npm - nmr-processing - Versions diffs - 21.2.4 → 22.0.0 - Mend

nmr-processing 21.2.4 → 22.0.0

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package/dist/nmr-processing.js +2 -2
package/package.json +3 -3

package/dist/nmr-processing.js CHANGED Viewed

@@ -1,2 +1,2 @@
-var mr=Object.defineProperty;var Ct=(e,n)=>{for(var t in n)mr(e,t,{get:n[t],enumerable:!0})};export*from"gyromagnetic-ratio";import{xEnsureFloat64 as cr}from"ml-spectra-processing";function E(e,n){let{windowData:t,output:s=new Float64Array(e)}=n,i=s.length;if(i!==t.length)throw new RangeError("window function and data should have the same length");for(let o=0;o<i;o++)s[o]*=t[o];return cr(s)}import{xDivide as dr,xMaxValue as gr}from"ml-spectra-processing";function en(e,n){let t=new Float64Array(n);for(let s=0;s<n;s++)t[s]=e(s);return t}function tn(e,n){let{dw:t}=n,{lineBroadening:s}=e,i=-s*Math.PI*t;return o=>Math.exp(i*o)}function nn(e,n){let{dw:t,length:s}=n,{lineBroadening:i,lineBroadeningCenter:o}=e;if(o>1||o<0)throw new Error("The lineBroadeningCenter of gaussian shape should be inside of the window function: 0 - 1");let a=Math.PI*i*t,r=o*(s-1);return l=>Math.exp(-1*((r-l)*a)**2)}function sn(e,n){return yt({exponent:1,...e},n)}function yt(e,n){let{length:t}=n,{exponent:s,offset:i}=e;if(t===void 0)throw new Error("length options should exists for sineBell shape");let o=Math.PI*i,a=Math.PI*(1-i)/(t-1);return r=>Math.sin(o+a*r)**s}function on(e,n){return yt({...e,exponent:2},n)}function an(e,n){let{length:t,dw:s}=n,i=-s/e.lineBroadening;return o=>{let a=Math.exp(i*o);return a/(a**2+Math.exp(-i*(o-t))**2)}}function rn(e,n){let{kind:t,options:s}=e;switch(t){case"exponential":return tn(s,n);case"gaussian":return nn(s,n);case"sineBell":return sn(s,n);case"sineSquare":return on(s,n);case"traf":return an(s,n);default:throw new Error(`Unknown distribution ${t}`)}}function ne(e){let{shapes:n,windowOptions:t}=e,s=new Float64Array(t.length).fill(1);for(let[i,o]of Object.entries(n)){let{options:a,apply:r=!0}=o;if(!r)continue;let l=en(rn({kind:i,options:a},t),t.length);E(s,{windowData:l,output:s})}return dr(s,gr(s),{output:s})}import{TopicMolecule as Sr}from"openchemlib-utils";import{Molecule as Or}from"openchemlib";import{agnes as fr}from"ml-hclust";import{Matrix as pr}from"ml-matrix";import{Molecule as cn}from"openchemlib";function ln(e,n={}){let t=n.output||structuredClone(e);for(let s of t)s.id=crypto.randomUUID();return t}var ur={h:"1H",c:"13C"};function mn(e){return Object.values(e).map(n=>ur[n.toLowerCase()])}function Cr(e){if(!e.from||!e.to)throw new Error("options from and to are mandatory")}async function se(e,n){Cr(n);let{from:t,to:s,minLength:i=0,maxLength:o,predictions:a,includeDiagonal:r=!1}=n,l={...n.joinDistance,H:.05,C:.5},{correlationPaths:m=yr(e,{fromLabel:t,toLabel:s,minLength:i,maxLength:o})}=n,c=e.getGroupedDiastereotopicAtomIDs()||[],d=[];for(let h of c||[])d.push({...h,pathInfo:structuredClone(m[h.atoms[0]])});let g=a[s],u=a[t];if(!u||!g)throw new Error("predictions are not availaible");let f={x:u,y:g},C={x:{},y:{}};for(let h in C)for(let D of f[h].joinedSignals){if(!D.diaIDs)throw new Error("Signal has not diaIDs");C[h][D.diaIDs[0]]=D}let y={};for(let h of d){let D=h.pathInfo;if(D.paths.length===0||!C.x[D.oclID])continue;let O=D.paths;for(let S of O){if(!C.y[m[S.to].oclID])continue;let x={x:D,y:m[S.to]},H=`${x.x.oclID}-${x.y.oclID}`;if(H===`${D.oclID}-${D.oclID}`||y[H])continue;let v={id:crypto.randomUUID(),x:0,y:0,z:100},P={id:crypto.randomUUID(),x:{delta:0,diaIDs:[],atoms:[]},y:{delta:0,diaIDs:[],atoms:[]},peaks:[]};for(let M of["x","y"]){let F=x[M].oclID;v[M]=C[M][F].delta,P[M].delta=C[M][F].delta,P[M].diaIDs=[F];let{atoms:R}=C[M][F];R&&(P[M].atoms=R)}P.peaks=[v],y[H]=P}}r&&Dr(y,{paths:m,signalsByDiaID:C});let p=Object.values(y),b=hr(p,{joinDistance:l,from:t,to:s});return{nuclei:mn({from:t,to:s}),joinedSignals:p,signals:br(p),zones:b}}function yr(e,n){let{fromLabel:t,toLabel:s,minLength:i,maxLength:o=Number.MAX_SAFE_INTEGER}=n,a=e.diaIDs,r=e.moleculeWithH,l=e.distanceMatrix,m=cn.getAtomicNoFromLabel(t),c=cn.getAtomicNoFromLabel(s),d=[];for(let g=0;g<r.getAllAtoms();g++){let u={oclID:a[g],paths:[]};for(let f=0;f<r.getAllAtoms();f++){if(g===f||r.getAtomicNo(f)!==c||r.getAtomicNo(g)!==m)continue;let C=l[g][f];C>=i&&C<=o&&u.paths.push({from:g,to:f})}d.push(u)}return d}function br(e){let n=[];for(let t of e)for(let s of t.x.atoms||[])for(let i of t.y.atoms||[]){let o=structuredClone(t);o.x.atoms=[s],o.y.atoms=[i],n.push(o)}return ln(n)}function Dr(e,n){let{paths:t=[],signalsByDiaID:s}=n;for(let i of t){let o=i.oclID;if(!s.x[o]||e[`${o}-${o}`])continue;let a=s.x[o].delta,r=s.y[o].delta,l={id:crypto.randomUUID(),x:{delta:a,diaIDs:[o],atoms:s.x[o].atoms},y:{delta:r,diaIDs:[o],atoms:s.y[o].atoms},peaks:[{id:crypto.randomUUID(),x:a,y:r,z:1,minX:a,maxX:a,minY:r,maxY:r}]};e[`${i.oclID}-${i.oclID}`]=l}}function hr(e,n){if(e.length===0)return[];let{joinDistance:t,from:s,to:i}=n,o=new pr(e.map(f=>[f.x.delta,f.y.delta])),a=o.minColumn(0),r=o.maxColumn(0),l=o.minColumn(1),m=o.maxColumn(1);o.mulColumn(0,1/(r-a)),o.mulColumn(1,1/(m-l));let c=Math.hypot(t[s]/(r-a),t[i]/(m-l)),d=fr(o.to2DArray(),{method:"centroid"}),g=dn([d],c),u=[];for(let f of g){let C=[];f.isLeaf&&C.push(e[f.index]);for(let y of f.children)for(let p of y.indices())C.push(e[p]);u.push({id:crypto.randomUUID(),...Hr(C,{joinDistance:t,from:s,to:i}),signals:C})}return u}function Hr(e,n){let{joinDistance:t,from:s,to:i}=n,o=Number.MAX_SAFE_INTEGER,a=Number.MAX_SAFE_INTEGER,r=Number.MIN_SAFE_INTEGER,l=Number.MIN_SAFE_INTEGER;for(let m of e)m.x.delta<o&&(o=m.x.delta),m.x.delta>r&&(r=m.x.delta),m.y.delta<a&&(a=m.y.delta),m.y.delta>l&&(l=m.y.delta);return{x:{from:o-t[s],to:r+t[s]},y:{from:a-t[i],to:l+t[i]}}}function dn(e,n){let t=e.length;for(let s=0;s<e.length;s++){let i=e[s];i.height>n&&(e.push(...i.children),e.splice(s--,1))}return e.length<t?dn(e,n):e}async function gn(e,n){let{minLength:t,maxLength:s,predictions:{H:i},includeDiagonal:o=!0,minCoupling:a=1.5}=n;if(!i)throw new Error("prediction is not availaible");let r={...n,from:"H",to:"H",includeDiagonal:o};return(!t||!s)&&(r.correlationPaths=xr(e,i,a)),se(e,r)}function xr(e,n,t){let s=e.diaIDs,i=[],o={},a=n.signals;for(let m of a){let c=m.diaIDs[0];o[c]??={};for(let d of m.js){if(!d.diaIDs||d.diaIDs.length===0)throw new Error("should contains assigned coupling by atoms");let g=d.diaIDs[0];o[c][g]=Math.max(d.coupling,o[c][g]??Number.MIN_SAFE_INTEGER)}}let r=e.moleculeWithH,l=Or.getAtomicNoFromLabel("H");for(let m=0;m<r.getAllAtoms();m++){let c={oclID:s[m],paths:[]};for(let d=0;d<r.getAllAtoms();d++)m!==d&&r.getAtomicNo(d)===l&&r.getAtomicNo(m)===l&&o[s[m]]?.[s[d]]>=t&&c.paths.push({from:m,to:d});i.push(c)}return i}function un(e,n){async function t(s){let i=await fetch(n,{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}: ${a}`)}let{data:o}=await i.json();return{nucleus:o.nucleus,joinedSignals:o.joinedSignals??[],signals:o.signals??[],ranges:o.ranges??[]}}return Object.defineProperty(t,"name",{value:`default${e[0].toUpperCase()}${e.slice(1)}Predictor`}),t}var fn=un("proton","https://nmr-prediction.service.zakodium.com/v1/predict/proton"),pn=un("carbon","https://nmr-prediction.service.zakodium.com/v1/predict/carbon");async function Me(e,n,t){let{cache:s,predictorOptions:i}=t;if(typeof s=="function"){let a=await s(e);if(a)return a}let o=await n(e,i);return typeof s=="function"&&await s(e,o),o}async function Cn(e,n={}){let{predictor:t=pn,predictorOptions:s={},cache:i}=n;return e.molecule.getAllAtoms()===0?{nucleus:"13C",joinedSignals:[],signals:[],ranges:[]}:Me(e,t,{cache:i,predictorOptions:s})}async function yn(e,n){let{minLength:t=2,maxLength:s=3,joinDistance:i}=n;return se(e,{...n,from:"H",to:"C",minLength:t,maxLength:s,joinDistance:i})}async function bn(e,n){let{minLength:t=1,maxLength:s=1,joinDistance:i}=n;return se(e,{...n,from:"H",to:"C",minLength:t,maxLength:s,joinDistance:i})}async function Dn(e,n={}){let{predictor:t=fn,cache:s,predictorOptions:i={}}=n;return e.molecule.getAllAtoms()===0?{nucleus:"1H",joinedSignals:[],signals:[],ranges:[]}:Me(e,t,{cache:s,predictorOptions:i})}function bt(e,n){if(e in n)return!0;let t="hsqc"in n||"hmbc"in n;return e==="C"?t:e==="H"?t||"cosy"in n:!1}var vr={cosy:{predictor:gn,required:["H"],message:"Proton prediction is missing so COSY could not be generated."},hsqc:{predictor:bn,required:["H","C"],message:"Carbon and / or proton prediction is missing so HSQC could not be generated."},hmbc:{predictor:yn,required:["H","C"],message:"Carbon and / or proton prediction is missing so HMBC could not be generated."}};async function W(e,n={}){let{logger:t,joinDistance:s={H:.05,C:.5},predictOptions:i={H:{},C:{},hsqc:{},hmbc:{},cosy:{}}}=n,o=new Sr(e),a=bt("H",i)?await Dn(o,{...i?.H}):void 0,r=bt("C",i)?await Cn(o,i?.C):void 0,l={},m=o.diaIDs,c={};hn(a,m)&&(c.H=a,"H"in i&&(l.proton=a)),hn(r,m)&&(c.C=r,"C"in i&&(l.carbon=r));let g=["cosy","hsqc","hmbc"].filter(f=>f in i).map(async f=>{let{predictor:C,required:y,message:p}=vr[f];if(y.every(b=>b in c)){let b=await C(o,{predictions:c,...i[f],joinDistance:s});return{key:f,result:b}}else t&&t.warn(p);return{key:f,result:void 0}}),u=await Promise.all(g);for(let{key:f,result:C}of u)C&&(l[f]=C);return{diaIDs:o.diaIDs,hoses:o.hoseCodes,distanceMatrix:o.distanceMatrix,moleculeWithHydrogens:o.moleculeWithH,groupedDiaIDs:o.getGroupedDiastereotopicAtomIDs()||[],molfile:o.toMolfile(),molfileWithH:o.toMolfileWithH(),spectra:l}}function hn(e,n=[]){if(!e||e.ranges.length===0)return!1;let{signals:t}=e;for(let s of t)if(!s.diaIDs?.every(o=>n.includes(o)))return!1;return!0}import{xIsMonotonic as Kr,xRescale as Qr,xSequentialFillFromTo as el}from"ml-spectra-processing";var _=[{label:"singlet",value:"s",multiplicity:1,names:[]},{label:"doublet",value:"d",multiplicity:2,names:[]},{label:"triplet",value:"t",multiplicity:3,names:[]},{label:"quartet",value:"q",multiplicity:4,names:[]},{label:"quintet",value:"i",acs:"quint",multiplicity:5,names:["quint","qui","qnt","pentet","pnt","pent"]},{label:"sextet",value:"h",multiplicity:6,names:["x","sxt","sext","hexuplet","hex"]},{label:"septet",value:"p",acs:"sept",multiplicity:7,names:["sept","spt","heptet","hpt","hept"]},{label:"octet",value:"o",multiplicity:8,names:["oct"]},{label:"nonet",value:"n",multiplicity:9,names:["non"]},{label:"multiplet",value:"m",multiplicity:null,names:["massive"]}];var Dt={};for(let{value:e,multiplicity:n,names:t}of _){n&&(Dt[e]=n-1);for(let s of t)n&&(Dt[s]=n-1)}var q=Dt;function ie(e){let n=structuredClone(e),t=e.reduce((s,i)=>{let{atoms:o=[]}=i;return Math.max(...o,s)},0)+1;for(let[s,i]of e.entries()){let{js:o=[],atoms:a=[t++]}=i,{newCouplings:r,tempSignals:l}=Pr(o,a,t+e.length);l.length>0&&n.push(...l),n[s].js=r,n[s].atoms=a}return n.sort((s,i)=>s.delta-i.delta),n}function Pr(e,n,t){let s=[];return{newCouplings:e.reduce((o,a)=>{let{atoms:r=[],multiplicity:l,coupling:m}=a;if(r.length===0&&m&&l){let c=[],d=q[l];for(let g=0;g<d;g++)t++,c.push({coupling:m,multiplicity:"d",atoms:[t]}),s.push(Fr(m,[t],n));o.push(...c)}else o.push(a);return o},[]),tempSignals:s}}function Fr(e,n,t){return{delta:1e5,atoms:n,js:[{coupling:e,atoms:t}]}}import{Matrix as Rr}from"ml-matrix";import{Matrix as ht}from"ml-matrix";import{simpleClustering as jr}from"ml-simple-clustering";function L(e){let{couplingConstants:n,connectivity:t}=e,s=ht.checkMatrix(n),i=t?ht.checkMatrix(t):Mr(s),{levels:o=Array.from({length:i.rows},()=>2),clusters:a=jr(i.to2DArray(),{out:"indexes"})}=e;return{...e,levels:o,clusters:a,connectivity:i,couplingConstants:s}}function Mr(e){let n=ht.ones(e.rows,e.rows);for(let t=0;t<e.rows;t++)for(let s=t;s<e.columns;s++)e.get(t,s)===0&&(n.set(t,s,0),n.set(s,t,0));return n}function wr(e){for(let n of e){if(!n.js)throw new Error("there is not js");if(!n.atoms)throw new Error("there is not atoms");for(let t of n.js)if(!t.atoms)throw new Error("there is not atoms")}}function U(e){wr(e);let n=e.length,t=[],s=Rr.zeros(n,n),i={};for(let o=0;o<n;o++){t.push(e[o].delta);let a=e[o].atoms[0];i[a]=o}for(let o=0;o<n;o++){let{atoms:a,js:r}=e[o],l=a[0];for(let m of r){let{coupling:c,atoms:d}=m,g=d[0];s.set(i[l],i[g],c),s.set(i[g],i[l],c)}}return L({couplingConstants:s,chemicalShifts:t})}import{generateSpectrum as Vr}from"spectrum-generator";import Tr from"binary-search";import{EVD as Er,Matrix as zr}from"ml-matrix";import{SparseMatrix as we}from"ml-sparse-matrix";import{SparseMatrix as Nr}from"ml-sparse-matrix";function Hn(e,n){let t=2*e*n,s=new Nr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+n+r,a+r,1)}return s}import{SparseMatrix as Ar}from"ml-sparse-matrix";function Ht(e,n){let t=2*e*n,s=new Ar(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+r,a+n+r,.5),s.set(o+n+r,a+r,.5)}return s}import{SparseMatrix as kr}from"ml-sparse-matrix";function Ot(e,n){let t=2*e*n,s=new kr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+r,a+n+r,-.5),s.set(o+n+r,a+r,.5)}return s}import{SparseMatrix as Ir}from"ml-sparse-matrix";function Re(e,n){let t=2*e*n,s=new Ir(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=o+n;for(let r=0;r<n;r++)s.set(o+r,o+r,.5),s.set(a+r,a+r,-.5)}return s}var xt=.01;function On(e,n={}){let{lineWidth:t=1,maxClusterSize:s=8,frequency:i=400}=n,o=L(e),a=o.chemicalShifts.slice();for(let m=0;m<a.length;m++)a[m]=a[m]*i;let r=o.levels,l=[];for(let m of o.clusters){let c=m.map(y=>y<0?-y-1:y),d=1,g=0,u=[],f=[];if(m.length>s){let y=0;for(;m[y++]<0;);y=m[y-1],u.push(-a[y]);for(let p=0;p<m.length;p++)if(m[p]<0){let b=o.couplingConstants.get(y,c[p])/2,h=u.length;for(let D=0;D<h;D++)u.push(u[D]+b),u[D]-=b}u.sort((p,b)=>p-b),g=u.length,d=1;for(let p=0;p<g;p++)f.push(1)}else{let y=Xr(a,o.couplingConstants,r,o.connectivity,c),p=y.rows,b=new Er(y),h=b.eigenvectorMatrix,D=b.realEigenvalues,O=new we(p,p),S=m.length;d=0;for(let F=0;F<S;F++){let R={rows:2**F},w={rows:2**(S-F-1)},j=Hn(R.rows,w.rows);m[F]>=0?(O.add(j.mul(m[F]+1)),d++):O.add(j.mul(m[F]))}let x=zr.zeros(p,p);O.forEachNonZero((F,R,w)=>{if(w>0)for(let j=0;j<h.columns;j++){let N=h.get(R,j);N!==0&&x.set(F,j,x.get(F,j)+N)}return w});let H=x.clone();O.forEachNonZero((F,R,w)=>{if(w<0)for(let j=0;j<h.columns;j++){let N=h.get(R,j);N!==0&&H.set(F,j,H.get(F,j)+N)}return w});let v=h.transpose();x=v.mmul(x);let P=new we(x.to2DArray(),{threshold:xt});H=v.mmul(H);let M=new we(H.to2DArray(),{threshold:xt});M.forEachNonZero((F,R,w)=>w),Br(M,xt),M.forEachNonZero((F,R,w)=>{let j=P.get(F,R);j=Math.min(Math.abs(j),Math.abs(w)),j*=j,g+=j;let N=D[F]-D[R],A=Tr(u,N,(k,X)=>k-X);return A<0?(u.splice(-1-A,0,N),f.splice(-1-A,0,j)):f[A]+=j,w})}let C=u.length;if(C>0){d/=g;let y=t/64,p=u[0],b=f[0],h=1;for(let D=1;D<C;D++)Math.abs(u[D]-p/h)<y?(b+=f[D],p+=u[D],h++):(l.push({x:-p/h/i,y:b*d}),p=u[D],b=f[D],h=1);l.push({x:-p/h/i,y:b*d})}}return l.filter(m=>m.x<1e3)}function Br(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function Xr(e,n,t,s,i){let o=1;for(let r of i)o*=t[r];let a=new we(o,o);for(let r=0;r<i.length;r++){let l=i[r],m={rows:2**r},c={rows:2**(i.length-r-1)},d=e[l],g=Re(m.rows,c.rows);a.add(g.mul(d));for(let u=0;u<i.length;u++){let f=i[u];if(s.get(l,f)===1){let C={rows:2**u},y={rows:2**(i.length-u-1)},p=Ht(m.rows,c.rows).mmul(Ht(C.rows,y.rows));p.add(Ot(m.rows,c.rows).mul(-1).mmul(Ot(C.rows,y.rows))),p.add(Re(m.rows,c.rows).mmul(Re(C.rows,y.rows))),a.add(p.mul(n.get(l,f)/2))}}}return a}import Yr from"binary-search";import{EVD as Wr,Matrix as Ur}from"ml-matrix";import{SparseMatrix as Y}from"ml-sparse-matrix";import{SparseMatrix as qr}from"ml-sparse-matrix";function xn(e){let n=(e-1)/2,t=[],s=[];for(let m=0;m<e;m++)t.push(e-1-m-n),s.push(Math.sqrt(n*(n+1)-t[m]*(t[m]+1)));let i=St(s,1,e,e);for(let m=0;m<e;m++)s[m]=Math.sqrt(n*(n+1)-t[m]*(t[m]-1));let o=St(s,-1,e,e),a=i.clone().add(o).mul(.5),r=o.clone().mul(-1).add(i).mul(-.5),l=St(t,0,e,e);return{x:a,y:r,z:l,m:o,p:i}}function St(e,n,t,s){let i=new qr(t,s,{initialCapacity:20});for(let o=0;o<e.length;o++)o-n>=0&&o-n<t&&o<s&&i.set(o-n,o,e[o]);return i}var Lr=xn(2);function He(e){return e===2?Lr:xn(e)}var Ne=.01;function Z(e,n={}){let{lineWidth:t=1,maxClusterSize:s=8,frequency:i=400}=n,o=L(e),a=o.chemicalShifts.slice();for(let m=0;m<a.length;m++)a[m]=a[m]*i;let r=o.levels,l=[];for(let m of o.clusters){let c=m.map(y=>y<0?-y-1:y),d=1,g=0,u=[],f=[];if(m.length>s){let y=0;for(;m[y++]<0;);y=m[y-1],u.push(-a[y]);for(let p=0;p<m.length;p++)if(m[p]<0){let b=o.couplingConstants.get(y,c[p])/2,h=u.length;for(let D=0;D<h;D++)u.push(u[D]+b),u[D]-=b}u.sort((p,b)=>p-b),g=u.length,d=1;for(let p=0;p<g;p++)f.push(1)}else{let y=Zr(a,o.couplingConstants,r,o.connectivity,c),p=y.rows,b=new Wr(y),h=b.eigenvectorMatrix,D=b.realEigenvalues,O=new Y(p,p),S=m.length;d=0;for(let F=0;F<S;F++){let R=He(r[c[F]]),w=1;for(let k=0;k<F;k++)w*=r[c[k]];let j=Y.eye(w);w=1;for(let k=F+1;k<S;k++)w*=r[c[k]];let N=Y.eye(w),A=j.kroneckerProduct(R.m).kroneckerProduct(N);m[F]>=0?(O.add(A.mul(m[F]+1)),d++):O.add(A.mul(m[F]))}let x=Ur.zeros(p,p);O.forEachNonZero((F,R,w)=>{if(w>0)for(let j=0;j<h.columns;j++){let N=h.get(R,j);N!==0&&x.set(F,j,x.get(F,j)+N)}return w});let H=x.clone();O.forEachNonZero((F,R,w)=>{if(w<0)for(let j=0;j<h.columns;j++){let N=h.get(R,j);N!==0&&H.set(F,j,H.get(F,j)+N)}return w});let v=h.transpose();x=v.mmul(x);let P=new Y(x.to2DArray(),{threshold:Ne});Sn(P,Ne),H=v.mmul(H);let M=new Y(H.to2DArray(),{threshold:Ne});M.forEachNonZero((F,R,w)=>w),Sn(M,Ne),M.forEachNonZero((F,R,w)=>{let j=x.get(F,R);j=Math.min(Math.abs(j),Math.abs(w)),j*=j,g+=j;let N=D[F]-D[R],A=Yr(u,N,(k,X)=>k-X);return A<0?(u.splice(-1-A,0,N),f.splice(-1-A,0,j)):f[A]+=j,w})}let C=u.length;if(C>0){d/=g;let y=t/64,p=u[0],b=f[0],h=1;for(let D=1;D<C;D++)Math.abs(u[D]-p/h)<y?