v+=p[h],y+=u[h],x++):(r.push({x:-y/x/i,y:vg}),y=u[h],v=p[h],x=1);r.push({x:-y/x/i,y:vg})}}return r.filter(m=>m.x<1e3)}function Jo(t,e){t.forEachNonZero((n,s,i)=>Math.abs(i)<=e?0:i)}function Cg(t,e,n,s,i){let o=1;for(let l of i)o=n[l];let a=new _.SparseMatrix(o,o);for(let l=0;l<i.length;l++){let r=i[l],m=_t(n[r]),c=1;for(let d=0;d<l;d++)c=n[i[d]];let g=_.SparseMatrix.eye(c);c=1;for(let d=l+1;d<i.length;d++)c=n[i[d]];let C=_.SparseMatrix.eye(c),u=t[r],p=g.kroneckerProduct(m.z).kroneckerProduct(C);a.add(p.mul(u));for(let d=0;d<i.length;d++){let f=i[d];if(s.get(r,f)===1){let y=_t(n[f]),v=1;for(let S=0;S<d;S++)v=n[i[S]];let x=_.SparseMatrix.eye(v);v=1;for(let S=d+1;S<i.length;S++)v=n[i[S]];let h=_.SparseMatrix.eye(v),D=g.kroneckerProduct(m.x).kroneckerProduct(C).mmul(x.kroneckerProduct(y.x).kroneckerProduct(h));D.add(g.kroneckerProduct(m.y).kroneckerProduct(C).mul(-1).mmul(x.kroneckerProduct(y.y).kroneckerProduct(h))),D.add(g.kroneckerProduct(m.z).kroneckerProduct(C).mmul(x.kroneckerProduct(y.z).kroneckerProduct(h))),a.add(D.mul(e.get(r,f)/2))}}}return a}function ss(t,e={}){let{lineWidth:n=1,frequency:s=400,from:i=0,to:o=10,nbPoints:a=1024,shape:l={kind:"gaussian"}}=e,r=et(t),m=n/s,c=it(r,e);return(0,Go.generateSpectrum)(c,{generator:{from:i,to:o,nbPoints:a},peakOptions:{shape:l,width:m}})}var Ko=require("ml-hclust"),Qo=require("ml-matrix");function ot(t,e={}){let n=et(t),{chemicalShifts:s,couplingConstants:i,connectivity:o}=n,{frequency:a=400,maxClusterSize:l=8}=e,r=ug(s,i,a),m=(0,Ko.agnes)(r,{method:"single",isDistanceMatrix:!0}),c=[],g=s.length;is(m,c,{maxClusterSize:l,force:!1,nSpins:g,connectivity:o});let C=pg(c,l),u=C.length,p=new Array(u);for(let d=0;d<u;d++){p[d]=[];for(let f=0;f<g;f++){let y=C[d][f];y!==0&&p[d].push(y<0?-(f+1):f)}}return p}function is(t,e,n){let{maxClusterSize:s,force:i,nSpins:o,connectivity:a}=n;if(!i&&t.size<=s)e.push($o(t.indices(),o));else for(let l of t.children)if(l.size<=s){let r=$o(l.indices(),o),m=0;for(let c=0;c<o;c++)if(r[c]===1){for(let g=0;g<o;g++)a.get(c,g)===1&&r[g]===0&&(r[g]=-1,m++);m++}m<=s?e.push(r):l.index<0?is(l,e,{maxClusterSize:s,force:!0,nSpins:o,connectivity:a}):(r[l.index]=2,e.push(r))}else is(l,e,{maxClusterSize:s,force:!1,nSpins:o,connectivity:a})}function ug(t,e,n){let s=e.rows,i=e.columns,o=Qo.Matrix.zeros(s,s);for(let a=0;a<s;a++)for(let l=a;l<i;l++){let r=e.get(a,l);if(t[a]-t[l]!==0){let 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c=st(t);c.clusters=ot(c,{frequency:n,maxClusterSize:m});let g=ss(c,{frequency:n,from:i,to:o,nbPoints:l,lineWidth:a,maxClusterSize:m,shape:s});return r&&(0,jt.xIsMonotonic)(g.y)===0&&(g.y=(0,jt.xRescale)(g.y,{max:r})),g}var os=require("gyromagnetic-ratio");function bn(t,e){let{nucleus:n,frequency:s}=e,i=(0,os.getGyromagneticRatio)(t),o=(0,os.getGyromagneticRatio)(n);if(!o\|\|!i)throw new Error(`${t} or ${n} is not supported`);return si/o}async function dg(t,e={}){let{logger:n,simulation:s={oneD:{},twoD:{}},prediction:i={}}=e,{spectra:o}=await G(t,{logger:n,...i}),a={proton:{from:0,to:14},carbon:{from:0,to:200},nbPoints:65536,frequency:400,lineWidth:1,...s.oneD\|\|{}},l={from:{x:a.proton.from,y:a.carbon.from},to:{x:a.proton.to,y:a.carbon.to},nbPoints:{x:1024,y:1024},...s.twoD\|\|{}};!("frequency"in s)&&n&&n.warn("Frequency is settled to 400 MHz");let{frequency:r=400}=s,m=[];for(let c in o)switch(c){case"carbon":case"proton":{m.push(Hg(o[c],{nbPoints:a.nbPoints,lineWidth:a.lineWidth,...a[c],experiment:c,frequency:r}));break}case"cosy":case"hsqc":case"hmbc":{m.push(yg(o[c],{...l,experiment:c,frequency:r}));break}default:break}return{spectra:m,molecules:[{molfile:t.toMolfile()}]}}function yg(t,e){let{signals:n,zones:s,nuclei:i}=t,{frequency:o,experiment:a}=e,l=hg(i),r=ta(i,o);return{data:{rr:{...ns(n,{...e,width:l,factor:3}),noise:.01}},info:{nucleus:i,originFrequency:r,baseFrequency:r,pulseSequence:a,experiment:"2d"},zones:{values:s}}}function hg(t){return t[0]===t[1]?.02:{x:.02,y:.2133}}function Hg(t,e){let{frequency:n=400,experiment:s}=e,{signals:i,nucleus:o}=t,a=ta(o,n),{x:l,y:r}=Zt(i,{...e,frequency:a});return{data:{x:Array.from(l),re:Array.from(r),im:null},info:{nucleus:t.nucleus,dimension:1,isComplex:!1,originFrequency:a,baseFrequency:a,pulseSequence:"prediction",experiment:s,isFt:!0},ranges:{values:t.ranges}}}function ta(t,e){return typeof t=="string"?bn(t,{nucleus:"1H",frequency:e}):t[0]===t[1]?`${e},${e}`:`${e},${bn(t[1],{nucleus:t[0],frequency:e})}`}var ls=z(require("ml-tree-set"));function na(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 f=l;c.error&&(f=Math.max(f,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 ea(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 f=0;f<t.length;f++){let y=t[f];y&&y!==""&&(C.push(f),g[y]\|\|(g[y]=[]),g[y].push(s[f])),y===""&&m++}if(m>i)return 0;let u=Object.keys(g);if(u.length===0)return 0;if(n)for(let f of u){let y=g[f],v=0;for(let h of y){let D=a[h];v+=D.allHydrogens}let{integration:x}=l[f];if(v-x>=.5)return 0}let p=r?Dg(t,e):1,d=m/c;return p-d}function Dg(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,d=Math.abs(g.delta-p);d<u?a+=1:(d=Math.abs(d-u),a+=-.25/ud+1)}}}return l>0&&(a/=l),a}function as(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:d}=t;if(Date.now()-l>a)return s;let f=d[e],y=u[f];for(let v of y){n[e]=v;let x=ea(n,{useIntegrationRestriction:p,diaIDPeerPossibleAssignment:d,nbAllowedUnAssigned:C,restrictionByCS:o,predictions:c,targets:m});if(x===0){v===""&&(n[e]=null);continue}e===i-1&&x>=g?Og(s,{predictions:c,partial:n,score:x,maxSolutions:r}):e<i-1&&as({nSources:i,restrictionByCS:o,timeout:a,timeStart:l,maxSolutions:r,targets:m,predictions:c,lowerBoundScore:g,nbAllowedUnAssigned:C,possibleAssignmentMap:u,useIntegrationRestriction:p,diaIDPeerPossibleAssignment:d},e+1,JSON.parse(JSON.stringify(n)),s)}}function Og(t,e){let{score:n,maxSolutions:s,partial:i,predictions:o}=e;t.nSolutions++;let a={assignment:JSON.parse(JSON.stringify(i)),score:n/xg(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 