nmr-processing 22.2.0 → 22.3.0

package/dist/nmr-processing.js

@@ -1,2 +1,2 @@
-var dr=Object.defineProperty;var pt=(e,n)=>{for(var t in n)dr(e,t,{get:n[t],enumerable:!0})};export*from"gyromagnetic-ratio";import{xEnsureFloat64 as ur}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 ur(s)}import{xDivide as fr,xMaxValue as pr}from"ml-spectra-processing";function Qt(e,n){let t=new Float64Array(n);for(let s=0;s<n;s++)t[s]=e(s);return t}function en(e,n){let{dw:t}=n,{lineBroadening:s}=e,i=-s*Math.PI*t;return o=>Math.exp(i*o)}function tn(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 nn(e,n){return Ct({exponent:1,...e},n)}function Ct(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 sn(e,n){return Ct({...e,exponent:2},n)}function on(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 an(e,n){let{kind:t,options:s}=e;switch(t){case"exponential":return en(s,n);case"gaussian":return tn(s,n);case"sineBell":return nn(s,n);case"sineSquare":return sn(s,n);case"traf":return on(s,n);default:throw new Error(`Unknown distribution ${t}`)}}function ne(e){let{shapes:n,windowOptions:t}=e,s=new Float64Array(t.length).fill(1);for(let[i,o]of Object.entries(n)){let{options:a,apply:r=!0}=o;if(!r)continue;let l=Qt(an({kind:i,options:a},t),t.length);E(s,{windowData:l,output:s})}return fr(s,pr(s),{output:s})}import{TopicMolecule as Fr}from"openchemlib-utils";import{Molecule as vr}from"openchemlib";import{agnes as yr}from"ml-hclust";import{Matrix as br}from"ml-matrix";import{Molecule as mn}from"openchemlib";function rn(e,n={}){let t=n.output||structuredClone(e);for(let s of t)s.id=crypto.randomUUID();return t}var Cr={h:"1H",c:"13C"};function ln(e){return Object.values(e).map(n=>Cr[n.toLowerCase()])}function Dr(e){if(!e.from||!e.to)throw new Error("options from and to are mandatory")}async function se(e,n){Dr(n);let{from:t,to:s,minLength:i=0,maxLength:o,predictions:a,includeDiagonal:r=!1}=n,l={...n.joinDistance,H:.05,C:.5},{correlationPaths:m=hr(e,{fromLabel:t,toLabel:s,minLength:i,maxLength:o})}=n,c=e.getGroupedDiastereotopicAtomIDs()||[],g=[];for(let D of c||[])g.push({...D,pathInfo:structuredClone(m[D.atoms[0]])});let d=a[s],u=a[t];if(!u||!d)throw new Error("predictions are not availaible");let f={x:u,y:d},C={x:{},y:{}};for(let D in C)for(let h of f[D].joinedSignals){if(!h.diaIDs)throw new Error("Signal has not diaIDs");C[D][h.diaIDs[0]]=h}let y={};for(let D of g){let h=D.pathInfo;if(h.paths.length===0||!C.x[h.oclID])continue;let O=h.paths;for(let S of O){if(!C.y[m[S.to].oclID])continue;let x={x:h,y:m[S.to]},H=`${x.x.oclID}-${x.y.oclID}`;if(H===`${h.oclID}-${h.oclID}`||y[H])continue;let v={id:crypto.randomUUID(),x:0,y:0,z:100},P={id:crypto.randomUUID(),x:{delta:0,diaIDs:[],atoms:[]},y:{delta:0,diaIDs:[],atoms:[]},peaks:[]};for(let M of["x","y"]){let F=x[M].oclID;v[M]=C[M][F].delta,P[M].delta=C[M][F].delta,P[M].diaIDs=[F];let{atoms:w}=C[M][F];w&&(P[M].atoms=w)}P.peaks=[v],y[H]=P}}r&&Or(y,{paths:m,signalsByDiaID:C});let p=Object.values(y),b=xr(p,{joinDistance:l,from:t,to:s});return{nuclei:ln({from:t,to:s}),joinedSignals:p,signals:Hr(p),zones:b}}function hr(e,n){let{fromLabel:t,toLabel:s,minLength:i,maxLength:o=Number.MAX_SAFE_INTEGER}=n,a=e.diaIDs,r=e.moleculeWithH,l=e.distanceMatrix,m=mn.getAtomicNoFromLabel(t),c=mn.getAtomicNoFromLabel(s),g=[];for(let d=0;d<r.getAllAtoms();d++){let u={oclID:a[d],paths:[]};for(let f=0;f<r.getAllAtoms();f++){if(d===f||r.getAtomicNo(f)!==c||r.getAtomicNo(d)!==m)continue;let C=l[d][f];C>=i&&C<=o&&u.paths.push({from:d,to:f})}g.push(u)}return g}function Hr(e){let n=[];for(let t of e)for(let s of t.x.atoms||[])for(let i of t.y.atoms||[]){let o=structuredClone(t);o.x.atoms=[s],o.y.atoms=[i],n.push(o)}return rn(n)}function Or(e,n){let{paths:t=[],signalsByDiaID:s}=n;for(let i of t){let o=i.oclID;if(!s.x[o]||e[`${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 xr(e,n){if(e.length===0)return[];let{joinDistance:t,from:s,to:i}=n,o=new br(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)),g=yr(o.to2DArray(),{method:"centroid"}),d=cn([g],c),u=[];for(let f of d){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(),...Sr(C,{joinDistance:t,from:s,to:i}),signals:C})}return u}function Sr(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 cn(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?cn(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=Pr(e,i,a)),se(e,r)}function Pr(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 g of m.js){if(!g.diaIDs||g.diaIDs.length===0)throw new Error("should contains assigned coupling by atoms");let d=g.diaIDs[0];o[c][d]=Math.max(g.coupling,o[c][d]??Number.MIN_SAFE_INTEGER)}}let r=e.moleculeWithH,l=vr.getAtomicNoFromLabel("H");for(let m=0;m<r.getAllAtoms();m++){let c={oclID:s[m],paths:[]};for(let g=0;g<r.getAllAtoms();g++)m!==g&&r.getAtomicNo(g)===l&&r.getAtomicNo(m)===l&&o[s[m]]?.[s[g]]>=t&&c.paths.push({from:m,to:g});i.push(c)}return i}function dn(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 un=dn("proton","https://nmr-prediction.service.zakodium.com/v1/predict/proton"),fn=dn("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 pn(e,n={}){let{predictor:t=fn,predictorOptions:s={},cache:i}=n;return e.molecule.getAllAtoms()===0?{nucleus:"13C",joinedSignals:[],signals:[],ranges:[]}:Me(e,t,{cache:i,predictorOptions:s})}async function Cn(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 yn(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 bn(e,n={}){let{predictor:t=un,cache:s,predictorOptions:i={}}=n;return e.molecule.getAllAtoms()===0?{nucleus:"1H",joinedSignals:[],signals:[],ranges:[]}:Me(e,t,{cache:s,predictorOptions:i})}function yt(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 jr={cosy:{predictor:gn,required:["H"],message:"Proton prediction is missing so COSY could not be generated."},hsqc:{predictor:yn,required:["H","C"],message:"Carbon and / or proton prediction is missing so HSQC could not be generated."},hmbc:{predictor:Cn,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 Fr(e),a=yt("H",i)?await bn(o,{...i?.H}):void 0,r=yt("C",i)?await pn(o,i?.C):void 0,l={},m=o.diaIDs,c={};Dn(a,m)&&(c.H=a,"H"in i&&(l.proton=a)),Dn(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}=jr[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 Dn(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 tl,xRescale as nl,xSequentialFillFromTo as sl}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 bt={};for(let{value:e,multiplicity:n,names:t}of _){n&&(bt[e]=n-1);for(let s of t)n&&(bt[s]=n-1)}var q=bt;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}=Mr(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 Mr(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(wr(m,[t],n));o.push(...c)}else o.push(a);return o},[]),tempSignals:s}}function wr(e,n,t){return{delta:1e5,atoms:n,js:[{coupling:e,atoms:t}]}}import{Matrix as Ar}from"ml-matrix";import{Matrix as Dt}from"ml-matrix";import{simpleClustering as Rr}from"ml-simple-clustering";function L(e){let{couplingConstants:n,connectivity:t}=e,s=Dt.checkMatrix(n),i=t?Dt.checkMatrix(t):Nr(s),{levels:o=Array.from({length:i.rows},()=>2),clusters:a=Rr(i.to2DArray(),{out:"indexes"})}=e;return{...e,levels:o,clusters:a,connectivity:i,couplingConstants:s}}function Nr(e){let n=Dt.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 kr(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){kr(e);let n=e.length,t=[],s=Ar.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 $r}from"spectrum-generator";import Br from"binary-search";import{EVD as Xr,Matrix as qr}from"ml-matrix";import{SparseMatrix as Re}from"ml-sparse-matrix";import{SparseMatrix as Ir}from"ml-sparse-matrix";function hn(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=2*i*n;for(let r=0;r<n;r++)s.set(o+n+r,a+r,1)}return s}import{SparseMatrix as Tr}from"ml-sparse-matrix";function ht(e,n){let t=2*e*n,s=new Tr(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 Er}from"ml-sparse-matrix";function Ht(e,n){let t=2*e*n,s=new Er(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 zr}from"ml-sparse-matrix";function we(e,n){let t=2*e*n,s=new zr(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 Ot=.01;function Hn(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=Yr(a,o.couplingConstants,r,o.connectivity,c),p=y.rows,b=new Xr(y),D=b.eigenvectorMatrix,h=b.realEigenvalues,O=new Re(p,p),S=m.length;g=0;for(let F=0;F<S;F++){let w={rows:2**F},R={rows:2**(S-F-1)},j=hn(w.rows,R.rows);m[F]>=0?(O.add(j.mul(m[F]+1)),g++):O.add(j.mul(m[F]))}let x=qr.zeros(p,p);O.forEachNonZero((F,w,R)=>{if(R>0)for(let j=0;j<D.columns;j++){let N=D.get(w,j);N!==0&&x.set(F,j,x.get(F,j)+N)}return R});let H=x.clone();O.forEachNonZero((F,w,R)=>{if(R<0)for(let j=0;j<D.columns;j++){let N=D.get(w,j);N!==0&&H.set(F,j,H.get(F,j)+N)}return R});let v=D.transpose();x=v.mmul(x);let P=new Re(x.to2DArray(),{threshold:Ot});H=v.mmul(H);let M=new Re(H.to2DArray(),{threshold:Ot});M.forEachNonZero((F,w,R)=>R),Lr(M,Ot),M.forEachNonZero((F,w,R)=>{let j=P.get(F,w);j=Math.min(Math.abs(j),Math.abs(R)),j*=j,d+=j;let N=h[F]-h[w],A=Br(u,N,(k,X)=>k-X);return A<0?(u.splice(-1-A,0,N),f.splice(-1-A,0,j)):f[A]+=j,R})}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 Lr(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function Yr(e,n,t,s,i){let o=1;for(let r of i)o*=t[r];let a=new Re(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=we(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(Ht(m.rows,c.rows).mul(-1).mmul(Ht(C.rows,y.rows))),p.add(we(m.rows,c.rows).mmul(we(C.rows,y.rows))),a.add(p.mul(n.get(l,f)/2))}}}return a}import Zr from"binary-search";import{EVD as Vr,Matrix as Gr}from"ml-matrix";import{SparseMatrix as Y}from"ml-sparse-matrix";import{SparseMatrix as Wr}from"ml-sparse-matrix";function On(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=xt(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=xt(s,-1,e,e),a=i.clone().add(o).mul(.5),r=o.clone().mul(-1).add(i).mul(-.5),l=xt(t,0,e,e);return{x:a,y:r,z:l,m:o,p:i}}function xt(e,n,t,s){let i=new Wr(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 Ur=On(2);function He(e){return e===2?Ur:On(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=Jr(a,o.couplingConstants,r,o.connectivity,c),p=y.rows,b=new Vr(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 w=He(r[c[F]]),R=1;for(let k=0;k<F;k++)R*=r[c[k]];let j=Y.eye(R);R=1;for(let k=F+1;k<S;k++)R*=r[c[k]];let N=Y.eye(R),A=j.kroneckerProduct(w.m).kroneckerProduct(N);m[F]>=0?(O.add(A.mul(m[F]+1)),g++):O.add(A.mul(m[F]))}let x=Gr.zeros(p,p);O.forEachNonZero((F,w,R)=>{if(R>0)for(let j=0;j<D.columns;j++){let N=D.get(w,j);N!==0&&x.set(F,j,x.get(F,j)+N)}return R});let H=x.clone();O.forEachNonZero((F,w,R)=>{if(R<0)for(let j=0;j<D.columns;j++){let N=D.get(w,j);N!==0&&H.set(F,j,H.get(F,j)+N)}return R});let v=D.transpose();x=v.mmul(x);let P=new Y(x.to2DArray(),{threshold:Ne});xn(P,Ne),H=v.mmul(H);let M=new Y(H.to2DArray(),{threshold:Ne});M.forEachNonZero((F,w,R)=>R),xn(M,Ne),M.forEachNonZero((F,w,R)=>{let j=x.get(F,w);j=Math.min(Math.abs(j),Math.abs(R)),j*=j,d+=j;let N=h[F]-h[w],A=Zr(u,N,(k,X)=>k-X);return A<0?