(b+=f[D],p+=u[D],h++):(l.push({x:-p/h/i,y:b*d}),p=u[D],b=f[D],h=1);l.push({x:-p/h/i,y:b*d})}}return l.filter(m=>m.x<1e3)}function Sn(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function Zr(e,n,t,s,i){let o=1;for(let r of i)o*=t[r];let a=new Y(o,o);for(let r=0;r<i.length;r++){let l=i[r],m=He(t[l]),c=1;for(let C=0;C<r;C++)c*=t[i[C]];let d=Y.eye(c);c=1;for(let C=r+1;C<i.length;C++)c*=t[i[C]];let g=Y.eye(c),u=e[l],f=d.kroneckerProduct(m.z).kroneckerProduct(g);a.add(f.mul(u));for(let C=0;C<i.length;C++){let y=i[C];if(s.get(l,y)===1){let p=He(t[y]),b=1;for(let S=0;S<C;S++)b*=t[i[S]];let h=Y.eye(b);b=1;for(let S=C+1;S<i.length;S++)b*=t[i[S]];let D=Y.eye(b),O=d.kroneckerProduct(m.x).kroneckerProduct(g).mmul(h.kroneckerProduct(p.x).kroneckerProduct(D));O.add(d.kroneckerProduct(m.y).kroneckerProduct(g).mul(-1).mmul(h.kroneckerProduct(p.y).kroneckerProduct(D))),O.add(d.kroneckerProduct(m.z).kroneckerProduct(g).mmul(h.kroneckerProduct(p.z).kroneckerProduct(D))),a.add(O.mul(n.get(l,y)/2))}}}return a}function vn(e,n={}){let t=L(e),{lineWidth:s=1,frequency:i=400,from:o=0,to:a=10,nbPoints:r=16*1024,noise:l,baseline:m,shape:c={kind:"gaussian"},isProton:d=t.levels.every(u=>u===2)}=n,g=d?On(t,n):Z(t,n);return Vr(g,{generator:{from:o,to:a,nbPoints:r},peakOptions:{shape:c,width:s/i},noise:l,baseline:m})}import{agnes as Gr}from"ml-hclust";import{Matrix as Jr}from"ml-matrix";function V(e,n={}){let t=L(e),{chemicalShifts:s,couplingConstants:i,connectivity:o}=t,{frequency:a=400,maxClusterSize:r=8}=n,l=$r(s,i,a),m=Gr(l,{method:"single",isDistanceMatrix:!0}),c=[],d=s.length;vt(m,c,{maxClusterSize:r,force:!1,nSpins:d,connectivity:o});let g=_r(c,r),u=g.length,f=[];for(let C=0;C<u;C++){let y=[];for(let p=0;p<d;p++){let b=g[C][p];b!==0&&y.push(b<0?-(p+1):p)}f.push(y)}return f}function vt(e,n,t){let{maxClusterSize:s,force:i,nSpins:o,connectivity:a}=t;if(!i&&e.size<=s)n.push(Pn(e.indices(),o));else for(let r of e.children)if(r.size<=s){let l=Pn(r.indices(),o),m=0;for(let c=0;c<o;c++)if(l[c]===1){for(let d=0;d<o;d++)a.get(c,d)===1&&l[d]===0&&(l[d]=-1,m++);m++}m<=s?n.push(l):r.index<0?vt(r,n,{maxClusterSize:s,force:!0,nSpins:o,connectivity:a}):(l[r.index]=2,n.push(l))}else vt(r,n,{maxClusterSize:s,force:!1,nSpins:o,connectivity:a})}function $r(e,n,t){let s=n.rows,i=n.columns,o=Jr.zeros(s,s);for(let a=0;a<s;a++)for(let r=a;r<i;r++){let l=n.get(a,r);if(e[a]-e[r]!==0){let m=1-Math.abs(l/((e[a]-e[r])*t));o.set(a,r,m),o.set(r,a,m)}else a===r||l!==0||(o.set(a,r,1),o.set(r,a,1))}return o.to2DArray()}function _r(e,n){for(let t=e.length-1;t>=0;t--){let s=e[t],i=s.length,o=0;for(;o<i&&s[o++]!==-1;);if(!(o>=i))for(let a=e.length-1;a>=t+1;a--){let r=e[a],l=0,m=0;for(let c=0;c<i;c++)s[c]*r[c]===-1&&m++,(s[c]!==0||r[c]!==0)&&l++;if(m>0&&l<=n){for(let c=0;c<i;c++)r[c]===1?s[c]=1:r[c]===-1&&s[c]!==1&&(s[c]=-1);e.splice(a,1)}}}return e}function Pn(e,n){let t=new Int16Array(n);for(let s of e)t[s]=1;return t}function tl(e){for(let n of e){if(!n.js)throw new Error("There is not js");if(!n.atoms)throw new Error("There is not atoms");for(let t of n.js)if(!t.atoms)throw new Error("There is not atoms")}}function Ae(e,n={}){let t=ie(e);tl(t);let{frequency:s=400,shape:i={kind:"gaussian"},from:o=0,to:a=10,lineWidth:r=1,nbPoints:l=16*1024,maxValue:m=1e8,maxClusterSize:c=8,...d}=n;if(t.length===0)return{x:el({from:o,to:a,size:l}),y:new Float64Array(l)};let g=U(t);g.clusters=V(g,{frequency:s,maxClusterSize:c});let u=vn(g,{frequency:s,from:o,to:a,nbPoints:l,lineWidth:r,shape:i,maxClusterSize:c,...d});return m&&Kr(u.y)===0&&(u.y=Qr(u.y,{max:m})),u}import{getGyromagneticRatio as Fn}from"gyromagnetic-ratio";function Oe(e,n){let{nucleus:t,frequency:s}=n,i=Fn(e),o=Fn(t);if(!o||!i)throw new Error(`${e} or ${t} is not supported`);return s*i/o}var F1=Oe;function jn(e,n){let{nbPoints:t,lineWidth:s,frequency:i}=n,o=[];for(let a in e)if(a==="proton"||a==="carbon"){let r=e[a];if(!r)continue;o.push(nl(r,{nbPoints:t,lineWidth:s,...n[a],experiment:a,frequency:i}))}return o}function nl(e,n){let{frequency:t=400,experiment:s}=n,{signals:i,nucleus:o}=e,a=Oe(o,{nucleus:"1H",frequency:t}),{x:r,y:l}=Ae(i,{...n,frequency:a});return{data:{x:r,re:l,im:null},info:{nucleus:e.nucleus,dimension:1,isComplex:!1,originFrequency:a,baseFrequency:a,pulseSequence:"prediction",experiment:s,isFt:!0},ranges:{values:e.ranges}}}import{xEnsureFloat64 as sl}from"ml-spectra-processing";import{generateSpectrum2D as il}from"spectrum-generator";function K(e){return typeof e!="object"?{x:e,y:e}:{...e}}function Mn(e,n={}){let{from:t=-1,to:s=12,nbPoints:i=512,factor:o=3}=n,{width:a=.02}=n,r={x:[],y:[],z:[]};for(let c of e)r.x.push(c.x.delta),r.y.push(c.y.delta),r.z.push(1e6);let{z:l,...m}=il(ol(r),{generator:{from:K(t),to:K(s),nbPoints:K(i)},peaks:{width:K(a),factor:o}});return{z:l.map(sl),...m}}function ol(e){let n=structuredClone(e);for(let t=0;t<n.x.length;t++)for(let s=t+1;s<n.x.length;s++)n.x[t]===n.x[s]&&n.y[t]===n.y[s]&&(n.z[t]+=n.z[s],n.x.splice(s,1),n.y.splice(s,1),n.z.splice(s,1),s--);return n}function Rn(e,n){let t=Oe(e[1],{nucleus:e[0],frequency:n});return[n,t]}function Nn(e,n){let t=[];for(let s in e){if(!rl(s)||!e[s])continue;let i=e[s];t.push(al(i,{experiment:s,...n}))}return t}function al(e,n){let{signals:t,zones:s,nuclei:i}=e,{experiment:o,frequency:a,width:r=ll(i),nbPoints:l}=n,m=Rn(i,a),c=n.fromTo[wn(i[0])],d=n.fromTo[wn(i[1])],g=ml(r,m),u=Mn(t,{from:{x:c.from,y:d.from},to:{x:c.to,y:d.to},nbPoints:l,factor:3,width:g}),f=m.join(",");return{data:{rr:{...u,noise:.01}},info:{nucleus:i,originFrequency:f,baseFrequency:f,pulseSequence:o,experiment:"2d"},zones:{values:s}}}function rl(e){return["cosy","hsqc","hmbc"].includes(e)}function ll(e){return{x:8,y:e[0]===e[1]?8:24}}function ml(e,n){let t=K(e);return{x:t.x/n[0],y:t.y/n[1]}}function wn(e){return e.includes("H")?"proton":"carbon"}async function Z1(e,n={}){let{logger:t,simulation:s={oneD:{},twoD:{}},prediction:i={}}=n,{spectra:o}=await W(e,{logger:t,...i});!("frequency"in s)&&t&&t.warn("Frequency is settled to 400 MHz");let{frequency:a=400}=s,r={proton:{from:-1,to:12},carbon:{from:-10,to:220},nbPoints:65536,lineWidth:1,...s.oneD},l={frequency:a,fromTo:{proton:r.proton,carbon:r.carbon},nbPoints:{x:1024,y:1024},...s.twoD},m=jn(o,{frequency:a,...r}),c=Nn(o,l);return{spectra:[...m,...c],molecules:[{molfile:e.toMolfile()}]}}import{TreeSet as ul}from"ml-tree-set";function An(e){let{restrictionByCS:n,predictions:t,targets:s,useIntegrationRestriction:i}=e,{tolerance:o,chemicalShiftRestriction:a}=n,r=Math.abs(o),l={};for(let m in t){let c=t[m];if(c.error&&(c.error=Math.abs(c.error)),l[m]=[],s)for(let d in s){let g=s[d],{nbAtoms:u}=c,{integration:f}=g;if(i&&f>0?u-f<1:!0)if(!a||c.delta===void 0)l[m].push(d);else{let y=r;c.error&&(y=Math.max(y,c.error));let p=g.signals&&g.signals.length>0?g.signals[0].delta:(g.to+g.from)/2;Math.abs(c.delta-p-r)<4*r&&l[m].push(d)}}l[m].push("*")}return l}function kn(e,n){let{useIntegrationRestriction:t,diaIDPeerPossibleAssignment:s,nbAllowedUnAssigned:i,restrictionByCS:o,predictions:a,targets:r}=n,{useChemicalShiftScore:l}=o,m=0,c=e.length,d={},g=[];for(let y=0;y<e.length;y++){let p=e[y];p&&p!=="*"&&(g.push(y),d[p]||(d[p]=[]),d[p].push(s[y])),p==="*"&&m++}if(m>i)return 0;let u=Object.keys(d);if(u.length===0)return 0;if(t)for(let y of u){let p=d[y],b=0;for(let D of p){let O=a[D];b+=O.allHydrogens}let{integration:h}=r[y];if(b-h>=.5)return 0}let f=l?cl(e,n):1,C=m/c;return f-C}function cl(e,n){let{tolerance:t}=n.restrictionByCS,{diaIDPeerPossibleAssignment:s,predictions:i,targets:o}=n,a=0,r=0;for(let l=0;l<e.length;l++){let m=e[l];if(m&&m!=="*"){r++;let c=s[l],d=i[c],g=o[m],u=t;if(d.error&&(u=Math.max(d.error,t)),d.delta===void 0)a+=1;else{let f=g.signals&&g.signals.length>0?g.signals[0].delta:(g.to+g.from)/2,C=Math.abs(d.delta-f);C<u?a+=1:(C=Math.abs(C-u),a+=-.25/u*C+1)}}}return r>0&&(a/=r),a}function Pt(e,n,t,s){let{nSources:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:l,targets:m,predictions:c,lowerBoundScore:d,nbAllowedUnAssigned:g,possibleAssignmentMap:u,useIntegrationRestriction:f,diaIDPeerPossibleAssignment:C}=e;if(Date.now()-r>a)return;let y=C[n],p=u[y];for(let b of p){t[n]=b;let h=kn(t,{useIntegrationRestriction:f,diaIDPeerPossibleAssignment:C,nbAllowedUnAssigned:g,restrictionByCS:o,predictions:c,targets:m});if(h===0){b==="*"&&(t[n]=null);continue}n===i-1&&h>=d?dl(s,{predictions:c,partial:t,score:h,maxSolutions:l}):n<i-1&&Pt({nSources:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:l,targets:m,predictions:c,lowerBoundScore:d,nbAllowedUnAssigned:g,possibleAssignmentMap:u,useIntegrationRestriction:f,diaIDPeerPossibleAssignment:C},n+1,structuredClone(t),s)}}function dl(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n;e.nSolutions++;let a={assignment:structuredClone(i),score:t/gl(i,o)};if(e.nSolutions>=s){let r=e.solutions.last();a.score>r.score&&(e.solutions.pollLast(),e.solutions.add(a))}else e.solutions.add(a),e.nSolutions++}function gl(e,n){let t=Object.keys(n).length,s=new Set(e),i=t-s.size;return i>0?2*i:1}var fl=(e,n)=>n.score-e.score;async function ke(e){let{restrictionByCS:n={},useIntegrationRestriction:t,timeout:s,minScore:i,nbAllowedUnAssigned:o,maxSolutions:a,targets:r,joinedSignals:l}=e,{tolerance:m=1,useChemicalShiftScore:c=!1,chemicalShiftRestriction:d=!0}=n,g=l.length,u={};for(let D of l){let O=D.diaIDs[0],S=D.atoms[0];u[O]={...D,diaIDIndex:S,allHydrogens:D.nbAtoms}}let f=An({restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:d},useIntegrationRestriction:t,predictions:u,targets:r}),C=Object.keys(f),y=new Array(g).fill(null),p={solutions:new ul(fl),nSolutions:0},b=Date.now();Pt({nSources:g,restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:d},timeout:s,timeStart:b,targets:r,predictions:u,maxSolutions:a,lowerBoundScore:i,nbAllowedUnAssigned:o,possibleAssignmentMap:f,diaIDPeerPossibleAssignment:C,useIntegrationRestriction:t},0,y,p);let h=[];for(let D of p.solutions.elements){let{assignment:O,score:S}=D,x=structuredClone(r);for(let H=0;H<O.length;H++){let v=O[H];if(typeof v!="string")continue;let P=x[v];P.diaIDs||(P.diaIDs=[]),v&&P.diaIDs.push(C[H])}h.push({score:S,assignment:Object.values(x)})}return h}function pl(e){for(let n of e){if(!n.atoms)throw new Error("signal has not atoms property");if(!n.diaIDs)throw new Error("signal has not diaIDs property");if(!n.nbAtoms)throw new Error("signal has not nbAtoms property")}}function Cl(e){for(let n of e)if(n.integration===void 0)throw new Error("ranges has not integration property")}async function mp(e,n,t={}){let{restrictionByCS:s,minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:r=6e3,predictionOptions:l={}}=t;if(!n)throw new Error("It is needed a OCL molecule instance to assign");let{spectra:m}=await W(n,{predictOptions:{H:l}}),c=m.proton?.joinedSignals||[];Cl(e),pl(c);let d={};for(let g of e){let{id:u=crypto.randomUUID()}=g;d[u]=structuredClone(g)}return ke({restrictionByCS:s,timeout:r,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:d,joinedSignals:c,useIntegrationRestriction:!0})}function yl(e){for(let n of e){if(!n.atoms)throw new Error("signal has not atoms property");if(!n.diaIDs)throw new Error("signal has not diaIDs property");if(!n.nbAtoms)throw new Error("signal has not nbAtoms property")}}function bl(e){let n=structuredClone(e);for(let t of n)t.integration===void 0&&(t.integration=0);return n}async function up(e,n,t={}){let{restrictionByCS:s={},minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:r=6e3,predictionOptions:l={}}=t,{spectra:m}=await W(n,{predictOptions:{C:l}}),c=m.carbon?.joinedSignals||[];yl(c);let d=bl(e),g={};for(let u of d){let{id:f=crypto.randomUUID()}=u;g[f]=structuredClone(u)}return ke({restrictionByCS:s,timeout:r,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:g,joinedSignals:c,useIntegrationRestriction:!1})}import{ensureHeterotopicChiralBonds as Xl}from"openchemlib-utils";import{TreeSet as Bn}from"ml-tree-set";import{getConnectivityMatrix as jl}from"openchemlib-utils";import{getCorrelationDelta as Dl}from"nmr-correlation";function In(e,n){let{restrictionByCS:t,predictions:s,targets:i}=n,{tolerance:o,chemicalShiftRestriction:a}=t,r=Object.keys(s);for(let l of r){let m=o[l],c=s[l],d=i[l];e[l]||(e[l]={});for(let g in c){let u=c[g];if(e[l][g]=[],d)for(let f in d){let C=d[f],{nbAtoms:y,protonsCount:p}=u,{integration:b,protonsCount:h}=C;if(b?l==="H"?y-b<1:h.length>0?h.includes(p):!0:!0)if(!a||u.delta===void 0)e[l][g].push(f);else{let O=Dl(C);if(O===void 0)throw new Error("Correlation has not delta");Math.abs(u.delta-O-m)<4*m&&e[l][g].push(f)}}e[l][g].push("*")}}return e}import{getCorrelationDelta as Hl}from"nmr-correlation";function hl(e,n,t){let s=e[0],{H:i=[]}=n[s].attachment,o=[{targetIDs:[s],attachments:new Set(i)}];for(let a=1;a<e.length;a++){let r=e[a],l=n[r],{H:m=[]}=l.attachment,c=!0;for(let d of o)if(m.some(u=>d.attachments.has(u))){c=!1,d.targetIDs.push(r);for(let u of m)d.attachments.add(u);break}c&&o.push({targetIDs:[r],attachments:new Set(m)})}return o.map(a=>({atomType:"C",targetIDs:a.targetIDs,integration:t?Array.from(a.attachments).reduce((r,l)=>t[l].integration+r,0):0}))}var Tn=hl;function En(e,n){let{diaIDPeerPossibleAssignment:t,infoByAtomTypes:s,restrictionByCS:i,predictions:o,targets:a,correlations:r}=n,{tolerance:l,useChemicalShiftScore:m}=i,c=0,d=0,g={},u={},f=Object.keys(e);for(let x of f){let H=0,{nbAllowedUnAssigned:v}=s[x],P={},M=e[x]||[];g[x]=P,u[x]=[],d+=M.length;for(let F=0;F<M.length;F++){let R=M[F];R&&R!=="*"&&(u[x].push(F),P[R]||(P[R]=[]),P[R].push(t[x][F])),R==="*"&&H++}if(H>v)return 0;c+=H}let C={};for(let x in g)C[x]=Object.keys(g[x]);if(Object.values(C).every(x=>x.length===0))return 0;let p=xl.bind({},o),b=[];for(let x in e)if(x==="C"&&C[x].length>0)b.push(...Tn(C[x],a[x],r));else for(let H of C[x])b.push({atomType:x,targetIDs:[H],integration:a.H[H].integration});for(let x of b){let{integration:H,atomType:v}=x;if(H===void 0||Number.isNaN(H))continue;let P=0;for(let M of x.targetIDs){let F=g[v][M];for(let R of F){let{prediction:w,atomType:j}=p(R);v===j&&(P+=w.allHydrogens)}}if(P-H>=5)return 0}let h=1,D=1;if(m){D=0,h=0;for(let x of Object.keys(e)){let H=e[x],v=a[x];for(let P=0;P<H.length;P++){let M=H[P];if(M&&M!=="*"){h++;let F=t[x][P],R=o[x][F],w=v[M],j=l[x];if(R.delta===void 0)D+=1;else{let N=Hl(w);if(N===void 0)throw new Error("correlation has not delta");let A=Math.abs(R.delta-N);A<j?D+=1:(A=Math.abs(A-j),D+=-.25/j*A+1)}}}}h>0&&(D/=h)}let O=0;if(Sl(C)>1){let x={},H=[];for(let P of Object.keys(u))H=H.concat(u[P].map(M=>({index:M,atomType:P})));for(let P=0;P<H.length;P++){let{atomType:M,index:F}=H[P],R=o[M][t[M][F]];for(let w=P+1;w<H.length;w++){let{atomType:j,index:N}=H[w],A=o[j][t[j][N]],X=R.pathLength[A.diaIDIndex]<5,De=e[M][F],he=e[j][N];if(!De||!he)continue;let pt=De>he?`${he} ${De}`:`${De} ${he}`,Kt=Ol({from:{targetID:De,atomType:M},to:{targetID:he,atomType:j}},a),Qt=X?Kt?1:0:Kt?0:1;x[pt]=x[pt]?Math.max(x[pt],Qt):Qt}}let v=0;for(let P in x)v+=x[P];O=v/(H.length*(H.length-1)/2)}let S=c/d;return D===0?O-S:O===0?D-S:(D+O)/2-S}function Ol(e,n){let{from:t,to:s}=e;if(t.targetID===s.targetID)return!0;let i=n[t.atomType][t.targetID],o=n[s.atomType][s.targetID];for(let a of o.link)for(let r of i.link)if(r.signal.id===a.signal.id)return!0;return!1}function xl(e,n){let t=Object.keys(e);for(let s of t){let i=e[s];if(!i)throw new Error(`prediction by ${s}`);if(i[n])return{atomType:s,prediction:i[n]}}throw new Error(`There is not prediction for ${n}`)}function Sl(e){let n=0;for(let t in e)n+=e[t].length;return n}function Ft(e,n,t,s){let{currentAtomTypes:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:l,targets:m,predictions:c,correlations:d,lowerBoundScore:g,possibleAssignmentMap:u,diaIDPeerPossibleAssignment:f}=e;if(!(Date.now()-r>a))for(let C of i){let{currentIndex:y,nSources:p}=n[C];if(y>=p-1&&t[C][y]!==null)continue;let b=f[C][y],h=u[C][b];for(let D of h){t[C][y]=D;let O=En(t,{diaIDPeerPossibleAssignment:f,infoByAtomTypes:n,restrictionByCS:o,predictions:c,correlations:d,targets:m});if(O!