xg(t,e){let n=Object.keys(e).length,s=new Set(t),i=n-s.size;return i>0?2i:1}var sa=(t,e)=>e.score-t.score;async function vn(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 ls.default(sa),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 d=na({restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:g},useIntegrationRestriction:n,predictions:p,targets:l}),f=Object.keys(d),y=bg(u);C={solutions:new ls.default(sa),nSolutions:0};let v=Date.now();as({nSources:u,restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:g},timeout:s,timeStart:v,targets:l,predictions:p,maxSolutions:a,lowerBoundScore:i,nbAllowedUnAssigned:o,possibleAssignmentMap:d,diaIDPeerPossibleAssignment:f,useIntegrationRestriction:n},0,y,C);let x=[];for(let h of C.solutions.elements){let{assignment:D,score:S}=h,O=JSON.parse(JSON.stringify(l));for(let H=0;H<D.length;H++){let b=O[D[H]];b.diaIDs\|\|(b.diaIDs=[]),D[H]&&b.diaIDs.push(f[H])}x.push({score:S,assignment:Object.values(O)})}return x}function bg(t,e=null){let n=new Array(t);for(let s=0;s<t;s++)n[s]=e;return n}function vg(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 Pg(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 G(e,{predictOptions:{H:r}}),c=m.proton?.joinedSignals\|\|[];Sg(t),vg(c);let g={};for(let C of t){let{id:u=(0,ia.v4)()}=C;g[u]=JSON.parse(JSON.stringify(C))}return vn({restrictionByCS:s,timeout:l,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:g,joinedSignals:c,useIntegrationRestriction:!0})}var oa=require("@lukeed/uuid");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 Mg(t){for(let e of t)e.integration===void 0&&(e.integration=0);return t}async function jg(t,e,n={}){let{restrictionByCS:s={},minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:l=6e3,predictionOptions:r={}}=n,{spectra:m}=await G(e,{predictOptions:{C:r}}),c=m.carbon?.joinedSignals\|\|[];Ng(c);let g=Mg(t),C={};for(let u of g){let{id:p=(0,oa.v4)()}=u;C[p]=JSON.parse(JSON.stringify(u))}return vn({restrictionByCS:s,timeout:l,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:C,joinedSignals:c,useIntegrationRestriction:!1})}var xa=require("openchemlib-utils");var ms=z(require("ml-tree-set")),ua=require("openchemlib-utils");var aa=require("nmr-correlation");function la(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 d=g[p],{nbAtoms:f,protonsCount:y}=u,{integration:v,protonsCount:x}=d;if(v?r==="H"?f-v<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,aa.getCorrelationDelta)(d);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 ma=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 ra=Rg;function ca(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 O of p){let H=0,{nbAllowedUnAssigned:b}=s[O],P={},R=t[O]\|\|[];C[O]=P,u[O]=[],g+=R.length;for(let j=0;j<R.length;j++){let A=R[j];A&&A!==""&&(u[O].push(j),P[A]\|\|(P[A]=[]),P[A].push(n[O][j])),A===""&&H++}if(H>b)return 0;c+=H}let d={};for(let O in C)d[O]=Object.keys(C[O]);let f=Object.values(d);if(f.reduce((O,H)=>H.length===0?O+1:O,0)===f.length)return 0;let y=Ag.bind({},o),v=[];for(let O in t)if(O==="C"&&d[O].length>0)v.push(...ra(d[O],a[O],l));else for(let H of d[O])v.push({atomType:O,targetIDs:[H],integration:a.H[H].integration});for(let O of v){let{integration:H,atomType:b}=O;if(H===void 0\|\|isNaN(H))continue;let P=0;for(let R of O.targetIDs){let j=C[b][R];for(let A of j){let{prediction:w,atomType:F}=y(A);b===F&&(P+=w.allHydrogens)}}if(P-H>=5)return 0}let x=1,h=1;if(m){h=0,x=0;for(let O of Object.keys(t)){let H=t[O],b=a[O];for(let P=0;P<H.length;P++){let R=H[P];if(R&&R!==""){x++;let j=n[O][P],A=o[O][j],w=b[R],F=r[O];if(typeof A.delta>"u")h+=1;else{let T=(0,ma.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(wg(d)>1){let O={},H=[];for(let P of Object.keys(u))H=H.concat(u[P].map(R=>({index:R,atomType:P})));for(let P=0;P<H.length;P++){let{atomType:R,index:j}=H[P],A=o[R][n[R][j]];for(let w=P+1;w<H.length;w++){let{atomType:F,index:T}=H[w],k=o[F][n[F][T]],K=A.pathLength[k.diaIDIndex]<5,At=t[R][j],wt=t[F][T];if(!At\|\|!wt)continue;let Wn=At>wt?`${wt} ${At}`:`${At} ${wt}`,Ms=Fg({from:{targetID:At,atomType:R},to:{targetID:wt,atomType:F}},a),js=K?Ms?1:0:Ms?0:1;O[Wn]=O[Wn]?Math.max(O[Wn],js):js}}let b=0;for(let P in O)b+=O[P];D=b/(H.length(H.length-1)/2)}let S=c/g;return h===0?D-S:D===0?h-S:(h+D)/2-S}function Fg(t,e){let{from:n,to:s}=t;if(n.targetID===s.targetID)return!0;let i=e[n.atomType][n.targetID],o=e[s.atomType][s.targetID];for(let a of o.link)for(let l of i.link)if(l.signal.id===a.signal.id)return!0;return!1}function Ag(t,e){let n=Object.keys(t);for(let s of n){let i=t[s];if(!i)throw new Error(`prediction by ${s}`);if(i[e])return{atomType:s,prediction:i[e]}}throw new Error(`There is not prediction for ${e}`)}function wg(t){let e=0;for(let n in t)e+=t[n].length;return e}function rs(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 d of i){let{currentIndex:f,nSources:y}=e[d];if(f>=y-1&&n[d][f]!==null)continue;let v=p[d][f],x=u[d][v];for(let h of x){n[d][f]=h;let D=ca(n,{diaIDPeerPossibleAssignment:p,infoByAtomTypes:e,restrictionByCS:o,predictions:c,correlations:g,targets:m});if(D!