(u.splice(-1-A,0,N),f.splice(-1-A,0,j)):f[A]+=j,R})}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 xn(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function Jr(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 Sn(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?Hn(t,n):Z(t,n);return $r(d,{generator:{from:o,to:a,nbPoints:r},peakOptions:{shape:c,width:s/i},noise:l,baseline:m})}import{agnes as _r}from"ml-hclust";import{Matrix as Kr}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=Qr(s,i,a),m=_r(l,{method:"single",isDistanceMatrix:!0}),c=[],g=s.length;St(m,c,{maxClusterSize:r,force:!1,nSpins:g,connectivity:o});let d=el(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 St(e,n,t){let{maxClusterSize:s,force:i,nSpins:o,connectivity:a}=t;if(!i&&e.size<=s)n.push(vn(e.indices(),o));else for(let r of e.children)if(r.size<=s){let l=vn(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?St(r,n,{maxClusterSize:s,force:!0,nSpins:o,connectivity:a}):(l[r.index]=2,n.push(l))}else St(r,n,{maxClusterSize:s,force:!1,nSpins:o,connectivity:a})}function Qr(e,n,t){let s=n.rows,i=n.columns,o=Kr.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 el(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 vn(e,n){let t=new Int16Array(n);for(let s of e)t[s]=1;return t}function il(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);il(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:sl({from:o,to:a,size:l}),y:new Float64Array(l)};let d=U(t);d.clusters=V(d,{frequency:s,maxClusterSize:c});let u=Sn(d,{frequency:s,from:o,to:a,nbPoints:l,lineWidth:r,shape:i,maxClusterSize:c,...g});return m&&tl(u.y)===0&&(u.y=nl(u.y,{max:m})),u}import{getGyromagneticRatio as Pn}from"gyromagnetic-ratio";function Oe(e,n){let{nucleus:t,frequency:s}=n,i=Pn(e),o=Pn(t);if(!o||!i)throw new Error(`${e} or ${t} is not supported`);return s*i/o}var L1=Oe;function Fn(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(ol(r,{nbPoints:t,lineWidth:s,...n[a],experiment:a,frequency:i}))}return o}function ol(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 al}from"ml-spectra-processing";import{generateSpectrum2D as rl}from"spectrum-generator";function K(e){return typeof e!="object"?{x:e,y:e}:{...e}}function jn(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}=rl(ll(r),{generator:{from:K(t),to:K(s),nbPoints:K(i)},peaks:{width:K(a),factor:o}});return{z:l.map(al),...m}}function ll(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 Mn(e,n){let t=Oe(e[1],{nucleus:e[0],frequency:n});return[n,t]}function Rn(e,n){let t=[];for(let s in e){if(!cl(s)||!e[s])continue;let i=e[s];t.push(ml(i,{experiment:s,...n}))}return t}function ml(e,n){let{signals:t,zones:s,nuclei:i}=e,{experiment:o,frequency:a,width:r=gl(i),nbPoints:l}=n,m=Mn(i,a),c=n.fromTo[wn(i[0])],g=n.fromTo[wn(i[1])],d=dl(r,m),u=jn(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 cl(e){return["cosy","hsqc","hmbc"].includes(e)}function gl(e){return{x:8,y:e[0]===e[1]?8:24}}function dl(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 rp(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=Fn(o,{frequency:a,...r}),c=Rn(o,l);return{spectra:[...m,...c],molecules:[{molfile:e.toMolfile()}]}}import{TreeSet as Cl}from"ml-tree-set";function Nn(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 An(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?ul(e,n):1,C=m/c;return f-C}function ul(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 vt(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=An(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?fl(s,{predictions:c,partial:t,score:D,maxSolutions:l}):n<i-1&&vt({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 fl(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n;e.nSolutions++;let 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 pl(e,n){let t=Object.keys(n).length,s=new Set(e),i=t-s.size;return i>0?2*i:1}var yl=(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=Nn({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 Cl(yl),nSolutions:0},b=Date.now();vt({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 bl(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 Dl(e){for(let n of e)if(n.integration===void 0)throw new Error("ranges has not integration property")}async function Sp(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||[];Dl(e),bl(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 hl(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 Hl(e){let n=structuredClone(e);for(let t of n)t.integration===void 0&&(t.integration=0);return n}async function jp(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||[];hl(c);let g=Hl(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 Yl}from"openchemlib-utils";import{TreeSet as zn}from"ml-tree-set";import{getConnectivityMatrix as Rl}from"openchemlib-utils";import{getCorrelationDelta as Ol}from"nmr-correlation";function kn(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=Ol(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 Sl}from"nmr-correlation";function xl(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 In=xl;function Tn(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 w=M[F];w&&w!=="*"&&(u[x].push(F),P[w]||(P[w]=[]),P[w].push(t[x][F])),w==="*"&&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=Pl.bind({},o),b=[];for(let x in e)if(x==="C"&&C[x].length>0)b.push(...In(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 w of F){let{prediction:R,atomType:j}=p(w);v===j&&(P+=R.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],w=o[x][F],R=v[M],j=l[x];if(w.delta===void 0)h+=1;else{let N=Sl(R);if(N===void 0)throw new Error("correlation has not delta");let A=Math.abs(w.delta-N);A<j?h+=1:(A=Math.abs(A-j),h+=-.25/j*A+1)}}}}D>0&&(h/=D)}let O=0;if(Fl(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],w=o[M][t[M][F]];for(let R=P+1;R<H.length;R++){let{atomType:j,index:N}=H[R],A=o[j][t[j][N]],X=w.pathLength[A.diaIDIndex]<5,De=e[M][F],he=e[j][N];if(!De||!he)continue;let ft=De>he?`${he} ${De}`:`${De} ${he}`,_t=vl({from:{targetID:De,atomType:M},to:{targetID:he,atomType:j}},a),Kt=X?_t?1:0:_t?0:1;x[ft]=x[ft]?Math.max(x[ft],Kt):Kt}}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 vl(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 Pl(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 Fl(e){let n=0;for(let t in e)n+=e[t].length;return n}function Pt(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=Tn(t,{diaIDPeerPossibleAssignment:f,infoByAtomTypes:n,restrictionByCS:o,predictions:c,correlations:g,targets:m});if(O!==0)if(Ml(i,n)&&O>=d)jl(s,{predictions:c,partial:t,score:O,maxSolutions:l});else{let S=structuredClone(n);S[C].currentIndex+=1,Pt({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 jl(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n,a={assignment:structuredClone(i),score:t/wl(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 Ml(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 wl(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 En(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 Bn=(e,n)=>n.score-e.score;function Nl(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 Al={C:(e,n)=>e.getAllHydrogens(n),H:()=>1};async function Xn(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 zn(Bn),nSolutions:0},C=Rl(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 El({molecule:t,predictedSignals:v,options:H,atomType:x});Nl(P),p[x]||(p[x]={});let M=0;for(let F of P){let w=F.diaIDs[0],R=F.atoms[0],j=Al[x](t,R);M+=F.nbAtoms*j,p[x][w]={...F,diaIDIndex:R,allHydrogens:F.nbAtoms*j,protonsCount:j,pathLength:C[R]}}for(let F in p[x])p[x][F].allHydrogens*=100/M;y[x]={nSources:P.length,currentIndex:0,nbAllowedUnAssigned:a[x]||0}}b=kn(b,{restrictionByCS:s,predictions:p,targets:d}),D={};for(let x in b)D[x]=Object.keys(b[x]);let O=Il(f,y,h);f={solutions:new zn(Bn),nSolutions:0};let S=Date.now();for(let x of O)Pt({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 kl({store:f,spectra:n,diaIDPeerPossibleAssignment:D,targets:d})}function kl(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]=En(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 Il(e,n,t){return e.nSolutions>0?e.solutions.elements.map(s=>{let i=s.assignment;for(let o of t)i[o]=qn(n[o].nSources);return i}):Tl(n,t)}function Tl(e,n){let t={},s=Object.keys(e);for(let i of s){let o=n.includes(i)?null:"*";t[i]=qn(e[i].nSources,o)}return[t]}function qn(e,n=null){let t=new Array(e);for(let s=0;s<e;s++)t[s]=n;return t}async function El(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 Ln(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 zl(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 zl(e),e}import{buildCorrelationData as Xl}from"nmr-correlation";function Yn(e=[]){let n=structuredClone(e),t=[];for(let s of n)if(G(s)){let{id:i,info:o}=s,a=Bl({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 Bl(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 Wn(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 Un(e,n={}){let{tolerance:t={C:.25,H:.05}}=n,s=Yn(e),o=Xl(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=Wn(r.attachment,o),a[m][l]=r)}return{targets:a,correlations:o}}function ql(e,n=[]){let t=Ll(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 Zn=ql;function Ll(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 cC(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(),Yl(f);let C=Ln(e.spectra),{targets:y,correlations:p}=Un(C,c),{assignmentOrder:b}=Zn(p,s);return await Xn({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 Wl={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 Ul(e){return typeof e=="string"&&Wl[e]!==void 0}function Q(e){return e===void 0?"signal":Ul(e)?e:"unspecified"}var Te=new Set(["signal"]);var Vn=_.toSorted((e,n)=>e.multiplicity===null&&n.multiplicity===null?0:e.multiplicity===null?1:n.multiplicity===null?-1:e.multiplicity-n.multiplicity),Ft=Vn.map(e=>e.value),Ee=Vn.map(e=>e.acs||e.value);import{Molecule as Zl}from"openchemlib";import{TopicMolecule as Vl}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 Gn(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 Jn(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 _n(e,n){let t=[],s=jt(n),i=n[0].nucleusType.atomicNumber;for(let o of e){let a=jt(o.from),r=$n(s,a),m=o[r?"to":"from"],c=r?a:jt(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 $n(e,n){for(let t of e)if(n.has(t))return!0;return!1}function jt(e){let n=e.filter(t=>t.shift!