==0)if(Pl(i,n)&&O>=g)vl(s,{predictions:c,partial:t,score:O,maxSolutions:l});else{let S=structuredClone(n);S[C].currentIndex+=1,Ft({currentAtomTypes:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:l,targets:m,predictions:c,correlations:d,lowerBoundScore:g,possibleAssignmentMap:u,diaIDPeerPossibleAssignment:f},S,structuredClone(t),s)}}}}function vl(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n,a={assignment:structuredClone(i),score:t/Fl(i,o)};if(e.nSolutions>=s){let r=e.solutions.last();a.score>r.score&&(e.solutions.pollLast(),e.solutions.add(a))}else e.solutions.add(a),e.nSolutions++}function Pl(e,n){let t=!0;for(let s of e){let{currentIndex:i,nSources:o}=n[s];t=t&&i>=o-1}return t}function Fl(e,n){let t=0;for(let s in n){let i=Object.keys(n[s]).length,o=new Set(e[s]);t+=i-o.size}return t>0?2*t:1}function G(e){return"ranges"in e}function zn(e,n){for(let t=0;t<n.length;t++){let s=n[t],i=G(s)?s.ranges:s.zones;for(let o=0;o<i.length;o++){let a=i[o].signals||[];for(let r=0;r<a.length;r++)if(e===a[r].id)return{spectrumIndex:t,signalIndex:r,elementIndex:o}}}throw new Error(`There is not a signal with ${e} ID`)}var Xn=(e,n)=>n.score-e.score;function Ml(e){let n=["nbAtoms","diaIDs","atoms"];for(let t of e)for(let s of n)if(!t[s])throw new Error(`property ${s} does not exist`)}var Rl={C:(e,n)=>e.getAllHydrogens(n),H:()=>1};async function qn(e){let{spectra:n,molecule:t,restrictionByCS:s,timeout:i,minScore:o,nbAllowedUnAssigned:a={},maxSolutions:r,correlations:l,assignmentOrder:m,predictionOptions:c,predictions:d={},targets:g}=e,u=o,f={solutions:new Bn(Xn),nSolutions:0},C=jl(t,{pathLength:!0}),y={},p={},b={},h={};for(let D of m){for(let x of D){let H={[x]:c[x]},v=d[x],P=await kl({molecule:t,predictedSignals:v,options:H,atomType:x});Ml(P),p[x]||(p[x]={});let M=0;for(let F of P){let R=F.diaIDs[0],w=F.atoms[0],j=Rl[x](t,w);M+=F.nbAtoms*j,p[x][R]={...F,diaIDIndex:w,allHydrogens:F.nbAtoms*j,protonsCount:j,pathLength:C[w]}}for(let F in p[x])p[x][F].allHydrogens*=100/M;y[x]={nSources:P.length,currentIndex:0,nbAllowedUnAssigned:a[x]||0}}b=In(b,{restrictionByCS:s,predictions:p,targets:g}),h={};for(let x in b)h[x]=Object.keys(b[x]);let O=Nl(f,y,D);f={solutions:new Bn(Xn),nSolutions:0};let S=Date.now();for(let x of O)Ft({currentAtomTypes:D,restrictionByCS:s,timeout:i,timeStart:S,targets:g,predictions:p,correlations:l,maxSolutions:r,lowerBoundScore:u,possibleAssignmentMap:b,diaIDPeerPossibleAssignment:h},y,x,f)}return wl({store:f,spectra:n,diaIDPeerPossibleAssignment:h,targets:g})}function wl(e){let{store:n,spectra:t,diaIDPeerPossibleAssignment:s,targets:i}=e,{solutions:o}=n,a={},r=Object.keys(i);for(let m of r){let c=i[m];for(let d in c){let g=c[d];for(let u of g.link){let f=u.signal.id;a[f]||(a[u.signal.id]=zn(f,t))}}}let l=[];for(let m of o.elements){let c=structuredClone(t),{assignment:d,score:g}=m,u=Object.keys(d);for(let f of u){let C=i[f],y=d[f];for(let p=0;p<y.length;p++){let b=y[p];if(b==="*"||!b)continue;let h=C[b],D=s[f][p];for(let O of h.link){let{spectrumIndex:S,elementIndex:x,signalIndex:H}=a[O.signal.id],v=c[S];if(G(v)){let{ranges:P}=v,F=P[x].signals[H];if(F.diaIDs||(F.diaIDs=[]),F.diaIDs.includes(D))continue;F.diaIDs.push(D)}else{let P=O.axis,M=v.zones[x].signals[H];if(M[P].diaIDs||(M[P].diaIDs=[]),M[P].diaIDs?.includes(D))continue;M[P].diaIDs?.push(D)}}}}l.push({score:g,assignment:c})}return l}function Nl(e,n,t){return e.nSolutions>0?e.solutions.elements.map(s=>{let i=s.assignment;for(let o of t)i[o]=Ln(n[o].nSources);return i}):Al(n,t)}function Al(e,n){let t={},s=Object.keys(e);for(let i of s){let o=n.includes(i)?null:"*";t[i]=Ln(e[i].nSources,o)}return[t]}function Ln(e,n=null){let t=new Array(e);for(let s=0;s<e;s++)t[s]=n;return t}async function kl(e){let{molecule:n,predictedSignals:t,options:s,atomType:i}=e;if(t)return t;let{spectra:o}=await W(n,{predictOptions:s});return o[i==="C"?"carbon":"proton"]?.joinedSignals||[]}function Yn(e=[]){let n=structuredClone(e),t=[];for(let s of n){if(!("info"in s))throw new Error("each spectrum should contain info properties with nucleus information");if(G(s)){let{info:i,id:o}=s,a=Ie(s.ranges);t.push({id:o,info:i,ranges:a})}else{let{info:i,id:o}=s,a=Ie(s.zones);t.push({id:o,info:i,zones:a})}}return t}function Il(e){for(let n of e){if(!n.id)throw new Error("A range/zone has not an ID");for(let t of n.signals||[])if(!t.id)throw new Error("A signal has not an ID")}}function Ie(e){for(let n of e){n.id||(n.id=crypto.randomUUID());for(let t of n.signals||[])t.id||(t.id=crypto.randomUUID())}return Il(e),e}import{buildCorrelationData as El}from"nmr-correlation";function Wn(e=[]){let n=structuredClone(e),t=[];for(let s of n)if(G(s)){let{id:i,info:o}=s,a=Tl({id:i,info:o,ranges:s.ranges});t.push({id:i,info:o,ranges:{values:a}})}else{let{id:i,info:o}=s;t.push({id:i,info:o,zones:{values:s.zones}})}return t}function Tl(e){if(e.info.nucleus!=="1H")return e.ranges;let n=e.ranges.reduce((t,s)=>t+(s.integration??0),0);for(let t of e.ranges)if(t.integration&&(t.integration*=100/n,t.signals)){let s=t.signals.reduce((i,o)=>i+(o.integration??0),0);for(let i of t.signals)i.integration?i.integration*=t.integration/s:i.integration=t.integration}return e.ranges}function Un(e,n){let{H:t=[]}=e,s=0;for(let i of t){let o=n[i];s+=Number(o.link[0].signal.integration)}return s}function Zn(e,n={}){let{tolerance:t={C:.25,H:.05}}=n,s=Wn(e),o=El(s,{tolerance:t}).values.map(r=>({...r,integration:0})),a={H:{},C:{}};for(let r of o){if(r.pseudo)continue;let{id:l,atomType:m}=r;(m==="H"||m==="C")&&(a[m][l]=r,m==="H"?a[m][l].integration=r.link[0].signal.integration||0:a[m][l].integration=Un(r.attachment,o),a[m][l]=r)}return{targets:a,correlations:o}}function zl(e,n=[]){let t=Bl(e),{hasHSQC:s,types:i}=t;if(n.length>0)return{assignmentOrder:n,experimentTypes:t};let o=[];return s?o.push(["C"],["H"]):o.push(i.filter(a=>a==="H"||a==="C")),{assignmentOrder:o,experimentTypes:t}}var Vn=zl;function Bl(e){let n=new Set;for(let t of e)for(let s of t.link){let i=s.experimentType;i==="1d"&&(i=s.atomType[0].toUpperCase()),n.add(i)}return{types:Array.from(n),hasProton:n.has("H"),hasCarbon:n.has("C"),hasHSQC:n.has("hsqc")}}async function Jp(e,n={}){let{restrictionByCS:t={},justAssign:s,minScore:i=.01,maxSolutions:o=10,nbAllowedUnAssigned:a,timeout:r=6e3,predictionOptions:l={},predictions:m={},correlation:c={}}=n,{tolerance:d={H:.2,C:1},useChemicalShiftScore:g=!1,chemicalShiftRestriction:u=!0}=t,f=e.molecule;if(!f)throw new Error("It is needed a molecule to assign");f.addImplicitHydrogens(),Xl(f);let C=Yn(e.spectra),{targets:y,correlations:p}=Zn(C,c),{assignmentOrder:b}=Vn(p,s);return await qn({restrictionByCS:{tolerance:d,useChemicalShiftScore:g,chemicalShiftRestriction:u},spectra:C,molecule:f,timeout:r,minScore:i,maxSolutions:o,assignmentOrder:b,nbAllowedUnAssigned:a,correlations:p,targets:y,predictionOptions:l,predictions:m})}var ql={unspecified:"Unspecified",unknown:"Unknown",signal:"Signal",residualSolvent:"Residual solvent",reference:"Reference",nmrSolvent:"NMR Solvent",impurity:"Impurity",standard:"Standard",artifact:"Artifact",p1:"Product 1",p2:"Product 2",p3:"Product 3"};function Ll(e){return typeof e=="string"&&ql[e]!==void 0}function Q(e){return e===void 0?"signal":Ll(e)?e:"unspecified"}var Te=new Set(["signal"]);var Gn=_.toSorted((e,n)=>e.multiplicity===null&&n.multiplicity===null?0:e.multiplicity===null?1:n.multiplicity===null?-1:e.multiplicity-n.multiplicity),jt=Gn.map(e=>e.value),Ee=Gn.map(e=>e.acs||e.value);import{Molecule as Yl}from"openchemlib";import{TopicMolecule as Wl}from"openchemlib-utils";function xe(e,n,t){let{name:s}=e,i=t[s],{idCode:o}=n[i];if(i===void 0)throw new Error("atom map does not exists");return{...e,idCode:o,atom:i}}function Jn(e,n,t){let s=[];for(let i of e){let{from:o,to:a}=i;s.push({...i,from:o.map(r=>xe(r,n,t)),to:a.map(r=>xe(r,n,t))})}return s}function $n(e,n,t){let s=[];for(let i of e){let{atoms:o}=i;s.push({...i,atoms:o.map(a=>xe(a,n,t))})}return s}function Kn(e,n){let t=[],s=Mt(n),i=n[0].nucleusType.atomicNumber;for(let o of e){let a=Mt(o.from),r=_n(s,a),m=o[r?"to":"from"],c=r?a:Mt(o.to),{nucleusType:{atomicNumber:d},idCode:g}=m[0];!_n(s,c)||d!==i||t.push({coupling:o.value,atoms:m.map(u=>u.atom),diaIDs:[g]})}return t}function _n(e,n){for(let t of e)if(n.has(t))return!0;return!1}function Mt(e){let n=e.filter(t=>t.shift!==null).map(t=>t.shift);return new Set(n)}function Qn(e,n,t){let s=new Set,i=[];for(let o of e){let{name:a}=o,r=n[a],{idCode:l}=t[r];if(!r)throw new Error("atom mapping does not exists");s.add(l),i.push(r)}return{diaIDs:Array.from(s),atoms:i}}function es(e){let n=[];for(let t of e){let{atoms:s=[],...i}=t;if(s.length>1)for(let o of s)n.push({...i,atoms:[o]});else n.push(t)}return n}function ts(e){let n=[];for(let t of e){let s=es(t.js);for(let i of t.atoms){let o={...t,atoms:[i],nbAtoms:1,js:s};n.push(o)}}return n}function ns(e,n){let{atomicNumber:t=1,atomMap:s,molfile:i}=n,o=[],a=Yl.fromMolfile(i),l=new Wl(a).diaIDsAndInfo,m=Jn(e.couplings,l,s),c=$n(e.shifts,l,s);for(let d of c){let{atoms:g,value:u}=d;if(!g.some(C=>C.nucleusType.atomicNumber===t))continue;let f={delta:u,nbAtoms:g.length,...Qn(g,s,l),js:Kn(m,g)};o.push(f)}return ts(o)}function ss(e){return{molarFraction:{value:e.v,low:e.vl,high:e.vh},fieldStrength:e.f,baseItensity:e.bi,intensityLimit:e.il,spinSystemFlags:e.sf,spinSystemType:em(e.sst),analysisType:e.at,inchiKey:e.ik,populations:Ul(e.p),lineShapes:Ql(e.l),shiftGroups:_l(e.sg),shifts:Zl(e.s),couplingGroups:Kl(e.cg),couplings:Vl(e.c),atoms:Gl(e.a),bonds:Jl(e.b)}}function Ul(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,population:{value:t.v,low:t.vl,high:t.vh},spinSystemFlags:t.sf});return n}function Zl(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,shiftGroup:t.sg});return n}function Vl(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,couplingGroup:t.cg,shifts:{from:t.s[0],to:t.s[1]}});return n}function Gl(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,nucleusType:tm(t.nc),cipRank:{canonical:t.crcan,rd:t.crrd,nmr:t.crnmr},ordinal:t.o,stereochemistryFlags:t.rs,spinSystemFlags:t.sf,formalcharge:t.fc,partialCharge:t.c,coordinates2D:t.c2d,coordinates3D:t.c3d,parent2D:t.p2d,shift:t.s});return n}function Jl(e){let n=[];for(let t of e)n.push({id:t.id,bondType:$l(t.b),stereochemistryFlags:t.rs,spinSystemFlags:t.sf,atoms:t.a});return n}function $l(e){switch(e){case 0:return"NONE";case 1:return"SINGLE";case 2:return"DOUBLE";case 3:return"TRIPLE";case 4:return"CONJUGATED";case 5:return"SINGLE_UP";case 6:return"SINGLE_DOWN";default:throw new Error(`Unknown bond type: ${e}`)}}function _l(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,shift:{value:t.v,low:t.vl,high:t.vh},spin2:t.s,spinCount:t.c,exchangeable:t.ex,spinSystemFlags:t.sf,gamma:t.g,iterationWeight:t.iw,response:{value:t.rs.v,low:t.rs.vl,high:t.rs.vh,sf:t.rs.sf},population:t.p,lineShape:t.l});return n}function Kl(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.parentID,name:t.name,remarks:t.remarks,coupling:{value:t.v,low:t.vl,high:t.vh},spinSystemFlags:t.sf,couplingType:t.t});return n}function Ql(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,spinSystemFlags:t.sf,lineWidth:{value:t.l.v,low:t.l.low,high:t.l.high},gaussian:{value:t.g.v,low:t.g.low,high:t.g.high}});return n}function em(e){switch(e){case 0:return"NONE";case 1:return"SOLUTE";case 2:return"SOLVENT";case 4:return"IMPURITY";case 8:return"REFERENCE";case 16:return"CALIBRANT";case 32:return"ERROR_MESSAGE";default:throw new Error(`Unexpected spinSystemType: ${e}`)}}function tm(e){return{atomicNumber:(e&65024)>>9,isotope:e&511}}function is(e,n){let{logger:t}=n;t.debug("Parsing CT json results");let s=ss(e),i=nm(s),o=sm(s);return{...s,shifts:i,couplings:o}}function nm(e){let n=e.shifts,t=im(e),s=os(e),i=[];for(let o of n){let a=t[o.shiftGroup];if(!a)throw new Error(`Shift group ${o.shiftGroup} not found`);let r=s[o.id];if(!r)throw new Error(`Atom not found: ${o.id}`);i.push({atoms:r,value:a.shift.value})}return i}function sm(e){let n=e.couplings,t=om(e.couplingGroups),s=os(e),i=[];for(let o of n){let a=t[o.couplingGroup];if(!a)throw new Error(`Coupling group ${o.couplingGroup} not found`);let r=s[o.shifts.from];if(!r)throw new Error(`Atom not found: ${o.shifts.from}`);let l=s[o.shifts.to];if(!l)throw new Error(`Atom not found: ${o.shifts.to}`);i.push({from:r,to:l,value:a.coupling.value})}return i}function os(e){let n={};for(let t of e.atoms){if(!t.shift)continue;let s=t.shift;n[s]||(n[s]=[]),n[s].push(t)}return n}function im(e){let n={};for(let t of e.shiftGroups)n[t.id]=t;return n}function om(e){let n={};for(let t of e)n[t.id]=t;return n}function as(e){let n={};for(let t of e)n[t.name]=t.ordinal;return n}function vC(e,n,t){let s=is(e,{logger:console}),i=as(s.atoms),o=ns(s,{atomMap:i,molfile:n,...t});return{...s,signals:o}}var FC=[{names:["acetic 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D=0;D<f.re.length;D++){let O=f.re[D]*c[D+r-p],S=f.im[D]*d[D+r-p],x=f.re[D]*d[D+r-p],H=f.im[D]*c[D+r-p];b+=O-S,h+=x+H}c[r-p-1]=b,d[r-p-1]=h}let C=new Float64Array(t.length),y=new Float64Array(s.length);return C.set(c.subarray(0,r),0),y.set(d.subarray(0,r),0),o<0?(C.set(t.slice(0,t.length-r),r),y.set(s.slice(0,t.length-r),r)):(C.set(t.slice(o),r),y.set(s.slice(o),r)),{re:C,im:y}}function Dm(e,n){let{U:t,V:s,svals:i}=ps(e),o=e.re.length,a=e.re[0].length,r=i.length,l=bm(i)*1e-7,m={re:new Float64Array(a),im:new Float64Array(a)};for(let c=0;c<a;c++){let d=0,g=0;for(let u=0;u<r;u++)if(i[u]>l){let f=0,C=0;for(let D=0;D<o;D++){let O=t.re[D][u]*n.re[D],S=-t.im[D][u]*n.im[D],x=t.re[D][u]*n.im[D],H=-t.im[D][u]*n.re[D];f+=O-S,C+=x+H}let y=f/i[u],p=C/i[u],b=s.re[c][u],h=s.im[c][u];d+=b*y-h*p,g+=b*p+h*y}m.re[c]=d,m.im[c]=g}return m}var Hm={updateXDomain:!0,updateYDomain:!0};function Om(e,n={}){if(!hs(e))throw new Error("Digital Filter is not applicable on this data");let{info:t,data:{re:s,im:i}}=e,{lpNumberOfCoefficients:o=0,tdOff:a=0}=t,{nbCoefficients:r=o,nbPoints:l=a/2,nbInputs:m=Math.floor(s.length/2-r-l)}=n,{re:c,im:d}=re({re:s,im:i},{nbCoefficients:r,nbInputs:m,nbPoints:l}),g=e.filters.find(f=>f.name==="backwardLinearPrediction");g&&(g.value={nbCoefficients:r,nbPoints:l,nbInputs:m});let u=e.data.x;Object.assign(e.data,{re:c,im:d,x:l<0?hm({from:0,size:c.length,step:u[1]-u[0]}):u})}function hs(e){return!!(e.info.isComplex&&e.info.isFid)}function xm(e,n){return{once:!0,reduce:n}}var Hs={name:"backwardLinearPrediction",label:"Backward Linear Prediction Filter",domainUpdateRules:Hm,apply:Om,reduce:xm,isApplicable:hs};import Zm from"ml-airpls";import{PolynomialRegression as Vm}from"ml-regression-polynomial";import{xyEquallySpaced as Gm}from"ml-spectra-processing";import{CholeskyDecomposition as Fm,Matrix as vs}from"ml-matrix";import{calculateAdaptiveWeights as jm,xMultiply as Mm}from"ml-spectra-processing";function Os(e,n,t){if(n===0)return 1;if(e===0||n>e)return 0;if(n>e-n&&(n=e-n),!t)return Sm(e,n);if(t[n]>0)return t[n];let s=1,i=e;for(let o=1;o<=n;o++){if(t[o]>0){i--,s=t[o];continue}s*=i--,s/=o,t[o]=s}return s}function Sm(e,n){let t=1,s=e;for(let i=1;i<=n;i++)t*=s--,t/=i;return t}import{Matrix as vm}from"ml-matrix";function xs(e){let n=e.rows,t=e.columns,s=new vm(n,n);for(let i=0;i<n;i++)for(let o=0;o<n;o++){let a=0;for(let r=0;r<t;r++)a+=e.get(o,r)*e.get(i,r);s.set(o,i,a)}return s}import{matrixCreateEmpty as Pm}from"ml-spectra-processing";function Ss(e,n){let t=e.rows,s=e.columns,i=n.columns;if(n.rows!==t)throw new Error("Matrix dimensions are incompatible for multiplication");let o=Pm({nbRows:s,nbColumns:i});for(let a=0;a<s;a++)for(let r=0;r<i;r++){let l=0;for(let m=0;m<t;m++)l+=e.get(m,a)*n.get(m,r);o[a][r]=l}return o}function Ps(e,n,t={}){let{maxIterations:s=100,tolerance:i=1e-6,factorStd:o=3,learningRate:a=.3,minWeight:r=.01}=t,l=new Float64Array(e.length).fill(1),m=e.slice(),c=new Float64Array(e.length),d=0,g=1/0,{logger:u}=t;for(;d<s&&g>i;){let f=Rm(e,{degree:n,weights:l,logger:u});if(!f)return m;l=jm(e,f,l,{minWeight:r,learningRate:a,factorStd:o}),g=wm(f,c,e.length),c.set(f),m=f,d++}return m}function Rm(e,n){let{degree:t,weights:s}=n;if(t<0)throw new Error("Degree must be non-negative.");if(e.length===0)return new Float64Array([]);let i=e.length,o=t,a=Math.max(1,i-1),r=new Float64Array(i);for(let c=0;c<i;c++)r[c]=c/a;let l=new Float64Array(o+1);for(let c=0;c<o+1;c++)l[c]=Os(o,c);let m=new vs(o+1,i);for(let c=0;c<i;c++)for(let d=0;d<=o;d++){let g=l[d]*r[c]**d*(1-r[c])**(o-d);m.set(d,c,s[c]*g)}try{let c=new Fm(xs(m));if(!c.isPositiveDefinite())throw new Error("Matrix is not positive definite");let d=Mm(e,s),g=vs.from1DArray(i,1,d),u=c.solve(m.mmul(g)),f=Ss(m,u);return s.map((C,y)=>f[y][0]/C)}catch(c){return n.logger&&n.logger.error(c),new Float64Array(e.length)}}function wm(e,n,t){let s=0;for(let i=0;i<t;i++)s+=(e[i]-(n[i]||0))**2;return Math.sqrt(s/t)}import{xSequentialFillFromStep as Nm,xWhittakerSmoother as Am}from"ml-spectra-processing";function Fs(e,n){let t=e.length;if(t===0)return new Float64Array(0);let s=n??Nm({from:0,step:1,size:t}),i=Am(e);return km(s,i)}function km(e,n){let t=e.length;if(t<2)throw new Error("At least 2 points are required for interpolation.");let s=new Float64Array(t-1);for(let u=0;u<t-1;u++)s[u]=e[u+1]-e[u];let i=new Float64Array(t-1);for(let u=0;u<t-1;u++)i[u]=(n[u+1]-n[u])/s[u];let o=t-2,a=new Float64Array(o-1),r=new Float64Array(o),l=new Float64Array(o-1),m=new Float64Array(o);for(let u=0;u<o;u++){let f=u+1;r[u]=2*(s[f-1]+s[f]),m[u]=6*(i[f]-i[f-1]),u>0&&(a[u-1]=s[f-1]),u<o-1&&(l[u]=s[f])}let c=new Float64Array(t).fill(0);if(o>=1){let u=new Float64Array(a),f=new Float64Array(r),C=new Float64Array(l),y=new Float64Array(m);for(let p=1;p<o;p++){let b=u[p-1]/f[p-1];f[p]-=b*C[p-1],y[p]-=b*y[p-1]}c[o]=y[o-1]/f[o-1];for(let p=o-2;p>=0;p--)c[p+1]=(y[p]-C[p]*c[p+2])/f[p]}let d=[];for(let u=0;u<t-1;u++){let f=n[u],C=(n[u+1]-n[u])/s[u]-s[u]*(2*c[u]+c[u+1])/6,y=c[u]/2,p=(c[u+1]-c[u])/(6*s[u]);d.push({a:f,b:C,c:y,d:p})}let g=new Float64Array(e.length);for(let u=0;u<e.length;u++){let f=e[u],C=0;for(;C<t-1&&e[C+1]<f;)C++;f<e[0]?C=0:f>e[t-1]&&(C=t-2);let y=e[C],p=f-y,b=d[C],h=b.a+b.b*p+b.c*p**2+b.d*p**3;g[u]=h}return g}import{DirectConvolution as Bm,FFTConvolution as Xm}from"ml-convolution";import{Matrix as qm}from"ml-matrix";import{xAdd as Lm,xWhittakerSmoother as Ym}from"ml-spectra-processing";import{Matrix as Im}from"ml-matrix";import{xMean as Tm,xStandardDeviation as Em}from"ml-spectra-processing";function qe(e){let n=[],t=[],{rows:s,columns:i}=e,[o,a]=zm(e);for(;a.length!