==0)if(Tg(i,e)&&D>=C)Ig(s,{predictions:c,partial:n,score:D,maxSolutions:r});else{let S=JSON.parse(JSON.stringify(e));S[d].currentIndex+=1,rs({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 Ig(t,e){let{score:n,maxSolutions:s,partial:i,predictions:o}=e,a={assignment:JSON.parse(JSON.stringify(i)),score:n/kg(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=!0;for(let s of t){let{currentIndex:i,nSources:o}=e[s];n=n&&i>=o-1}return n}function kg(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 at(t){return"ranges"in t}function ga(t,e){for(let n=0;n<e.length;n++){let s=e[n],i=at(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 Ca=(t,e)=>e.score-t.score;function Eg(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 zg={C:(t,e)=>t.getAllHydrogens(e),H:()=>1};async function pa(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 ms.default(Ca),nSolutions:0},d=(0,ua.getConnectivityMatrix)(n,{pathLength:!0}),f={},y={},v={},x={};for(let h of m){for(let O of h){let H={};H[O]=c[O];let b=g[O],P=await Wg({molecule:n,predictedSignals:b,options:H,atomType:O});Eg(P),y[O]\|\|(y[O]={});let R=0;for(let j of P){let A=j.diaIDs[0],w=j.atoms[0],F=zg[O](n,w);R+=j.nbAtomsF,y[O][A]={...j,diaIDIndex:w,allHydrogens:j.nbAtomsF,protonsCount:F,pathLength:d[w]}}for(let j in y[O])y[O][j].allHydrogens=100/R;f[O]={nSources:P.length,currentIndex:0,nbAllowedUnAssigned:a[O]\|\|0}}v=la(v,{restrictionByCS:s,predictions:y,targets:C}),x={};for(let O in v)x[O]=Object.keys(v[O]);let D=Xg(p,f,h);p={solutions:new ms.default(Ca),nSolutions:0};let S=Date.now();for(let O of D)rs({currentAtomTypes:h,restrictionByCS:s,timeout:i,timeStart:S,targets:C,predictions:y,correlations:r,maxSolutions:l,lowerBoundScore:u,possibleAssignmentMap:v,diaIDPeerPossibleAssignment:x},f,O,p)}return qg({store:p,spectra:e,diaIDPeerPossibleAssignment:x,targets:C})}function qg(t){let{store:e,spectra:n,diaIDPeerPossibleAssignment:s,targets:i}=t,{solutions:o}=e,a={},l=Object.keys(i);for(let m of l){let c=i[m];for(let g in c){let C=c[g];for(let u of C.link){let p=u.signal.id;a[p]\|\|(a[u.signal.id]=ga(p,n))}}}let r=[];for(let m of o.elements){let c=JSON.parse(JSON.stringify(n)),{assignment:g,score:C}=m,u=Object.keys(g);for(let p of u){let d=i[p],f=g[p];for(let y=0;y<f.length;y++){let v=f[y];if(v===""\|\|!v)continue;let x=d[v],h=s[p][y];for(let D of x.link){let{spectrumIndex:S,elementIndex:O,signalIndex:H}=a[D.signal.id],b=c[S];if(at(b)){let{ranges:P}=b,j=P[O].signals[H];if(j.diaIDs\|\|(j.diaIDs=[]),j.diaIDs.includes(h))continue;j.diaIDs.push(h)}else{let P=D.axis,R=b.zones[O].signals[H];if(R[P].diaIDs\|\|(R[P].diaIDs=[]),R[P].diaIDs?.includes(h))continue;R[P].diaIDs?.push(h)}}}}r.push({score:C,assignment:c})}return r}function Xg(t,e,n){return t.nSolutions>0?t.solutions.elements.map(s=>{let i=s.assignment;for(let o of n)i[o]=fa(e[o].nSources);return i}):Bg(e,n)}function Bg(t,e){let n={},s=Object.keys(t);for(let i of s){let o=e.includes(i)?null:"";n[i]=fa(t[i].nSources,o)}return[n]}function fa(t,e=null){let n=new Array(t);for(let s=0;s<t;s++)n[s]=e;return n}async function Wg(t){let{molecule:e,predictedSignals:n,options:s,atomType:i}=t;if(n)return n;let{spectra:o}=await G(e,{predictOptions:s});return o[i==="C"?"carbon":"proton"]?.joinedSignals\|\|[]}var cs=require("@lukeed/uuid");function da(t=[]){let e=JSON.parse(JSON.stringify(t)),n=[];for(let s of e){if(!("info"in s))throw new Error("each spectrum should contain info properties with nucleus information");let{info:i,id:o}=s;if(at(s)){let a=Sn(s.ranges);n.push({id:o,info:i,ranges:a})}else{let a=Sn(s.zones);n.push({id:o,info:i,zones:a})}}return n}function Yg(t){for(let e of t){if(!e.id)throw new Error("A range/zone has not an ID");for(let n of e.signals\|\|[])if(!n.id)throw new Error("A signal has not an ID")}}function Sn(t){for(let e of t){e.id\|\|(e.id=(0,cs.v4)());for(let n of e.signals\|\|[])n.id\|\|(n.id=(0,cs.v4)())}return Yg(t),t}var Ha=require("nmr-correlation");function ya(t=[]){let e=JSON.parse(JSON.stringify(t)),n=[];for(let s of e){let{id:i,info:o}=s;if(at(s)){let a=Lg({id:i,info:o,ranges:s.ranges});n.push({id:i,info:o,ranges:{values:a}})}else n.push({id:i,info:o,zones:{values:s.zones}})}return n}function Lg(t){if(t.info.nucleus!=="1H")return t.ranges;let e=t.ranges.reduce((n,s)=>s.integration?n+s.integration:n,0);for(let n of t.ranges)if(n.integration&&(n.integration=100/e,n.signals)){let s=n.signals.reduce((i,o)=>o.integration?i+o.integration:i,0);for(let i of n.signals)i.integration?i.integration=n.integration/s:i.integration=n.integration}return t.ranges}function ha(t,e){let{H:n=[]}=t.attachment,s=0;for(let i of n){let o=e[i];s+=Number(o.link[0].signal.integration)}return s}function Da(t,e={}){let{tolerance:n={C:.25,H:.05}}=e,s=ya(t),{values:i}=(0,Ha.buildCorrelationData)(s,{tolerance:n}),o={};for(let a of i){if(a.pseudo)continue;let{id:l,atomType:r}=a;o[r]\|\|(o[r]={}),o[r][l]=a,r==="H"?o[r][l].integration=a.link[0].signal.integration:o[r][l].integration=ha(a,i)}return{targets:o,correlations:i}}function _g(t,e=[]){let n=Zg(t),{hasHSQC:s,types:i}=n;if(e.length>0)return{assignmentOrder:e,experimentTypes:n};let o=[];return s?o.push(["C"],["H"]):o.push(i.filter(a=>a==="H"\|\|a==="C")),{assignmentOrder:o,experimentTypes:n}}var Oa=_g;function Zg(t){let e=[];for(let n of t){let s=n.experimentType;s==="1d"&&(s=`${n.atomType.toUpperCase()}`),e.includes(s)\|\|e.push(s);for(let i of 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Na=require("is-any-array"),B=z(require("numeral"));var Sa=require("ml-spectra-processing");function ba(t,e){let n=t.reduce((s,i)=>{if(isNaN(nt[i]))throw new Error(`pattern ${i} is not in ${Object.keys(nt).join(" ")}`);return s+nt[i]},0);if(!Nt[n])throw new Error(`The joined pattern from ${t.join(",")} doesn't exist`);return e?.acsFormat?Bt[n]:Nt[n]}var gs=(t,e)=>t.localeCompare(e),Jg=(t,e)=>gs(t.diaIDs.sort(gs).join(" "),e.diaIDs.sort(gs).join(" ")),Pa=(t,e,n)=>Math.abs(t.coupling-e.coupling)<n,Vg=(t,e,n)=>Jg(t,e)===0&&Pa(t,e,n);function Cs(t,e={}){let{tolerance:n=.05,ignoreDiaIDs:s=!1,acsFormat:i=!1}=e;return!t.js\|\|t.js.length<2?t:s?($g(t),va(t,Pa,{tolerance:n,acsFormat:i})):(Gg(t),va(t,Vg,{tolerance:n,acsFormat:i}))}function va(t,e,n){let{tolerance:s,acsFormat:i}=n;t.js.sort((l,r)=>r.coupling-l.coupling);let o=[t.js[0]],a=[o];for(let l=1;l<t.js.length;l++){let r=t.js[l];e(o[o.length-1],r,s)?o.push(r):(o=[r],a.push(o))}t.js=[];for(let l of a){let 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s="",i=[],o=[t.from,t.to];if(t.signals&&(t.signals=t.signals.filter(a=>!ja(a.kind,n.filter))),t.signals&&t.signals.length>0){let a=t.signals;if(a.length>1){n.ascending===!0&&a.sort((m,c)=>m.delta-c.delta);let l=(0,B.default)(Math.max(...o)),r=(0,B.default)(Math.min(...o));if(s+=`${r.format(n.deltaFormat)}-${l.format(n.deltaFormat)}`,s+=` (${Ma(t,n)}`,a.some(m=>m.multiplicity\|\|m.js&&m.js.length>0))for(let m of a){i=[],m.delta!