==null).map(t=>t.shift);return new Set(n)}function Kn(e,n,t){let s=new Set,i=[];for(let o of e){let{name:a}=o,r=n[a],{idCode:l}=t[r];if(!r)throw new Error("atom mapping does not exists");s.add(l),i.push(r)}return{diaIDs:Array.from(s),atoms:i}}function Qn(e){let n=[];for(let t of e){let{atoms:s=[],...i}=t;if(s.length>1)for(let o of s)n.push({...i,atoms:[o]});else n.push(t)}return n}function es(e){let n=[];for(let t of e){let s=Qn(t.js);for(let i of t.atoms){let o={...t,atoms:[i],nbAtoms:1,js:s};n.push(o)}}return n}function ts(e,n){let{atomicNumber:t=1,atomMap:s,molfile:i}=n,o=[],a=Zl.fromMolfile(i),l=new Vl(a).diaIDsAndInfo,m=Gn(e.couplings,l,s),c=Jn(e.shifts,l,s);for(let g of c){let{atoms:d,value:u}=g;if(!d.some(C=>C.nucleusType.atomicNumber===t))continue;let f={delta:u,nbAtoms:d.length,...Kn(d,s,l),js:_n(m,d)};o.push(f)}return es(o)}function ns(e){return{molarFraction:{value:e.v,low:e.vl,high:e.vh},fieldStrength:e.f,baseItensity:e.bi,intensityLimit:e.il,spinSystemFlags:e.sf,spinSystemType:sm(e.sst),analysisType:e.at,inchiKey:e.ik,populations:Gl(e.p),lineShapes:nm(e.l),shiftGroups:em(e.sg),shifts:Jl(e.s),couplingGroups:tm(e.cg),couplings:$l(e.c),atoms:_l(e.a),bonds:Kl(e.b)}}function Gl(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 Jl(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 $l(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 _l(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,nucleusType:im(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 Kl(e){let n=[];for(let t of e)n.push({id:t.id,bondType:Ql(t.b),stereochemistryFlags:t.rs,spinSystemFlags:t.sf,atoms:t.a});return n}function Ql(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 em(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 tm(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 nm(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 sm(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 im(e){return{atomicNumber:(e&65024)>>9,isotope:e&511}}function ss(e,n){let{logger:t}=n;t.debug("Parsing CT json results");let s=ns(e),i=om(s),o=am(s);return{...s,shifts:i,couplings:o}}function om(e){let n=e.shifts,t=rm(e),s=is(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 am(e){let n=e.couplings,t=lm(e.couplingGroups),s=is(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 is(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 rm(e){let n={};for(let t of e.shiftGroups)n[t.id]=t;return n}function lm(e){let n={};for(let t of e)n[t.id]=t;return n}function os(e){let n={};for(let t of e)n[t.name]=t.ordinal;return n}function XC(e,n,t){let s=ss(e,{logger:console}),i=os(s.atoms),o=ts(s,{atomMap:i,molfile:n,...t});return{...s,signals:o}}var LC=[{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 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grease\u1DA0"],smiles:"",ranges:[],nucleus:"1H",solvent:"D\u2082O",id:"e29fb191-db1b-45f2-8c2f-85d7229fb1ae"},{names:["hexamethylbenzene"],smiles:"CC1=C(C(=C(C(=C1C)C)C)C)C",ranges:[],nucleus:"1H",solvent:"D\u2082O",id:"9fb191db-1ba5-428c-af85-d7229fb1aed3"},{names:["n-hexane"],smiles:"CCCCCC",ranges:[],nucleus:"1H",solvent:"D\u2082O",id:"b191db1b-a5f2-4c2f-85d7-229fb1aed368"},{names:["HMDSO"],smiles:"C[Si](C)(C)O[Si](C)(C)C",ranges:[{signals:[{js:[],delta:.28,multiplicity:"s",assignment:"CH\u2083"}],integration:18,from:.275,to:.28500000000000003}],nucleus:"1H",solvent:"D\u2082O",id:"91db1ba5-f28c-4f85-9722-9fb1aed36811"},{names:["HMPA"],smiles:"CN(C)P(=O)(N(C)C)N(C)C",ranges:[{signals:[{js:[{coupling:9.5,multiplicity:"d"}],delta:2.61,assignment:"CH\u2083"}],integration:18,from:2.5931249999999997,to:2.626875}],nucleus:"1H",solvent:"D\u2082O",id:"db1ba5f2-8c2f-45d7-a29f-b1aed3681147"},{names:["hydrogen"],smiles:"",ranges:[],nucleus:"1H",solvent:"D\u2082O",id:"1ba5f28c-2f85-4722-9fb1-aed368114712"},{names:["imidazole"],smiles:"C1=CN=CN1",ranges:[{signals:[{js:[],delta:7.78,multiplicity:"s",assignment:"CH(2)"}],integration:1,from:7.775,to:7.785},{signals:[{js:[],delta:7.14,multiplicity:"s",assignment:"CH(4,5)"}],integration:2,from:7.135,to:7.145}],nucleus:"1H",solvent:"D\u2082O",id:"a5f28c2f-85d7-429f-b1ae-d36811471295"},{names:["methane"],smiles:"C",ranges:[{signals:[{js:[],delta:.18,multiplicity:"s",assignment:"CH\u2084"}],integration:4,from:.175,to:.185}],nucleus:"1H",solvent:"D\u2082O",id:"f28c2f85-d722-4fb1-aed3-6811471295bc"},{names:["methanol"],smiles:"CO",ranges:[{signals:[{js:[],delta:3.34,multiplicity:"s",assignment:"CH\u2083"}],integration:3,from:3.335,to:3.3449999999999998}],nucleus:"1H",solvent:"D\u2082O",id:"8c2f85d7-229f-41ae-9368-11471295bc05"},{names:["nitromethane"],smiles:"C[N+](=O)[O-]",ranges:[{signals:[{js:[],delta:4.4,multiplicity:"s",assignment:"CH\u2083"}],integration:3,from:4.3950000000000005,to:4.405}],nucleus:"1H",solvent:"D\u2082O",id:"2f85d722-9fb1-4ed3-a811-471295bc05d0"},{names:["n-pentane"],smiles:"CCCCC",ranges:[],nucleus:"1H",solvent:"D\u2082O",id:"85d7229f-b1ae-4368-9147-1295bc05d0d6"},{names:["propane"],smiles:"CCC",ranges:[{signals:[{js:[{coupling:7.3,multiplicity:"t"}],delta:.88,assignment:"CH\u2083"}],integration:6,from:.85675,to:.90325},{signals:[{js:[{coupling:7.3,multiplicity:"sept"}],delta:1.3,assignment:"CH\u2082"}],integration:2,from:1.24025,to:1.35975}],nucleus:"1H",solvent:"D\u2082O",id:"d7229fb1-aed3-4811-8712-95bc05d0d6a8"},{names:["2-propanol"],smiles:"CC(O)C",ranges:[{signals:[{js:[{coupling:6,multiplicity:"d"}],delta:1.17,assignment:"CH\u2083"}],integration:6,from:1.1575,to:1.1824999999999999},{signals:[{js:[{coupling:6,multiplicity:"sept"}],delta:4.02,assignment:"CH"}],integration:1,from:3.9699999999999998,to:4.069999999999999}],nucleus:"1H",solvent:"D\u2082O",id:"229fb1ae-d368-4147-9295-bc05d0d6a885"},{names:["propylene"],smiles:"CC=C",ranges:[{signals:[{js:[{coupling:6.4,multiplicity:"d"},{coupling:1.5,multiplicity:"t"}],delta:1.7,assignment:"CH\u2083"}],integration:3,from:1.68325,to:1.71675},{signals:[{js:[{coupling:10,multiplicity:"d"}],delta:4.95,assignment:"CH\u2082(1)"}],integration:1,from:4.9325,to:4.9675},{signals:[{js:[{coupling:17,multiplicity:"d"}],delta:5.06,assignment:"CH\u2082(2)"}],integration:1,from:5.0337499999999995,to:5.08625},{signals:[{js:[],delta:5.9,assignment:"CH",multiplicity:"m"}],integration:1,from:5.875,to:5.925000000000001}],nucleus:"1H",solvent:"D\u2082O",id:"9fb1aed3-6811-4712-95bc-05d0d6a88510"},{names:["pyridine"],smiles:"C1=CC=NC=C1",ranges:[{signals:[{js:[],delta:8.52,assignment:"CH(2,6)",multiplicity:"m"}],integration:2,from:8.495,to:8.545},{signals:[{js:[],delta:7.45,assignment:"CH(3,5)",multiplicity:"m"}],integration:2,from:7.425,to:7.4750000000000005},{signals:[{js:[],delta:7.87,assignment:"CH(4)",multiplicity:"m"}],integration:1,from:7.845,to:7.8950000000000005}],nucleus:"1H",solvent:"D\u2082O",id:"b1aed368-1147-4295-bc05-d0d6a88510f8"},{names:["pyrrole"],smiles:"C1=CNC=C1",ranges:[{signals:[{js:[],delta:6.93,assignment:"CH(2,5)",multiplicity:"m"}],integration:2,from:6.904999999999999,to:6.955},{signals:[{js:[],delta:6.26,assignment:"CH(3,4)",multiplicity:"m"}],integration:2,from:6.234999999999999,to:6.285}],nucleus:"1H",solvent:"D\u2082O",id:"aed36811-4712-45bc-85d0-d6a88510f8b5"},{names:["pyrrolidine"],smiles:"C1CCNC1",ranges:[{signals:[{js:[],delta:3.07,assignment:"CH\u2082(2,5)",multiplicity:"m"}],integration:4,from:3.045,to:3.0949999999999998},{signals:[{js:[],delta:1.87,assignment:"CH\u2082(3,4)",multiplicity:"m"}],integration:4,from:1.8450000000000002,to:1.895}],nucleus:"1H",solvent:"D\u2082O",id:"d3681147-1295-4c05-90d6-a88510f8b557"},{names:["silicone 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Mt(e,n){let{x:t,re:s,im:i}=e,o=ne({shapes:n,windowOptions:{dw:t[1]-t[0],length:s.length}}),a=E(s,{windowData:o}),r=E(i,{windowData:o});return{x:t,re:a,im:r}}var fm={updateXDomain:!0,updateYDomain:!1},pm={exponential:{apply:!0,options:{lineBroadening:.3}},sineBell:{apply:!1,options:{offset:0}},sineSquare:{apply:!1,options:{offset:0}},traf:{apply:!1,options:{lineBroadening:.3}},gaussian:{apply:!1,options:{lineBroadening:.3,lineBroadeningCenter:0}}};function Cm(e,n){if(!ls(e))throw new Error("apodization not applicable on this data");let{x:t,re:s,im:i}=e.data,o=Mt({x:t,re:s,im:i},n);e.data={...e.data,...o}}function ls(e){return!!(e.info.isComplex&&e.info.isFid)}function ym(e,n){return{once:!0,reduce:n}}var ms={name:"apodization",label:"Apodization / Window functions",domainUpdateRules:fm,apply:Cm,reduce:ym,isApplicable:ls};import{xSequentialFillFromStep as xm}from"ml-spectra-processing";import{xEnsureFloat64 as bs,xMaxValue as Hm}from"ml-spectra-processing";import{matrixCreateEmpty as cs}from"ml-spectra-processing";function J(e,n){let t=cs({nbRows:e,nbColumns:n}),s=cs({nbRows:e,nbColumns:n});return{re:t,im:s}}function wt(e,n){let t=e.re.length,s=n.re[0].length,i=n.re.length,o=J(t,s);for(let a=0;a<t;a++)for(let r=0;r<s;r++)for(let l=0;l<i;l++){let m=e.re[a][l]*n.re[l][r],c=e.im[a][l]*n.im[l][r],g=e.re[a][l]*n.im[l][r],d=e.im[a][l]*n.re[l][r];o.re[a][r]+=m-c,o.im[a][r]+=g+d}return o}function fs(e){let n=e.re.length,t=e.re[0].length,s=n>=t,i=ps(e),o=Dm(i),a=s?wt(o,i):wt(i,o),{eigenvalues:r,eigenvectors:l}=bm(a,Math.min(n,t)),m=r.map(D=>Math.sqrt(Math.max(0,D))),[c,g]=s?[l,[n,t]]:[l,[t,n]],[d,u]=g,f=J(d,u),[C,y]=s?[f,c]:[c,f];for(let D=0;D<g[1];D++)if(!(m[D]<1e-6))for(let h=0;h<g[0];h++){let O=0,S=0;for(let x=0;x<(s?t:n);x++){let H=s?i:o,v=H.re[h][x]*c.re[x][D],P=H.im[h][x]*c.im[x][D],M=H.re[h][x]*c.im[x][D],F=H.im[h][x]*c.re[x][D];O+=v-P,S+=M+F}f.re[h][D]=O/m[D],f.im[h][D]=S/m[D]}let p=us(C,n,Math.min(n,t)),b=us(y,t,Math.min(n,t));return{U:p,V:b,svals:m}}function 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m=Array.from({length:n},(d,u)=>u);m.sort((d,u)=>Math.abs(a[u])-Math.abs(a[d]));let c=m.map(d=>a[d]),g=J(i,n);for(let d=0;d<i;d++)for(let u=0;u<n;u++)Math.abs(c[u])<1e-10?(g.re[d][u]=0,g.im[d][u]=0):(g.re[d][u]=r.re[d][m[u]],g.im[d][u]=r.im[d][m[u]]);return{eigenvalues:c,eigenvectors:g}}function gs(e){let n=0;for(let t=0;t<e.re.length;t++)n+=e.re[t]*e.re[t]+e.im[t]*e.im[t];return Math.sqrt(n)}function ds(e,n){let t=Rt(e.re.length);for(let s=0;s<e.re.length;s++)t.re[s]=e.re[s]*n,t.im[s]=e.im[s]*n;return t}function us(e,n,t){let s=J(n,t),i=Math.min(n,e.re.length),o=Math.min(t,e.re[0].length);for(let a=0;a<i;a++)for(let r=0;r<o;r++)s.re[a][r]=e.re[a][r],s.im[a][r]=e.im[a][r];return s}function Dm(e){let n=e.re.length,t=e.re[0].length,s=J(t,n);for(let i=0;i<n;i++)for(let o=0;o<t;o++)s.re[o][i]=e.re[i][o],s.im[o][i]=-e.im[i][o];return s}function hm(e,n=1e-10){for(let t of e.im)for(let s of t)if(Math.abs(s)>n)return!1;return!0}function 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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 Om(e,n){let{U:t,V:s,svals:i}=fs(e),o=e.re.length,a=e.re[0].length,r=i.length,l=Hm(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 Sm={updateXDomain:!0,updateYDomain:!0};function vm(e,n={}){if(!Ds(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?xm({from:0,size:c.length,step:u[1]-u[0]}):u})}function Ds(e){return!!(e.info.isComplex&&e.info.isFid)}function Pm(e,n){return{once:!0,reduce:n}}var hs={name:"backwardLinearPrediction",label:"Backward Linear Prediction Filter",domainUpdateRules:Sm,apply:vm,reduce:Pm,isApplicable:Ds};import Jm from"ml-airpls";import{PolynomialRegression as $m}from"ml-regression-polynomial";import{xyEquallySpaced as _m}from"ml-spectra-processing";import{CholeskyDecomposition as wm,Matrix as Ss}from"ml-matrix";import{calculateAdaptiveWeights as Rm,xMultiply as Nm}from"ml-spectra-processing";function Hs(e,n,t){if(n===0)return 1;if(e===0||n>e)return 0;if(n>e-n&&(n=e-n),!t)return Fm(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 Fm(e,n){let t=1,s=e;for(let i=1;i<=n;i++)t*=s--,t/=i;return t}import{Matrix as jm}from"ml-matrix";function Os(e){let n=e.rows,t=e.columns,s=new jm(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 Mm}from"ml-spectra-processing";function xs(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=Mm({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 vs(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=Am(e,{degree:n,weights:l,logger:u});if(!f)return m;l=Rm(e,f,l,{minWeight:r,learningRate:a,factorStd:o}),d=km(f,c,e.length),c.set(f),m=f,g++}return m}function Am(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]=Hs(o,c);let m=new Ss(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 wm(Os(m));if(!c.isPositiveDefinite())throw new Error("Matrix is not positive definite");let g=Nm(e,s),d=Ss.from1DArray(i,1,g),u=c.solve(m.mmul(d)),f=xs(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 km(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 Im,xWhittakerSmoother as Tm}from"ml-spectra-processing";function Ps(e,n){let t=e.length;if(t===0)return new Float64Array(0);let s=n??Im({from:0,step:1,size:t}),i=Tm(e);return Em(s,i)}function Em(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 Lm,FFTConvolution as Ym}from"ml-convolution";import{Matrix as Wm}from"ml-matrix";import{xAdd as Um,xWhittakerSmoother as Zm}from"ml-spectra-processing";import{Matrix as zm}from"ml-matrix";import{xMean as Bm,xStandardDeviation as Xm}from"ml-spectra-processing";function qe(e){let n=[],t=[],{rows:s,columns:i}=e,[o,a]=qm(e);for(;a.length!