==t.length;)if(a.length>0){[o,n]=[[],o],[a,t]=[[],a];let c=Tm(t),d=Em(t,{mean:c}),g=c+3*d;for(let u=0;u<t.length;u++)t[u]<=g&&(o.push(n[u]),a.push(t[u]))}else o=n,a=t;let r=Im.zeros(s,i);for(let c of o){let d=c/i|0,g=c%i;r.set(d,g,1)}let l=(c,d)=>{let g=js(c,s),u=js(d,i),f=0;for(let C=g.from;C<g.to;C++)for(let y=u.from;y<u.to;y++)r.get(C,y)<1&&(f+=1);return f>0},m=r.clone();for(let c=0;c<s;c++)for(let d=0;d<i;d++)r.get(c,d)>0&&l(c,d)&&m.set(c,d,0);return m}function js(e,n){return{from:Math.max(e-5,0),to:Math.min(e+5,n)}}function zm(e){let n=e.mean()+3*e.standardDeviation(),t=[],s=[],{rows:i,columns:o}=e;for(let a=0;a<i;a++)for(let r=0;r<o;r++){let l=e.get(a,r);l<=n&&(t.push(a*o+r),s.push(l))}return[t,s]}function Rs(e,n){let t=Wm(e,n),s=qe(t).to1DArray(),{lambda:i=150,maxIterations:o=1}=n;return Ym(e,{lambda:i,controlPoints:s,maxIterations:o})}function Ms(e,n,t=1){let s=n.convolve(e),i=[];for(let o of s)i.push(Math.abs(o/t));return i}function Wm(e,n){let t=e.length,{scale:s=11}=n,i=Um(s),o=s>32?new Xm(t,i):new Bm(t,i),a=Ms(e,o,s),r=Ms(a,o,s);return new qm([Lm(a,r)])}function Um(e){let n=[];for(let t=0;t<e;t++)n.push(1);for(let t=0;t<e;t++)n.push(-1);return n.push(0),n}var Jm={updateXDomain:!1,updateYDomain:!1};function $m(e,n){if(!ws(e))throw new Error("Baseline correction not applicable on this data");let{algorithm:t}=n,{x:s,re:i}=e.data,o;switch(t){case"airpls":o=Zm(s,i,n).corrected;break;case"polynomial":{let{degree:a,zones:r}=n,l=Gm({x:s,y:i},{numberOfPoints:4096,zones:r}),c=new Vm(l.x,l.y,a,{interceptAtZero:!1}).predict(s);o=new Float64Array(s.length);for(let d=0;d<i.length;d++)o[d]=i[d]-c[d]}break;case"whittaker":{let a=Rs(i,n);o=new Float64Array(s.length);for(let r=0;r<i.length;r++)o[r]=i[r]-a[r]}break;case"bernstein":{let{degree:a}=n,r=Ps(i,a,n);o=new Float64Array(s.length);for(let l=0;l<i.length;l++)o[l]=i[l]-r[l]}break;case"cubic":{let a=Fs(i,s);o=new Float64Array(s.length);for(let r=0;r<i.length;r++)o[r]=i[r]-a[r]}break;default:throw new Error(`baselineCorrection: algorithm unknown: ${t}`)}Object.assign(e.data,{re:o})}function ws(e){return!e.info.isFid}function _m(e,n){return{once:!0,reduce:n}}var Ns={name:"baselineCorrection",label:"Baseline correction",domainUpdateRules:Jm,apply:$m,reduce:_m,isApplicable:ws};var Km={updateXDomain:!0,updateYDomain:!0};function Qm(e,n){if(!As(e))throw new Error("Digital filter is not applicable on this data");let{digitalFilterValue:t}=n,s=new Float64Array(e.data.re),i=new Float64Array(e.data.im),o=new Float64Array(s.length),a=new Float64Array(i.length),r=Math.floor(t);o.set(s.slice(r)),a.set(i.slice(r)),e.data.re=o,e.data.im=a}function As(e){return!!(e.info.isComplex&&e.info.isFid)}function ec(e,n){return{once:!0,reduce:n}}var ks={name:"digitalFilter",label:"Digital Filter",domainUpdateRules:Km,apply:Qm,reduce:ec,isApplicable:As};import{xEnsureFloat64 as At,xyEquallySpaced as Is}from"ml-spectra-processing";var tc={updateXDomain:!1,updateYDomain:!1};function nc(e,n={}){if(!Ts(e))throw new Error("Equally spaced is not applicable on this data");let{from:t,to:s,numberOfPoints:i,exclusions:o}=n,{x:a,re:r,im:l}=e.data,m=Is({x:a,y:r},{from:t,to:s,numberOfPoints:i,exclusions:o});if(e.data.x=At(m.x),e.data.re=At(m.y),l){let c=Is({x:a,y:r},{from:t,to:s,numberOfPoints:i,exclusions:o});e.data.im=At(c.y)}}function Ts(e){return!!(e.info.isComplex&&!e.info.isFid)}function sc(e,n){return{once:!1,reduce:n}}var Es={name:"equallySpaced",label:"Equally spaced",domainUpdateRules:tc,apply:nc,reduce:sc,isApplicable:Ts};import{xySetYValue as zs}from"ml-spectra-processing";var ic={updateXDomain:!1,updateYDomain:!1};function oc(e,n){if(!Bs(e))throw new Error("Exclusion zones filter not applicable on this data");let{x:t,re:s,im:i}=e.data;e.data.re=Float64Array.from(zs({x:t,y:s},{zones:n}).y),e.data.im=i&&Float64Array.from(zs({x:t,y:s},{zones:n}).y)}function Bs(e){return!!e.info.isFt}function ac(e,n){return{once:!0,reduce:rc(e.concat(n))}}var Xs={name:"exclusionZones",label:"Exclusion zones",domainUpdateRules:ic,apply:oc,reduce:ac,isApplicable:Bs};function rc(e=[],n={}){let{from:t=Number.NEGATIVE_INFINITY,to:s=Number.POSITIVE_INFINITY}=n;t>s&&([t,s]=[s,t]),e=e.map(a=>a.from>a.to?{...a,from:a.to,to:a.from}:{...a}),e.sort((a,r)=>a.from!==r.from?a.from-r.from:a.to-r.to);for(let a of e)t>a.from&&(a.from=t),s<a.to&&(a.to=s);if(e=e.filter(a=>a.from<=a.to),e.length===0)return[];let i=e[0],o=[i];for(let a=1;a<e.length;a++){let r=e[a];r.from<=i.to?i.to<r.to&&(i.to=r.to):(i=r,o.push(i))}return o}import{isPowerOfTwo as cc,reimFFT as dc,reimPhaseCorrection as gc,xMean as Ls,xMultiply as uc}from"ml-spectra-processing";var z=Math.PI/180;import{nextPowerOfTwo as lc,xSequentialFillFromStep as mc}from"ml-spectra-processing";function qs(e){let{x:n,re:t,im:s}=e.data,i=lc(n.length),o=new Float64Array(i),a=new Float64Array(i);o.set(t.slice(0,i)),a.set(s.slice(0,i));let r=mc({from:n[0],size:i,step:n[1]-n[0]});e.data={...e.data,re:o,im:a,x:r}}var fc={updateXDomain:!0,updateYDomain:!0};function pc(e){if(!Ys(e))throw new Error("fft not applicable on this data");Dc(e);let n=e.filters.some(o=>o.name==="digitalFilter"&&o.enabled),{info:{aqMod:t}}=e;t===1&&bc(e),cc(e.data.x.length)||qs(e);let{data:s,info:i}=e;if(Object.assign(s,dc({re:s.re,im:i.reverse?uc(s.im,-1):s.im},{applyZeroShift:!0})),n){let{digitalFilter:o=0}=i,a=Math.floor(o),r=(o-a)*Math.PI*2,l=a%2?180*z:0;Object.assign(s,gc(s,l,-r,{reverse:!0}))}e.data.x=yc(e),e.info={...e.info,isFid:!1,isFt:!0}}function Ys(e){return!!(e.info.isComplex&&e.info.isFid)}function Cc(e,n){return{once:!0,reduce:n}}function yc(e){let n=e.info,t=Number(n.baseFrequency),s=Number(n.frequencyOffset),i=Number(n.spectralWidth),o=s/t,a=.5*i,r=e.data.x.length,l=o-a,m=i/(r-1),c=new Float64Array(r);for(let d=0;d<r;d++)c[d]=l,l+=m;return c}function bc(e){let n=e.data,t=n.re.length,s=new Float64Array(n.re),i=new Float64Array(n.im),o=Ls(n.re.slice(t*.75>>0,t)),a=Ls(n.im.slice(t*.75>>0,t));for(let r=0;r<t;r++)s[r]-=o,i[r]-=a;return Object.assign(e.data,{re:s,im:i}),e}function Dc(e){let{data:n}=e;if(n.x.length!==n.re.length||n.x.length!==n.im.length)throw new Error("The length of data should be equal")}var Ws={name:"fft",label:"FFT",domainUpdateRules:fc,apply:pc,reduce:Cc,isApplicable:Ys};import{xSequentialFillFromStep as Oc}from"ml-spectra-processing";import{Matrix as hc,SVD as Hc}from"ml-matrix";function Us(e,n){let{nbCoefficients:t,nbInputs:s,nbPoints:i}=n;if(e.length<s+t+i)throw new RangeError("data length should be bigger than nbInputs + nbCoefficients + nbPoints");let o=e.length-i-2,a=[];for(let d=0;d<s;d++){let g=new Float64Array(t);for(let u=0;u<t;u++)g[u]=e[o-d-u];a.push(g)}let r=new Hc(a),l=new Float64Array(s);for(let d=0;d<s;d++)l[d]=e[o-d+1];let m=r.solve(hc.from1DArray(l.length,1,l)).to1DArray(),{output:c=Float64Array.from(e)}=n;for(let d=0;d<i;d++){let g=0;for(let u=0;u<m.length;u++)g+=m[u]*c[o+1+d-u];c[o+d+2]=g}return{output:c,predicted:c.slice(o+2)}}function le(e,n){let{re:t,im:s}=e,{nbCoefficients:i,nbPoints:o,nbInputs:a=t.length}=n,r=Math.abs(o),l=o<0?r:0,m=2*Math.ceil((a+r+i)/2);if(t.length<m-l)throw new RangeError(`The sum of nbPoints, nbInputs and nbCoefficients should be less than data length (${t.length})`);let c=new Float64Array(2*m),d=t.length-m+l;for(let f=0;f<m-l;f++)c.set([t[d+f],s[d+f]],2*f);Us(c,{nbInputs:a*2,nbCoefficients:i,nbPoints:r*2,output:c});let g=new Float64Array(t.length+l),u=new Float64Array(l+s.length);o<0?(g.set(t),u.set(s)):(g.set(t.slice(0,t.length-o)),u.set(s.slice(0,s.length-o)));for(let f=0;f<2*r;f+=2)g[g.length-1-(f>>1)]=c[c.length-2-f],u[g.length-1-(f>>1)]=c[c.length-1-f];return{re:g,im:u}}function me(e,n,t){let s=2*e,i=2*n;if(t===0){if(s<n)return 0;if(n<s&&s<i)return n;if(i<s)return t-n}return n<t?t-n:0}var xc={updateXDomain:!0,updateYDomain:!0};function Sc(e,n={}){if(!Zs(e))throw new Error("Digital filter is not applicable on this data");let{info:t,data:{re:s,im:i}}=e,{lpNumberOfCoefficients:o=0,linearPredictionBin:a=0,spectrumSize:r=s.length,numberOfPoints:l=s.length}=t,{nbPoints:m=me(r,l,a)/-2,nbCoefficients:c=o,nbInputs:d=Math.floor(s.length-m-c)}=n,g=e.filters.find(y=>y.name==="forwardLinearPrediction");g&&(g.value={nbCoefficients:c,nbPoints:m,nbInputs:d});let{re:u,im:f}=le({re:s,im:i},{nbCoefficients:c,nbInputs:d,nbPoints:m}),{data:{x:C}}=e;Object.assign(e.data,{re:u,im:f,x:m<0?Oc({from:0,size:u.length,step:C[1]-C[0]}):C})}function Zs(e){return!!(e.info.isComplex&&e.info.isFid)}function vc(e,n){return{once:!0,reduce:n}}var Vs={name:"forwardLinearPrediction",label:"Forward Linear Prediction Filter",domainUpdateRules:xc,apply:Sc,reduce:vc,isApplicable:Zs};import{reimAbsolute as Pc,reimAutoPhaseCorrection as Fc,reimPhaseCorrection as jc,xEnsureFloat64 as Gs}from"ml-spectra-processing";var Mc={updateXDomain:!1,updateYDomain:!1};function Rc(e,n={}){if(!_s(e))throw new Error("Phase correction not applicable on this data");let{absolute:t=!1}=n,s=e.filters?.find(i=>i.name==="phaseCorrection");if(t){let{re:i,im:o}=e.data;e.data.re=Pc({re:i,im:o}),e.data.im=void 0,s&&(s.value={...s.value,ph0:0,ph1:0,absolute:t})}else if("ph0"in n&&"ph1"in n){let{ph0:i=0,ph1:o=0}=n;Js(e,{ph0:i,ph1:o}),s&&(s.value={...s.value,absolute:t})}else{let i=$s(e);if(i.ph0===0&&i.ph1===0&&(i=$s(e,{magnitudeMode:!0})),Js(e,i),s){let{ph0:o,ph1:a}=i;s.value={...s.value,absolute:t,ph0:o,ph1:a}}}}function Js(e,n){let{ph0:t,ph1:s}=n,{re:i,im:o}=e.data,a=jc({re:i,im:o},t*Math.PI/180,s*Math.PI/180,{reverse:!0});e.data={...e.data,re:Gs(a.re),im:Gs(a.im)}}function $s(e,n={}){let{minRegSize:t=5,maxDistanceToJoin:s=128,magnitudeMode:i=!1,factorNoise:o=5,reverse:a=!0}=n;return Fc(e.data,{minRegSize:t,maxDistanceToJoin:s,magnitudeMode:i,factorNoise:o,reverse:a})}function _s(e){return!!(e.info.isComplex&&!e.info.isFid)}function wc(e,n){return{once:!0,reduce:n}}var Ks={name:"phaseCorrection",label:"Phase 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p=e([u-y*m/c,y]);p<a&&([a,d]=[p,y])}t=d-C,s=d+C,i--}return{ph0:u-d*m/c,ph1:d}}function md(e){let{pivot:t,absolute:s,phases:i,threshold:o}=e,{rows:a,columns:r}=s,l=new Ke(a,r,{threshold:0}),m=new Ke(a,r,{threshold:0}),{x:c,y:d}=t;for(let H=d-40;H<d+40;H++)for(let v=c-40;v<c+40;v++)l.set(H,v,s.get(H,v)),m.set(H,v,i.get(H,v));let g=Po(l,m,o),u=-15,f=15,C=12,y=0,p=Number.MAX_SAFE_INTEGER,b=Number.MAX_SAFE_INTEGER,h=15;for(;C>0&&y!==p;){p=y;for(let H=u;H<f+1;H+=h){let v=g([H,0]);v<=b&&([b,y]=[v,H])}u=y+Math.sign(y)*h,f=u,C--}u=y-15,f=y+15;let D=5;for(C=5;C>0;){let H=(f-u)/(D-1);for(let v=u;v<=f;v+=H){let P=g([v,0]);P<b&&([b,y]=[P,v])}u=y-H,f=y+H,C--}let O=s.get(d,c),S=i.get(d,c);return O*Math.cos(S+y*z)<0?y-Math.sign(y)*180:y}function cd(e,n={}){let{re:t,im:s}=e,{transpose:i=!1}=n,o=i?new xo(new _e(t)):new _e(t),a=i?new xo(new _e(s)):new _e(s),{rows:r,columns:l}=o,m=ad({nbRows:r,nbColumns:l});for(let y=0;y<r;y++)for(let 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a=0;a<s.length;a++)s[a]=s[a].replace(/ *[,;]+$/,"").replaceAll(/  +/g," ").trim();e.parts=s}import{Matrix as nu,SVD as su}from"ml-matrix";function k8(e,n){let{nbCoefficients:t,nbInputs:s,nbPoints:i}=n;if(e.length<s+t+i)throw new RangeError("data length should be bigger than nbInputs + nbCoefficients + nbPoints");let o=[];for(let c=0;c<s;c++){let d=new Float64Array(t);for(let g=0;g<t;g++)d[g]=e[c+g+i+1];o.push(d)}let a=new su(o),r=new Float64Array(s);for(let c=0;c<s;c++)r[c]=e[c+i];let l=a.solve(nu.from1DArray(r.length,1,r)).to1DArray(),{output:m=Float64Array.from(e)}=n;for(let c=0;c<i;c++){let d=0;for(let g=0;g<l.length;g++)d+=l[g]*m[g+i-c];m[i-c-1]=d}return{output:m,predicted:m.slice(0,i)}}import{reimPhaseCorrection as xa,xMinValue as iu,xSubtract as Oa}from"ml-spectra-processing";import{analyseMultiplet as ou}from"multiplet-analysis";var au={minimalResolution:.1,critFoundJ:.75,maxTestedJ:17,minTestedJ:1,takeBestPartMultiplet:!0,correctVerticalOffset:!0,symmetrizeEachStep:!1,decreasingJvalues:!0,makeShortCutForSpeed:!0};function z8(e,n={}){let{x:t}=e,{re:s,im:i}=structuredClone(e),{autoPhase:o,analyzer:a={}}=n;if(o&&i){let r=iu(s);r>0&&(s=Oa(s,r),i&&(i=Oa(i,r)));let l=ru(s,i);s=xa({re:s,im:i},Sa(l),0).re}return ou({x:t,y:s},{...au,...a})}function ru(e,n){let t=-180,s=180,i=6,o=10,a=0,r=Number.MAX_SAFE_INTEGER;for(;o>0;){let l=(s-t)/(i+1);for(let m=t;m<=s;m+=l){let c=xa({re:e,im:n},Sa(m),0),d=lu(c.re);d<r&&([r,a]=[d,m])}t=a-l,s=a+l,o--}return a}function Sa(e){return e*Math.PI/180}function lu(e){let n=0;for(let t of e)t<0&&(n-=t);return n}import{gsd as mu,joinBroadPeaks as cu,optimizePeaks as du,setShape as gu}from"ml-gsd";import{savitzkyGolay as uu}from"ml-signal-processing";import{xAbsoluteMedian as fu,xMaxAbsoluteValue as Fa,xNoiseSanPlot as pu,xWhittakerSmoother as Cu,xyExtract as yu}from"ml-spectra-processing";function rt(e,n){return tt(e,{...n,convertTo:"hz"})}function $(e,n){let{from:t,to:s,frequency:i,noiseLevel:o,thresholdFactor:a=3,minMaxRatio:r=.05,broadRatio:l=25e-5,useSanPlot:m=!1,smoothY:c=!0,optimize:d=!1,groupingFactor:g=2,factorLimits:u=2,realTopDetection:f=!0,shape:C={kind:"gaussian"},optimization:y={kind:"lm"},broadWidth:p=.25,sgOptions:b={},direction:h="positive",peakDetectionAlgorithm:D="auto",sensitivity:O=100}=n,S=1/i/(e.x[1]-e.x[0]),x=Math.max(Math.round(S/2),5),{windowSize:H=x-x%2+1,polynomial:v=3}=b;if(!H)throw new Zt({windowSize:H,ws:x,pointsPerHz:S,frequency:i,x:e.x.slice(0,2),sgOptions:b,autoWindowSizeFormula:"ws - (ws % 2) + 1",pointsPerHzFormula:"1 / frequency / (x[1] - x[0])"});if(e.x.length<H)return[];let P,{maxAbsDdY:M}=n;if(t!==void 0&&s!==void 0){if(!("maxAbsDdY"in n)){let j=uu(e,{windowSize:H,polynomial:v,derivative:2});M=Fa(j.data.y)}P=yu(e,{zones:[{from:t,to:s}]})}else P=e;hu(O);let F=O!==100?Cu(P.y,{lambda:50.1-O/2,maxIterations:1}):P.y,R=Du(P.y,{noiseLevel:o,useSanPlot:m,thresholdFactor:a}),w={shape:C,smoothedY:F,maxAbsDdY:M,frequency:i,broadWidth:p,optimize:d,factorLimits:u,groupingFactor:g,maxCriteria:!0,peakDetectionAlgorithm:D,sgOptions:{windowSize:H,polynomial:v},minMaxRatio:r,broadRatio:l,noiseLevel:R.positive,smoothY:c,optimization:y,realTopDetection:f};switch(h){case"positive":return Ut(P,w);case"negative":return va(P,R,w);case"both":return[...Ut(P,w),...va(P,R,w)];default:{let j=h;throw new Error(`Unknown distribution ${j}`)}}}function va(e,n,t){return t.noiseLevel=n.negative,t.maxCriteria=!1,Ut(e,t)}function 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Zt=class extends Error{data;constructor(n){super("windowSize must be an odd integer >= 5, check data property of this error for contextual information"),this.data=n}};function hu(e){if(e<1||e>100)throw new RangeError("The value of sensitivity should lie between (1, 100)")}import{xGetFromToIndex as Uu,xyMaxYPoint as Zu}from"ml-spectra-processing";function ja(e){e.sort((n,t)=>n.from-t.from);for(let n=0;n<e.length-1;n++){let t=e[n],s=e[n+1];t.to>s.from&&(t.id=crypto.randomUUID(),t.to=Math.max(s.to,t.to),t.signals&&s.signals&&(t.signals=t.signals.concat(s.signals)),t.integration!==void 0&&(t.integration+=s.integration||0),e.splice(n+1,1),n--)}return e}var lt=["s","d","t","q","quint","h","sept","o","n"];var Hu={jAxis:"x",intensity:"intensity"};function Ou(e){if(!("symRank"in e))throw new Error("Internal error, symRank was not calculated");if(!("mask"in e))throw new Error("Internal Error, mask was not added")}var Na={compilePattern:(e,n={})=>{let{jAxisKey:t=Hu,symRatio:s=2.5}=n,i=ju(e,{...n,symRatio:s,maxError:2.5,iteration:1,jAxisKey:t});if(i.multiplicity="m",i.asymmetric=!0,Ou(i),i.symRank>=.95&&i.peaksComp.length<32){i.asymmetric=!1;let o,a,r,l=1,m=[];for(let c=0;c<9;c++){let d=Mu(i,c),g=!1;if(d.length===1&&c===0)g=!0;else if(d.length<=1)continue;let u=Fu(d);a=2**c;let f=null,C=1;for(;!g&&(f=Pu(u,a))!==null&&C<400;){let y=new Array(f.length);l=1;for(let D=0;D<f.length;D++){y[D]=new Array(f[D]);for(let O=0;O<f[D];O++)y[D][O]=l++}m=[];let p=1;m.push(d[1].x-d[0].x),o=d[0].x,y[0].splice(0,1),y[1].splice(0,1),l=1;let b=2;for(r=2**c-1;m.length<c&&b<r&&l<d.length;){for(C+=1,p++;l<d.length&&y[l].length===0;)l++;if(l<d.length){m.push(d[l].x-d[0].x),y[l].splice(0,1),b++;for(let D=2;D<=p;D++){let O=0;for(let S=0;S<D;S++)O+=m[S];for(let S=1;S<y.length;S++)if(Math.abs(d[S].x-(o+O))<.25){y[S].splice(0,1),b++;break}}}}let h=vu(m);g=!0;for(let 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ye(e,n,t={}){let{solvent:s,symRatio:i=1.5,integrationSum:o=100,joinOverlapRanges:a=!0,clean:r=.4,compile:l=!1,integralType:m="sum",frequency:c=400,frequencyCluster:d=16,keepPeaks:g=!1,nucleus:u="1H"}=t,f={solvent:s,integrationSum:o,integralType:m,frequencyCluster:d,frequency:c,nucleus:u};if(n.length===0)return[];e.x[0]>e.x[1]&&(e.x=e.x.toReversed(),e.y=e.y.toReversed());let{peaks:C,solventSignals:y}=wu(e,n,f),p=te(e,C,f);if(r)for(let h=0;h<p.length;h++)Math.abs(p[h].integralData.value)<r&&p.splice(h,1);if(l){let h,D;for(let O=0;O<p.length;O++){p[O]=Na.compilePattern(p[O],{symRatio:i});let S=p[O];if(S.maskPattern&&S.multiplicity!=="m"&&S.multiplicity!==""){Ru(S),h=0,D=0;let x=[];for(let H=S.maskPattern.length-1;H>=0;H--)if(D+=Se(S.peaks[H],c),!S.maskPattern[H]){let v=S.peaks.splice(H,1)[0];x.push({x:v.x,y:v.intensity,width:v.width}),S.mask.splice(H,1),S.mask2.splice(H,1),S.maskPattern.splice(H,1),S.nbPeaks--,h+=Se(v,c)}if(x.length>0){h=h*S.integralData.value/D,S.integralData.value-=h;let H=[];for(let P=x.length-1;P>=0;P--)H.push(x[P]);f.integrationSum=Math.abs(h);let v=te(e,H,f);for(let P of v)p.push(P)}}}st(p,o)}if(p.push(...y),p.sort((h,D)=>h.delta-D.delta),r)for(let h=p.length-1;h>=0;h--)Math.abs(p[h].integralData.value)<r&&p.splice(h,1);let b=[];for(let h=0;h<p.length;h++){let D=p[h],O={id:crypto.randomUUID(),from:D.integralData.from,to:D.integralData.to,integration:D.integralData.value,assignment:D.assignment},S={delta:D.delta,kind:D.kind||"signal",multiplicity:D.multiplicity,assignment:D.assignment};g&&(S.peaks=D.peaks.map(x=>{let{intensity:H,...v}=x;return{y:H,...v}})),D.nmrJs&&(S.js=D.nmrJs),O.signals=[S],b[h]=O}return a&&(b=ja(b)),b}function wu(e,n,t){let s=[],i=[];for(let c of 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P7(e,n){let{from:t,to:s}=n.peakPicking,{fromIndex:i,toIndex:o}=Uu(e.x,{from:t,to:s}),a=n.peakPicking.sgOptions?.windowSize??7;if(o-i<=a)return n.logger?.info("Too small window for accurate multiplicity determination"),[{from:e.x[i],to:e.x[o],signals:[{delta:Zu(e,{fromIndex:i,toIndex:o}).x,multiplicity:"",js:[]}]}];let{ranges:r={}}=n,{nucleus:l=""}=r;switch(l){case"1H":return za(e,n);case"13C":return Ia(e,n);default:return Ta(e,n)}}import{BaseRegression as Vu}from"ml-regression-base";import{SimpleLinearRegression as Gu}from"ml-regression-simple-linear";import{xyCheck as Ju}from"ml-spectra-processing";function w7(e,n){Ju(e,{minLength:2});let{x:t,y:s}=e,{gyromagneticRatio:i,gradientPulseDuration:o,timeCorrection:a}=n,r=new Float64Array(t.length),l=new Float64Array(t.length);for(let f=0;f<t.length;f++)r[f]=Math.log(s[f]),l[f]=t[f]**2;let m=new Gu(l,r),{slope:c,intercept:d}=m.toJSON(),g=-c/a/(i*o)**2,u=Math.exp(d);return{regression:new Jt(g,u,n),coefficient:g,signalAbsenseDiffussion:u}}var 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i.json();return{nucleus:o.nucleus,joinedSignals:o.joinedSignals??