==void 0&&(s=lC(s),s+=(0,B.default)(m.delta).format(n.deltaFormat));let c={from:Number.MIN_SAFE_INTEGER,to:Number.MAX_SAFE_INTEGER};Nn(c,m,i,n),i.length>0&&(s+=` (${i.join(", ")})`)}s+=")"}else if(i=[],a[0].delta!==void 0)s+=(0,B.default)(a[0].delta).format(n.deltaFormat),Nn(t,a[0],i,n),i.length>0&&(s+=` (${i.join(", ")})`);else{let l=(0,B.default)(Math.max(...o)),r=(0,B.default)(Math.min(...o));s+=`${r.format(n.deltaFormat)}-${l.format(n.deltaFormat)}`,Nn(t,a[0],i,n),i.length>0&&(s+=` (${i})`)}}else{let 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hC(t,e){let{from:n,to:s}=pC(e.nucleus),i=Number.MAX_SAFE_INTEGER,o=Number.MIN_SAFE_INTEGER;for(let r of t)for(let m of r.signals\|\|[])i>m.delta&&(i=m.delta),o<m.delta&&(o=m.delta);let{from:a=Math.min(i-.5,n),to:l=Math.max(o+.5,s)}=e;return{from:a,to:l}}var Ba=require("@lukeed/uuid"),Wa=require("ml-levenberg-marquardt"),Ya=require("ml-peak-shape-generator"),La=require("ml-spectra-processing");var Ia=z(require("ml-direct"));function Ta(t,e,n){let{minValues:s,maxValues:i,directOptions:o={}}=n,a=HC(t,e),l=(0,Ia.default)(a,s,i,o),{optima:r}=l;return{error:l.minFunctionValue,iterations:l.iterations,parameterValues:r[0]}}function HC(t,e){let{x:n,y:s}=t,i=n.length;return o=>{let a=e(o),l=0;for(let r=0;r<i;r++)l+=(s[r]-a(n[r]))2;return l}}var Ea=require("ml-peak-shape-generator"),za=require("ml-spectra-processing");var Ut={delta:{init:t=>t.signal.delta,min:t=>t.signal.delta-t.shape.fwhm2,max:t=>t.signal.delta+t.shape.fwhm2,gradientDifference:()=>.002},intensity:{init:t=>t.signal.intensity\|\|1,min:()=>0,max:()=>1.5,gradientDifference:()=>.001},fwhm:{init:t=>t.shape.fwhm,min:t=>t.shape.fwhm.25,max:t=>t.shape.fwhm4,gradientDifference:t=>t.shape.fwhm.002},mu:{init:t=>t.shape.mu\|\|.5,min:()=>0,max:()=>1,gradientDifference:()=>.01},coupling:{init:t=>t.jCoupling.coupling,min:t=>t.jCoupling.coupling.8,max:t=>t.jCoupling.coupling1.2,gradientDifference:()=>.01}};function Ft(t,e){let{frequency:n,maxClusterSize:s=1}=e,i=Rt(t),o=st(i);o.clusters=ot(o,{frequency:n,maxClusterSize:s});let a=it(o,e).filter(r=>r.x<1e3),l=a.reduce((r,m)=>m.y>r?m.y:r,Number.MIN_SAFE_INTEGER);for(let r of a)r.y/=l;return a}var ka=["init","min","max","gradientDifference"];function qa(t,e,n,s){let i=0,o=[],{shape:a={kind:"gaussian"},baseline:l=n.min,lineWidth:r=1,frequency:m}=s,c=DC({signals:e,data:t,shiftValue:l,frequency:m,range:n.range});for(let g of c){let{shape:C={...a}}=g;C.fwhm\|\|(C.fwhm=r),C.fwhm/=m;let u=(0,Ea.getShape1D)(C),p=["delta","intensity",...u.getParameters()],d={min:[],max:[],init:[],gradientDifference:[]};for(let h of p)for(let D of ka)d[D].push(OC({signal:g,frequency:m,parameter:h,property:D,minMaxY:n,shapeFct:u}));for(let h of g.js\|\|[])for(let D of ka){let S="coupling",O=s?.parameters?.[S]?.[D];if(O)if(typeof O=="number")d[D].push(Jt(O,S,D,n,m,s.baseline));else{let b=O({jCoupling:h});d[D].push(Jt(b,S,D,n,m,s.baseline))}if(!Ut[S])throw new Error(`No default parameter for ${S}`);let H=Ut[S][D];d[D].push(H({jCoupling:h}))}let f=i,y=f+p.length-1,v=y+1,x=v+g.js.length-1;i+=x-f+1,o.push({shape:C,shapeFct:u,signal:g,parameters:p,propertiesValues:d,fromIndex:f,toIndex:y,fromIndexCoupling:v,toIndexCoupling:x})}return o}function DC(t){let{signals:e,data:n,frequency:s,shiftValue:i,range:o}=t,a=l=>{let r=Ft([l],{frequency:s,maxClusterSize:1}),m=r.reduce((g,C)=>C.y>g.y?C:g,r[0]),{y:c}=(0,za.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 OC(t){let{signal:e,frequency:n,parameter:s,property:i,minMaxY:o,shapeFct:a}=t,l=e?.parameters?.[s]?.[i];if(l)return Jt(l,s,i,o,n,t.baseline);let r=t?.parameters?.[s]?.[i];if(r){if(typeof r=="number")return Jt(r,s,i,o,n,t.baseline);{let c=r(e);return Jt(c,s,i,o,n,t.baseline)}}if(!Ut[s])throw new Error(`No default parameter for ${s}`);let m=Ut[s][i];return m({signal:e,shape:a})}function Jt(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 xC={maxClusterSize:1};function Xa(t,e){let n={...xC,...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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P=0;P<b.parameters.length;P++)C[f]=b.propertiesValues.min[P],u[f]=b.propertiesValues.max[P],p[f]=b.propertiesValues.init[P],d[f++]=b.propertiesValues.gradientDifference[P];for(let P=b.parameters.length;P<b.parameters.length+b.signal.js.length;P++)C[f]=b.propertiesValues.min[P],u[f]=b.propertiesValues.max[P],p[f]=b.propertiesValues.init[P],d[f++]=b.propertiesValues.gradientDifference[P]}let y=Xa(r,i),{kind:v,options:x}=s,[h,D]=v==="direct"?[Ta,vC]:[Wa.levenbergMarquardt,bC],O=h({x:t.x,y:c},y,{minValues:C,maxValues:u,initialValues:p,gradientDifference:d,...D,...x}).parameterValues,H=[];for(let b of r){let{fromIndexCoupling:P}=b,R=b.signal.js.map((T,k)=>(T.coupling=O[P+k],T)),j=O[b.fromIndex],A=Ft([{delta:j,js:R}],i),w=O[b.fromIndex+1]l.range+m,F=[];for(let{x:T,y:k}of A){let E={id:(0,Ba.v4)(),x:T,y:wk,width:0,shape:{...b.shape}};for(let K=2;K<b.parameters.length;K++)E.shape[b.parameters[K]]=O[b.fromIndex+K];E.shape.fwhm=i.frequency,E.width=(0,Ya.getShape1D)(E.shape).fwhmToWidth(E.shape.fwhm),F.push(E)}H.push({delta:j,js:R,shape:{...F[0].shape},intensity:w,peaks:F})}return H}var _a=require("ml-spectra-processing");var PC=Math.PI2;function NC(t,e){let{lb:n=1,from:s=0,to:i=10,nbPoints:o=1024,frequency:a=400,maxClusterSize:l=8}=e,r=st(t);r.clusters=ot(r,{frequency:a,maxClusterSize:l});let m=it(r,{frequency:a}),c=new Float64Array(o),g=new Float64Array(o),C=Math.abs(i-s),u=o/(Ca),p=(0,_a.xSequentialFillFromTo)({size:o,from:0,to:u});for(let y of m){let{x:v,y:x}=y,h=vaPC;for(let D=0;D<o;D++)c[D]+=xMath.cos(hp[D]),g[D]+=xMath.sin(hp[D])}let{windowData:d,...f}=U({re:c,im:g},{pointsToShift:0,compose:{length:o,shapes:[{start:0,shape:{kind:"exponential",options:{dw:u/(o-1),lb:n}}}]}});return f}function us(t){return t.getAllAtoms()<1}var Za=require("openchemlib/full");function MC(t){return t?.match(/V[23]0/)?!us(Za.Molecule.fromMolfile(t)):!1}var Mn=[];for(let{label:t,value:e,names:n}of L)Mn.push(t,e,...n);Mn=Mn.sort((t,e)=>e.length-t.length);function Vt(t){if(t=t.replace(/broad/g,""),t=t.replace(/br\.?