==t.length;)if(a.length>0){[o,n]=[[],o],[a,t]=[[],a];let c=Bm(t),g=Xm(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=zm.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=Fs(c,s),u=Fs(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 Fs(e,n){return{from:Math.max(e-5,0),to:Math.min(e+5,n)}}function qm(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 Ms(e,n){let t=Vm(e,n),s=qe(t).to1DArray(),{lambda:i=150,maxIterations:o=1}=n;return Zm(e,{lambda:i,controlPoints:s,maxIterations:o})}function js(e,n,t=1){let s=n.convolve(e),i=[];for(let o of s)i.push(Math.abs(o/t));return i}function Vm(e,n){let t=e.length,{scale:s=11}=n,i=Gm(s),o=s>32?new Ym(t,i):new Lm(t,i),a=js(e,o,s),r=js(a,o,s);return new Wm([Um(a,r)])}function Gm(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 Km={updateXDomain:!1,updateYDomain:!1};function Qm(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=Jm(s,i,n).corrected;break;case"polynomial":{let{degree:a,zones:r}=n,l=_m({x:s,y:i},{numberOfPoints:4096,zones:r}),c=new $m(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=Ms(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=vs(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=Ps(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 ec(e,n){return{once:!0,reduce:n}}var Rs={name:"baselineCorrection",label:"Baseline correction",domainUpdateRules:Km,apply:Qm,reduce:ec,isApplicable:ws};var tc={updateXDomain:!0,updateYDomain:!0};function nc(e,n){if(!Ns(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 Ns(e){return!!(e.info.isComplex&&e.info.isFid)}function sc(e,n){return{once:!0,reduce:n}}var As={name:"digitalFilter",label:"Digital Filter",domainUpdateRules:tc,apply:nc,reduce:sc,isApplicable:Ns};import{xEnsureFloat64 as Nt,xyEquallySpaced as ks}from"ml-spectra-processing";var ic={updateXDomain:!1,updateYDomain:!1};function oc(e,n={}){if(!Is(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=ks({x:a,y:r},{from:t,to:s,numberOfPoints:i,exclusions:o});if(e.data.x=Nt(m.x),e.data.re=Nt(m.y),l){let c=ks({x:a,y:r},{from:t,to:s,numberOfPoints:i,exclusions:o});e.data.im=Nt(c.y)}}function Is(e){return!!(e.info.isComplex&&!e.info.isFid)}function ac(e,n){return{once:!1,reduce:n}}var Ts={name:"equallySpaced",label:"Equally spaced",domainUpdateRules:ic,apply:oc,reduce:ac,isApplicable:Is};import{xySetYValue as Es}from"ml-spectra-processing";var rc={updateXDomain:!1,updateYDomain:!1};function lc(e,n){if(!zs(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(Es({x:t,y:s},{zones:n}).y),e.data.im=i&&Float64Array.from(Es({x:t,y:s},{zones:n}).y)}function zs(e){return!!e.info.isFt}function mc(e,n){return{once:!0,reduce:cc(e.concat(n))}}var Bs={name:"exclusionZones",label:"Exclusion zones",domainUpdateRules:rc,apply:lc,reduce:mc,isApplicable:zs};function cc(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 uc,reimFFT as fc,reimPhaseCorrection as pc,xMean as qs,xMultiply as Cc}from"ml-spectra-processing";var z=Math.PI/180;import{nextPowerOfTwo as gc,xSequentialFillFromStep as dc}from"ml-spectra-processing";function Xs(e){let{x:n,re:t,im:s}=e.data,i=gc(n.length),o=new Float64Array(i),a=new Float64Array(i);o.set(t.slice(0,i)),a.set(s.slice(0,i));let r=dc({from:n[0],size:i,step:n[1]-n[0]});e.data={...e.data,re:o,im:a,x:r}}var yc={updateXDomain:!0,updateYDomain:!0};function bc(e){if(!Ls(e))throw new Error("fft not applicable on this data");Oc(e);let n=e.filters.some(o=>o.name==="digitalFilter"&&o.enabled),{info:{aqMod:t}}=e;t===1&&Hc(e),uc(e.data.x.length)||Xs(e);let{data:s,info:i}=e;if(Object.assign(s,fc({re:s.re,im:i.reverse?Cc(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,pc(s,l,-r,{reverse:!0}))}e.data.x=hc(e),e.info={...e.info,isFid:!1,isFt:!0}}function Ls(e){return!!(e.info.isComplex&&e.info.isFid)}function Dc(e,n){return{once:!0,reduce:n}}function hc(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 Hc(e){let n=e.data,t=n.re.length,s=new Float64Array(n.re),i=new Float64Array(n.im),o=qs(n.re.slice(t*.75>>0,t)),a=qs(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 Oc(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 Ys={name:"fft",label:"FFT",domainUpdateRules:yc,apply:bc,reduce:Dc,isApplicable:Ls};import{xSequentialFillFromStep as vc}from"ml-spectra-processing";import{Matrix as xc,SVD as Sc}from"ml-matrix";function Ws(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 Sc(a),l=new Float64Array(s);for(let g=0;g<s;g++)l[g]=e[o-g+1];let m=r.solve(xc.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);Ws(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 Pc={updateXDomain:!0,updateYDomain:!0};function Fc(e,n={}){if(!Us(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?vc({from:0,size:u.length,step:C[1]-C[0]}):C})}function Us(e){return!!(e.info.isComplex&&e.info.isFid)}function jc(e,n){return{once:!0,reduce:n}}var Zs={name:"forwardLinearPrediction",label:"Forward Linear Prediction Filter",domainUpdateRules:Pc,apply:Fc,reduce:jc,isApplicable:Us};import{reimAbsolute as Mc,reimAutoPhaseCorrection as wc,reimPhaseCorrection as Rc,xEnsureFloat64 as Vs}from"ml-spectra-processing";var Nc={updateXDomain:!1,updateYDomain:!1};function Ac(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=Mc({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;Gs(e,{ph0:i,ph1:o}),s&&(s.value={...s.value,absolute:t})}else{let i=Js(e);if(i.ph0===0&&i.ph1===0&&(i=Js(e,{magnitudeMode:!0})),Gs(e,i),s){let{ph0:o,ph1:a}=i;s.value={...s.value,absolute:t,ph0:o,ph1:a}}}}function Gs(e,n){let{ph0:t,ph1:s}=n,{re:i,im:o}=e.data,a=Rc({re:i,im:o},t*Math.PI/180,s*Math.PI/180,{reverse:!0});e.data={...e.data,re:Vs(a.re),im:Vs(a.im)}}function Js(e,n={}){let{minRegSize:t=5,maxDistanceToJoin:s=128,magnitudeMode:i=!1,factorNoise:o=5,reverse:a=!0}=n;return wc(e.data,{minRegSize:t,maxDistanceToJoin:s,magnitudeMode:i,factorNoise:o,reverse:a})}function $s(e){return!!(e.info.isComplex&&!e.info.isFid)}function kc(e,n){return{once:!0,reduce:n}}var _s={name:"phaseCorrection",label:"Phase 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fd(e,n){let t=ra(e,n),{rowAssignments:s,gain:i}=ia(t,{maximaze:!1});if(i===-1)return[];let o=[],a=Number.NEGATIVE_INFINITY;for(let r of s)a<n[r].y&&(a=n[r].y),o.push({...n[r]});for(let r of o)r.y/=a;return o}function ra(e,n){let t=n.length,s=e.length,i=new gd(s,t);for(let o=0;o<s;o++)for(let a=0;a<t;a++)i.set(o,a,Math.abs(e[o].x-n[a].x));return i}import{xyObjectCheck as pd,xyObjectMinMaxValues as Cd}from"ml-spectra-processing";function la(e,n){pd(e,{minLength:1});let{minX:t,maxX:s,thresholdFactor:i=.2}=n,{minY:o,maxY:a}=Cd(e),r=yd(o,a)*i,l=e[0],m=Number.MAX_SAFE_INTEGER;for(let c of e)if(Math.abs(c.y)>=r){let g=Math.min(c.x-t,s-c.x);g<m&&(m=g,l=c)}return l}function yd(e,n){return Math.max(Math.abs(e),Math.abs(n))}function ma(e){return e.getAllAtoms()<1}import{Molecule as bd}from"openchemlib";function Fb(e){return e?.match(/V[23]0/)?!ma(bd.fromMolfile(e)):!1}import{xyIntegration as Dd}from"ml-spectra-processing";function Se(e,n){return Math.abs(e.intensity*e.width/n*1.57)}function 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0||r.from>a.to?(a={id:crypto.randomUUID(),from:r.from,to:r.to,integration:r.original.nbAtoms,signals:[r.original]},o.push(a)):(a.integration+=r.original.nbAtoms,r.to>a.to&&(a.to=r.to),a.signals.push(r.original));return o}import{gyromagneticRatio as Sa}from"gyromagnetic-ratio";function W8(e){if(e in Sa)return e;if(e.toLowerCase()==="proton")return"1H";let n=e.replaceAll(/[^0-9]/g,"");if(!n)return e;for(let t in Sa)if(t.includes(n))return t;return e}function G8(e,n={}){let{logger:t}=n,s={info:{dimension:1},ranges:[],acsString:e,normalized:e.replace(/\.\s*$/,"").replaceAll(/[\r\n\t]/g," ").replaceAll(/[;:]/g,",").replaceAll("}",")").replaceAll("{","(").replaceAll(/[\u2011\u2012\u2013\u2014\u2015\u2212]/g,"-")};return Cu(s),fu(s,n),t?.info(`Found: ${s.ranges.length} ranges`),s}function fu(e,n={}){let{logger:t}=n;for(let s of e.parts)if(s.toLowerCase().includes("nmr"))pu(e,s);else{e.info.frequency||(e.info.frequency=400,t?.warn("Frequency not defined, assuming 400 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Gt=class extends mf{coefficient;signalAbsenseDiffussion;gyromagneticRatio;gradientPulseDuration;timeCorrection;constructor(n,t,s){let{gyromagneticRatio:i,gradientPulseDuration:o,timeCorrection:a}=s;super(),this.coefficient=n,this.signalAbsenseDiffussion=t,this.gyromagneticRatio=i,this.gradientPulseDuration=o,this.timeCorrection=a}_predict(n){return this.signalAbsenseDiffussion*Math.exp(-this.timeCorrection*this.coefficient*(n*this.gyromagneticRatio*this.gradientPulseDuration)**2)}};import{levenbergMarquardt as df}from"ml-levenberg-marquardt";import{BaseRegression as uf}from"ml-regression-base";import{xyCheck as ff}from"ml-spectra-processing";var pf={damping:1.5,maxIterations:100,errorTolerance:1e-8};function 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br}from"ml-hclust";import{Matrix as Dr}from"ml-matrix";import{Molecule as dn}from"openchemlib";function cn(e,n={}){let t=n.output||structuredClone(e);for(let s of t)s.id=crypto.randomUUID();return t}var yr={h:"1H",c:"13C"};function gn(e){return Object.values(e).map(n=>yr[n.toLowerCase()])}function hr(e){if(!e.from||!e.to)throw new Error("options from and to are mandatory")}async function se(e,n){hr(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=Hr(e,{fromLabel:t,toLabel:s,minLength:i,maxLength:o})}=n,c=e.getGroupedDiastereotopicAtomIDs()||[],g=[];for(let h of c||[])g.push({...h,pathInfo:structuredClone(m[h.atoms[0]])});let d=a[s],u=a[t];if(!u||!d)throw new Error("predictions are not availaible");let f={x:u,y:d},C={x:{},y:{}};for(let h in C)for(let b of f[h].joinedSignals){if(!b.diaIDs)throw new Error("Signal has not diaIDs");C[h][b.diaIDs[0]]=b}let y={};for(let h of g){let b=h.pathInfo;if(b.paths.length===0||!C.x[b.oclID])continue;let O=b.paths;for(let v of O){if(!C.y[m[v.to].oclID])continue;let x={x:b,y:m[v.to]},H=`${x.x.oclID}-${x.y.oclID}`;if(H===`${b.oclID}-${b.oclID}`||y[H])continue;let S={id:crypto.randomUUID(),x:0,y:0,z:100},P={id:crypto.randomUUID(),x:{delta:0,diaIDs:[],atoms:[]},y:{delta:0,diaIDs:[],atoms:[]},peaks:[]};for(let M of["x","y"]){let F=x[M].oclID;S[M]=C[M][F].delta,P[M].delta=C[M][F].delta,P[M].diaIDs=[F];let{atoms:R}=C[M][F];R&&(P[M].atoms=R)}P.peaks=[S],y[H]=P}}r&&xr(y,{paths:m,signalsByDiaID:C});let p=Object.values(y),D=Sr(p,{joinDistance:l,from:t,to:s});return{nuclei:gn({from:t,to:s}),joinedSignals:p,signals:Or(p),zones:D}}function Hr(e,n){let{fromLabel:t,toLabel:s,minLength:i,maxLength:o=Number.MAX_SAFE_INTEGER}=n,a=e.diaIDs,r=e.moleculeWithH,l=e.distanceMatrix,m=dn.getAtomicNoFromLabel(t),c=dn.getAtomicNoFromLabel(s),g=[];for(let d=0;d<r.getAllAtoms();d++){let u={oclID:a[d],paths:[]};for(let f=0;f<r.getAllAtoms();f++){if(d===f||r.getAtomicNo(f)!==c||r.getAtomicNo(d)!