[],signals:o.signals??[],ranges:o.ranges??[]}}return Object.defineProperty(t,"name",{value:`default${e[0].toUpperCase()}${e.slice(1)}Predictor`}),t}var fn=un("proton","https://nmr-prediction.service.zakodium.com/v1/predict/proton"),pn=un("carbon","https://nmr-prediction.service.zakodium.com/v1/predict/carbon");async function Me(e,n,t){let{cache:s,predictorOptions:i}=t;if(typeof s=="function"){let a=await s(e);if(a)return a}let o=await n(e,i);return typeof s=="function"&&await s(e,o),o}async function Cn(e,n={}){let{predictor:t=pn,predictorOptions:s={},cache:i}=n;return e.molecule.getAllAtoms()===0?{nucleus:"13C",joinedSignals:[],signals:[],ranges:[]}:Me(e,t,{cache:i,predictorOptions:s})}async function yn(e,n){let{minLength:t=2,maxLength:s=3,joinDistance:i}=n;return se(e,{...n,from:"H",to:"C",minLength:t,maxLength:s,joinDistance:i})}async function bn(e,n){let{minLength:t=1,maxLength:s=1,joinDistance:i}=n;return se(e,{...n,from:"H",to:"C",minLength:t,maxLength:s,joinDistance:i})}async function Dn(e,n={}){let{predictor:t=fn,cache:s,predictorOptions:i={}}=n;return e.molecule.getAllAtoms()===0?{nucleus:"1H",joinedSignals:[],signals:[],ranges:[]}:Me(e,t,{cache:s,predictorOptions:i})}function bt(e,n){if(e in n)return!0;let t="hsqc"in n||"hmbc"in n;return e==="C"?t:e==="H"?t||"cosy"in n:!1}var Sr={cosy:{predictor:dn,required:["H"],message:"Proton prediction is missing so COSY could not be generated."},hsqc:{predictor:bn,required:["H","C"],message:"Carbon and / or proton prediction is missing so HSQC could not be generated."},hmbc:{predictor:yn,required:["H","C"],message:"Carbon and / or proton prediction is missing so HMBC could not be generated."}};async function W(e,n={}){let{logger:t,joinDistance:s={H:.05,C:.5},predictOptions:i={H:{},C:{},hsqc:{},hmbc:{},cosy:{}}}=n,o=new xr(e),a=bt("H",i)?await Dn(o,{...i?.H}):void 0,r=bt("C",i)?await Cn(o,i?.C):void 0,l={},m=o.diaIDs,c={};hn(a,m)&&(c.H=a,"H"in i&&(l.proton=a)),hn(r,m)&&(c.C=r,"C"in i&&(l.carbon=r));let d=["cosy","hsqc","hmbc"].filter(f=>f in i).map(async f=>{let{predictor:C,required:y,message:p}=Sr[f];if(y.every(b=>b in c)){let b=await C(o,{predictions:c,...i[f],joinDistance:s});return{key:f,result:b}}else t&&t.warn(p);return{key:f,result:void 0}}),u=await Promise.all(d);for(let{key:f,result:C}of u)C&&(l[f]=C);return{diaIDs:o.diaIDs,hoses:o.hoseCodes,distanceMatrix:o.distanceMatrix,moleculeWithHydrogens:o.moleculeWithH,groupedDiaIDs:o.getGroupedDiastereotopicAtomIDs()||[],molfile:o.toMolfile(),molfileWithH:o.toMolfileWithH(),spectra:l}}function hn(e,n=[]){if(!e||e.ranges.length===0)return!1;let{signals:t}=e;for(let s of t)if(!s.diaIDs?.every(o=>n.includes(o)))return!1;return!0}import{xIsMonotonic as _r,xRescale as Kr,xSequentialFillFromTo as Qr}from"ml-spectra-processing";var _=[{label:"singlet",value:"s",multiplicity:1,names:[]},{label:"doublet",value:"d",multiplicity:2,names:[]},{label:"triplet",value:"t",multiplicity:3,names:[]},{label:"quartet",value:"q",multiplicity:4,names:[]},{label:"quintet",value:"i",acs:"quint",multiplicity:5,names:["quint","qui","qnt","pentet","pnt","pent"]},{label:"sextet",value:"h",multiplicity:6,names:["x","sxt","sext","hexuplet","hex"]},{label:"septet",value:"p",acs:"sept",multiplicity:7,names:["sept","spt","heptet","hpt","hept"]},{label:"octet",value:"o",multiplicity:8,names:["oct"]},{label:"nonet",value:"n",multiplicity:9,names:["non"]},{label:"multiplet",value:"m",multiplicity:null,names:["massive"]}];var Dt={};for(let{value:e,multiplicity:n,names:t}of _){n&&(Dt[e]=n-1);for(let s of t)n&&(Dt[s]=n-1)}var q=Dt;function ie(e){let n=structuredClone(e),t=e.reduce((s,i)=>{let{atoms:o=[]}=i;return Math.max(...o,s)},0)+1;for(let[s,i]of e.entries()){let{js:o=[],atoms:a=[t++]}=i,{newCouplings:r,tempSignals:l}=vr(o,a,t+e.length);l.length>0&&n.push(...l),n[s].js=r,n[s].atoms=a}return n.sort((s,i)=>s.delta-i.delta),n}function vr(e,n,t){let s=[];return{newCouplings:e.reduce((o,a)=>{let{atoms:r=[],multiplicity:l,coupling:m}=a;if(r.length===0&&m&&l){let c=[],g=q[l];for(let d=0;d<g;d++)t++,c.push({coupling:m,multiplicity:"d",atoms:[t]}),s.push(Pr(m,[t],n));o.push(...c)}else o.push(a);return o},[]),tempSignals:s}}function Pr(e,n,t){return{delta:1e5,atoms:n,js:[{coupling:e,atoms:t}]}}import{Matrix as Mr}from"ml-matrix";import{Matrix as ht}from"ml-matrix";import{simpleClustering as Fr}from"ml-simple-clustering";function L(e){let{couplingConstants:n,connectivity:t}=e,s=ht.checkMatrix(n),i=t?ht.checkMatrix(t):jr(s),{levels:o=Array.from({length:i.rows},()=>2),clusters:a=Fr(i.to2DArray(),{out:"indexes"})}=e;return{...e,levels:o,clusters:a,connectivity:i,couplingConstants:s}}function jr(e){let n=ht.ones(e.rows,e.rows);for(let t=0;t<e.rows;t++)for(let s=t;s<e.columns;s++)e.get(t,s)===0&&(n.set(t,s,0),n.set(s,t,0));return n}function Rr(e){for(let n of e){if(!n.js)throw new Error("there is not js");if(!n.atoms)throw new Error("there is not atoms");for(let t of n.js)if(!t.atoms)throw new Error("there is not atoms")}}function U(e){Rr(e);let n=e.length,t=[],s=Mr.zeros(n,n),i={};for(let o=0;o<n;o++){t.push(e[o].delta);let a=e[o].atoms[0];i[a]=o}for(let o=0;o<n;o++){let{atoms:a,js:r}=e[o],l=a[0];for(let m of r){let{coupling:c,atoms:g}=m,d=g[0];s.set(i[l],i[d],c),s.set(i[d],i[l],c)}}return L({couplingConstants:s,chemicalShifts:t})}import{generateSpectrum as Zr}from"spectrum-generator";import Ir from"binary-search";import{EVD as Tr,Matrix as Er}from"ml-matrix";import{SparseMatrix as we}from"ml-sparse-matrix";import{SparseMatrix as wr}from"ml-sparse-matrix";function Hn(e,n){let t=2*e*n,s=new wr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+n+r,a+r,1)}return s}import{SparseMatrix as Nr}from"ml-sparse-matrix";function Ht(e,n){let t=2*e*n,s=new Nr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+r,a+n+r,.5),s.set(o+n+r,a+r,.5)}return s}import{SparseMatrix as Ar}from"ml-sparse-matrix";function Ot(e,n){let t=2*e*n,s=new Ar(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=2*i*n;for(let r=0;r<n;r++)s.set(o+r,a+n+r,-.5),s.set(o+n+r,a+r,.5)}return s}import{SparseMatrix as kr}from"ml-sparse-matrix";function Re(e,n){let t=2*e*n,s=new kr(t,t,{initialCapacity:2*e*n});for(let i=0;i<e;i++){let o=2*i*n,a=o+n;for(let r=0;r<n;r++)s.set(o+r,o+r,.5),s.set(a+r,a+r,-.5)}return s}var xt=.01;function On(e,n={}){let{lineWidth:t=1,maxClusterSize:s=8,frequency:i=400}=n,o=L(e),a=o.chemicalShifts.slice();for(let m=0;m<a.length;m++)a[m]=a[m]*i;let r=o.levels,l=[];for(let m of o.clusters){let c=m.map(y=>y<0?-y-1:y),g=1,d=0,u=[],f=[];if(m.length>s){let y=0;for(;m[y++]<0;);y=m[y-1],u.push(-a[y]);for(let p=0;p<m.length;p++)if(m[p]<0){let b=o.couplingConstants.get(y,c[p])/2,D=u.length;for(let h=0;h<D;h++)u.push(u[h]+b),u[h]-=b}u.sort((p,b)=>p-b),d=u.length,g=1;for(let p=0;p<d;p++)f.push(1)}else{let y=Br(a,o.couplingConstants,r,o.connectivity,c),p=y.rows,b=new Tr(y),D=b.eigenvectorMatrix,h=b.realEigenvalues,O=new we(p,p),S=m.length;g=0;for(let F=0;F<S;F++){let R={rows:2**F},w={rows:2**(S-F-1)},j=Hn(R.rows,w.rows);m[F]>=0?(O.add(j.mul(m[F]+1)),g++):O.add(j.mul(m[F]))}let x=Er.zeros(p,p);O.forEachNonZero((F,R,w)=>{if(w>0)for(let j=0;j<D.columns;j++){let N=D.get(R,j);N!==0&&x.set(F,j,x.get(F,j)+N)}return w});let H=x.clone();O.forEachNonZero((F,R,w)=>{if(w<0)for(let j=0;j<D.columns;j++){let N=D.get(R,j);N!==0&&H.set(F,j,H.get(F,j)+N)}return w});let v=D.transpose();x=v.mmul(x);let P=new we(x.to2DArray(),{threshold:xt});H=v.mmul(H);let M=new we(H.to2DArray(),{threshold:xt});M.forEachNonZero((F,R,w)=>w),zr(M,xt),M.forEachNonZero((F,R,w)=>{let j=P.get(F,R);j=Math.min(Math.abs(j),Math.abs(w)),j*=j,d+=j;let N=h[F]-h[R],A=Ir(u,N,(k,X)=>k-X);return A<0?(u.splice(-1-A,0,N),f.splice(-1-A,0,j)):f[A]+=j,w})}let C=u.length;if(C>0){g/=d;let y=t/64,p=u[0],b=f[0],D=1;for(let h=1;h<C;h++)Math.abs(u[h]-p/D)<y?(b+=f[h],p+=u[h],D++):(l.push({x:-p/D/i,y:b*g}),p=u[h],b=f[h],D=1);l.push({x:-p/D/i,y:b*g})}}return l.filter(m=>m.x<1e3)}function zr(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function Br(e,n,t,s,i){let o=1;for(let r of i)o*=t[r];let a=new we(o,o);for(let r=0;r<i.length;r++){let l=i[r],m={rows:2**r},c={rows:2**(i.length-r-1)},g=e[l],d=Re(m.rows,c.rows);a.add(d.mul(g));for(let u=0;u<i.length;u++){let f=i[u];if(s.get(l,f)===1){let C={rows:2**u},y={rows:2**(i.length-u-1)},p=Ht(m.rows,c.rows).mmul(Ht(C.rows,y.rows));p.add(Ot(m.rows,c.rows).mul(-1).mmul(Ot(C.rows,y.rows))),p.add(Re(m.rows,c.rows).mmul(Re(C.rows,y.rows))),a.add(p.mul(n.get(l,f)/2))}}}return a}import Lr from"binary-search";import{EVD as Yr,Matrix as Wr}from"ml-matrix";import{SparseMatrix as Y}from"ml-sparse-matrix";import{SparseMatrix as Xr}from"ml-sparse-matrix";function xn(e){let n=(e-1)/2,t=[],s=[];for(let m=0;m<e;m++)t.push(e-1-m-n),s.push(Math.sqrt(n*(n+1)-t[m]*(t[m]+1)));let i=St(s,1,e,e);for(let m=0;m<e;m++)s[m]=Math.sqrt(n*(n+1)-t[m]*(t[m]-1));let o=St(s,-1,e,e),a=i.clone().add(o).mul(.5),r=o.clone().mul(-1).add(i).mul(-.5),l=St(t,0,e,e);return{x:a,y:r,z:l,m:o,p:i}}function St(e,n,t,s){let i=new Xr(t,s,{initialCapacity:20});for(let o=0;o<e.length;o++)o-n>=0&&o-n<t&&o<s&&i.set(o-n,o,e[o]);return i}var qr=xn(2);function He(e){return e===2?qr:xn(e)}var Ne=.01;function Z(e,n={}){let{lineWidth:t=1,maxClusterSize:s=8,frequency:i=400}=n,o=L(e),a=o.chemicalShifts.slice();for(let m=0;m<a.length;m++)a[m]=a[m]*i;let r=o.levels,l=[];for(let m of o.clusters){let c=m.map(y=>y<0?-y-1:y),g=1,d=0,u=[],f=[];if(m.length>s){let y=0;for(;m[y++]<0;);y=m[y-1],u.push(-a[y]);for(let p=0;p<m.length;p++)if(m[p]<0){let b=o.couplingConstants.get(y,c[p])/2,D=u.length;for(let h=0;h<D;h++)u.push(u[h]+b),u[h]-=b}u.sort((p,b)=>p-b),d=u.length,g=1;for(let p=0;p<d;p++)f.push(1)}else{let y=Ur(a,o.couplingConstants,r,o.connectivity,c),p=y.rows,b=new Yr(y),D=b.eigenvectorMatrix,h=b.realEigenvalues,O=new Y(p,p),S=m.length;g=0;for(let F=0;F<S;F++){let R=He(r[c[F]]),w=1;for(let k=0;k<F;k++)w*=r[c[k]];let j=Y.eye(w);w=1;for(let k=F+1;k<S;k++)w*=r[c[k]];let N=Y.eye(w),A=j.kroneckerProduct(R.m).kroneckerProduct(N);m[F]>=0?(O.add(A.mul(m[F]+1)),g++):O.add(A.mul(m[F]))}let x=Wr.zeros(p,p);O.forEachNonZero((F,R,w)=>{if(w>0)for(let j=0;j<D.columns;j++){let N=D.get(R,j);N!==0&&x.set(F,j,x.get(F,j)+N)}return w});let H=x.clone();O.forEachNonZero((F,R,w)=>{if(w<0)for(let j=0;j<D.columns;j++){let N=D.get(R,j);N!==0&&H.set(F,j,H.get(F,j)+N)}return w});let v=D.transpose();x=v.mmul(x);let P=new Y(x.to2DArray(),{threshold:Ne});Sn(P,Ne),H=v.mmul(H);let M=new Y(H.to2DArray(),{threshold:Ne});M.forEachNonZero((F,R,w)=>w),Sn(M,Ne),M.forEachNonZero((F,R,w)=>{let j=x.get(F,R);j=Math.min(Math.abs(j),Math.abs(w)),j*=j,d+=j;let N=h[F]-h[R],A=Lr(u,N,(k,X)=>k-X);return A<0?(u.splice(-1-A,0,N),f.splice(-1-A,0,j)):f[A]+=j,w})}let C=u.length;if(C>0){g/=d;let y=t/64,p=u[0],b=f[0],D=1;for(let h=1;h<C;h++)Math.abs(u[h]-p/D)<y?(b+=f[h],p+=u[h],D++):(l.push({x:-p/D/i,y:b*g}),p=u[h],b=f[h],D=1);l.push({x:-p/D/i,y:b*g})}}return l.filter(m=>m.x<1e3)}function Sn(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function Ur(e,n,t,s,i){let o=1;for(let r of i)o*=t[r];let a=new Y(o,o);for(let r=0;r<i.length;r++){let l=i[r],m=He(t[l]),c=1;for(let C=0;C<r;C++)c*=t[i[C]];let g=Y.eye(c);c=1;for(let C=r+1;C<i.length;C++)c*=t[i[C]];let d=Y.eye(c),u=e[l],f=g.kroneckerProduct(m.z).kroneckerProduct(d);a.add(f.mul(u));for(let C=0;C<i.length;C++){let y=i[C];if(s.get(l,y)===1){let p=He(t[y]),b=1;for(let S=0;S<C;S++)b*=t[i[S]];let D=Y.eye(b);b=1;for(let S=C+1;S<i.length;S++)b*=t[i[S]];let h=Y.eye(b),O=g.kroneckerProduct(m.x).kroneckerProduct(d).mmul(D.kroneckerProduct(p.x).kroneckerProduct(h));O.add(g.kroneckerProduct(m.y).kroneckerProduct(d).mul(-1).mmul(D.kroneckerProduct(p.y).kroneckerProduct(h))),O.add(g.kroneckerProduct(m.z).kroneckerProduct(d).mmul(D.kroneckerProduct(p.z).kroneckerProduct(h))),a.add(O.mul(n.get(l,y)/2))}}}return a}function vn(e,n={}){let t=L(e),{lineWidth:s=1,frequency:i=400,from:o=0,to:a=10,nbPoints:r=16*1024,noise:l,baseline:m,shape:c={kind:"gaussian"},isProton:g=t.levels.every(u=>u===2)}=n,d=g?On(t,n):Z(t,n);return Zr(d,{generator:{from:o,to:a,nbPoints:r},peakOptions:{shape:c,width:s/i},noise:l,baseline:m})}import{agnes as Vr}from"ml-hclust";import{Matrix as Gr}from"ml-matrix";function V(e,n={}){let t=L(e),{chemicalShifts:s,couplingConstants:i,connectivity:o}=t,{frequency:a=400,maxClusterSize:r=8}=n,l=Jr(s,i,a),m=Vr(l,{method:"single",isDistanceMatrix:!0}),c=[],g=s.length;vt(m,c,{maxClusterSize:r,force:!1,nSpins:g,connectivity:o});let d=$r(c,r),u=d.length,f=[];for(let C=0;C<u;C++){let y=[];for(let p=0;p<g;p++){let b=d[C][p];b!==0&&y.push(b<0?-(p+1):p)}f.push(y)}return f}function vt(e,n,t){let{maxClusterSize:s,force:i,nSpins:o,connectivity:a}=t;if(!i&&e.size<=s)n.push(Pn(e.indices(),o));else for(let r of e.children)if(r.size<=s){let l=Pn(r.indices(),o),m=0;for(let c=0;c<o;c++)if(l[c]===1){for(let g=0;g<o;g++)a.get(c,g)===1&&l[g]===0&&(l[g]=-1,m++);m++}m<=s?n.push(l):r.index<0?vt(r,n,{maxClusterSize:s,force:!0,nSpins:o,connectivity:a}):(l[r.index]=2,n.push(l))}else vt(r,n,{maxClusterSize:s,force:!1,nSpins:o,connectivity:a})}function Jr(e,n,t){let s=n.rows,i=n.columns,o=Gr.zeros(s,s);for(let a=0;a<s;a++)for(let r=a;r<i;r++){let l=n.get(a,r);if(e[a]-e[r]!==0){let m=1-Math.abs(l/((e[a]-e[r])*t));o.set(a,r,m),o.set(r,a,m)}else a===r||l!==0||(o.set(a,r,1),o.set(r,a,1))}return o.to2DArray()}function $r(e,n){for(let t=e.length-1;t>=0;t--){let s=e[t],i=s.length,o=0;for(;o<i&&s[o++]!==-1;);if(!(o>=i))for(let a=e.length-1;a>=t+1;a--){let r=e[a],l=0,m=0;for(let c=0;c<i;c++)s[c]*r[c]===-1&&m++,(s[c]!==0||r[c]!==0)&&l++;if(m>0&&l<=n){for(let c=0;c<i;c++)r[c]===1?s[c]=1:r[c]===-1&&s[c]!==1&&(s[c]=-1);e.splice(a,1)}}}return e}function Pn(e,n){let t=new Int16Array(n);for(let s of e)t[s]=1;return t}function el(e){for(let n of e){if(!n.js)throw new Error("There is not js");if(!n.atoms)throw new Error("There is not atoms");for(let t of n.js)if(!t.atoms)throw new Error("There is not atoms")}}function Ae(e,n={}){let t=ie(e);el(t);let{frequency:s=400,shape:i={kind:"gaussian"},from:o=0,to:a=10,lineWidth:r=1,nbPoints:l=16*1024,maxValue:m=1e8,maxClusterSize:c=8,...g}=n;if(t.length===0)return{x:Qr({from:o,to:a,size:l}),y:new Float64Array(l)};let d=U(t);d.clusters=V(d,{frequency:s,maxClusterSize:c});let u=vn(d,{frequency:s,from:o,to:a,nbPoints:l,lineWidth:r,shape:i,maxClusterSize:c,...g});return m&&_r(u.y)===0&&(u.y=Kr(u.y,{max:m})),u}import{getGyromagneticRatio as Fn}from"gyromagnetic-ratio";function Oe(e,n){let{nucleus:t,frequency:s}=n,i=Fn(e),o=Fn(t);if(!o||!i)throw new Error(`${e} or ${t} is not supported`);return s*i/o}var F1=Oe;function jn(e,n){let{nbPoints:t,lineWidth:s,frequency:i}=n,o=[];for(let a in e)if(a==="proton"||a==="carbon"){let r=e[a];if(!r)continue;o.push(tl(r,{nbPoints:t,lineWidth:s,...n[a],experiment:a,frequency:i}))}return o}function tl(e,n){let{frequency:t=400,experiment:s}=n,{signals:i,nucleus:o}=e,a=Oe(o,{nucleus:"1H",frequency:t}),{x:r,y:l}=Ae(i,{...n,frequency:a});return{data:{x:r,re:l,im:null},info:{nucleus:e.nucleus,dimension:1,isComplex:!1,originFrequency:a,baseFrequency:a,pulseSequence:"prediction",experiment:s,isFt:!0},ranges:{values:e.ranges}}}import{xEnsureFloat64 as nl}from"ml-spectra-processing";import{generateSpectrum2D as sl}from"spectrum-generator";function K(e){return typeof e!="object"?{x:e,y:e}:{...e}}function Mn(e,n={}){let{from:t=-1,to:s=12,nbPoints:i=512,factor:o=3}=n,{width:a=.02}=n,r={x:[],y:[],z:[]};for(let c of e)r.x.push(c.x.delta),r.y.push(c.y.delta),r.z.push(1e6);let{z:l,...m}=sl(il(r),{generator:{from:K(t),to:K(s),nbPoints:K(i)},peaks:{width:K(a),factor:o}});return{z:l.map(nl),...m}}function il(e){let n=structuredClone(e);for(let t=0;t<n.x.length;t++)for(let s=t+1;s<n.x.length;s++)n.x[t]===n.x[s]&&n.y[t]===n.y[s]&&(n.z[t]+=n.z[s],n.x.splice(s,1),n.y.splice(s,1),n.z.splice(s,1),s--);return n}function Rn(e,n){let t=Oe(e[1],{nucleus:e[0],frequency:n});return[n,t]}function Nn(e,n){let t=[];for(let s in e){if(!al(s)||!e[s])continue;let i=e[s];t.push(ol(i,{experiment:s,...n}))}return t}function ol(e,n){let{signals:t,zones:s,nuclei:i}=e,{experiment:o,frequency:a,width:r=rl(i),nbPoints:l}=n,m=Rn(i,a),c=n.fromTo[wn(i[0])],g=n.fromTo[wn(i[1])],d=ll(r,m),u=Mn(t,{from:{x:c.from,y:g.from},to:{x:c.to,y:g.to},nbPoints:l,factor:3,width:d}),f=m.join(",");return{data:{rr:{...u,noise:.01}},info:{nucleus:i,originFrequency:f,baseFrequency:f,pulseSequence:o,experiment:"2d"},zones:{values:s}}}function al(e){return["cosy","hsqc","hmbc"].includes(e)}function rl(e){return{x:8,y:e[0]===e[1]?8:24}}function ll(e,n){let t=K(e);return{x:t.x/n[0],y:t.y/n[1]}}function wn(e){return e.includes("H")?"proton":"carbon"}async function Z1(e,n={}){let{logger:t,simulation:s={oneD:{},twoD:{}},prediction:i={}}=n,{spectra:o}=await W(e,{logger:t,...i});!