/g,""),/^\s$/.exec(t))return[];let e=new RegExp(Mn.join("\|"),"g"),n=t.match(e);return n?n.map(s=>s.trim()):[t]}function jn(t){let e=/ (?<before>[^(]?) $ (?<inside>.?) $ (?<after>.?) /.exec(t);return e?e.groups:{before:t,inside:"",after:""}}function Rn(t,e={}){let{nucleus:n,frequency:s,logger:i}=e,o=jn(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 d=c.filter(y=>y.match(/(Hz\|J\|^[0-9.]+$)/)).map(y=>Number(y.replace(/J[0-9.]\s=/,"J =").replace(/[^0-9.]/g,""))),f=Vt(g.multiplicity\|\|"");if(f.length===d.length)for(let y=0;y<f.length;y++)g.js?g.js.push({coupling:d[y],multiplicity:f[y]}):i.error(`A range has not couplings: ${t}`);if(C.from===C.to&&(C={...C,...Lt(g,{nucleus:n,frequency:s})}),isNaN(C.from)\|\|isNaN(C.to)){i.error(`A range could not be parsed: ${t}`);return}return C}function jC(t,e={}){let{logger:n}=e,s={info:{dimension:1},ranges:[],acsString:t,normalized:t.replace(/\.\s$/,"").replace(/[\r\n\t]/g," ").replace(/[;:]/g,",").replace(/\}/g,")").replace(/\{/g,"(").replace(/[\u2011\u2012\u2013\u2014\u2015\u2212]/g,"-")};return AC(s),RC(s,e),n?.info(`Found: ${s.ranges.length} ranges`),s}function RC(t,e={}){let{logger:n}=e;for(let s of t.parts)if(s.toLowerCase().includes("nmr"))FC(t,s);else{t.info.frequency\|\|(t.info.frequency=400,n?.warn("Frequency not defined, assuming 400 MHz")),t.info.nucleus\|\|(t.info.nucleus="1H",n?.warn("Nucleus not defined, assuming 1H"));let i=Rn(s,{...t.info,logger:n});i&&t.ranges.push(i)}}function FC(t,e){let n=jn(e),s=n.before.replace(/[ -]nmr[ -]/i,"").replace(/[ -]/g,"");if(/^[0-9]+[A-Z][a-z]?$/.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$1")),n.inside){let i=n.inside.split(/[,]/),o=i.filter(l=>/[0-9]{2}/.exec(l));if(o.length){let l=o[0].replace(/[^0-9]/g,"");l.length>1&&(t.info.frequency=Number(l))}let a=i.filter(l=>!l.match(/[0-9]{2}/));a.length&&(t.info.solvent=a[0])}}function AC(t){let e=[],n=0;for(let a=0;a<t.normalized.length;a++)",;)".includes(t.normalized[a])&&(e.push(t.normalized.slice(n,a+1)),n=a+1);e.push(t.normalized.slice(n));let s=[],i="",o=0;for(let a of e)i+=a,o+=(a.match(/$/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(/ [,;]+$/,"").replace(/ +/g," ").trim();t.parts=s}var ps=require("gyromagnetic-ratio");function wC(t){if(ps.gyromagneticRatio[t])return t;if(t.toLowerCase()==="proton")return"1H";let e=t.replace(/[^0-9]/g,"");if(!e)return t;for(let n in ps.gyromagneticRatio)if(n.includes(e))return n;return t}var lt=require("ml-gsd"),Ja=require("ml-signal-processing"),$=require("ml-spectra-processing");function Fn(t,e){return pn(t,{...e,convertTo:"hz"})}function ys(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:d={kind:"lm"},broadWidth:f=.25,sgOptions:y={},direction:v="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 An({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 O,{maxAbsDdY:H}=e;if(n!==void 0&&s!==void 0){if(!("maxAbsDdY"in e)){let R=(0,Ja.savitzkyGolay)(t,{windowSize:D,polynomial:S,derivative:2});H=(0,$.xMaxAbsoluteValue)(R.data.y)}O=(0,$.xyExtract)(t,{zones:[{from:n,to:s}]})}else O=t;let b=TC(O.y,{noiseLevel:o,useSanPlot:m,thresholdFactor:a}),P={shape:p,maxAbsDdY:H,frequency:i,broadWidth:f,optimize:g,factorLimits:C,maxCriteria:!0,sgOptions:{windowSize:D,polynomial:S},minMaxRatio:l,broadRatio:r,noiseLevel:b.positive,smoothY:c,optimization:d,realTopDetection:u};switch(v){case"positive":return ds(O,P);case"negative":return Ua(O,b,P);case"both":return[...ds(O,P),...Ua(O,b,P)];default:throw Error(`Unknown distribution ${v}`)}}function Ua(t,e,n){return n.noiseLevel=e.negative,n.maxCriteria=!1,ds(t,n)}function ds(t,e){let{shape:n,maxAbsDdY:s,frequency:i,broadWidth:o,optimize:a,maxCriteria:l,factorLimits:r,sgOptions:m,minMaxRatio:c,broadRatio:g,noiseLevel:C,smoothY:u,optimization:p,realTopDetection:d}=e,f=(0,lt.gsd)(t,{sgOptions:m,maxCriteria:l,minMaxRatio:c,noiseLevel:C,smoothY:u,realTopDetection:d}),y=(0,lt.setShape)(f,{output:f,shape:n}),v=o?(0,lt.joinBroadPeaks)(y,{shape:n,broadWidth:o,optimization:p,broadRatio:IC(f,{maxAbsDdY:s,broadRatio:g})}).map(fs):y.map(fs);return Fn(a?(0,lt.optimizePeaks)(t,v,{shape:n,factorLimits:r,optimization:p}).map(fs):v,{frequency:i})}function IC(t,e={}){let{maxAbsDdY:n,broadRatio:s=.0025}=e;if(n&&t.length>0){let i=(0,$.xMaxAbsoluteValue)(t.map(o=>o.ddY));return sn/i}return s}function TC(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,$.xNoiseSanPlot)(t,{factorStd:i}):o((0,$.xAbsoluteMedian)(t)i)}function fs(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 An=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 Tn=require("ml-spectra-processing");var Ds=require("@lukeed/uuid"),nl=require("ml-spectra-processing");var Va=require("@lukeed/uuid");function Ga(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,Va.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 wn=["s","d","t","q","quint","h","sept","o","n"],kC=2.5,EC=1,zC={jAxis:"x",intensity:"intensity"};function qC(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 In={compilePattern:(t,e={})=>{let{jAxisKey:n=zC,symRatio:s=2.5}=e,i=_C(t,{...e,symRatio:s,maxError:kC,iteration:1,jAxisKey:n});if(i.multiplicity="m",i.asymmetric=!0,qC(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=ZC(i,c),C=!1;if(g.length===1&&c===0)C=!0;else if(g.length<=1)continue;let u=LC(g);a=2c;let p=null,d=1;for(;!C&&(p=YC(u,a))!==null&&d<400;){let f=new Array(p.length);r=1;for(let h=0;h<p.length;h++){f[h]=new Array(p[h]);for(let D=0;D<p[h];D++)f[h][D]=r++}m=[];let y=1;m.push(g[1].x-g[0].x),o=g[0].x,f[0].splice(0,1),f[1].splice(0,1),r=1;let v=2;for(l=2c-1;m.length<c&&v<l&&r<g.length;){for(d+=1,y++;r<g.length&&f[r].length===0;)r++;if(r<g.length){m.push(g[r].x-g[0].x),f[r].splice(0,1),v++;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<f.length;S++)if(Math.abs(g[S].x-(o+D))<.25){f[S].splice(0,1),v++;break}}}}let x=WC(m);C=!0;for(let h=0;h<x.length;h++)x[h].intensity!