==m)continue;let C=l[d][f];C>=i&&C<=o&&u.paths.push({from:d,to:f})}g.push(u)}return g}function Or(e){let n=[];for(let t of e)for(let s of t.x.atoms||[])for(let i of t.y.atoms||[]){let o=structuredClone(t);o.x.atoms=[s],o.y.atoms=[i],n.push(o)}return cn(n)}function xr(e,n){let{paths:t=[],signalsByDiaID:s}=n;for(let i of t){let o=i.oclID;if(!s.x[o]||e[`${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 Sr(e,n){if(e.length===0)return[];let{joinDistance:t,from:s,to:i}=n,o=new Dr(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)),g=br(o.to2DArray(),{method:"centroid"}),d=un([g],c),u=[];for(let f of d){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(),...vr(C,{joinDistance:t,from:s,to:i}),signals:C})}return u}function vr(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 un(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?un(e,n):e}async function fn(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=Fr(e,i,a)),se(e,r)}function Fr(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 g of m.js){if(!g.diaIDs||g.diaIDs.length===0)throw new Error("should contains assigned coupling by atoms");let d=g.diaIDs[0];o[c][d]=Math.max(g.coupling,o[c][d]??Number.MIN_SAFE_INTEGER)}}let r=e.moleculeWithH,l=Pr.getAtomicNoFromLabel("H");for(let m=0;m<r.getAllAtoms();m++){let c={oclID:s[m],paths:[]};for(let g=0;g<r.getAllAtoms();g++)m!==g&&r.getAtomicNo(g)===l&&r.getAtomicNo(m)===l&&o[s[m]]?.[s[g]]>=t&&c.paths.push({from:m,to:g});i.push(c)}return i}function pn(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 Cn=pn("proton","https://nmr-prediction.service.zakodium.com/v1/predict/proton"),yn=pn("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 bn(e,n={}){let{predictor:t=yn,predictorOptions:s={},cache:i}=n;return e.molecule.getAllAtoms()===0?{nucleus:"13C",joinedSignals:[],signals:[],ranges:[]}:Me(e,t,{cache:i,predictorOptions:s})}async function Dn(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 hn(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 Hn(e,n={}){let{predictor:t=Cn,cache:s,predictorOptions:i={}}=n;return e.molecule.getAllAtoms()===0?{nucleus:"1H",joinedSignals:[],signals:[],ranges:[]}:Me(e,t,{cache:s,predictorOptions:i})}function yt(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 Mr={cosy:{predictor:fn,required:["H"],message:"Proton prediction is missing so COSY could not be generated."},hsqc:{predictor:hn,required:["H","C"],message:"Carbon and / or proton prediction is missing so HSQC could not be generated."},hmbc:{predictor:Dn,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 jr(e),a=yt("H",i)?await Hn(o,{...i?.H}):void 0,r=yt("C",i)?await bn(o,i?.C):void 0,l={},m=o.diaIDs,c={};On(a,m)&&(c.H=a,"H"in i&&(l.proton=a)),On(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}=Mr[f];if(y.every(D=>D in c)){let D=await C(o,{predictions:c,...i[f],joinDistance:s});return{key:f,result:D}}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 On(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 nl,xRescale as sl,xSequentialFillFromTo as il}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 bt={};for(let{value:e,multiplicity:n,names:t}of _){n&&(bt[e]=n-1);for(let s of t)n&&(bt[s]=n-1)}var q=bt;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}=Rr(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 Rr(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(wr(m,[t],n));o.push(...c)}else o.push(a);return o},[]),tempSignals:s}}function wr(e,n,t){return{delta:1e5,atoms:n,js:[{coupling:e,atoms:t}]}}import{Matrix as kr}from"ml-matrix";import{Matrix as Dt}from"ml-matrix";import{simpleClustering as Nr}from"ml-simple-clustering";function L(e){let{couplingConstants:n,connectivity:t}=e,s=Dt.checkMatrix(n),i=t?Dt.checkMatrix(t):Ar(s),{levels:o=Array.from({length:i.rows},()=>2),clusters:a=Nr(i.to2DArray(),{out:"indexes"})}=e;return{...e,levels:o,clusters:a,connectivity:i,couplingConstants:s}}function Ar(e){let n=Dt.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 Ir(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){Ir(e);let n=e.length,t=[],s=kr.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 _r}from"spectrum-generator";import Xr from"binary-search";import{EVD as qr,Matrix as Lr}from"ml-matrix";import{SparseMatrix as we}from"ml-sparse-matrix";import{SparseMatrix as Tr}from"ml-sparse-matrix";function xn(e,n){let t=2*e*n,s=new Tr(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 Er}from"ml-sparse-matrix";function ht(e,n){let t=2*e*n,s=new Er(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 zr}from"ml-sparse-matrix";function Ht(e,n){let t=2*e*n,s=new zr(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 Br}from"ml-sparse-matrix";function Re(e,n){let t=2*e*n,s=new Br(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 Ot=.01;function Sn(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 D=o.couplingConstants.get(y,c[p])/2,h=u.length;for(let b=0;b<h;b++)u.push(u[b]+D),u[b]-=D}u.sort((p,D)=>p-D),d=u.length,g=1;for(let p=0;p<d;p++)f.push(1)}else{let y=Wr(a,o.couplingConstants,r,o.connectivity,c),p=y.rows,D=new qr(y),h=D.eigenvectorMatrix,b=D.realEigenvalues,O=new we(p,p),v=m.length;g=0;for(let F=0;F<v;F++){let R={rows:2**F},w={rows:2**(v-F-1)},j=xn(R.rows,w.rows);m[F]>=0?(O.add(j.mul(m[F]+1)),g++):O.add(j.mul(m[F]))}let x=Lr.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 S=h.transpose();x=S.mmul(x);let P=new we(x.to2DArray(),{threshold:Ot});H=S.mmul(H);let M=new we(H.to2DArray(),{threshold:Ot});M.forEachNonZero((F,R,w)=>w),Yr(M,Ot),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=b[F]-b[R],A=Xr(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],D=f[0],h=1;for(let b=1;b<C;b++)Math.abs(u[b]-p/h)<y?(D+=f[b],p+=u[b],h++):(l.push({x:-p/h/i,y:D*g}),p=u[b],D=f[b],h=1);l.push({x:-p/h/i,y:D*g})}}return l.filter(m=>m.x<1e3)}function Yr(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function Wr(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(Ht(m.rows,c.rows).mul(-1).mmul(Ht(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 Vr from"binary-search";import{EVD as Gr,Matrix as Jr}from"ml-matrix";import{SparseMatrix as Y}from"ml-sparse-matrix";import{SparseMatrix as Ur}from"ml-sparse-matrix";function vn(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=xt(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=xt(s,-1,e,e),a=i.clone().add(o).mul(.5),r=o.clone().mul(-1).add(i).mul(-.5),l=xt(t,0,e,e);return{x:a,y:r,z:l,m:o,p:i}}function xt(e,n,t,s){let i=new Ur(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 Zr=vn(2);function He(e){return e===2?Zr:vn(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 D=o.couplingConstants.get(y,c[p])/2,h=u.length;for(let b=0;b<h;b++)u.push(u[b]+D),u[b]-=D}u.sort((p,D)=>p-D),d=u.length,g=1;for(let p=0;p<d;p++)f.push(1)}else{let y=$r(a,o.couplingConstants,r,o.connectivity,c),p=y.rows,D=new Gr(y),h=D.eigenvectorMatrix,b=D.realEigenvalues,O=new Y(p,p),v=m.length;g=0;for(let F=0;F<v;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<v;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=Jr.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 S=h.transpose();x=S.mmul(x);let P=new Y(x.to2DArray(),{threshold:Ne});Pn(P,Ne),H=S.mmul(H);let M=new Y(H.to2DArray(),{threshold:Ne});M.forEachNonZero((F,R,w)=>w),Pn(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=b[F]-b[R],A=Vr(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],D=f[0],h=1;for(let b=1;b<C;b++)Math.abs(u[b]-p/h)<y?(D+=f[b],p+=u[b],h++):(l.push({x:-p/h/i,y:D*g}),p=u[b],D=f[b],h=1);l.push({x:-p/h/i,y:D*g})}}return l.filter(m=>m.x<1e3)}function Pn(e,n){e.forEachNonZero((t,s,i)=>Math.abs(i)<=n?0:i)}function $r(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]),D=1;for(let v=0;v<C;v++)D*=t[i[v]];let h=Y.eye(D);D=1;for(let v=C+1;v<i.length;v++)D*=t[i[v]];let b=Y.eye(D),O=g.kroneckerProduct(m.x).kroneckerProduct(d).mmul(h.kroneckerProduct(p.x).kroneckerProduct(b));O.add(g.kroneckerProduct(m.y).kroneckerProduct(d).mul(-1).mmul(h.kroneckerProduct(p.y).kroneckerProduct(b))),O.add(g.kroneckerProduct(m.z).kroneckerProduct(d).mmul(h.kroneckerProduct(p.z).kroneckerProduct(b))),a.add(O.mul(n.get(l,y)/2))}}}return a}function Fn(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?Sn(t,n):Z(t,n);return _r(d,{generator:{from:o,to:a,nbPoints:r},peakOptions:{shape:c,width:s/i},noise:l,baseline:m})}import{agnes as Kr}from"ml-hclust";import{Matrix as Qr}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=el(s,i,a),m=Kr(l,{method:"single",isDistanceMatrix:!0}),c=[],g=s.length;St(m,c,{maxClusterSize:r,force:!1,nSpins:g,connectivity:o});let d=tl(c,r),u=d.length,f=[];for(let C=0;C<u;C++){let y=[];for(let p=0;p<g;p++){let D=d[C][p];D!==0&&y.push(D<0?-(p+1):p)}f.push(y)}return f}function St(e,n,t){let{maxClusterSize:s,force:i,nSpins:o,connectivity:a}=t;if(!i&&e.size<=s)n.push(jn(e.indices(),o));else for(let r of e.children)if(r.size<=s){let l=jn(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?St(r,n,{maxClusterSize:s,force:!0,nSpins:o,connectivity:a}):(l[r.index]=2,n.push(l))}else St(r,n,{maxClusterSize:s,force:!1,nSpins:o,connectivity:a})}function el(e,n,t){let s=n.rows,i=n.columns,o=Qr.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 tl(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 jn(e,n){let t=new Int16Array(n);for(let s of e)t[s]=1;return t}function ol(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);ol(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:il({from:o,to:a,size:l}),y:new Float64Array(l)};let d=U(t);d.clusters=V(d,{frequency:s,maxClusterSize:c});let u=Fn(d,{frequency:s,from:o,to:a,nbPoints:l,lineWidth:r,shape:i,maxClusterSize:c,...g});return m&&nl(u.y)===0&&(u.y=sl(u.y,{max:m})),u}import{getGyromagneticRatio as Mn}from"gyromagnetic-ratio";function Oe(e,n){let{nucleus:t,frequency:s}=n,i=Mn(e),o=Mn(t);if(!o||!i)throw new Error(`${e} or ${t} is not supported`);return s*i/o}var Z1=Oe;function Rn(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(al(r,{nbPoints:t,lineWidth:s,...n[a],experiment:a,frequency:i}))}return o}function al(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 rl}from"ml-spectra-processing";import{generateSpectrum2D as ll}from"spectrum-generator";function K(e){return typeof e!="object"?{x:e,y:e}:{...e}}function wn(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}=ll(ml(r),{generator:{from:K(t),to:K(s),nbPoints:K(i)},peaks:{width:K(a),factor:o}});return{z:l.map(rl),...m}}function ml(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 Nn(e,n){let t=Oe(e[1],{nucleus:e[0],frequency:n});return[n,t]}function kn(e,n){let t=[];for(let s in e){if(!gl(s)||!e[s])continue;let i=e[s];t.push(cl(i,{experiment:s,...n}))}return t}function cl(e,n){let{signals:t,zones:s,nuclei:i}=e,{experiment:o,frequency:a,width:r=dl(i),nbPoints:l}=n,m=Nn(i,a),c=n.fromTo[An(i[0])],g=n.fromTo[An(i[1])],d=ul(r,m),u=wn(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 gl(e){return["cosy","hsqc","hmbc"].includes(e)}function dl(e){return{x:8,y:e[0]===e[1]?8:24}}function ul(e,n){let t=K(e);return{x:t.x/n[0],y:t.y/n[1]}}function An(e){return e.includes("H")?"proton":"carbon"}async function gp(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=Rn(o,{frequency:a,...r}),c=kn(o,l);return{spectra:[...m,...c],molecules:[{molfile:e.toMolfile()}]}}import{TreeSet as yl}from"ml-tree-set";function In(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 Tn(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],D=0;for(let b of p){let O=a[b];D+=O.allHydrogens}let{integration:h}=r[y];if(D-h>=.5)return 0}let f=l?fl(e,n):1,C=m/c;return f-C}function fl(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 vt(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 D of p){t[n]=D;let h=Tn(t,{useIntegrationRestriction:f,diaIDPeerPossibleAssignment:C,nbAllowedUnAssigned:d,restrictionByCS:o,predictions:c,targets:m});if(h===0){D==="*"&&(t[n]=null);continue}n===i-1&&h>=g?pl(s,{predictions:c,partial:t,score:h,maxSolutions:l}):n<i-1&&vt({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 pl(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n;e.nSolutions++;let a={assignment:structuredClone(i),score:t/Cl(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 Cl(e,n){let t=Object.keys(n).length,s=new Set(e),i=t-s.size;return i>0?2*i:1}var bl=(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 b of l){let O=b.diaIDs[0],v=b.atoms[0];u[O]={...b,diaIDIndex:v,allHydrogens:b.nbAtoms}}let f=In({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 yl(bl),nSolutions:0},D=Date.now();vt({nSources:d,restrictionByCS:{tolerance:m,useChemicalShiftScore:c,chemicalShiftRestriction:g},timeout:s,timeStart:D,targets:r,predictions:u,maxSolutions:a,lowerBoundScore:i,nbAllowedUnAssigned:o,possibleAssignmentMap:f,diaIDPeerPossibleAssignment:C,useIntegrationRestriction:t},0,y,p);let h=[];for(let b of p.solutions.elements){let{assignment:O,score:v}=b,x=structuredClone(r);for(let H=0;H<O.length;H++){let S=O[H];if(typeof S!