("frequency"in s)&&t&&t.warn("Frequency is settled to 400 MHz");let{frequency:a=400}=s,r={proton:{from:-1,to:12},carbon:{from:-10,to:220},nbPoints:65536,lineWidth:1,...s.oneD},l={frequency:a,fromTo:{proton:r.proton,carbon:r.carbon},nbPoints:{x:1024,y:1024},...s.twoD},m=jn(o,{frequency:a,...r}),c=Nn(o,l);return{spectra:[...m,...c],molecules:[{molfile:e.toMolfile()}]}}import{TreeSet as dl}from"ml-tree-set";function An(e){let{restrictionByCS:n,predictions:t,targets:s,useIntegrationRestriction:i}=e,{tolerance:o,chemicalShiftRestriction:a}=n,r=Math.abs(o),l={};for(let m in t){let c=t[m];if(c.error&&(c.error=Math.abs(c.error)),l[m]=[],s)for(let g in s){let d=s[g],{nbAtoms:u}=c,{integration:f}=d;if(i&&f>0?u-f<1:!0)if(!a||c.delta===void 0)l[m].push(g);else{let y=r;c.error&&(y=Math.max(y,c.error));let p=d.signals&&d.signals.length>0?d.signals[0].delta:(d.to+d.from)/2;Math.abs(c.delta-p-r)<4*r&&l[m].push(g)}}l[m].push("*")}return l}function kn(e,n){let{useIntegrationRestriction:t,diaIDPeerPossibleAssignment:s,nbAllowedUnAssigned:i,restrictionByCS:o,predictions:a,targets:r}=n,{useChemicalShiftScore:l}=o,m=0,c=e.length,g={},d=[];for(let y=0;y<e.length;y++){let p=e[y];p&&p!=="*"&&(d.push(y),g[p]||(g[p]=[]),g[p].push(s[y])),p==="*"&&m++}if(m>i)return 0;let u=Object.keys(g);if(u.length===0)return 0;if(t)for(let y of u){let p=g[y],b=0;for(let h of p){let O=a[h];b+=O.allHydrogens}let{integration:D}=r[y];if(b-D>=.5)return 0}let f=l?ml(e,n):1,C=m/c;return f-C}function ml(e,n){let{tolerance:t}=n.restrictionByCS,{diaIDPeerPossibleAssignment:s,predictions:i,targets:o}=n,a=0,r=0;for(let l=0;l<e.length;l++){let m=e[l];if(m&&m!=="*"){r++;let c=s[l],g=i[c],d=o[m],u=t;if(g.error&&(u=Math.max(g.error,t)),g.delta===void 0)a+=1;else{let f=d.signals&&d.signals.length>0?d.signals[0].delta:(d.to+d.from)/2,C=Math.abs(g.delta-f);C<u?a+=1:(C=Math.abs(C-u),a+=-.25/u*C+1)}}}return r>0&&(a/=r),a}function Pt(e,n,t,s){let{nSources:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:l,targets:m,predictions:c,lowerBoundScore:g,nbAllowedUnAssigned:d,possibleAssignmentMap:u,useIntegrationRestriction:f,diaIDPeerPossibleAssignment:C}=e;if(Date.now()-r>a)return;let y=C[n],p=u[y];for(let b of p){t[n]=b;let D=kn(t,{useIntegrationRestriction:f,diaIDPeerPossibleAssignment:C,nbAllowedUnAssigned:d,restrictionByCS:o,predictions:c,targets:m});if(D===0){b==="*"&&(t[n]=null);continue}n===i-1&&D>=g?cl(s,{predictions:c,partial:t,score:D,maxSolutions:l}):n<i-1&&Pt({nSources:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:l,targets:m,predictions:c,lowerBoundScore:g,nbAllowedUnAssigned:d,possibleAssignmentMap:u,useIntegrationRestriction:f,diaIDPeerPossibleAssignment:C},n+1,structuredClone(t),s)}}function cl(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n;e.nSolutions++;let a={assignment:structuredClone(i),score:t/gl(i,o)};if(e.nSolutions>=s){let r=e.solutions.last();a.score>r.score&&(e.solutions.pollLast(),e.solutions.add(a))}else e.solutions.add(a),e.nSolutions++}function gl(e,n){let t=Object.keys(n).length,s=new Set(e),i=t-s.size;return i>0?2*i:1}var ul=(e,n)=>n.score-e.score;async function ke(e){let{restrictionByCS:n={},useIntegrationRestriction:t,timeout:s,minScore:i,nbAllowedUnAssigned:o,maxSolutions:a,targets:r,joinedSignals:l}=e,{tolerance:m=1,useChemicalShiftScore:c=!1,chemicalShiftRestriction:g=!0}=n,d=l.length,u={};for(let h of l){let O=h.diaIDs[0],S=h.atoms[0];u[O]={...h,diaIDIndex:S,allHydrogens:h.nbAtoms}}let f=An({restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:g},useIntegrationRestriction:t,predictions:u,targets:r}),C=Object.keys(f),y=new Array(d).fill(null),p={solutions:new dl(ul),nSolutions:0},b=Date.now();Pt({nSources:d,restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:g},timeout:s,timeStart:b,targets:r,predictions:u,maxSolutions:a,lowerBoundScore:i,nbAllowedUnAssigned:o,possibleAssignmentMap:f,diaIDPeerPossibleAssignment:C,useIntegrationRestriction:t},0,y,p);let D=[];for(let h of p.solutions.elements){let{assignment:O,score:S}=h,x=structuredClone(r);for(let H=0;H<O.length;H++){let v=O[H];if(typeof v!="string")continue;let P=x[v];(!P.signals||P.signals.length===0)&&(P.signals=[{delta:(P.to+P.from)/2}]);let M=P.signals[0];M.diaIDs||(M.diaIDs=[]),v&&M.diaIDs.push(C[H])}D.push({score:S,assignment:Object.values(x)})}return D}function fl(e){for(let n of e){if(!n.atoms)throw new Error("signal has not atoms property");if(!n.diaIDs)throw new Error("signal has not diaIDs property");if(!n.nbAtoms)throw new Error("signal has not nbAtoms property")}}function pl(e){for(let n of e)if(n.integration===void 0)throw new Error("ranges has not integration property")}async function mp(e,n,t={}){let{restrictionByCS:s,minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:r=6e3,predictionOptions:l={}}=t;if(!n)throw new Error("It is needed a OCL molecule instance to assign");let{spectra:m}=await W(n,{predictOptions:{H:l}}),c=m.proton?.joinedSignals||[];pl(e),fl(c);let g={};for(let d of e){let{id:u=crypto.randomUUID()}=d;g[u]=structuredClone(d)}return ke({restrictionByCS:s,timeout:r,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:g,joinedSignals:c,useIntegrationRestriction:!0})}function Cl(e){for(let n of e){if(!n.atoms)throw new Error("signal has not atoms property");if(!n.diaIDs)throw new Error("signal has not diaIDs property");if(!n.nbAtoms)throw new Error("signal has not nbAtoms property")}}function yl(e){let n=structuredClone(e);for(let t of n)t.integration===void 0&&(t.integration=0);return n}async function up(e,n,t={}){let{restrictionByCS:s={},minScore:i=1,maxSolutions:o=10,nbAllowedUnAssigned:a=0,timeout:r=6e3,predictionOptions:l={}}=t,{spectra:m}=await W(n,{predictOptions:{C:l}}),c=m.carbon?.joinedSignals||[];Cl(c);let g=yl(e),d={};for(let u of g){let{id:f=crypto.randomUUID()}=u;d[f]=structuredClone(u)}return ke({restrictionByCS:s,timeout:r,minScore:i,nbAllowedUnAssigned:a,maxSolutions:o,targets:d,joinedSignals:c,useIntegrationRestriction:!1})}import{ensureHeterotopicChiralBonds as Bl}from"openchemlib-utils";import{TreeSet as Bn}from"ml-tree-set";import{getConnectivityMatrix as Fl}from"openchemlib-utils";import{getCorrelationDelta as bl}from"nmr-correlation";function In(e,n){let{restrictionByCS:t,predictions:s,targets:i}=n,{tolerance:o,chemicalShiftRestriction:a}=t,r=Object.keys(s);for(let l of r){let m=o[l],c=s[l],g=i[l];e[l]||(e[l]={});for(let d in c){let u=c[d];if(e[l][d]=[],g)for(let f in g){let C=g[f],{nbAtoms:y,protonsCount:p}=u,{integration:b,protonsCount:D}=C;if(b?l==="H"?y-b<1:D.length>0?D.includes(p):!0:!0)if(!a||u.delta===void 0)e[l][d].push(f);else{let O=bl(C);if(O===void 0)throw new Error("Correlation has not delta");Math.abs(u.delta-O-m)<4*m&&e[l][d].push(f)}}e[l][d].push("*")}}return e}import{getCorrelationDelta as hl}from"nmr-correlation";function Dl(e,n,t){let s=e[0],{H:i=[]}=n[s].attachment,o=[{targetIDs:[s],attachments:new Set(i)}];for(let a=1;a<e.length;a++){let r=e[a],l=n[r],{H:m=[]}=l.attachment,c=!0;for(let g of o)if(m.some(u=>g.attachments.has(u))){c=!1,g.targetIDs.push(r);for(let u of m)g.attachments.add(u);break}c&&o.push({targetIDs:[r],attachments:new Set(m)})}return o.map(a=>({atomType:"C",targetIDs:a.targetIDs,integration:t?Array.from(a.attachments).reduce((r,l)=>t[l].integration+r,0):0}))}var Tn=Dl;function En(e,n){let{diaIDPeerPossibleAssignment:t,infoByAtomTypes:s,restrictionByCS:i,predictions:o,targets:a,correlations:r}=n,{tolerance:l,useChemicalShiftScore:m}=i,c=0,g=0,d={},u={},f=Object.keys(e);for(let x of f){let H=0,{nbAllowedUnAssigned:v}=s[x],P={},M=e[x]||[];d[x]=P,u[x]=[],g+=M.length;for(let F=0;F<M.length;F++){let R=M[F];R&&R!=="*"&&(u[x].push(F),P[R]||(P[R]=[]),P[R].push(t[x][F])),R==="*"&&H++}if(H>v)return 0;c+=H}let C={};for(let x in d)C[x]=Object.keys(d[x]);if(Object.values(C).every(x=>x.length===0))return 0;let p=Ol.bind({},o),b=[];for(let x in e)if(x==="C"&&C[x].length>0)b.push(...Tn(C[x],a[x],r));else for(let H of C[x])b.push({atomType:x,targetIDs:[H],integration:a.H[H].integration});for(let x of b){let{integration:H,atomType:v}=x;if(H===void 0||Number.isNaN(H))continue;let P=0;for(let M of x.targetIDs){let F=d[v][M];for(let R of F){let{prediction:w,atomType:j}=p(R);v===j&&(P+=w.allHydrogens)}}if(P-H>=5)return 0}let D=1,h=1;if(m){h=0,D=0;for(let x of Object.keys(e)){let H=e[x],v=a[x];for(let P=0;P<H.length;P++){let M=H[P];if(M&&M!=="*"){D++;let F=t[x][P],R=o[x][F],w=v[M],j=l[x];if(R.delta===void 0)h+=1;else{let N=hl(w);if(N===void 0)throw new Error("correlation has not delta");let A=Math.abs(R.delta-N);A<j?h+=1:(A=Math.abs(A-j),h+=-.25/j*A+1)}}}}D>0&&(h/=D)}let O=0;if(xl(C)>1){let x={},H=[];for(let P of Object.keys(u))H=H.concat(u[P].map(M=>({index:M,atomType:P})));for(let P=0;P<H.length;P++){let{atomType:M,index:F}=H[P],R=o[M][t[M][F]];for(let w=P+1;w<H.length;w++){let{atomType:j,index:N}=H[w],A=o[j][t[j][N]],X=R.pathLength[A.diaIDIndex]<5,De=e[M][F],he=e[j][N];if(!De||!he)continue;let pt=De>he?`${he} ${De}`:`${De} ${he}`,Kt=Hl({from:{targetID:De,atomType:M},to:{targetID:he,atomType:j}},a),Qt=X?Kt?1:0:Kt?0:1;x[pt]=x[pt]?Math.max(x[pt],Qt):Qt}}let v=0;for(let P in x)v+=x[P];O=v/(H.length*(H.length-1)/2)}let S=c/g;return h===0?O-S:O===0?h-S:(h+O)/2-S}function Hl(e,n){let{from:t,to:s}=e;if(t.targetID===s.targetID)return!0;let i=n[t.atomType][t.targetID],o=n[s.atomType][s.targetID];for(let a of o.link)for(let r of i.link)if(r.signal.id===a.signal.id)return!0;return!1}function Ol(e,n){let t=Object.keys(e);for(let s of t){let i=e[s];if(!i)throw new Error(`prediction by ${s}`);if(i[n])return{atomType:s,prediction:i[n]}}throw new Error(`There is not prediction for ${n}`)}function xl(e){let n=0;for(let t in e)n+=e[t].length;return n}function Ft(e,n,t,s){let{currentAtomTypes:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:l,targets:m,predictions:c,correlations:g,lowerBoundScore:d,possibleAssignmentMap:u,diaIDPeerPossibleAssignment:f}=e;if(!(Date.now()-r>a))for(let C of i){let{currentIndex:y,nSources:p}=n[C];if(y>=p-1&&t[C][y]!==null)continue;let b=f[C][y],D=u[C][b];for(let h of D){t[C][y]=h;let O=En(t,{diaIDPeerPossibleAssignment:f,infoByAtomTypes:n,restrictionByCS:o,predictions:c,correlations:g,targets:m});if(O!==0)if(vl(i,n)&&O>=d)Sl(s,{predictions:c,partial:t,score:O,maxSolutions:l});else{let S=structuredClone(n);S[C].currentIndex+=1,Ft({currentAtomTypes:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:l,targets:m,predictions:c,correlations:g,lowerBoundScore:d,possibleAssignmentMap:u,diaIDPeerPossibleAssignment:f},S,structuredClone(t),s)}}}}function Sl(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n,a={assignment:structuredClone(i),score:t/Pl(i,o)};if(e.nSolutions>=s){let r=e.solutions.last();a.score>r.score&&(e.solutions.pollLast(),e.solutions.add(a))}else e.solutions.add(a),e.nSolutions++}function vl(e,n){let t=!0;for(let s of e){let{currentIndex:i,nSources:o}=n[s];t=t&&i>=o-1}return t}function Pl(e,n){let t=0;for(let s in n){let i=Object.keys(n[s]).length,o=new Set(e[s]);t+=i-o.size}return t>0?2*t:1}function G(e){return"ranges"in e}function zn(e,n){for(let t=0;t<n.length;t++){let s=n[t],i=G(s)?s.ranges:s.zones;for(let o=0;o<i.length;o++){let a=i[o].signals||[];for(let r=0;r<a.length;r++)if(e===a[r].id)return{spectrumIndex:t,signalIndex:r,elementIndex:o}}}throw new Error(`There is not a signal with ${e} ID`)}var Xn=(e,n)=>n.score-e.score;function jl(e){let n=["nbAtoms","diaIDs","atoms"];for(let t of e)for(let s of n)if(!t[s])throw new Error(`property ${s} does not exist`)}var Ml={C:(e,n)=>e.getAllHydrogens(n),H:()=>1};async function qn(e){let{spectra:n,molecule:t,restrictionByCS:s,timeout:i,minScore:o,nbAllowedUnAssigned:a={},maxSolutions:r,correlations:l,assignmentOrder:m,predictionOptions:c,predictions:g={},targets:d}=e,u=o,f={solutions:new Bn(Xn),nSolutions:0},C=Fl(t,{pathLength:!0}),y={},p={},b={},D={};for(let h of m){for(let x of h){let H={[x]:c[x]},v=g[x],P=await Al({molecule:t,predictedSignals:v,options:H,atomType:x});jl(P),p[x]||(p[x]={});let M=0;for(let F of P){let R=F.diaIDs[0],w=F.atoms[0],j=Ml[x](t,w);M+=F.nbAtoms*j,p[x][R]={...F,diaIDIndex:w,allHydrogens:F.nbAtoms*j,protonsCount:j,pathLength:C[w]}}for(let F in p[x])p[x][F].allHydrogens*=100/M;y[x]={nSources:P.length,currentIndex:0,nbAllowedUnAssigned:a[x]||0}}b=In(b,{restrictionByCS:s,predictions:p,targets:d}),D={};for(let x in b)D[x]=Object.keys(b[x]);let O=wl(f,y,h);f={solutions:new Bn(Xn),nSolutions:0};let S=Date.now();for(let x of O)Ft({currentAtomTypes:h,restrictionByCS:s,timeout:i,timeStart:S,targets:d,predictions:p,correlations:l,maxSolutions:r,lowerBoundScore:u,possibleAssignmentMap:b,diaIDPeerPossibleAssignment:D},y,x,f)}return Rl({store:f,spectra:n,diaIDPeerPossibleAssignment:D,targets:d})}function Rl(e){let{store:n,spectra:t,diaIDPeerPossibleAssignment:s,targets:i}=e,{solutions:o}=n,a={},r=Object.keys(i);for(let m of r){let c=i[m];for(let g in c){let d=c[g];for(let u of d.link){let f=u.signal.id;a[f]||(a[u.signal.id]=zn(f,t))}}}let l=[];for(let m of o.elements){let c=structuredClone(t),{assignment:g,score:d}=m,u=Object.keys(g);for(let f of u){let C=i[f],y=g[f];for(let p=0;p<y.length;p++){let b=y[p];if(b==="*"||!b)continue;let D=C[b],h=s[f][p];for(let O of D.link){let{spectrumIndex:S,elementIndex:x,signalIndex:H}=a[O.signal.id],v=c[S];if(G(v)){let{ranges:P}=v,F=P[x].signals[H];if(F.diaIDs||(F.diaIDs=[]),F.diaIDs.includes(h))continue;F.diaIDs.push(h)}else{let P=O.axis,M=v.zones[x].signals[H];if(M[P].diaIDs||(M[P].diaIDs=[]),M[P].diaIDs?.includes(h))continue;M[P].diaIDs?.push(h)}}}}l.push({score:d,assignment:c})}return l}function wl(e,n,t){return e.nSolutions>0?e.solutions.elements.map(s=>{let i=s.assignment;for(let o of t)i[o]=Ln(n[o].nSources);return i}):Nl(n,t)}function Nl(e,n){let t={},s=Object.keys(e);for(let i of s){let o=n.includes(i)?null:"*";t[i]=Ln(e[i].nSources,o)}return[t]}function Ln(e,n=null){let t=new Array(e);for(let s=0;s<e;s++)t[s]=n;return t}async function Al(e){let{molecule:n,predictedSignals:t,options:s,atomType:i}=e;if(t)return t;let{spectra:o}=await W(n,{predictOptions:s});return o[i==="C"?"carbon":"proton"]?.joinedSignals||[]}function Yn(e=[]){let n=structuredClone(e),t=[];for(let s of n){if(!("info"in s))throw new Error("each spectrum should contain info properties with nucleus information");if(G(s)){let{info:i,id:o}=s,a=Ie(s.ranges);t.push({id:o,info:i,ranges:a})}else{let{info:i,id:o}=s,a=Ie(s.zones);t.push({id:o,info:i,zones:a})}}return t}function kl(e){for(let n of e){if(!n.id)throw new Error("A range/zone has not an ID");for(let t of n.signals||[])if(!t.id)throw new Error("A signal has not an ID")}}function Ie(e){for(let n of e){n.id||(n.id=crypto.randomUUID());for(let t of n.signals||[])t.id||(t.id=crypto.randomUUID())}return kl(e),e}import{buildCorrelationData as Tl}from"nmr-correlation";function Wn(e=[]){let n=structuredClone(e),t=[];for(let s of n)if(G(s)){let{id:i,info:o}=s,a=Il({id:i,info:o,ranges:s.ranges});t.push({id:i,info:o,ranges:{values:a}})}else{let{id:i,info:o}=s;t.push({id:i,info:o,zones:{values:s.zones}})}return t}function Il(e){if(e.info.nucleus!=="1H")return e.ranges;let n=e.ranges.reduce((t,s)=>t+(s.integration??0),0);for(let t of e.ranges)if(t.integration&&(t.integration*=100/n,t.signals)){let s=t.signals.reduce((i,o)=>i+(o.integration??0),0);for(let i of t.signals)i.integration?i.integration*=t.integration/s:i.integration=t.integration}return e.ranges}function Un(e,n){let{H:t=[]}=e,s=0;for(let i of t){let o=n[i];s+=Number(o.link[0].signal.integration)}return s}function Zn(e,n={}){let{tolerance:t={C:.25,H:.05}}=n,s=Wn(e),o=Tl(s,{tolerance:t}).values.map(r=>({...r,integration:0})),a={H:{},C:{}};for(let r of o){if(r.pseudo)continue;let{id:l,atomType:m}=r;(m==="H"||m==="C")&&(a[m][l]=r,m==="H"?a[m][l].integration=r.link[0].signal.integration||0:a[m][l].integration=Un(r.attachment,o),a[m][l]=r)}return{targets:a,correlations:o}}function El(e,n=[]){let t=zl(e),{hasHSQC:s,types:i}=t;if(n.length>0)return{assignmentOrder:n,experimentTypes:t};let o=[];return s?o.push(["C"],["H"]):o.push(i.filter(a=>a==="H"||a==="C")),{assignmentOrder:o,experimentTypes:t}}var Vn=El;function zl(e){let n=new Set;for(let t of e)for(let s of t.link){let i=s.experimentType;i==="1d"&&(i=s.atomType[0].toUpperCase()),n.add(i)}return{types:Array.from(n),hasProton:n.has("H"),hasCarbon:n.has("C"),hasHSQC:n.has("hsqc")}}async function Jp(e,n={}){let{restrictionByCS:t={},justAssign:s,minScore:i=.01,maxSolutions:o=10,nbAllowedUnAssigned:a,timeout:r=6e3,predictionOptions:l={},predictions:m={},correlation:c={}}=n,{tolerance:g={H:.2,C:1},useChemicalShiftScore:d=!1,chemicalShiftRestriction:u=!0}=t,f=e.molecule;if(!f)throw new Error("It is needed a molecule to assign");f.addImplicitHydrogens(),Bl(f);let C=Yn(e.spectra),{targets:y,correlations:p}=Zn(C,c),{assignmentOrder:b}=Vn(p,s);return await qn({restrictionByCS:{tolerance:g,useChemicalShiftScore:d,chemicalShiftRestriction:u},spectra:C,molecule:f,timeout:r,minScore:i,maxSolutions:o,assignmentOrder:b,nbAllowedUnAssigned:a,correlations:p,targets:y,predictionOptions:l,predictions:m})}var Xl={unspecified:"Unspecified",unknown:"Unknown",signal:"Signal",residualSolvent:"Residual solvent",reference:"Reference",nmrSolvent:"NMR Solvent",impurity:"Impurity",standard:"Standard",artifact:"Artifact",p1:"Product 1",p2:"Product 2",p3:"Product 3"};function ql(e){return typeof e=="string"&&Xl[e]!==void 0}function Q(e){return e===void 0?"signal":ql(e)?e:"unspecified"}var Te=new Set(["signal"]);var Gn=_.toSorted((e,n)=>e.multiplicity===null&&n.multiplicity===null?0:e.multiplicity===null?1:n.multiplicity===null?-1:e.multiplicity-n.multiplicity),jt=Gn.map(e=>e.value),Ee=Gn.map(e=>e.acs||e.value);import{Molecule as Ll}from"openchemlib";import{TopicMolecule as Yl}from"openchemlib-utils";function xe(e,n,t){let{name:s}=e,i=t[s],{idCode:o}=n[i];if(i===void 0)throw new Error("atom map does not exists");return{...e,idCode:o,atom:i}}function Jn(e,n,t){let s=[];for(let i of e){let{from:o,to:a}=i;s.push({...i,from:o.map(r=>xe(r,n,t)),to:a.map(r=>xe(r,n,t))})}return s}function $n(e,n,t){let s=[];for(let i of e){let{atoms:o}=i;s.push({...i,atoms:o.map(a=>xe(a,n,t))})}return s}function Kn(e,n){let t=[],s=Mt(n),i=n[0].nucleusType.atomicNumber;for(let o of e){let a=Mt(o.from),r=_n(s,a),m=o[r?"to":"from"],c=r?a:Mt(o.to),{nucleusType:{atomicNumber:g},idCode:d}=m[0];!