==p[h]&&(C=!1)}C&&XC(i,m)}}for(let o of i.peaksComp)o.x/=i.observe,o.width=i.observe;return i}};function XC(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=BC(t,e),t.pattern=t.multiplicity}function BC(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:wn[i]}),s+=wn[i],i=1);let a=e.length-1;o.push({coupling:Math.abs(e[a]),multiplicity:wn[i]}),s+=wn[i],t.nmrJs=o}else s="s",Math.abs(t.startX-t.stopX)t.observe>16&&(s="br s");return s}function WC(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 YC(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 LC(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 _C(t,e){let n=hs(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=hs(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 hs(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 H=0;H<C.length;H++){let b=a.peaks[H];C[H]={x:b[i]a.observe,intensity:b[o],width:b.width/a.observe}}for(let H=C.length-2;H>=0;H--)Math.abs(C[H].x-C[H+1].x)<.25&&(C[H].x=C[H].xC[H].intensity+C[H+1].xC[H+1].intensity,C[H].intensity=C[H].intensity+C[H+1].intensity,C[H].x/=C[H].intensity,C[H].intensity/=2,C[H].width+=C[H+1].width,C.splice(H+1,1));a.peaksComp=C;let u=C.length,p=new Array(u);a.mask=p;let d=0,f=C.length-1,y=a.deltaa.observe,v=[(C[0].x+C[u-1].x)/2,1],x=Math.min($a(Math.abs(y-v[0])),e.maxError),h=0;for(let H=0;H<u;H++)p[H]=!0,h+=C[H].intensity;for(;d<=f;){if(p[d]=!0,p[f]=!0,d===f)u>2&&Math.abs(C[d].x-y)>x&&(p[d]=!1);else if(l=Math.max(C[d].intensity,C[f].intensity),r=Math.min(C[d].intensity,C[f].intensity),c=l/r,c>n)C[d].intensity===r?(p[d]=!1,f++):(p[f]=!1,d--);else{let H=Math.abs(C[d].x-y),b=Math.abs(C[f].x-y);Math.abs(H-b)<x?(m=Math.min(C[d].intensity,C[f].intensity),g=Math.min(C[d].width,C[f].width),C[d].intensity=m,C[f].intensity=m,C[d].width=g,C[f].width=g,v=[v[0]+(C[f].x+C[d].x)/2,v[1]+1]):Math.max(H,b)===b?(p[f]=!1,d--):(p[d]=!1,f++)}if(d++,f--,s===1&&(y=Ka(C,p),isNaN(y)))return a.symRank=0,a;x=$a(Math.abs(y-v[0]/v[1]))}for(let H=u-1;H>=0;H--)p[H]===!1&&C.splice(H,1);if(y=Ka(C),isNaN(y))return a.symRank=0,a;a.delta=y/a.observe;let D=0,S=0;if(C.length>1){for(let H=Math.ceil(C.length/2)-1;H>=0;H--)D+=(3+Math.min(Math.abs(C[H].x-y),Math.abs(C[C.length-1-H].x-y)))/(3+Math.max(Math.abs(C[H].x-y),Math.abs(C[C.length-1-H].x-y)))C[H].intensity,S+=C[H].intensity;D/=S}else C.length===1&&(D=1);let O=0;for(let H of C)O+=H.intensity;if(D-=(h-O)/h.12,D>.8&&D<.97&&s<2)return hs(a,{...e,maxError:EC,iteration:2});if(C.length>1){let H;for(let b=Math.ceil(C.length/2)-1;b>=0;b--)H=(C[b].x-C[C.length-1-b].x)/2,C[b].x=y+H,C[C.length-1-b].x=y-H}return a.symRank=D,a}function $a(t){let e=t2.5;return e<.75&&(e=.75),e>3&&(e=3),e}function ZC(t,e){let n=JSON.parse(JSON.stringify(t.peaksComp)),s=0,i=0;for(let a of n)s+=a.intensity;s=2*e/s,t.mask2=t.mask.slice();let o=t.mask2.length-1;for(let a=n.length-1;a>=0;a--){for(n[a].intensity=s;o>=0&&!t.mask2[o];)o--;n[a].intensity<.75?(n.splice(a,1),t.mask2[o]=!1):i+=n[a].intensity,o--}i=2*e/i;for(let a=n.length-1;a>=0;a--)n[a].intensity=i;return n}function Ka(t,e=[]){let n=0,s=0,i;if(e.length>0)for(let o=0;o<t.length;o++)e[o]&&(i=Qa(t[o]),n+=i,s+=it[o].x);else for(let o of t)i=Qa(o),n+=i,s+=io.x;return s/n}function Qa(t){return Math.abs(t.intensityt.width1.57)}function UC(t){if(!t.mask)throw new Error("Internal Error, mask was not added");if(!t.mask2)throw new Error("Internal Error, mask2 was not added");if(!t.maskPattern)throw new Error("Internal Error, maskPattern was not added")}var tl=(t,e,n)=>({id:(0,Ds.v4)(),delta:NaN,nbPeaks:1,kind:"signal",startX:t.x-t.width/e,stopX:t.x+t.width/e,observe:e,nucleus:n,integralData:{from:t.x-t.width3/e,to:t.x+t.width3/e,value:0},peaks:[{x:t.x,intensity:t.y,width:t.width}]});function el(t,e,n={}){let{symRatio:s=1.5,integrationSum:i=100,joinOverlapRanges:o=!0,clean:a=.4,compile:l=!0,integralType:r="sum",frequency:m=400,frequencyCluster:c=16,keepPeaks:g=!1,nucleus:C="1H"}=n,u={integrationSum:i,integralType:r,frequencyCluster:c,frequency:m,nucleus:C};if(e.length===0)return[];t.x[0]>t.x[1]&&(t.x=t.x.reverse(),t.y=t.y.reverse());let p=Gt(t,e,u);if(a)for(let f=0;f<p.length;f++)Math.abs(p[f].integralData.value)<a&&p.splice(f,1);if(l){let f,y;for(let v=0;v<p.length;v++){p[v]=In.compilePattern(p[v],{symRatio:s});let x=p[v];if(x.maskPattern&&x.multiplicity!=="m"&&x.multiplicity!==""){UC(x),f=0,y=0;let h=[];for(let D=x.maskPattern.length-1;D>=0;D--)if(y+=Hs(x.peaks[D],m),!x.maskPattern[D]){let S=x.peaks.splice(D,1)[0];h.push({x:S.x,y:S.intensity,width:S.width}),x.mask.splice(D,1),x.mask2.splice(D,1),x.maskPattern.splice(D,1),x.nbPeaks--,f+=Hs(S,m)}if(h.length>0){f=fx.integralData.value/y,x.integralData.value-=f;let D=[];for(let O=h.length-1;O>=0;O--)D.push(h[O]);u.integrationSum=Math.abs(f);let S=Gt(t,D,u);for(let O of S)p.push(O)}}}sl(p,i)}if(p.sort((f,y)=>y.delta-f.delta),a)for(let f=p.length-1;f>=0;f--)Math.abs(p[f].integralData.value)<a&&p.splice(f,1);let d=[];for(let f=0;f<p.length;f++){let y=p[f],v={id:(0,Ds.v4)(),from:y.integralData.from,to:y.integralData.to,integration:y.integralData.value},x={delta:y.delta,kind:y.kind\|\|"signal",multiplicity:y.multiplicity};g&&(x.peaks=y.peaks.map(h=>{let D={y:h.intensity,...h};return delete D.intensity,D})),y.nmrJs&&(x.js=y.nmrJs),v.signals=[x],d[f]=v}return o&&(d=Ga(d)),d}function 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JC(t,e){let{from:n,to:s}=e.peakPicking,{fromIndex:i,toIndex:o}=(0,Tn.xGetFromToIndex)(t.x,{from:n,to:s});if(o-i<7)return e.logger?.info("Too small window for accurate multiplicity determination"),[{from:t.x[i],to:t.x[o],signals:[{delta:(0,Tn.xyMaxYPoint)(t,{from:i,to:o}).x,multiplicity:"",js:[]}]}];let a=ys(t,e.peakPicking);return a=Ge(a,e.impurities),el(t,a,e.ranges)}var il=require("ml-gsd");function VC(t,e,n){let{frequency:s}=n,i=fn(e,{frequency:s}),o=(0,il.optimizePeaks)(t,i,n);return Fn(o,{frequency:s,output:o})}var ol=require("ml-levenberg-marquardt"),al=require("ml-regression-base"),ll=require("ml-spectra-processing"),GC={damping:1.5,maxIterations:100,errorTolerance:1e-8};function 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Hl(t){let e=mu(t),n=t.slice(),s;for(let a=n.length-1;a>=0;a--){let l=n[a];if(l.peaks&&l.peaks.length>1&&e[a][1]++,e[a][0]===1){let r=Dl(n,e,l,-1,!0);r>=0&&(e[a][1]+=2,e[r][1]+=2)}}for(let a=n.length-1;a>=0;a--){let l=n[a];e[a][0]===0&&(s=ru(n,e,l,!0),e[a][1]+=s)}let i=0;for(let a=n.length-1;a>=0;a--)e[a][0]!