="string")continue;let P=x[S];(!P.signals||P.signals.length===0)&&(P.signals=[{delta:(P.to+P.from)/2}]);let M=P.signals[0];M.diaIDs||(M.diaIDs=[]),S&&M.diaIDs.push(C[H])}h.push({score:v,assignment:Object.values(x)})}return h}function Dl(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 hl(e){for(let n of e)if(n.integration===void 0)throw new Error("ranges has not integration property")}async function jp(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||[];hl(e),Dl(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 Hl(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 Ol(e){let n=structuredClone(e);for(let t of n)t.integration===void 0&&(t.integration=0);return n}async function Np(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||[];Hl(c);let g=Ol(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 Wl}from"openchemlib-utils";import{TreeSet as qn}from"ml-tree-set";import{getConnectivityMatrix as Nl}from"openchemlib-utils";import{getCorrelationDelta as xl}from"nmr-correlation";function En(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:D,protonsCount:h}=C;if(D?l==="H"?y-D<1:h.length>0?h.includes(p):!0:!0)if(!a||u.delta===void 0)e[l][d].push(f);else{let O=xl(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 vl}from"nmr-correlation";function Sl(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 zn=Sl;function Bn(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:S}=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>S)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=Fl.bind({},o),D=[];for(let x in e)if(x==="C"&&C[x].length>0)D.push(...zn(C[x],a[x],r));else for(let H of C[x])D.push({atomType:x,targetIDs:[H],integration:a.H[H].integration});for(let x of D){let{integration:H,atomType:S}=x;if(H===void 0||Number.isNaN(H))continue;let P=0;for(let M of x.targetIDs){let F=d[S][M];for(let R of F){let{prediction:w,atomType:j}=p(R);S===j&&(P+=w.allHydrogens)}}if(P-H>=5)return 0}let h=1,b=1;if(m){b=0,h=0;for(let x of Object.keys(e)){let 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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 Fl(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 jl(e){let n=0;for(let t in e)n+=e[t].length;return n}function Pt(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 D=f[C][y],h=u[C][D];for(let b of h){t[C][y]=b;let O=Bn(t,{diaIDPeerPossibleAssignment:f,infoByAtomTypes:n,restrictionByCS:o,predictions:c,correlations:g,targets:m});if(O!==0)if(Rl(i,n)&&O>=d)Ml(s,{predictions:c,partial:t,score:O,maxSolutions:l});else{let v=structuredClone(n);v[C].currentIndex+=1,Pt({currentAtomTypes:i,restrictionByCS:o,timeout:a,timeStart:r,maxSolutions:l,targets:m,predictions:c,correlations:g,lowerBoundScore:d,possibleAssignmentMap:u,diaIDPeerPossibleAssignment:f},v,structuredClone(t),s)}}}}function Ml(e,n){let{score:t,maxSolutions:s,partial:i,predictions:o}=n,a={assignment:structuredClone(i),score:t/wl(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 Rl(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 wl(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 Xn(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 Ln=(e,n)=>n.score-e.score;function Al(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 kl={C:(e,n)=>e.getAllHydrogens(n),H:()=>1};async function Yn(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 qn(Ln),nSolutions:0},C=Nl(t,{pathLength:!0}),y={},p={},D={},h={};for(let b of m){for(let x of b){let H={[x]:c[x]},S=g[x],P=await zl({molecule:t,predictedSignals:S,options:H,atomType:x});Al(P),p[x]||(p[x]={});let M=0;for(let F of P){let R=F.diaIDs[0],w=F.atoms[0],j=kl[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}}D=En(D,{restrictionByCS:s,predictions:p,targets:d}),h={};for(let x in D)h[x]=Object.keys(D[x]);let O=Tl(f,y,b);f={solutions:new qn(Ln),nSolutions:0};let v=Date.now();for(let x of O)Pt({currentAtomTypes:b,restrictionByCS:s,timeout:i,timeStart:v,targets:d,predictions:p,correlations:l,maxSolutions:r,lowerBoundScore:u,possibleAssignmentMap:D,diaIDPeerPossibleAssignment:h},y,x,f)}return Il({store:f,spectra:n,diaIDPeerPossibleAssignment:h,targets:d})}function Il(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]=Xn(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 D=y[p];if(D==="*"||!D)continue;let h=C[D],b=s[f][p];for(let O of h.link){let{spectrumIndex:v,elementIndex:x,signalIndex:H}=a[O.signal.id],S=c[v];if(G(S)){let{ranges:P}=S,F=P[x].signals[H];if(F.diaIDs||(F.diaIDs=[]),F.diaIDs.includes(b))continue;F.diaIDs.push(b)}else{let P=O.axis,M=S.zones[x].signals[H];if(M[P].diaIDs||(M[P].diaIDs=[]),M[P].diaIDs?.includes(b))continue;M[P].diaIDs?.push(b)}}}}l.push({score:d,assignment:c})}return l}function Tl(e,n,t){return e.nSolutions>0?e.solutions.elements.map(s=>{let i=s.assignment;for(let o of t)i[o]=Wn(n[o].nSources);return i}):El(n,t)}function El(e,n){let t={},s=Object.keys(e);for(let i of s){let o=n.includes(i)?null:"*";t[i]=Wn(e[i].nSources,o)}return[t]}function Wn(e,n=null){let t=new Array(e);for(let s=0;s<e;s++)t[s]=n;return t}async function zl(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 Un(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 Bl(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 Bl(e),e}import{buildCorrelationData as ql}from"nmr-correlation";function Zn(e=[]){let n=structuredClone(e),t=[];for(let s of n)if(G(s)){let{id:i,info:o}=s,a=Xl({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 Xl(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 Vn(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 Gn(e,n={}){let{tolerance:t={C:.25,H:.05}}=n,s=Zn(e),o=ql(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=Vn(r.attachment,o),a[m][l]=r)}return{targets:a,correlations:o}}function Ll(e,n=[]){let t=Yl(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 Jn=Ll;function Yl(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 fC(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(),Wl(f);let C=Un(e.spectra),{targets:y,correlations:p}=Gn(C,c),{assignmentOrder:D}=Jn(p,s);return await Yn({restrictionByCS:{tolerance:g,useChemicalShiftScore:d,chemicalShiftRestriction:u},spectra:C,molecule:f,timeout:r,minScore:i,maxSolutions:o,assignmentOrder:D,nbAllowedUnAssigned:a,correlations:p,targets:y,predictionOptions:l,predictions:m})}var Ul={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 Zl(e){return typeof e=="string"&&Ul[e]!==void 0}function Q(e){return e===void 0?"signal":Zl(e)?e:"unspecified"}var Te=new Set(["signal"]);var $n=_.toSorted((e,n)=>e.multiplicity===null&&n.multiplicity===null?0:e.multiplicity===null?1:n.multiplicity===null?-1:e.multiplicity-n.multiplicity),Ft=$n.map(e=>e.value),Ee=$n.map(e=>e.acs||e.value);import{Molecule as Vl}from"openchemlib";import{TopicMolecule as Gl}from"openchemlib-utils";function xe(e,n,t){let{name:s}=e,i=t[s],{idCode:o}=n[i];if(i===void 0)throw new Error("atom map does not exists");return{...e,idCode:o,atom:i}}function _n(e,n,t){let s=[];for(let i of e){let{from:o,to:a}=i;s.push({...i,from:o.map(r=>xe(r,n,t)),to:a.map(r=>xe(r,n,t))})}return s}function Kn(e,n,t){let s=[];for(let i of e){let{atoms:o}=i;s.push({...i,atoms:o.map(a=>xe(a,n,t))})}return s}function es(e,n){let t=[],s=jt(n),i=n[0].nucleusType.atomicNumber;for(let o of e){let a=jt(o.from),r=Qn(s,a),m=o[r?"to":"from"],c=r?a:jt(o.to),{nucleusType:{atomicNumber:g},idCode:d}=m[0];!Qn(s,c)||g!==i||t.push({coupling:o.value,atoms:m.map(u=>u.atom),diaIDs:[d]})}return t}function Qn(e,n){for(let t of e)if(n.has(t))return!0;return!1}function jt(e){let n=e.filter(t=>t.shift!==null).map(t=>t.shift);return new Set(n)}function ts(e,n,t){let s=new Set,i=[];for(let o of e){let{name:a}=o,r=n[a],{idCode:l}=t[r];if(!r)throw new Error("atom mapping does not exists");s.add(l),i.push(r)}return{diaIDs:Array.from(s),atoms:i}}function ns(e){let n=[];for(let t of e){let{atoms:s=[],...i}=t;if(s.length>1)for(let o of s)n.push({...i,atoms:[o]});else n.push(t)}return n}function ss(e){let n=[];for(let t of e){let s=ns(t.js);for(let i of t.atoms){let o={...t,atoms:[i],nbAtoms:1,js:s};n.push(o)}}return n}function is(e,n){let{atomicNumber:t=1,atomMap:s,molfile:i}=n,o=[],a=Vl.fromMolfile(i),l=new Gl(a).diaIDsAndInfo,m=_n(e.couplings,l,s),c=Kn(e.shifts,l,s);for(let g of c){let{atoms:d,value:u}=g;if(!d.some(C=>C.nucleusType.atomicNumber===t))continue;let f={delta:u,nbAtoms:d.length,...ts(d,s,l),js:es(m,d)};o.push(f)}return ss(o)}function os(e){return{molarFraction:{value:e.v,low:e.vl,high:e.vh},fieldStrength:e.f,baseItensity:e.bi,intensityLimit:e.il,spinSystemFlags:e.sf,spinSystemType:im(e.sst),analysisType:e.at,inchiKey:e.ik,populations:Jl(e.p),lineShapes:sm(e.l),shiftGroups:tm(e.sg),shifts:$l(e.s),couplingGroups:nm(e.cg),couplings:_l(e.c),atoms:Kl(e.a),bonds:Ql(e.b)}}function Jl(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 $l(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 _l(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 Kl(e){let n=[];for(let t of e)n.push({id:t.id,parentID:t.pid,name:t.n,remarks:t.r,nucleusType:om(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 Ql(e){let n=[];for(let t of e)n.push({id:t.id,bondType:em(t.b),stereochemistryFlags:t.rs,spinSystemFlags:t.sf,atoms:t.a});return n}function em(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 tm(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 nm(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 sm(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 im(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 om(e){return{atomicNumber:(e&65024)>>9,isotope:e&511}}function as(e,n){let{logger:t}=n;t.debug("Parsing CT json results");let s=os(e),i=am(s),o=rm(s);return{...s,shifts:i,couplings:o}}function am(e){let n=e.shifts,t=lm(e),s=rs(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 rm(e){let n=e.couplings,t=mm(e.couplingGroups),s=rs(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 rs(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 lm(e){let n={};for(let t of 