_n(s,c)||g!==i||t.push({coupling:o.value,atoms:m.map(u=>u.atom),diaIDs:[d]})}return t}function _n(e,n){for(let t of e)if(n.has(t))return!0;return!1}function Mt(e){let n=e.filter(t=>t.shift!==null).map(t=>t.shift);return new Set(n)}function Qn(e,n,t){let s=new Set,i=[];for(let o of e){let{name:a}=o,r=n[a],{idCode:l}=t[r];if(!r)throw new Error("atom mapping does not exists");s.add(l),i.push(r)}return{diaIDs:Array.from(s),atoms:i}}function es(e){let n=[];for(let t of e){let{atoms:s=[],...i}=t;if(s.length>1)for(let o of s)n.push({...i,atoms:[o]});else n.push(t)}return n}function ts(e){let n=[];for(let t of e){let s=es(t.js);for(let i of t.atoms){let o={...t,atoms:[i],nbAtoms:1,js:s};n.push(o)}}return n}function ns(e,n){let{atomicNumber:t=1,atomMap:s,molfile:i}=n,o=[],a=Ll.fromMolfile(i),l=new Yl(a).diaIDsAndInfo,m=Jn(e.couplings,l,s),c=$n(e.shifts,l,s);for(let g of c){let{atoms:d,value:u}=g;if(!d.some(C=>C.nucleusType.atomicNumber===t))continue;let f={delta:u,nbAtoms:d.length,...Qn(d,s,l),js:Kn(m,d)};o.push(f)}return ts(o)}function ss(e){return{molarFraction:{value:e.v,low:e.vl,high:e.vh},fieldStrength:e.f,baseItensity:e.bi,intensityLimit:e.il,spinSystemFlags:e.sf,spinSystemType:Ql(e.sst),analysisType:e.at,inchiKey:e.ik,populations:Wl(e.p),lineShapes:Kl(e.l),shiftGroups:$l(e.sg),shifts:Ul(e.s),couplingGroups:_l(e.cg),couplings:Zl(e.c),atoms:Vl(e.a),bonds:Gl(e.b)}}function Wl(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,population:{value:t.v,low:t.vl,high:t.vh},spinSystemFlags:t.sf});return n}function Ul(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,shiftGroup:t.sg});return n}function Zl(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,couplingGroup:t.cg,shifts:{from:t.s[0],to:t.s[1]}});return n}function Vl(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,nucleusType:em(t.nc),cipRank:{canonical:t.crcan,rd:t.crrd,nmr:t.crnmr},ordinal:t.o,stereochemistryFlags:t.rs,spinSystemFlags:t.sf,formalcharge:t.fc,partialCharge:t.c,coordinates2D:t.c2d,coordinates3D:t.c3d,parent2D:t.p2d,shift:t.s});return n}function Gl(e){let n=[];for(let t of e)n.push({id:t.id,bondType:Jl(t.b),stereochemistryFlags:t.rs,spinSystemFlags:t.sf,atoms:t.a});return n}function Jl(e){switch(e){case 0:return"NONE";case 1:return"SINGLE";case 2:return"DOUBLE";case 3:return"TRIPLE";case 4:return"CONJUGATED";case 5:return"SINGLE_UP";case 6:return"SINGLE_DOWN";default:throw new Error(`Unknown bond type: ${e}`)}}function $l(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,shift:{value:t.v,low:t.vl,high:t.vh},spin2:t.s,spinCount:t.c,exchangeable:t.ex,spinSystemFlags:t.sf,gamma:t.g,iterationWeight:t.iw,response:{value:t.rs.v,low:t.rs.vl,high:t.rs.vh,sf:t.rs.sf},population:t.p,lineShape:t.l});return n}function _l(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.parentID,name:t.name,remarks:t.remarks,coupling:{value:t.v,low:t.vl,high:t.vh},spinSystemFlags:t.sf,couplingType:t.t});return n}function Kl(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,spinSystemFlags:t.sf,lineWidth:{value:t.l.v,low:t.l.low,high:t.l.high},gaussian:{value:t.g.v,low:t.g.low,high:t.g.high}});return n}function Ql(e){switch(e){case 0:return"NONE";case 1:return"SOLUTE";case 2:return"SOLVENT";case 4:return"IMPURITY";case 8:return"REFERENCE";case 16:return"CALIBRANT";case 32:return"ERROR_MESSAGE";default:throw new Error(`Unexpected spinSystemType: ${e}`)}}function em(e){return{atomicNumber:(e&65024)>>9,isotope:e&511}}function is(e,n){let{logger:t}=n;t.debug("Parsing CT json results");let s=ss(e),i=tm(s),o=nm(s);return{...s,shifts:i,couplings:o}}function tm(e){let n=e.shifts,t=sm(e),s=os(e),i=[];for(let o of n){let a=t[o.shiftGroup];if(!a)throw new Error(`Shift group ${o.shiftGroup} not found`);let r=s[o.id];if(!r)throw new Error(`Atom not found: ${o.id}`);i.push({atoms:r,value:a.shift.value})}return i}function nm(e){let n=e.couplings,t=im(e.couplingGroups),s=os(e),i=[];for(let o of n){let a=t[o.couplingGroup];if(!a)throw new Error(`Coupling group ${o.couplingGroup} not found`);let r=s[o.shifts.from];if(!r)throw new Error(`Atom not found: ${o.shifts.from}`);let l=s[o.shifts.to];if(!l)throw new Error(`Atom not found: ${o.shifts.to}`);i.push({from:r,to:l,value:a.coupling.value})}return i}function os(e){let n={};for(let t of e.atoms){if(!t.shift)continue;let s=t.shift;n[s]||(n[s]=[]),n[s].push(t)}return n}function sm(e){let n={};for(let t of e.shiftGroups)n[t.id]=t;return n}function im(e){let n={};for(let t of e)n[t.id]=t;return n}function as(e){let n={};for(let t of e)n[t.name]=t.ordinal;return n}function vC(e,n,t){let s=is(e,{logger:console}),i=as(s.atoms),o=ns(s,{atomMap:i,molfile:n,...t});return{...s,signals:o}}var FC=[{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",id:"c647453c-30a3-4743-b982-7e05ad6a4b5e"},{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",id:"47453c30-a327-43b9-827e-05ad6a4b5ee9"},{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",id:"453c30a3-2743-4982-be05-ad6a4b5ee993"},{names:["benzene"],smiles:"c1ccccc1",ranges:[{signals:[{delta:128.84,assignment:"CH"}],from:128.835,to:128.845}],nucleus:"13C",solvent:"THF-d\u2088",id:"3c30a327-43b9-427e-85ad-6a4b5ee993c8"},{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",id:"30a32743-b982-4e05-ad6a-4b5ee993c878"},{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",id:"a32743b9-827e-45ad-aa4b-5ee993c8784f"},{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",id:"2743b982-7e05-4d6a-8b5e-e993c8784fdf"},{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",id:"43b9827e-05ad-4a4b-9ee9-93c8784fdf0b"},{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",id:"b9827e05-ad6a-4b5e-a993-c8784fdf0b20"},{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",id:"827e05ad-6a4b-4ee9-93c8-784fdf0b20e0"},{names:["cyclohexane"],smiles:"C1CCCCC1",ranges:[{signals:[{delta:27.58,assignment:"CH\u2082"}],from:27.575,to:27.584999999999997}],nucleus:"13C",solvent:"THF-d\u2088",id:"7e05ad6a-4b5e-4993-8878-4fdf0b20e0a9"},{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",id:"05ad6a4b-5ee9-43c8-b84f-df0b20e0a9d7"},{names:["dichloromethane"],smiles:"ClCCl",ranges:[{signals:[{delta:54.67,assignment:"CH\u2082"}],from:54.665,to:54.675000000000004}],nucleus:"13C",solvent:"THF-d\u2088",id:"ad6a4b5e-e993-4878-8fdf-0b20e0a9d783"},{names:["diethyl 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h=0;h<f.re.length;h++){let O=f.re[h]*c[h+r-p],S=f.im[h]*g[h+r-p],x=f.re[h]*g[h+r-p],H=f.im[h]*c[h+r-p];b+=O-S,D+=x+H}c[r-p-1]=b,g[r-p-1]=D}let C=new Float64Array(t.length),y=new Float64Array(s.length);return C.set(c.subarray(0,r),0),y.set(g.subarray(0,r),0),o<0?(C.set(t.slice(0,t.length-r),r),y.set(s.slice(0,t.length-r),r)):(C.set(t.slice(o),r),y.set(s.slice(o),r)),{re:C,im:y}}function bm(e,n){let{U:t,V:s,svals:i}=ps(e),o=e.re.length,a=e.re[0].length,r=i.length,l=ym(i)*1e-7,m={re:new Float64Array(a),im:new Float64Array(a)};for(let c=0;c<a;c++){let g=0,d=0;for(let u=0;u<r;u++)if(i[u]>l){let f=0,C=0;for(let h=0;h<o;h++){let O=t.re[h][u]*n.re[h],S=-t.im[h][u]*n.im[h],x=t.re[h][u]*n.im[h],H=-t.im[h][u]*n.re[h];f+=O-S,C+=x+H}let y=f/i[u],p=C/i[u],b=s.re[c][u],D=s.im[c][u];g+=b*y-D*p,d+=b*p+D*y}m.re[c]=g,m.im[c]=d}return m}var hm={updateXDomain:!0,updateYDomain:!0};function Hm(e,n={}){if(!hs(e))throw new Error("Digital Filter is not applicable on this data");let{info:t,data:{re:s,im:i}}=e,{lpNumberOfCoefficients:o=0,tdOff:a=0}=t,{nbCoefficients:r=o,nbPoints:l=a/2,nbInputs:m=Math.floor(s.length/2-r-l)}=n,{re:c,im:g}=re({re:s,im:i},{nbCoefficients:r,nbInputs:m,nbPoints:l}),d=e.filters.find(f=>f.name==="backwardLinearPrediction");d&&(d.value={nbCoefficients:r,nbPoints:l,nbInputs:m});let u=e.data.x;Object.assign(e.data,{re:c,im:g,x:l<0?Dm({from:0,size:c.length,step:u[1]-u[0]}):u})}function hs(e){return!!(e.info.isComplex&&e.info.isFid)}function Om(e,n){return{once:!0,reduce:n}}var Hs={name:"backwardLinearPrediction",label:"Backward Linear Prediction Filter",domainUpdateRules:hm,apply:Hm,reduce:Om,isApplicable:hs};import Um from"ml-airpls";import{PolynomialRegression as Zm}from"ml-regression-polynomial";import{xyEquallySpaced as Vm}from"ml-spectra-processing";import{CholeskyDecomposition as Pm,Matrix as vs}from"ml-matrix";import{calculateAdaptiveWeights as Fm,xMultiply as jm}from"ml-spectra-processing";function Os(e,n,t){if(n===0)return 1;if(e===0||n>e)return 0;if(n>e-n&&(n=e-n),!t)return xm(e,n);if(t[n]>0)return t[n];let s=1,i=e;for(let o=1;o<=n;o++){if(t[o]>0){i--,s=t[o];continue}s*=i--,s/=o,t[o]=s}return s}function xm(e,n){let t=1,s=e;for(let i=1;i<=n;i++)t*=s--,t/=i;return t}import{Matrix as Sm}from"ml-matrix";function xs(e){let n=e.rows,t=e.columns,s=new Sm(n,n);for(let i=0;i<n;i++)for(let o=0;o<n;o++){let a=0;for(let r=0;r<t;r++)a+=e.get(o,r)*e.get(i,r);s.set(o,i,a)}return s}import{matrixCreateEmpty as vm}from"ml-spectra-processing";function Ss(e,n){let t=e.rows,s=e.columns,i=n.columns;if(n.rows!==t)throw new Error("Matrix dimensions are incompatible for multiplication");let o=vm({nbRows:s,nbColumns:i});for(let a=0;a<s;a++)for(let r=0;r<i;r++){let l=0;for(let m=0;m<t;m++)l+=e.get(m,a)*n.get(m,r);o[a][r]=l}return o}function Ps(e,n,t={}){let{maxIterations:s=100,tolerance:i=1e-6,factorStd:o=3,learningRate:a=.3,minWeight:r=.01}=t,l=new Float64Array(e.length).fill(1),m=e.slice(),c=new Float64Array(e.length),g=0,d=1/0,{logger:u}=t;for(;g<s&&d>i;){let f=Mm(e,{degree:n,weights:l,logger:u});if(!f)return m;l=Fm(e,f,l,{minWeight:r,learningRate:a,factorStd:o}),d=Rm(f,c,e.length),c.set(f),m=f,g++}return m}function Mm(e,n){let{degree:t,weights:s}=n;if(t<0)throw new Error("Degree must be non-negative.");if(e.length===0)return new Float64Array([]);let i=e.length,o=t,a=Math.max(1,i-1),r=new Float64Array(i);for(let c=0;c<i;c++)r[c]=c/a;let l=new Float64Array(o+1);for(let c=0;c<o+1;c++)l[c]=Os(o,c);let m=new vs(o+1,i);for(let c=0;c<i;c++)for(let g=0;g<=o;g++){let d=l[g]*r[c]**g*(1-r[c])**(o-g);m.set(g,c,s[c]*d)}try{let c=new Pm(xs(m));if(!c.isPositiveDefinite())throw new Error("Matrix is not positive definite");let g=jm(e,s),d=vs.from1DArray(i,1,g),u=c.solve(m.mmul(d)),f=Ss(m,u);return s.map((C,y)=>f[y][0]/C)}catch(c){return n.logger&&n.logger.error(c),new Float64Array(e.length)}}function Rm(e,n,t){let s=0;for(let i=0;i<t;i++)s+=(e[i]-(n[i]||0))**2;return Math.sqrt(s/t)}import{xSequentialFillFromStep as wm,xWhittakerSmoother as Nm}from"ml-spectra-processing";function Fs(e,n){let t=e.length;if(t===0)return new Float64Array(0);let s=n??wm({from:0,step:1,size:t}),i=Nm(e);return Am(s,i)}function Am(e,n){let t=e.length;if(t<2)throw new Error("At least 2 points are required for interpolation.");let s=new Float64Array(t-1);for(let u=0;u<t-1;u++)s[u]=e[u+1]-e[u];let i=new Float64Array(t-1);for(let u=0;u<t-1;u++)i[u]=(n[u+1]-n[u])/s[u];let o=t-2,a=new Float64Array(o-1),r=new Float64Array(o),l=new Float64Array(o-1),m=new Float64Array(o);for(let u=0;u<o;u++){let f=u+1;r[u]=2*(s[f-1]+s[f]),m[u]=6*(i[f]-i[f-1]),u>0&&(a[u-1]=s[f-1]),u<o-1&&(l[u]=s[f])}let c=new Float64Array(t).fill(0);if(o>=1){let u=new Float64Array(a),f=new Float64Array(r),C=new Float64Array(l),y=new Float64Array(m);for(let p=1;p<o;p++){let b=u[p-1]/f[p-1];f[p]-=b*C[p-1],y[p]-=b*y[p-1]}c[o]=y[o-1]/f[o-1];for(let p=o-2;p>=0;p--)c[p+1]=(y[p]-C[p]*c[p+2])/f[p]}let g=[];for(let u=0;u<t-1;u++){let f=n[u],C=(n[u+1]-n[u])/s[u]-s[u]*(2*c[u]+c[u+1])/6,y=c[u]/2,p=(c[u+1]-c[u])/(6*s[u]);g.push({a:f,b:C,c:y,d:p})}let d=new Float64Array(e.length);for(let u=0;u<e.length;u++){let f=e[u],C=0;for(;C<t-1&&e[C+1]<f;)C++;f<e[0]?C=0:f>e[t-1]&&(C=t-2);let y=e[C],p=f-y,b=g[C],D=b.a+b.b*p+b.c*p**2+b.d*p**3;d[u]=D}return d}import{DirectConvolution as zm,FFTConvolution as Bm}from"ml-convolution";import{Matrix as Xm}from"ml-matrix";import{xAdd as qm,xWhittakerSmoother as Lm}from"ml-spectra-processing";import{Matrix as km}from"ml-matrix";import{xMean as Im,xStandardDeviation as Tm}from"ml-spectra-processing";function qe(e){let n=[],t=[],{rows:s,columns:i}=e,[o,a]=Em(e);for(;a.length!==t.length;)if(a.length>0){[o,n]=[[],o],[a,t]=[[],a];let c=Im(t),g=Tm(t,{mean:c}),d=c+3*g;for(let u=0;u<t.length;u++)t[u]<=d&&(o.push(n[u]),a.push(t[u]))}else o=n,a=t;let r=km.zeros(s,i);for(let c of o){let g=c/i|0,d=c%i;r.set(g,d,1)}let l=(c,g)=>{let d=js(c,s),u=js(g,i),f=0;for(let C=d.from;C<d.to;C++)for(let y=u.from;y<u.to;y++)r.get(C,y)<1&&(f+=1);return f>0},m=r.clone();for(let c=0;c<s;c++)for(let g=0;g<i;g++)r.get(c,g)>0&&l(c,g)&&m.set(c,g,0);return m}function js(e,n){return{from:Math.max(e-5,0),to:Math.min(e+5,n)}}function Em(e){let n=e.mean()+3*e.standardDeviation(),t=[],s=[],{rows:i,columns:o}=e;for(let a=0;a<i;a++)for(let r=0;r<o;r++){let l=e.get(a,r);l<=n&&(t.push(a*o+r),s.push(l))}return[t,s]}function Rs(e,n){let t=Ym(e,n),s=qe(t).to1DArray(),{lambda:i=150,maxIterations:o=1}=n;return Lm(e,{lambda:i,controlPoints:s,maxIterations:o})}function Ms(e,n,t=1){let s=n.convolve(e),i=[];for(let o of s)i.push(Math.abs(o/t));return i}function Ym(e,n){let t=e.length,{scale:s=11}=n,i=Wm(s),o=s>32?new Bm(t,i):new zm(t,i),a=Ms(e,o,s),r=Ms(a,o,s);return new Xm([qm(a,r)])}function Wm(e){let n=[];for(let t=0;t<e;t++)n.push(1);for(let t=0;t<e;t++)n.push(-1);return n.push(0),n}var Gm={updateXDomain:!1,updateYDomain:!1};function Jm(e,n){if(!ws(e))throw new Error("Baseline correction not applicable on this data");let{algorithm:t}=n,{x:s,re:i}=e.data,o;switch(t){case"airpls":o=Um(s,i,n).corrected;break;case"polynomial":{let{degree:a,zones:r}=n,l=Vm({x:s,y:i},{numberOfPoints:4096,zones:r}),c=new Zm(l.x,l.y,a,{interceptAtZero:!1}).predict(s);o=new Float64Array(s.length);for(let g=0;g<i.length;g++)o[g]=i[g]-c[g]}break;case"whittaker":{let a=Rs(i,n);o=new Float64Array(s.length);for(let r=0;r<i.length;r++)o[r]=i[r]-a[r]}break;case"bernstein":{let{degree:a}=n,r=Ps(i,a,n);o=new Float64Array(s.length);for(let l=0;l<i.length;l++)o[l]=i[l]-r[l]}break;case"cubic":{let a=Fs(i,s);o=new Float64Array(s.length);for(let r=0;r<i.length;r++)o[r]=i[r]-a[r]}break;default:throw new Error(`baselineCorrection: algorithm unknown: ${t}`)}Object.assign(e.data,{re:o})}function ws(e){return!e.info.isFid}function $m(e,n){return{once:!0,reduce:n}}var Ns={name:"baselineCorrection",label:"Baseline correction",domainUpdateRules:Gm,apply:Jm,reduce:$m,isApplicable:ws};var _m={updateXDomain:!0,updateYDomain:!0};function Km(e,n){if(!As(e))throw new Error("Digital filter is not applicable on this data");let{digitalFilterValue:t}=n,s=new Float64Array(e.data.re),i=new Float64Array(e.data.im),o=new Float64Array(s.length),a=new Float64Array(i.length),r=Math.floor(t);o.set(s.slice(r)),a.set(i.slice(r)),e.data.re=o,e.data.im=a}function As(e){return!!(e.info.isComplex&&e.info.isFid)}function Qm(e,n){return{once:!0,reduce:n}}var ks={name:"digitalFilter",label:"Digital Filter",domainUpdateRules:_m,apply:Km,reduce:Qm,isApplicable:As};import{xEnsureFloat64 as At,xyEquallySpaced as Is}from"ml-spectra-processing";var ec={updateXDomain:!1,updateYDomain:!1};function tc(e,n={}){if(!Ts(e))throw new Error("Equally spaced is not applicable on this data");let{from:t,to:s,numberOfPoints:i,exclusions:o}=n,{x:a,re:r,im:l}=e.data,m=Is({x:a,y:r},{from:t,to:s,numberOfPoints:i,exclusions:o});if(e.data.x=At(m.x),e.data.re=At(m.y),l){let c=Is({x:a,y:r},{from:t,to:s,numberOfPoints:i,exclusions:o});e.data.im=At(c.y)}}function Ts(e){return!!(e.info.isComplex&&!e.info.isFid)}function nc(e,n){return{once:!1,reduce:n}}var Es={name:"equallySpaced",label:"Equally spaced",domainUpdateRules:ec,apply:tc,reduce:nc,isApplicable:Ts};import{xySetYValue as zs}from"ml-spectra-processing";var sc={updateXDomain:!1,updateYDomain:!1};function ic(e,n){if(!Bs(e))throw new Error("Exclusion zones filter not applicable on this data");let{x:t,re:s,im:i}=e.data;e.data.re=Float64Array.from(zs({x:t,y:s},{zones:n}).y),e.data.im=i&&Float64Array.from(zs({x:t,y:s},{zones:n}).y)}function Bs(e){return!!e.info.isFt}function oc(e,n){return{once:!0,reduce:ac(e.concat(n))}}var Xs={name:"exclusionZones",label:"Exclusion zones",domainUpdateRules:sc,apply:ic,reduce:oc,isApplicable:Bs};function ac(e=[],n={}){let{from:t=Number.NEGATIVE_INFINITY,to:s=Number.POSITIVE_INFINITY}=n;t>s&&([t,s]=[s,t]),e=e.map(a=>a.from>a.to?{...a,from:a.to,to:a.from}:{...a}),e.sort((a,r)=>a.from!==r.from?a.from-r.from:a.to-r.to);for(let a of e)t>a.from&&(a.from=t),s<a.to&&(a.to=s);if(e=e.filter(a=>a.from<=a.to),e.length===0)return[];let i=e[0],o=[i];for(let a=1;a<e.length;a++){let r=e[a];r.from<=i.to?i.to<r.to&&(i.to=r.to):(i=r,o.push(i))}return o}import{isPowerOfTwo as mc,reimFFT as cc,reimPhaseCorrection as gc,xMean as Ls,xMultiply as dc}from"ml-spectra-processing";var z=Math.PI/180;import{nextPowerOfTwo as rc,xSequentialFillFromStep as lc}from"ml-spectra-processing";function qs(e){let{x:n,re:t,im:s}=e.data,i=rc(n.length),o=new Float64Array(i),a=new Float64Array(i);o.set(t.slice(0,i)),a.set(s.slice(0,i));let r=lc({from:n[0],size:i,step:n[1]-n[0]});e.data={...e.data,re:o,im:a,x:r}}var uc={updateXDomain:!0,updateYDomain:!0};function fc(e){if(!Ys(e))throw new Error("fft not applicable on this data");bc(e);let n=e.filters.some(o=>o.name==="digitalFilter"&&o.enabled),{info:{aqMod:t}}=e;t===1&&yc(e),mc(e.data.x.length)||qs(e);let{data:s,info:i}=e;if(Object.assign(s,cc({re:s.re,im:i.reverse?dc(s.im,-1):s.im},{applyZeroShift:!0})),n){let{digitalFilter:o=0}=i,a=Math.floor(o),r=(o-a)*Math.PI*2,l=a%2?180*z:0;Object.assign(s,gc(s,l,-r,{reverse:!0}))}e.data.x=Cc(e),e.info={...e.info,isFid:!1,isFt:!0}}function Ys(e){return!!