==0&&e[a][1]>2&&(i++,i+=lu(n,e,n[a],e[a])),e[a][1]>=2&&e[a][0]===0&&i++;let o=new Array(i);i--;for(let a=n.length-1;a>=0;a--)(e[a][0]!==0&&e[a][1]>2\|\|e[a][0]===0&&e[a][1]>1)&&(o[i--]=n[a]);return o}function lu(t,e,n,s){let i=Dl(t,e,n,-s[0],!0),o=0,a,l=null;i<0&&(a={x:{nucleus:n.x.nucleus,resolution:n.x.resolution,delta:n.y.delta},y:{nucleus:n.y.nucleus,resolution:n.y.resolution,delta:n.x.delta},peaks:[{x:n.y.delta,y:n.x.delta,z:1}]},t.push(a),l=[-s[0],s[1]],e.push(l),o++);let r,m=!1,c=!1;for(let g=t.length-1;g>=0;g--)r=t[g],e[g][0]===0&&(Math.abs(r.x.delta-n.x.delta)<.05&&(m=!0),Math.abs(r.y.delta-n.y.delta)<.05&&(c=!0));return 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o=t.length-1;o>=0;o--)if(e[o][0]===s&&cu(n,t[o],i)<.05){if(i){let a=n.x.delta,l=t[o].x.delta;t[o].y.delta=a,n.y.delta=l}else{let a=(t[o].x.delta+n.x.delta)/2,l=(t[o].y.delta+n.y.delta)/2;t[o].x.delta=a,t[o].y.delta=l,n.x.delta=a,n.y.delta=l}return o}return-1}function mu(t){let e=new Array(t.length);for(let n=t.length-1;n>=0;n--)if(e[n]=[0,0],Math.abs(t[n].x.delta-t[n].y.delta)<=.05){e[n][1]=1;let s=(t[n].x.delta2+t[n].y.delta)/3;t[n].x.delta=s,t[n].y.delta=s}else t[n].x.delta-t[n].y.delta>0?e[n][0]=1:e[n][0]=-1;return e}function cu(t,e,n){return Math.sqrt(n?(t.x.delta-e.y.delta)2+(t.y.delta-e.x.delta)2:(t.x.delta-e.x.delta)2+(t.y.delta-e.y.delta)2)}function Ol(t,e){let{minX:n,maxX:s,minY:i,maxY:o}=t,a=e.width,l=t.z[0].length,r=t.z.length,m=(o-i)/(r-1),c=(s-n)/(l-1),g=a-r,C=Math.max(a-l,0);C%2&&C++,g%2&&g++;let u=C/2,p=g/2,d=[];for(let f=0;f<r+g;f++)d.push(new Float64Array(l+C));for(let f=0;f<r;f++)for(let 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v=(0,He.matrixMinMaxZ)(u),O=(0,He.matrixMinMaxZ)(b),y={re:{...i,z:u,minZ:v.min,maxZ:v.max},im:{...s,z:b,minZ:O.min,maxZ:O.max}};if(d<0){let{minY:H,maxY:S}=i,D=(S-H)/(l-1),h=S+Dp;y.re.maxY=h,y.im.maxY=h}Object.assign(e.data,y)}function Ps(e){return!!(e.info.isComplex&&e.info.isFid)}function bm(){return{once:!0,reduce:void 0}}var mn={};I(mn,{DOMAIN_UPDATE_RULES:()=>hm,apply:()=>Hm,id:()=>Ms,isApplicable:()=>js,name:()=>ym,reduce:()=>Dm});function Ns(e,n){let{digitalFilterValue:t=0}=n,i=new Float64Array(e.re),s=new Float64Array(e.im),o=Math.floor(t),a=0;o+=0;let l=new Float64Array(i.length),r=new Float64Array(s.length);return l.set(i.slice(o)),l.set(i.slice(a,o),i.length-o),r.set(s.slice(o)),r.set(s.slice(a,o),s.length-o),{re:l,im:r}}var Ms="digitalFilter2D",ym="Digital filter on Dimension 1",hm={updateXDomain:!1,updateYDomain:!1};function Hm(e,n={}){if(!js(e))throw new Error("Digital filter on dimension 1 is not applicable on this data");let{data:{re:t,im:i}}=e,s=t.z,o=i.z,a=s.length,l=[],r=[],{digitalFilterValue:m}=n;if(!m\|\|m===0)return;let c=e.filters.find(g=>g.name===Ms);c&&(c.value={digitalFilterValue:m});for(let g=0;g<a;g++){let{re:d,im:f}=Ns({re:s[g],im:o[g]},{digitalFilterValue:m});l.push(d),r.push(f)}Object.assign(e.data.re,{z:l}),Object.assign(e.data.im,{z:r})}function js(e){return!!(e.info.isComplex&&e.info.isFid)}function Dm(){return{once:!0,reduce:void 0}}var Cn={};I(Cn,{DOMAIN_UPDATE_RULES:()=>vm,apply:()=>Sm,id:()=>Om,isApplicable:()=>As,name:()=>xm,reduce:()=>Pm});var fn=require("ml-spectra-processing");var gn=require("ml-matrix"),me=require("ml-spectra-processing");var cn=require("ml-spectra-processing");function Rs(e,n={}){let{digitalFilterValue:t=0}=n,i=e.re.length,s=new Float64Array(e.re),o=new Float64Array(e.im),a=(0,cn.xMean)(e.re.slice(i.75>>0,i-t)),l=(0,cn.xMean)(e.im.slice(i.75>>0,i-t));for(let r=t;r<i-t;r++)s[r]-=a,o[r]-=l;return{re:s,im:o}}function dn(e,n={}){let{re:t,im:i}=e,s=t.length,o=t[0].length,{reverse:a,digitalFilterValue:l=0}=n,r=new gn.Matrix(s,o),m=new gn.Matrix(s,o),{phaseCorrection:c={}}=n,{ph0:g,ph1:d,mode:f="no"}=c;for(let C=0;C<s;C++){let p={re:t[C],im:a?(0,me.xMultiply)(i[C],-1):i[C]};Object.assign(p,Rs(p,{digitalFilterValue:l})),Object.assign(p,(0,me.reimFFT)(p,{applyZeroShift:!0}));let u=lMath.PI2;u>0&&Object.assign(p,(0,me.reimPhaseCorrection)(p,0,-u,{reverse:!0})),f==="pk"&&g!==void 0&&d!==void 0&&Object.assign(p,(0,me.reimPhaseCorrection)(p,gMath.PI/180,dMath.PI/180,{reverse:!0})),r.setRow(C,p.re),m.setRow(C,p.im)}return{re:r,im:m}}var Q=require("ml-spectra-processing");function Fs(e){let{re:{z:n},im:{z:t}}=e,i=[],s=[];for(let o=0;o<n.length;o+=2){let a=n[o],l=t[o],r=n[o+1],m=t[o+1];i.push((0,Q.xSubtract)((0,Q.xMultiply)(m,-1),l)),i.push((0,Q.xSubtract)(r,a)),s.push((0,Q.xAdd)(r,a)),s.push((0,Q.xSubtract)(m,l))}return{re:i,im:s}}var Om="fftDimension1",xm="FFT Dimension 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t={re:ce.Matrix.checkMatrix(e.re),im:ce.Matrix.checkMatrix(e.im)},i=t.re.rows,s=t.re.columns,{acquisitionScheme:o,reverse:a}=n,l={...n},r={};if(o==="notPhaseSensitive"){let m=new ce.Matrix(i,s),c=new ce.Matrix(i,s);for(let g=0;g<s;g++){let d={re:t.re.getColumn(g),im:a\|\|o==="notPhaseSensitive"?(0,ee.xMultiply)(t.im.getColumn(g),-1):t.im.getColumn(g)};d.re[0]=.5,d.im[0]=.5;let{re:f,im:C}=ws(d,l);m.setColumn(g,f),c.setColumn(g,C)}r.rr=m,r.ir=c}else for(let m in t){let c=o==="SEQ"?i:i/2,g=new ce.Matrix(c,s),d=new ce.Matrix(c,s);for(let f=0;f<s;f++){let C=Nm(t[m],{acquisitionScheme:o,index:f,reverse:a});C.re[0]=.5,C.im[0]=.5;let{re:p,im:u}=ws(C,l);g.setColumn(f,p),d.setColumn(f,u)}m==="re"?(r.rr=g,r.ri=d):(r.ir=g,r.ii=d)}return r}function ws(e,n){let{acquisitionScheme:t,phaseCorrection:i={}}=n;e.re[0]=.5,e.im[0]=.5;let s=(0,ee.reimFFT)(e,{applyZeroShift:t!