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grease\u1DA0"],smiles:"",ranges:[],nucleus:"1H",solvent:"D\u2082O",id:"e29fb191-db1b-45f2-8c2f-85d7229fb1ae"},{names:["hexamethylbenzene"],smiles:"CC1=C(C(=C(C(=C1C)C)C)C)C",ranges:[],nucleus:"1H",solvent:"D\u2082O",id:"9fb191db-1ba5-428c-af85-d7229fb1aed3"},{names:["n-hexane"],smiles:"CCCCCC",ranges:[],nucleus:"1H",solvent:"D\u2082O",id:"b191db1b-a5f2-4c2f-85d7-229fb1aed368"},{names:["HMDSO"],smiles:"C[Si](C)(C)O[Si](C)(C)C",ranges:[{signals:[{js:[],delta:.28,multiplicity:"s",assignment:"CH\u2083"}],integration:18,from:.275,to:.28500000000000003}],nucleus:"1H",solvent:"D\u2082O",id:"91db1ba5-f28c-4f85-9722-9fb1aed36811"},{names:["HMPA"],smiles:"CN(C)P(=O)(N(C)C)N(C)C",ranges:[{signals:[{js:[{coupling:9.5,multiplicity:"d"}],delta:2.61,assignment:"CH\u2083"}],integration:18,from:2.5931249999999997,to:2.626875}],nucleus:"1H",solvent:"D\u2082O",id:"db1ba5f2-8c2f-45d7-a29f-b1aed3681147"},{names:["hydrogen"],smiles:"",ranges:[],nucleus:"1H",solvent:"D\u2082O",id:"1ba5f28c-2f85-4722-9fb1-aed368114712"},{names:["imidazole"],smiles:"C1=CN=CN1",ranges:[{signals:[{js:[],delta:7.78,multiplicity:"s",assignment:"CH(2)"}],integration:1,from:7.775,to:7.785},{signals:[{js:[],delta:7.14,multiplicity:"s",assignment:"CH(4,5)"}],integration:2,from:7.135,to:7.145}],nucleus:"1H",solvent:"D\u2082O",id:"a5f28c2f-85d7-429f-b1ae-d36811471295"},{names:["methane"],smiles:"C",ranges:[{signals:[{js:[],delta:.18,multiplicity:"s",assignment:"CH\u2084"}],integration:4,from:.175,to:.185}],nucleus:"1H",solvent:"D\u2082O",id:"f28c2f85-d722-4fb1-aed3-6811471295bc"},{names:["methanol"],smiles:"CO",ranges:[{signals:[{js:[],delta:3.34,multiplicity:"s",assignment:"CH\u2083"}],integration:3,from:3.335,to:3.3449999999999998}],nucleus:"1H",solvent:"D\u2082O",id:"8c2f85d7-229f-41ae-9368-11471295bc05"},{names:["nitromethane"],smiles:"C[N+](=O)[O-]",ranges:[{signals:[{js:[],delta:4.4,multiplicity:"s",assignment:"CH\u2083"}],integration:3,from:4.3950000000000005,to:4.405}],nucleus:"1H",solvent:"D\u2082O",id:"2f85d722-9fb1-4ed3-a811-471295bc05d0"},{names:["n-pentane"],smiles:"CCCCC",ranges:[],nucleus:"1H",solvent:"D\u2082O",id:"85d7229f-b1ae-4368-9147-1295bc05d0d6"},{names:["propane"],smiles:"CCC",ranges:[{signals:[{js:[{coupling:7.3,multiplicity:"t"}],delta:.88,assignment:"CH\u2083"}],integration:6,from:.85675,to:.90325},{signals:[{js:[{coupling:7.3,multiplicity:"sept"}],delta:1.3,assignment:"CH\u2082"}],integration:2,from:1.24025,to:1.35975}],nucleus:"1H",solvent:"D\u2082O",id:"d7229fb1-aed3-4811-8712-95bc05d0d6a8"},{names:["2-propanol"],smiles:"CC(O)C",ranges:[{signals:[{js:[{coupling:6,multiplicity:"d"}],delta:1.17,assignment:"CH\u2083"}],integration:6,from:1.1575,to:1.1824999999999999},{signals:[{js:[{coupling:6,multiplicity:"sept"}],delta:4.02,assignment:"CH"}],integration:1,from:3.9699999999999998,to:4.069999999999999}],nucleus:"1H",solvent:"D\u2082O",id:"229fb1ae-d368-4147-9295-bc05d0d6a885"},{names:["propylene"],smiles:"CC=C",ranges:[{signals:[{js:[{coupling:6.4,multiplicity:"d"},{coupling:1.5,multiplicity:"t"}],delta:1.7,assignment:"CH\u2083"}],integration:3,from:1.68325,to:1.71675},{signals:[{js:[{coupling:10,multiplicity:"d"}],delta:4.95,assignment:"CH\u2082(1)"}],integration:1,from:4.9325,to:4.9675},{signals:[{js:[{coupling:17,multiplicity:"d"}],delta:5.06,assignment:"CH\u2082(2)"}],integration:1,from:5.0337499999999995,to:5.08625},{signals:[{js:[],delta:5.9,assignment:"CH",multiplicity:"m"}],integration:1,from:5.875,to:5.925000000000001}],nucleus:"1H",solvent:"D\u2082O",id:"9fb1aed3-6811-4712-95bc-05d0d6a88510"},{names:["pyridine"],smiles:"C1=CC=NC=C1",ranges:[{signals:[{js:[],delta:8.52,assignment:"CH(2,6)",multiplicity:"m"}],integration:2,from:8.495,to:8.545},{signals:[{js:[],delta:7.45,assignment:"CH(3,5)",multiplicity:"m"}],integration:2,from:7.425,to:7.4750000000000005},{signals:[{js:[],delta:7.87,assignment:"CH(4)",multiplicity:"m"}],integration:1,from:7.845,to:7.8950000000000005}],nucleus:"1H",solvent:"D\u2082O",id:"b1aed368-1147-4295-bc05-d0d6a88510f8"},{names:["pyrrole"],smiles:"C1=CNC=C1",ranges:[{signals:[{js:[],delta:6.93,assignment:"CH(2,5)",multiplicity:"m"}],integration:2,from:6.904999999999999,to:6.955},{signals:[{js:[],delta:6.26,assignment:"CH(3,4)",multiplicity:"m"}],integration:2,from:6.234999999999999,to:6.285}],nucleus:"1H",solvent:"D\u2082O",id:"aed36811-4712-45bc-85d0-d6a88510f8b5"},{names:["pyrrolidine"],smiles:"C1CCNC1",ranges:[{signals:[{js:[],delta:3.07,assignment:"CH\u2082(2,5)",multiplicity:"m"}],integration:4,from:3.045,to:3.0949999999999998},{signals:[{js:[],delta:1.87,assignment:"CH\u2082(3,4)",multiplicity:"m"}],integration:4,from:1.8450000000000002,to:1.895}],nucleus:"1H",solvent:"D\u2082O",id:"d3681147-1295-4c05-90d6-a88510f8b557"},{names:["silicone 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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?Sm({from:0,size:c.length,step:u[1]-u[0]}):u})}function Os(e){return!!(e.info.isComplex&&e.info.isFid)}function Fm(e,n){return{once:!0,reduce:n}}var xs={name:"backwardLinearPrediction",label:"Backward Linear Prediction Filter",domainUpdateRules:vm,apply:Pm,reduce:Fm,isApplicable:Os};import $m from"ml-airpls";import{PolynomialRegression as _m}from"ml-regression-polynomial";import{xyEquallySpaced as Km}from"ml-spectra-processing";import{CholeskyDecomposition as wm,Matrix as Fs}from"ml-matrix";import{calculateAdaptiveWeights as Nm,xMultiply as Am}from"ml-spectra-processing";function Ss(e,n,t){if(n===0)return 1;if(e===0||n>e)return 0;if(n>e-n&&(n=e-n),!t)return jm(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 jm(e,n){let t=1,s=e;for(let i=1;i<=n;i++)t*=s--,t/=i;return t}import{Matrix as Mm}from"ml-matrix";function vs(e){let n=e.rows,t=e.columns,s=new Mm(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 Rm}from"ml-spectra-processing";function Ps(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=Rm({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 js(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=km(e,{degree:n,weights:l,logger:u});if(!f)return m;l=Nm(e,f,l,{minWeight:r,learningRate:a,factorStd:o}),d=Im(f,c,e.length),c.set(f),m=f,g++}return m}function km(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]=Ss(o,c);let m=new Fs(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 wm(vs(m));if(!c.isPositiveDefinite())throw new Error("Matrix is not positive definite");let g=Am(e,s),d=Fs.from1DArray(i,1,g),u=c.solve(m.mmul(d)),f=Ps(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 Im(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 Tm,xWhittakerSmoother as Em}from"ml-spectra-processing";function Ms(e,n){let t=e.length;if(t===0)return new Float64Array(0);let s=n??Tm({from:0,step:1,size:t}),i=Em(e);return zm(s,i)}function zm(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 D=u[p-1]/f[p-1];f[p]-=D*C[p-1],y[p]-=D*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,D=g[C],h=D.a+D.b*p+D.c*p**2+D.d*p**3;d[u]=h}return d}import{DirectConvolution as Ym,FFTConvolution as Wm}from"ml-convolution";import{Matrix as Um}from"ml-matrix";import{xAdd as Zm,xWhittakerSmoother as Vm}from"ml-spectra-processing";import{Matrix as Bm}from"ml-matrix";import{xMean as Xm,xStandardDeviation as qm}from"ml-spectra-processing";function qe(e){let n=[],t=[],{rows:s,columns:i}=e,[o,a]=Lm(e);for(;a.length!==t.length;)if(a.length>0){[o,n]=[[],o],[a,t]=[[],a];let c=Xm(t),g=qm(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=Bm.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=Rs(c,s),u=Rs(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 Rs(e,n){return{from:Math.max(e-5,0),to:Math.min(e+5,n)}}function Lm(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 Ns(e,n){let t=Gm(e,n),s=qe(t).to1DArray(),{lambda:i=150,maxIterations:o=1}=n;return Vm(e,{lambda:i,controlPoints:s,maxIterations:o})}function ws(e,n,t=1){let s=n.convolve(e),i=[];for(let o of s)i.push(Math.abs(o/t));return i}function Gm(e,n){let t=e.length,{scale:s=11}=n,i=Jm(s),o=s>32?new Wm(t,i):new Ym(t,i),a=ws(e,o,s),r=ws(a,o,s);return new Um([Zm(a,r)])}function Jm(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 Qm={updateXDomain:!1,updateYDomain:!1};function ec(e,n){if(!As(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=$m(s,i,n).corrected;break;case"polynomial":{let{degree:a,zones:r}=n,l=Km({x:s,y:i},{numberOfPoints:4096,zones:r}),c=new _m(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=Ns(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=js(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=Ms(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 As(e){return!e.info.isFid}function tc(e,n){return{once:!0,reduce:n}}var ks={name:"baselineCorrection",label:"Baseline correction",domainUpdateRules:Qm,apply:ec,reduce:tc,isApplicable:As};var nc={updateXDomain:!0,updateYDomain:!0};function sc(e,n){if(!Is(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 Is(e){return!!(e.info.isComplex&&e.info.isFid)}function ic(e,n){return{once:!0,reduce:n}}var Ts={name:"digitalFilter",label:"Digital Filter",domainUpdateRules:nc,apply:sc,reduce:ic,isApplicable:Is};import{xEnsureFloat64 as Nt,xyEquallySpaced as Es}from"ml-spectra-processing";var oc={updateXDomain:!1,updateYDomain:!1};function ac(e,n={}){if(!zs(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=Es({x:a,y:r},{from:t,to:s,numberOfPoints:i,exclusions:o});if(e.data.x=Nt(m.x),e.data.re=Nt(m.y),l){let c=Es({x:a,y:r},{from:t,to:s,numberOfPoints:i,exclusions:o});e.data.im=Nt(c.y)}}function zs(e){return!!(e.info.isComplex&&!e.info.isFid)}function rc(e,n){return{once:!1,reduce:n}}var Bs={name:"equallySpaced",label:"Equally spaced",domainUpdateRules:oc,apply:ac,reduce:rc,isApplicable:zs};import{xySetYValue as Xs}from"ml-spectra-processing";var lc={updateXDomain:!1,updateYDomain:!1};function mc(e,n){if(!qs(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(Xs({x:t,y:s},{zones:n}).y),e.data.im=i&&Float64Array.from(Xs({x:t,y:s},{zones:n}).y)}function qs(e){return!!e.info.isFt}function cc(e,n){return{once:!0,reduce:gc(e.concat(n))}}var Ls={name:"exclusionZones",label:"Exclusion zones",domainUpdateRules:lc,apply:mc,reduce:cc,isApplicable:qs};function gc(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 fc,reimFFT as pc,reimPhaseCorrection as Cc,xMean as Ws,xMultiply as yc}from"ml-spectra-processing";var T=Math.PI/180;import{nextPowerOfTwo as dc,xSequentialFillFromStep as uc}from"ml-spectra-processing";function Ys(e){let{x:n,re:t,im:s}=e.data,i=dc(n.length),o=new Float64Array(i),a=new Float64Array(i);o.set(t.slice(0,i)),a.set(s.slice(0,i));let r=uc({from:n[0],size:i,step:n[1]-n[0]});e.data={...e.data,re:o,im:a,x:r}}var bc={updateXDomain:!0,updateYDomain:!0};function Dc(e){if(!Us(e))throw new Error("fft not applicable on this data");xc(e);let n=e.filters.some(o=>o.name==="digitalFilter"&&o.enabled),{info:{aqMod:t}}=e;t===1&&Oc(e),fc(e.data.x.length)||Ys(e);let{data:s,info:i}=e;if(Object.assign(s,pc({re:s.re,im:i.reverse?yc(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*T:0;Object.assign(s,Cc(s,l,-r,{reverse:!0}))}e.data.x=Hc(e),e.info={...e.info,isFid:!1,isFt:!0}}function Us(e){return!!(e.info.isComplex&&e.info.isFid)}function hc(e,n){return{once:!0,reduce:n}}function Hc(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 Oc(e){let n=e.data,t=n.re.length,s=new Float64Array(n.re),i=new Float64Array(n.im),o=Ws(n.re.slice(t*.75>>0,t)),a=Ws(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 xc(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 Zs={name:"fft",label:"FFT",domainUpdateRules:bc,apply:Dc,reduce:hc,isApplicable:Us};import{xSequentialFillFromStep as Pc}from"ml-spectra-processing";import{Matrix as Sc,SVD as vc}from"ml-matrix";function Vs(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 vc(a),l=new Float64Array(s);for(let g=0;g<s;g++)l[g]=e[o-g+1];let m=r.solve(Sc.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);Vs(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 Fc={updateXDomain:!0,updateYDomain:!0};function jc(e,n={}){if(!Gs(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?Pc({from:0,size:u.length,step:C[1]-C[0]}):C})}function Gs(e){return!!