(e.info.isComplex&&e.info.isFid)}function pc(e,n){return{once:!0,reduce:n}}function Cc(e){let n=e.info,t=Number(n.baseFrequency),s=Number(n.frequencyOffset),i=Number(n.spectralWidth),o=s/t,a=.5*i,r=e.data.x.length,l=o-a,m=i/(r-1),c=new Float64Array(r);for(let g=0;g<r;g++)c[g]=l,l+=m;return c}function yc(e){let n=e.data,t=n.re.length,s=new Float64Array(n.re),i=new Float64Array(n.im),o=Ls(n.re.slice(t*.75>>0,t)),a=Ls(n.im.slice(t*.75>>0,t));for(let r=0;r<t;r++)s[r]-=o,i[r]-=a;return Object.assign(e.data,{re:s,im:i}),e}function bc(e){let{data:n}=e;if(n.x.length!==n.re.length||n.x.length!==n.im.length)throw new Error("The length of data should be equal")}var Ws={name:"fft",label:"FFT",domainUpdateRules:uc,apply:fc,reduce:pc,isApplicable:Ys};import{xSequentialFillFromStep as Hc}from"ml-spectra-processing";import{Matrix as Dc,SVD as hc}from"ml-matrix";function Us(e,n){let{nbCoefficients:t,nbInputs:s,nbPoints:i}=n;if(e.length<s+t+i)throw new RangeError("data length should be bigger than nbInputs + nbCoefficients + nbPoints");let o=e.length-i-2,a=[];for(let g=0;g<s;g++){let d=new Float64Array(t);for(let u=0;u<t;u++)d[u]=e[o-g-u];a.push(d)}let r=new hc(a),l=new Float64Array(s);for(let g=0;g<s;g++)l[g]=e[o-g+1];let m=r.solve(Dc.from1DArray(l.length,1,l)).to1DArray(),{output:c=Float64Array.from(e)}=n;for(let g=0;g<i;g++){let d=0;for(let u=0;u<m.length;u++)d+=m[u]*c[o+1+g-u];c[o+g+2]=d}return{output:c,predicted:c.slice(o+2)}}function le(e,n){let{re:t,im:s}=e,{nbCoefficients:i,nbPoints:o,nbInputs:a=t.length}=n,r=Math.abs(o),l=o<0?r:0,m=2*Math.ceil((a+r+i)/2);if(t.length<m-l)throw new RangeError(`The sum of nbPoints, nbInputs and nbCoefficients should be less than data length (${t.length})`);let c=new Float64Array(2*m),g=t.length-m+l;for(let f=0;f<m-l;f++)c.set([t[g+f],s[g+f]],2*f);Us(c,{nbInputs:a*2,nbCoefficients:i,nbPoints:r*2,output:c});let d=new Float64Array(t.length+l),u=new Float64Array(l+s.length);o<0?(d.set(t),u.set(s)):(d.set(t.slice(0,t.length-o)),u.set(s.slice(0,s.length-o)));for(let f=0;f<2*r;f+=2)d[d.length-1-(f>>1)]=c[c.length-2-f],u[d.length-1-(f>>1)]=c[c.length-1-f];return{re:d,im:u}}function me(e,n,t){let s=2*e,i=2*n;if(t===0){if(s<n)return 0;if(n<s&&s<i)return n;if(i<s)return t-n}return n<t?t-n:0}var Oc={updateXDomain:!0,updateYDomain:!0};function xc(e,n={}){if(!Zs(e))throw new Error("Digital filter is not applicable on this data");let{info:t,data:{re:s,im:i}}=e,{lpNumberOfCoefficients:o=0,linearPredictionBin:a=0,spectrumSize:r=s.length,numberOfPoints:l=s.length}=t,{nbPoints:m=me(r,l,a)/-2,nbCoefficients:c=o,nbInputs:g=Math.floor(s.length-m-c)}=n,d=e.filters.find(y=>y.name==="forwardLinearPrediction");d&&(d.value={nbCoefficients:c,nbPoints:m,nbInputs:g});let{re:u,im:f}=le({re:s,im:i},{nbCoefficients:c,nbInputs:g,nbPoints:m}),{data:{x:C}}=e;Object.assign(e.data,{re:u,im:f,x:m<0?Hc({from:0,size:u.length,step:C[1]-C[0]}):C})}function Zs(e){return!!(e.info.isComplex&&e.info.isFid)}function Sc(e,n){return{once:!0,reduce:n}}var Vs={name:"forwardLinearPrediction",label:"Forward Linear Prediction Filter",domainUpdateRules:Oc,apply:xc,reduce:Sc,isApplicable:Zs};import{reimAbsolute as vc,reimAutoPhaseCorrection as Pc,reimPhaseCorrection as Fc,xEnsureFloat64 as Gs}from"ml-spectra-processing";var jc={updateXDomain:!1,updateYDomain:!1};function Mc(e,n={}){if(!_s(e))throw new Error("Phase correction not applicable on this data");let{absolute:t=!1}=n,s=e.filters?.find(i=>i.name==="phaseCorrection");if(t){let{re:i,im:o}=e.data;e.data.re=vc({re:i,im:o}),e.data.im=void 0,s&&(s.value={...s.value,ph0:0,ph1:0,absolute:t})}else if("ph0"in n&&"ph1"in n){let{ph0:i=0,ph1:o=0}=n;Js(e,{ph0:i,ph1:o}),s&&(s.value={...s.value,absolute:t})}else{let i=$s(e);if(i.ph0===0&&i.ph1===0&&(i=$s(e,{magnitudeMode:!0})),Js(e,i),s){let{ph0:o,ph1:a}=i;s.value={...s.value,absolute:t,ph0:o,ph1:a}}}}function Js(e,n){let{ph0:t,ph1:s}=n,{re:i,im:o}=e.data,a=Fc({re:i,im:o},t*Math.PI/180,s*Math.PI/180,{reverse:!0});e.data={...e.data,re:Gs(a.re),im:Gs(a.im)}}function $s(e,n={}){let{minRegSize:t=5,maxDistanceToJoin:s=128,magnitudeMode:i=!1,factorNoise:o=5,reverse:a=!0}=n;return Pc(e.data,{minRegSize:t,maxDistanceToJoin:s,magnitudeMode:i,factorNoise:o,reverse:a})}function _s(e){return!!(e.info.isComplex&&!e.info.isFid)}function Rc(e,n){return{once:!0,reduce:n}}var Ks={name:"phaseCorrection",label:"Phase 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0||r.from>a.to?(a={id:crypto.randomUUID(),from:r.from,to:r.to,integration:r.original.nbAtoms,signals:[r.original]},o.push(a)):(a.integration+=r.original.nbAtoms,r.to>a.to&&(a.to=r.to),a.signals.push(r.original));return o}import{gyromagneticRatio as ha}from"gyromagnetic-ratio";function F8(e){if(e in ha)return e;if(e.toLowerCase()==="proton")return"1H";let n=e.replaceAll(/[^0-9]/g,"");if(!n)return e;for(let t in ha)if(t.includes(n))return t;return e}function w8(e,n={}){let{logger:t}=n,s={info:{dimension:1},ranges:[],acsString:e,normalized:e.replace(/\.\s*$/,"").replaceAll(/[\r\n\t]/g," ").replaceAll(/[;:]/g,",").replaceAll("}",")").replaceAll("{","(").replaceAll(/[\u2011\u2012\u2013\u2014\u2015\u2212]/g,"-")};return tu(s),Qd(s,n),t?.info(`Found: ${s.ranges.length} ranges`),s}function Qd(e,n={}){let{logger:t}=n;for(let s of e.parts)if(s.toLowerCase().includes("nmr"))eu(e,s);else{e.info.frequency||(e.info.frequency=400,t?.warn("Frequency not defined, assuming 400 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a=0;a<s.length;a++)s[a]=s[a].replace(/ *[,;]+$/,"").replaceAll(/  +/g," ").trim();e.parts=s}import{Matrix as nu,SVD as su}from"ml-matrix";function k8(e,n){let{nbCoefficients:t,nbInputs:s,nbPoints:i}=n;if(e.length<s+t+i)throw new RangeError("data length should be bigger than nbInputs + nbCoefficients + nbPoints");let o=[];for(let c=0;c<s;c++){let g=new Float64Array(t);for(let d=0;d<t;d++)g[d]=e[c+d+i+1];o.push(g)}let a=new su(o),r=new Float64Array(s);for(let c=0;c<s;c++)r[c]=e[c+i];let l=a.solve(nu.from1DArray(r.length,1,r)).to1DArray(),{output:m=Float64Array.from(e)}=n;for(let c=0;c<i;c++){let g=0;for(let d=0;d<l.length;d++)g+=l[d]*m[d+i-c];m[i-c-1]=g}return{output:m,predicted:m.slice(0,i)}}import{reimPhaseCorrection as Oa,xMinValue as iu,xSubtract as Ha}from"ml-spectra-processing";import{analyseMultiplet as ou}from"multiplet-analysis";var au={minimalResolution:.1,critFoundJ:.75,maxTestedJ:17,minTestedJ:1,takeBestPartMultiplet:!0,correctVerticalOffset:!0,symmetrizeEachStep:!1,decreasingJvalues:!0,makeShortCutForSpeed:!0};function z8(e,n={}){let{x:t}=e,{re:s,im:i}=structuredClone(e),{autoPhase:o,analyzer:a={}}=n;if(o&&i){let r=iu(s);r>0&&(s=Ha(s,r),i&&(i=Ha(i,r)));let l=ru(s,i);s=Oa({re:s,im:i},xa(l),0).re}return ou({x:t,y:s},{...au,...a})}function ru(e,n){let t=-180,s=180,i=6,o=10,a=0,r=Number.MAX_SAFE_INTEGER;for(;o>0;){let l=(s-t)/(i+1);for(let m=t;m<=s;m+=l){let c=Oa({re:e,im:n},xa(m),0),g=lu(c.re);g<r&&([r,a]=[g,m])}t=a-l,s=a+l,o--}return a}function xa(e){return e*Math.PI/180}function lu(e){let n=0;for(let t of e)t<0&&(n-=t);return n}import{gsd as mu,joinBroadPeaks as cu,optimizePeaks as gu,setShape as du}from"ml-gsd";import{savitzkyGolay as uu}from"ml-signal-processing";import{xAbsoluteMedian as fu,xMaxAbsoluteValue as Pa,xNoiseSanPlot as pu,xWhittakerSmoother as Cu,xyExtract as yu}from"ml-spectra-processing";function rt(e,n){return tt(e,{...n,convertTo:"hz"})}function $(e,n){let{from:t,to:s,frequency:i,noiseLevel:o,thresholdFactor:a=3,minMaxRatio:r=.05,broadRatio:l=25e-5,useSanPlot:m=!1,smoothY:c=!0,optimize:g=!1,groupingFactor:d=2,factorLimits:u=2,realTopDetection:f=!0,shape:C={kind:"gaussian"},optimization:y={kind:"lm"},broadWidth:p=.25,sgOptions:b={},direction:D="positive",peakDetectionAlgorithm:h="auto",sensitivity:O=100}=n,S=1/i/(e.x[1]-e.x[0]),x=Math.max(Math.round(S/2),5),{windowSize:H=x-x%2+1,polynomial:v=3}=b;if(!H)throw new Zt({windowSize:H,ws:x,pointsPerHz:S,frequency:i,x:e.x.slice(0,2),sgOptions:b,autoWindowSizeFormula:"ws - (ws % 2) + 1",pointsPerHzFormula:"1 / frequency / (x[1] - x[0])"});if(e.x.length<H)return[];let P,{maxAbsDdY:M}=n;if(t!==void 0&&s!==void 0){if(!("maxAbsDdY"in n)){let j=uu(e,{windowSize:H,polynomial:v,derivative:2});M=Pa(j.data.y)}P=yu(e,{zones:[{from:t,to:s}]})}else P=e;hu(O);let F=O!==100?Cu(P.y,{lambda:50.1-O/2,maxIterations:1}):P.y,R=Du(P.y,{noiseLevel:o,useSanPlot:m,thresholdFactor:a}),w={shape:C,smoothedY:F,maxAbsDdY:M,frequency:i,broadWidth:p,optimize:g,factorLimits:u,groupingFactor:d,maxCriteria:!0,peakDetectionAlgorithm:h,sgOptions:{windowSize:H,polynomial:v},minMaxRatio:r,broadRatio:l,noiseLevel:R.positive,smoothY:c,optimization:y,realTopDetection:f};switch(D){case"positive":return Ut(P,w);case"negative":return Sa(P,R,w);case"both":return[...Ut(P,w),...Sa(P,R,w)];default:{let j=D;throw new Error(`Unknown distribution ${j}`)}}}function Sa(e,n,t){return t.noiseLevel=n.negative,t.maxCriteria=!1,Ut(e,t)}function Ut(e,n){let{shape:t,maxAbsDdY:s,smoothedY:i,frequency:o,broadWidth:a,optimize:r,maxCriteria:l,groupingFactor:m,factorLimits:c,sgOptions:g,minMaxRatio:d,broadRatio:u,noiseLevel:f,smoothY:C,optimization:y,realTopDetection:p,peakDetectionAlgorithm:b}=n,D=mu({...e,y:i},{sgOptions:g,maxCriteria:l,minMaxRatio:d,noiseLevel:f,smoothY:C,realTopDetection:p,peakDetectionAlgorithm:b}),h=du(D,{output:D,shape:t}),O=a?cu(h,{shape:t,broadWidth:a,optimization:y,broadRatio:bu(D,{maxAbsDdY:s,broadRatio:u})}).map(Wt):h.map(Wt);return rt(r?gu(e,O,{shape:t,groupingFactor:m,factorLimits:c,optimization:y}).map(Wt):O,{frequency:o})}function bu(e,n={}){let{maxAbsDdY:t,broadRatio:s=.0025}=n;if(t&&e.length>0){let i=Pa(e.map(o=>o.ddY));return s*t/i}return s}function va(e){return{positive:e,negative:-e}}function Du(e,n){let{noiseLevel:t,useSanPlot:s,thresholdFactor:i}=n;return t?va(t):s?pu(e,{factorStd:i}):va(fu(e)*i)}function Wt(e){let{id:n,shape:t,x:s,y:i,width:o}=e;return{id:n,x:s,y:i,width:o,shape:t}}var Zt=class extends Error{data;constructor(n){super("windowSize must be an odd integer >= 5, check data property of this error for contextual information"),this.data=n}};function hu(e){if(e<1||e>100)throw new RangeError("The value of sensitivity should lie between (1, 100)")}import{xGetFromToIndex as Uu,xyMaxYPoint as Zu}from"ml-spectra-processing";function Fa(e){e.sort((n,t)=>n.from-t.from);for(let n=0;n<e.length-1;n++){let t=e[n],s=e[n+1];t.to>s.from&&(t.id=crypto.randomUUID(),t.to=Math.max(s.to,t.to),t.signals&&s.signals&&(t.signals=t.signals.concat(s.signals)),t.integration!==void 0&&(t.integration+=s.integration||0),e.splice(n+1,1),n--)}return e}var lt=["s","d","t","q","quint","h","sept","o","n"];var Hu={jAxis:"x",intensity:"intensity"};function Ou(e){if(!("symRank"in e))throw new Error("Internal error, symRank was not calculated");if(!("mask"in e))throw new Error("Internal Error, mask was not added")}var wa={compilePattern:(e,n={})=>{let{jAxisKey:t=Hu,symRatio:s=2.5}=n,i=ju(e,{...n,symRatio:s,maxError:2.5,iteration:1,jAxisKey:t});if(i.multiplicity="m",i.asymmetric=!0,Ou(i),i.symRank>=.95&&i.peaksComp.length<32){i.asymmetric=!1;let o,a,r,l=1,m=[];for(let c=0;c<9;c++){let g=Mu(i,c),d=!1;if(g.length===1&&c===0)d=!0;else if(g.length<=1)continue;let u=Fu(g);a=2**c;let f=null,C=1;for(;!d&&(f=Pu(u,a))!==null&&C<400;){let y=new Array(f.length);l=1;for(let h=0;h<f.length;h++){y[h]=new Array(f[h]);for(let O=0;O<f[h];O++)y[h][O]=l++}m=[];let p=1;m.push(g[1].x-g[0].x),o=g[0].x,y[0].splice(0,1),y[1].splice(0,1),l=1;let b=2;for(r=2**c-1;m.length<c&&b<r&&l<g.length;){for(C+=1,p++;l<g.length&&y[l].length===0;)l++;if(l<g.length){m.push(g[l].x-g[0].x),y[l].splice(0,1),b++;for(let h=2;h<=p;h++){let O=0;for(let S=0;S<h;S++)O+=m[S];for(let S=1;S<y.length;S++)if(Math.abs(g[S].x-(o+O))<.25){y[S].splice(0,1),b++;break}}}}let D=vu(m);d=!0;for(let 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ye(e,n,t={}){let{solvent:s,symRatio:i=1.5,integrationSum:o=100,joinOverlapRanges:a=!0,clean:r=.4,compile:l=!1,integralType:m="sum",frequency:c=400,frequencyCluster:g=16,keepPeaks:d=!1,nucleus:u="1H"}=t,f={solvent:s,integrationSum:o,integralType:m,frequencyCluster:g,frequency:c,nucleus:u};if(n.length===0)return[];e.x[0]>e.x[1]&&(e.x=e.x.toReversed(),e.y=e.y.toReversed());let{peaks:C,solventSignals:y}=wu(e,n,f),p=te(e,C,f);if(r)for(let D=0;D<p.length;D++)Math.abs(p[D].integralData.value)<r&&p.splice(D,1);if(l){let D,h;for(let O=0;O<p.length;O++){p[O]=wa.compilePattern(p[O],{symRatio:i});let S=p[O];if(S.maskPattern&&S.multiplicity!=="m"&&S.multiplicity!==""){Ru(S),D=0,h=0;let x=[];for(let H=S.maskPattern.length-1;H>=0;H--)if(h+=Se(S.peaks[H],c),!S.maskPattern[H]){let v=S.peaks.splice(H,1)[0];x.push({x:v.x,y:v.intensity,width:v.width}),S.mask.splice(H,1),S.mask2.splice(H,1),S.maskPattern.splice(H,1),S.nbPeaks--,D+=Se(v,c)}if(x.length>0){D=D*S.integralData.value/h,S.integralData.value-=D;let H=[];for(let P=x.length-1;P>=0;P--)H.push(x[P]);f.integrationSum=Math.abs(D);let v=te(e,H,f);for(let P of v)p.push(P)}}}st(p,o)}if(p.push(...y),p.sort((D,h)=>D.delta-h.delta),r)for(let D=p.length-1;D>=0;D--)Math.abs(p[D].integralData.value)<r&&p.splice(D,1);let b=[];for(let D=0;D<p.length;D++){let h=p[D],O={id:crypto.randomUUID(),from:h.integralData.from,to:h.integralData.to,integration:h.integralData.value},S={delta:h.delta,kind:h.kind||"signal",multiplicity:h.multiplicity,assignment:h.assignment};d&&(S.peaks=h.peaks.map(x=>{let{intensity:H,...v}=x;return{y:H,...v}})),h.nmrJs&&(S.js=h.nmrJs),O.signals=[S],b[D]=O}return a&&(b=Fa(b)),b}function wu(e,n,t){let s=[],i=[];for(let c of 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Na=[{names:["CD2Cl2"],smiles:"[2H]C([2H])(Cl)Cl",ranges:[{signals:[{delta:53.5,assignment:"CD2",js:[{spin:1,nbCouplings:2,coupling:27.6}]}],from:53.73,to:54.73}],nucleus:"13C",solvent:"cd2cl2"},{names:["CDCl3"],smiles:"[2H]C(Cl)(Cl)Cl",ranges:[{signals:[{delta:77,assignment:"CD",js:[{spin:1,nbCouplings:1,coupling:32.2}]}],from:76.58,to:77.45}],nucleus:"13C",solvent:"cdcl3"},{names:["DMSO-d6"],smiles:"C([2H])([2H])([2H])S(=O)C([2H])([2H])[2H]",ranges:[{signals:[{delta:40,assignment:"CD3",js:[{spin:1,nbCouplings:3,coupling:21}]}],from:39.15,to:40.78}],nucleus:"13C",solvent:"dmso"},{names:["C6H6","Benzene"],smiles:"",ranges:[{signals:[{delta:127.7,assignment:"CD",js:[{spin:1,nbCouplings:1,coupling:24.26}]}],from:127.45,to:127.92}],nucleus:"13C",solvent:"c6h6"}];function Au(e,n){let{frequency:t,solventFeatures:s,tolerance:i=.1,minScore:o=.99}=n,{delta:a,js:r}=s.ranges[0].signals[0],l=Bu(r[0],t),m=e.map(Tu),c=Iu(m,l,{delta:a,minScore:o,tolerance:i});if(c.length>0)for(let g of 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P7(e,n){let{from:t,to:s}=n.peakPicking,{fromIndex:i,toIndex:o}=Uu(e.x,{from:t,to:s}),a=n.peakPicking.sgOptions?.windowSize??7;if(o-i<=a)return n.logger?.info("Too small window for accurate multiplicity determination"),[{from:e.x[i],to:e.x[o],signals:[{delta:Zu(e,{fromIndex:i,toIndex:o}).x,multiplicity:"",js:[]}]}];let{ranges:r={}}=n,{nucleus:l=""}=r;switch(l){case"1H":return Ea(e,n);case"13C":return ka(e,n);default:return Ia(e,n)}}import{BaseRegression as Vu}from"ml-regression-base";import{SimpleLinearRegression as Gu}from"ml-regression-simple-linear";import{xyCheck as Ju}from"ml-spectra-processing";function w7(e,n){Ju(e,{minLength:2});let{x:t,y:s}=e,{gyromagneticRatio:i,gradientPulseDuration:o,timeCorrection:a}=n,r=new Float64Array(t.length),l=new Float64Array(t.length);for(let f=0;f<t.length;f++)r[f]=Math.log(s[f]),l[f]=t[f]**2;let m=new Gu(l,r),{slope:c,intercept:g}=m.toJSON(),d=-c/a/(i*o)**2,u=Math.exp(g);return{regression:new Jt(d,u,n),coefficient:d,signalAbsenseDiffussion:u}}var 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XYAutoPeaksPickingWindowSizeError,Rt as apodizationXReIm,E as apodize,Rn as calculateRelativeFrequency,FC as carbonImpurities,It as checkIntegralKind,j6 as checkMultiplicity,Ee as couplingACSPatterns,jt as couplingPatterns,ne as createApodizationWindowData,gm as default1DApodization,Q as ensureValidSignalKind,Ui as fftDirectDimension,Qi as fftIndirectDimension,Go as findMultiplet,ia as findPivot,up as get13CAssignments,Le as get1DErrorFactor,mp as get1HAssignments,Yo as get2DErrorFactor,Jp as getAssignments,A2 as getBaselineZones,U2 as getBaselineZonesByDietrich,BC as getDatabase,F1 as getFrequency,Tt as getPeakDelta,Oe as getRelativeFrequency,ge as getShiftX,oa as isEmptyMolecule,cb as isMolfileNotEmpty,ci as isRangeExists,Wo as isZoneExists,gi as mapIntegrals,di as mapPeaks,fi as mapRanges,Zo as mapZones,Hb as markSolventPeaks,h6 as matrixToBoxPlot,v6 as matrixToStocsy,F8 as normalizeNucleus,g8 as optimizeSignals,vC as parseCT,Z6 as peakToXY,_o as peaksToFID,$o as peaksToXY,W as predict,Z1 as predictSpectra,ls as protonImpurities,ze as rangeFromSignal,Ab as rangesToACS,Ib as rangesToTSV,Xb as rangesToXY,re as reimComplexBackwardLinearPrediction,w8 as resurrect,ot as signalJoinCouplings,Xl as signalKindLabelMapping,Te as signalKindsToInclude,Ze as signalMultiplicityPattern,Mn as signals2DToZ,p8 as signalsJoin,H8 as signalsToFID,S8 as signalsToRanges,Ae as signalsToXY,vn as simulate1D,na as solventSuppression,ae as splitPatterns,A6 as translateMultiplet,pi as updateIntegralsRelativeValues,bi as updateRanges,yi as updateRangesRelativeValues,k8 as xBackwardLinearPrediction,Us as xForwardLinearPrediction,z8 as xreimMultipletAnalysis,$ as xyAutoPeaksPicking,P7 as xyAutoRangesPicking,w7 as xyCalculateDiffussionCoefficient,T7 as xyCalculateT1,J7 as xyGetPivot,X7 as xyKineticFirstOrder,U7 as xyPeaksOptimization,vo as xyzAutoPhaseCorrection,Ga as xyzAutoSignalsPicking,uD as xyzAutoZonesPicking,Lt as xyzPhaseCorrection};