=="SEQ"}),{mode:o,ph0:a,ph1:l}=i;return(o&&o==="mc"\|\|t==="notPhaseSensitive")&&Object.assign(s,{re:(0,ee.reimAbsolute)(s),im:new 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hn={};I(hn,{DOMAIN_UPDATE_RULES:()=>qm,apply:()=>Xm,id:()=>qs,isApplicable:()=>Xs,name:()=>zm,reduce:()=>Bm});var De=require("ml-spectra-processing");var qs="flpDimension2",zm="Fordward-LP Dimension 2",qm={updateXDomain:!0,updateYDomain:!0};function Xm(e,n={}){if(!Xs(e))throw new Error("Forward Linear Prediction on dimension 2 is not applicable on this data");let{info:t,data:{re:i,im:s}}=e,o=i.z,a=s.z,l=o.length,r=o[0].length,{lpNumberOfCoefficients:m=[0,0],linearPredictionBin:c=[0,0],spectrumSize:g=[r,l],numberOfPoints:d=[r,l]}=t,{nbPoints:f=be(g[1],d[1],c[1])/-2,nbCoefficients:C=m[1],nbInputs:p=Math.floor(l-C-(f<0?0:f))}=n,u=e.filters.find(D=>D.name===qs);if(u&&(u.value={nbCoefficients:C,nbPoints:f,nbInputs:p}),Math.abs(f)===0\|\|C===0)return;let b=f<0?-1f:0,v=(0,De.matrixCreateEmpty)({nbRows:l+b,nbColumns:r}),O=(0,De.matrixCreateEmpty)({nbRows:l+b,nbColumns:r});for(let 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",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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Zo=require("ml-sparse-matrix");function Uo(e){let n=(e-1)/2,t=new Array(e),i=new Array(e);for(let m=0;m<e;m++)t[m]=e-1-m-n,i[m]=Math.sqrt(n(n+1)-t[m](t[m]+1));let s=ni(i,1,e,e);for(let m=0;m<e;m++)i[m]=Math.sqrt(n(n+1)-t[m](t[m]-1));let o=ni(i,-1,e,e),a=s.clone().add(o).mul(.5),l=o.clone().mul(-1).add(s).mul(-.5),r=ni(t,0,e,e);return{x:a,y:l,z:r,m:o,p:s}}function ni(e,n,t,i){let s=new Zo.SparseMatrix(t,i,{initialCapacity:20});for(let o=0;o<e.length;o++)o-n>=0&&o-n<t&&o<i&&s.set(o-n,o,e[o]);return s}var d0=Uo(2);function _e(e){return e===2?d0:Uo(e)}var Ht=.01;function se(e,n={}){let{lineWidth:t=1,maxClusterSize:i=8,frequency:s=400}=n,o=ne(e),a=o.chemicalShifts.slice();for(let m=0;m<a.length;m++)a[m]=a[m]s;let l=o.levels,r=[];for(let m of o.clusters){let c=m.map(u=>u<0?-u-1:u),g=1,d=0,f=[],C=[];if(m.length>i){let u=0;for(;m[u++]<0;);u=m[u-1],f.push(-a[u]);for(let b=0;b<m.length;b++)if(m[b]<0){let v=o.couplingConstants.get(u,c[b])/2,O=f.length;for(let 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_.SparseMatrix(h.to2DArray(),{threshold:Ht});R.forEachNonZero((j,A,w)=>w),Jo(R,Ht),R.forEachNonZero((j,A,w)=>{let F=D.get(j,A);F=Math.min(Math.abs(F),Math.abs(w)),F=F,d+=F;let T=y[j]-y[A],k=(0,Vo.default)(f,T,(E,K)=>E-K);k<0?(f.splice(-1-k,0,T),C.splice(-1-k,0,F)):C[k]+=F})}let p=f.length;if(p>0){g/=d;let u=t/64,b=f[0],v=C[0],O=1;for(let y=1;y<p;y++)Math.abs(f[y]-b/O)<u?(v+=C[y],b+=f[y],O++):(r.push({x:-b/O/s,y:vg}),b=f[y],v=C[y],O=1);r.push({x:-b/O/s,y:vg})}}return r.filter(m=>m.x<1e3)}function Jo(e,n){e.forEachNonZero((t,i,s)=>Math.abs(s)<=n?0:s)}function f0(e,n,t,i,s){let o=1;for(let l of s)o=t[l];let a=new _.SparseMatrix(o,o);for(let l=0;l<s.length;l++){let r=s[l],m=_e(t[r]),c=1;for(let p=0;p<l;p++)c=t[s[p]];let g=_.SparseMatrix.eye(c);c=1;for(let p=l+1;p<s.length;p++)c=t[s[p]];let d=_.SparseMatrix.eye(c),f=e[r],C=g.kroneckerProduct(m.z).kroneckerProduct(d);a.add(C.mul(f));for(let p=0;p<s.length;p++){let u=s[p];if(i.get(r,u)===1){let b=_e(t[u]),v=1;for(let S=0;S<p;S++)v=t[s[S]];let O=_.SparseMatrix.eye(v);v=1;for(let S=p+1;S<s.length;S++)v=t[s[S]];let y=_.SparseMatrix.eye(v),H=g.kroneckerProduct(m.x).kroneckerProduct(d).mmul(O.kroneckerProduct(b.x).kroneckerProduct(y));H.add(g.kroneckerProduct(m.y).kroneckerProduct(d).mul(-1).mmul(O.kroneckerProduct(b.y).kroneckerProduct(y))),H.add(g.kroneckerProduct(m.z).kroneckerProduct(d).mmul(O.kroneckerProduct(b.z).kroneckerProduct(y))),a.add(H.mul(n.get(r,u)/2))}}}return a}function ii(e,n={}){let{lineWidth:t=1,frequency:i=400,from:s=0,to:o=10,nbPoints:a=1024,shape:l={kind:"gaussian"}}=n,r=ne(e),m=t/i,c=se(r,n);return(0,Go.generateSpectrum)(c,{generator:{from:s,to:o,nbPoints:a},peakOptions:{shape:l,width:m}})}var Ko=require("ml-hclust"),Qo=require("ml-matrix");function oe(e,n={}){let t=ne(e),{chemicalShifts:i,couplingConstants:s,connectivity:o}=t,{frequency:a=400,maxClusterSize:l=8}=n,r=C0(i,s,a),m=(0,Ko.agnes)(r,{method:"single",isDistanceMatrix:!0}),c=[],g=i.length;si(m,c,{maxClusterSize:l,force:!1,nSpins:g,connectivity:o});let d=u0(c,l),f=d.length,C=new Array(f);for(let p=0;p<f;p++){C[p]=[];for(let u=0;u<g;u++){let b=d[p][u];b!==0&&C[p].push(b<0?-(u+1):u)}}return C}function si(e,n,t){let{maxClusterSize:i,force:s,nSpins:o,connectivity:a}=t;if(!s&&e.size<=i)n.push($o(e.indices(),o));else for(let l of e.children)if(l.size<=i){let r=$o(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<=i?n.push(r):l.index<0?si(l,n,{maxClusterSize:i,force:!0,nSpins:o,connectivity:a}):(r[l.index]=2,n.push(r))}else si(l,n,{maxClusterSize:i,force:!1,nSpins:o,connectivity:a})}function C0(e,n,t){let i=n.rows,s=n.columns,o=Qo.Matrix.zeros(i,i);for(let a=0;a<i;a++)for(let l=a;l<s;l++){let r=n.get(a,l);if(e[a]-e[l]!==0){let 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el=(e,n,t)=>({id:(0,Hi.v4)(),delta:NaN,nbPeaks:1,kind:"signal",startX:e.x-e.width/n,stopX:e.x+e.width/n,observe:n,nucleus:t,integralData:{from:e.x-e.width3/n,to:e.x+e.width3/n,value:0},peaks:[{x:e.x,intensity:e.y,width:e.width}]});function nl(e,n,t={}){let{symRatio:i=1.5,integrationSum:s=100,joinOverlapRanges:o=!0,clean:a=.4,compile:l=!0,integralType:r="sum",frequency:m=400,frequencyCluster:c=16,keepPeaks:g=!1,nucleus:d="1H"}=t,f={integrationSum:s,integralType:r,frequencyCluster:c,frequency:m,nucleus:d};if(n.length===0)return[];e.x[0]>e.x[1]&&(e.x=e.x.reverse(),e.y=e.y.reverse());let C=Ge(e,n,f);if(a)for(let u=0;u<C.length;u++)Math.abs(C[u].integralData.value)<a&&C.splice(u,1);if(l){let u,b;for(let v=0;v<C.length;v++){C[v]=wt.compilePattern(C[v],{symRatio:i});let O=C[v];if(O.maskPattern&&O.multiplicity!=="m"&&O.multiplicity!==""){Jg(O),u=0,b=0;let y=[];for(let H=O.maskPattern.length-1;H>=0;H--)if(b+=hi(O.peaks[H],m),!O.maskPattern[H]){let 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