(e.info.isComplex&&e.info.isFid)}function Mc(e,n){return{once:!0,reduce:n}}var Js={name:"forwardLinearPrediction",label:"Forward Linear Prediction Filter",domainUpdateRules:Fc,apply:jc,reduce:Mc,isApplicable:Gs};import{reimAbsolute as Rc,reimAutoPhaseCorrection as wc,reimPhaseCorrection as Nc,xEnsureFloat64 as $s}from"ml-spectra-processing";var Ac={updateXDomain:!1,updateYDomain:!1};function kc(e,n={}){if(!Qs(e))throw new Error("Phase correction not applicable on this data");let{absolute:t=!1}=n,s=e.filters?.find(i=>i.name==="phaseCorrection");if(t){let{re:i,im:o}=e.data;e.data.re=Rc({re:i,im:o}),e.data.im=void 0,s&&(s.value={...s.value,ph0:0,ph1:0,absolute:t})}else if("ph0"in n&&"ph1"in n){let{ph0:i=0,ph1:o=0}=n;_s(e,{ph0:i,ph1:o}),s&&(s.value={...s.value,absolute:t})}else{let i=Ks(e);if(i.ph0===0&&i.ph1===0&&(i=Ks(e,{magnitudeMode:!0})),_s(e,i),s){let{ph0:o,ph1:a}=i;s.value={...s.value,absolute:t,ph0:o,ph1:a}}}}function _s(e,n){let{ph0:t,ph1:s}=n,{re:i,im:o}=e.data,a=Nc({re:i,im:o},t*Math.PI/180,s*Math.PI/180,{reverse:!0});e.data={...e.data,re:$s(a.re),im:$s(a.im)}}function Ks(e,n={}){let{minRegSize:t=5,maxDistanceToJoin:s=128,magnitudeMode:i=!1,factorNoise:o=5,reverse:a=!0}=n;return wc(e.data,{minRegSize:t,maxDistanceToJoin:s,magnitudeMode:i,factorNoise:o,reverse:a})}function Qs(e){return!!(e.info.isComplex&&!e.info.isFid)}function Ic(e,n){return{once:!0,reduce:n}}var ei={name:"phaseCorrection",label:"Phase 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m=a;m<s-a;m++)i[m]-=r,o[m]-=l;return{re:i,im:o}}function _i(e,n={}){let{re:t,im:s}=e,i=t.length,o=T0(t[0].length),{reverse:a,digitalFilterValue:r=0}=n,l=new Ji(i,o),m=new Ji(i,o),{phaseCorrection:c={}}=n,g=o>t[0].length,{ph0:d,ph1:u,mode:f="no"}=c,C=Math.floor(r),y=r*Math.PI*2,p=C%2?180*T:0;for(let D=0;D<i;D++){let h={re:t[D],im:a?B0(s[D],-1):s[D]};Object.assign(h,Gi(h,{digitalFilterValue:r})),g&&Object.assign(h,z0(h,o)),Object.assign(h,E0(h,{applyZeroShift:!0})),y>0&&Object.assign(h,$i(h,p,-y,{reverse:!0})),f==="pk"&&d!==void 0&&u!==void 0&&Object.assign(h,$i(h,d*Math.PI/180,u*Math.PI/180,{reverse:!0})),l.setRow(D,h.re),m.setRow(D,h.im)}return{re:l,im:m}}import{xAdd as X0,xMultiply as q0,xSubtract as zt}from"ml-spectra-processing";function Ki(e){let{re:{z:n},im:{z:t}}=e,s=[],i=[],o=n.length,a=o-o%2;for(let r=0;r<a;r+=2){let l=n[r],m=t[r],c=n[r+1],g=t[r+1];s.push(zt(q0(g,-1),m),zt(c,l)),i.push(X0(c,l),zt(g,m))}return{re:s,im:i}}import{matrixCreateEmpty as Qi,nextPowerOfTwo as L0}from"ml-spectra-processing";function eo(e){let{data:n,info:t,meta:s={}}=e,{nuslist:i,NusTD:o}=s,a=t.acquisitionScheme?.toLowerCase(),r=n.re.z[0].length,l=L0(o[1]),m={re:[],im:[]};if(a==="echo-antiecho"){let c=i.map(d=>d*2),g=["re","im"];for(let d of g){let u=n[d].z,f=Qi({nbRows:l,nbColumns:r,ArrayConstructor:Float64Array}),C=n.re.z.length/2;for(let y=0;y<C;y++){let p=c[y];f[p].set(u[2*y]),f[p+1].set(u[2*y+1])}m[d]=f}}else{let c=["re","im"];for(let g of c){let d=n[g].z,u=Qi({nbRows:l,nbColumns:r,ArrayConstructor:Float64Array}),f=n.re.z.length;for(let C=0;C<f;C++){let y=i[C];u[y].set(d[C])}m[g]=u}}e.data={re:{...n.re,z:m.re},im:{...n.im,z:m.im}}}var Y0={updateXDomain:!0,updateYDomain:!0};function W0(e,n){if(!no(e))throw new Error("fft dimension 1 not applicable on this data");let{data:t,info:s,meta:{nuslist:i=[]}={}}=e,{digitalFilter:o=0,reverse:a=[!1,!1]}=s,r=s.acquisitionScheme?.toLowerCase();if(t.re.z.length!==t.im.z.length||t.re.z[0].length!==t.im.z[0].length)throw new RangeError("real and imaginary data must have the same dimensionality");let l=r==="echo-antiecho"?Ki(t):{re:t.re.z,im:t.im.z},m=_i(l,{acquisitionScheme:r,...n,reverse:a[0],digitalFilterValue:o});e.data.re.z=m.re.to2DArray().map(to),e.data.im.z=m.im.to2DArray().map(to);let{isFid:c,...g}=s;e.info={...g,isFid:!1,isFtDimensionOne:!0},i.length>0&&eo(e)}function no(e){return!!(e.info.isComplex&&e.info.isFid)}function U0(e,n){return{once:!0,reduce:n}}var so={name:"fftDimension1",label:"FFT Dimension 1",domainUpdateRules:Y0,apply:W0,reduce:U0,isApplicable:no};import{matrixMinMaxZ as Q0}from"ml-spectra-processing";import{Matrix as ue}from"ml-matrix";import{isPowerOfTwo as Z0,nextPowerOfTwo as oo,reimAbsolute as V0,reimFFT as G0,reimPhaseCorrection as J0,reimZeroFilling as $0,xMultiply as _0}from"ml-spectra-processing";function ao(e,n={}){let t={re:ue.checkMatrix(e.re),im:ue.checkMatrix(e.im)},s=oo(t.re.rows),i=t.re.columns,{acquisitionScheme:o,reverse:a}=n,r={...n},l={};if(o==="notPhaseSensitive"){let m=new ue(s,i),c=new ue(s,i);for(let g=0;g<i;g++){let d={re:t.re.getColumn(g),im:_0(t.im.getColumn(g),-1)},{re:u,im:f}=io(d,r);m.setColumn(g,u),c.setColumn(g,f)}l.rr=m,l.ir=c}else for(let m in t){let c=o==="SEQ"?s:s/2,g=new ue(c,i),d=new ue(c,i);for(let u=0;u<i;u++){let f=K0(t[m],{acquisitionScheme:o,index:u,reverse:a}),{re:C,im:y}=io(f,r);g.setColumn(u,C),d.setColumn(u,y)}m==="re"?(l.rr=g,l.ri=d):(l.ir=g,l.ii=d)}return l}function io(e,n){let{acquisitionScheme:t,phaseCorrection:s={}}=n;if(e.re[0]*=.5,e.im[0]*=.5,!Z0(e.re.length)){let l=oo(e.re.length);Object.assign(e,$0(e,l))}let i=G0(e,{applyZeroShift:t!=="SEQ"}),{mode:o,ph0:a,ph1:r}=s;return(o&&o==="mc"||t==="notPhaseSensitive")&&Object.assign(i,{re:V0(i),im:new Float64Array(e.re.length)}),o==="pk"&&a!==void 0&&r!==void 0&&Object.assign(i,J0(i,a*Math.PI/180,r*Math.PI/180)),i}function K0(e,n){let{index:t}=n,s=(n.acquisitionScheme||"").toLocaleLowerCase();if(s==="seq")return{re:e.getColumn(t),im:new Float64Array(e.rows)};let i=e.rows/2,o=new Float64Array(i),a=new Float64Array(i);if(n.reverse||s==="notphasesensitive")for(let l=0;l<i;l++)o[l]=e.get(2*l,t),a[l]=-e.get(2*l+1,t);else for(let l=0;l<i;l++)o[l]=e.get(2*l,t),a[l]=e.get(2*l+1,t);if(["states-tppi","tppi"].includes(s))for(let l=0;l<i;l+=2)o[l]*=-1,a[l]*=-1;return{re:o,im:a}}function ro(e){let n=[],t=[];for(let s=0;s<e.baseFrequency.length;s++){let i=e.baseFrequency[s],o=e.frequencyOffset[s],a=e.spectralWidth[s],r=o/i;n.push(r-a*.5),t.push(r+a*.5)}return{minX:n[0],maxX:t[0],minY:n[1],maxY:t[1]}}var eg={updateXDomain:!0,updateYDomain:!0};function tg(e,n){if(!lo(e))throw new Error("fft dimension 2 not applicable on this data");let{data:t,info:s}=e,i=s.acquisitionScheme;if(t.re.z.length!==t.im.z.length||t.re.z[0].length!==t.im.z[0].length)throw new RangeError("real and imaginary data must have the same dimensionality");let o={re:t.re.z,im:t.im.z},{reverse:a=[!1,!1]}=s,r=ao({re:o.re,im:o.im},{reverse:a[1],acquisitionScheme:i,...n});e.data={...ng(r,s)},e.info={...s,isFt:!0}}function ng(e,n){let t={},{acquisitionScheme:s}=n,i=ro(n),o=a=>{for(let r of a){let l=Object.values(e[r])[0],{min:m,max:c}=Q0(l);t[r]={z:l,maxZ:c,minZ:m,...i}}return t};return o(s==="notPhaseSensitive"?["rr","ir"]:["rr","ir","ri","ii"])}function lo(e){let{isComplex:n,isFtDimensionOne:t,isFt:s}=e.info;return!!(n&&t&&!s)}function sg(e,n){return{once:!0,reduce:n}}var mo={name:"fftDimension2",label:"FFT Dimension 2",domainUpdateRules:eg,apply:tg,reduce:sg,isApplicable:lo};import{matrixMinMaxZ as co}from"ml-spectra-processing";var ig={updateXDomain:!0,updateYDomain:!0};function og(e,n={}){if(!go(e))throw new Error("Forward Linear Prediction on dimension 1 is not applicable on this 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fo,matrixMinMaxZ as po}from"ml-spectra-processing";var rg={updateXDomain:!0,updateYDomain:!0};function lg(e,n={}){if(!Co(e))throw new Error("Forward linear prediction on dimension 2 is not applicable on this data");let{info:t,data:{re:s,im:i}}=e,o=s.z,a=i.z,r=o.length,l=o[0].length,{lpNumberOfCoefficients:m=[0,0],linearPredictionBin:c=[0,0],spectrumSize:g=[l,r],numberOfPoints:d=[l,r]}=t,{nbPoints:u=me(g[1],d[1],c[1])/-2,nbCoefficients:f=m[1],nbInputs:C=Math.floor(r-f-Math.max(u,0))}=n,y=e.filters.find(x=>x.name==="flpDimension2");if(y&&(y.value={nbCoefficients:f,nbPoints:u,nbInputs:C}),Math.abs(u)===0||f===0)return;let p=u<0?-1*u:0,D=fo({nbRows:r+p,nbColumns:l}),h=fo({nbRows:r+p,nbColumns:l});for(let x=0;x<l;x++){let{re:H,im:S}=le({re:I(o,x),im:I(a,x)},{nbPoints:u,nbCoefficients:f,nbInputs:C});E(D,H,x),E(h,S,x)}let b=po(D),O=po(h),v={re:{...s,z:D,minZ:b.min,maxZ:b.max},im:{...i,z:h,minZ:O.min,maxZ:O.max}};Object.assign(e.data,v)}function Co(e){let{isComplex:n,isFt:t,isFtDimensionOne:s}=e.info;return!!(n&&s&&!t)}function mg(e,n){return{once:!0,reduce:n}}var yo={name:"flpDimension2",label:"Fordward-LP Dimension 2",domainUpdateRules:rg,apply:lg,reduce:mg,isApplicable:Co};import{matrixMinMaxZ as Oo,nextPowerOfTwo as pg,xHilbertTransform as xo}from"ml-spectra-processing";import{matrixCreateEmpty as Ge,matrixMaxAbsoluteZ as cg,matrixTranspose as bo,nextPowerOfTwo as gg,reimFFT as Ho,reimZeroFilling as dg,xHilbertTransform as ug,xMultiply as Bt}from"ml-spectra-processing";function qt(e,n){let{nusLength:t,nusIndices:s}=n,i=gg(t),o=e.re.z[0].length,a={re:Ge({nbRows:o,nbColumns:i*4}),im:Ge({nbRows:o,nbColumns:i*4})},r={re:Ge({nbRows:o,nbColumns:i*4}),im:Ge({nbRows:o,nbColumns:i*4})};for(let b=0;b<o;b++){let O=I(e.re.z,b),v=Bt(I(e.im.z,b),-1);O[0]*=.5,v[0]*=.5;let x=dg({re:O,im:v},i*4),H=Ho(x,{applyZeroShift:!0});a.re[b].set(H.re),a.im[b].set(H.im)}let 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Xt(e,n={}){let{inverse:t=!1}=n,s=e.re.length,{re:i,im:o}=e;for(let a=0;a<s;a++){let r=Ho({re:i[a],im:t?Bt(ug(i[a]),-1):o[a]},{inverse:t,applyZeroShift:!0});e.re[a].set(r.re),e.im[a].set(r.im)}return e}var Cg={updateXDomain:!0,updateYDomain:!0};function yg(e){if(!So(e))throw new Error("fft dimension 2 not applicable on this data");let{data:n,meta:t={},info:s}=e;if(n.re.z.length!==n.im.z.length||n.re.z[0].length!==n.im.z[0].length)throw new RangeError("real and imaginary data must have the same dimensionality");let i=s.acquisitionScheme?.toLowerCase(),{nuslist:o,NusTD:a}=t,r={re:n.re,im:n.im},l=pg(a[1]),m={re:[],im:[]};if(i==="echo-antiecho"){l/=2;let d=r.re.z,u=d.length/2,f=[],C=[];for(let b=0;b<u;b++)f.push(d[2*b]),C.push(d[2*b+1]);let y={re:{...r.re,z:f},im:{...r.im,z:C}},p=qt(y,{nusIndices:o,nusLength:l}),D=[],h=p.re.z.length;for(let b=0;b<h;b++)D.push(p.re.z[b],p.im.z[b]);m.re=D;for(let b=0;b<h;b++)m.im.push(xo(p.re.z[b]),xo(p.im.z[b]))}else{let d=qt(r,{nusIndices:o,nusLength:l});m.re=d.re.z,m.im=d.im.z}let c=Oo(m.re),g=Oo(m.im);e.data={re:{...r.re,z:m.re,minZ:c.min,maxZ:c.max},im:{...r.im,z:m.im,minZ:g.min,maxZ:g.max}}}function So(e){let{nuslist:n}=e.meta??{},{isComplex:t,isFtDimensionOne:s,isFt:i}=e.info;return!!(n.length>0&&t&&s&&!i)}function bg(e,n){return{once:!0,reduce:n}}var vo={name:"nusDimension2",label:"NUS Reconstruction",domainUpdateRules:Cg,apply:yg,reduce:bg,isApplicable:So};import{Matrix as _e,MatrixTransposeView as jo,WrapperMatrix2D as Hg}from"ml-matrix";import{SparseMatrix as Ke}from"ml-sparse-matrix";import{matrixCreateEmpty as Og,xMaxIndex as xg}from"ml-spectra-processing";function fe(e){if(["rr","ir","ri","ii"].some(n=>!(n in e)))throw new Error("four quadrants should has ir, ri and ii quadrants")}function Je(e){if(["rr","ri"].some(n=>!(n in e)))throw new Error("Two quadrants should has ri quadrant")}import{reimPhaseCorrection as hg}from"ml-spectra-processing";import{Matrix as 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Mo(e,n={}){let{absolute:t,phases:s,threshold:i,nonZeros:o}=Pg(e,n),a=wo(t,s,i),{columns:r,rows:l,values:m}=o,c=xg(m),g={x:r[c],y:l[c]};return Sg(a,{pivot:g,absolute:t,phases:s,threshold:i})}function Sg(e,n){let t=-30,s=30,i=8,o=Number.MAX_SAFE_INTEGER,a=Number.MAX_SAFE_INTEGER,{pivot:r,absolute:l}=n,{x:m}=r,{columns:c}=l,g=0,d=30,u=vg(n);for(;i>0&&g!==o;){o=g;for(let C=t;C<=s+1;C+=d){let y=e([u-C*m/c,C]);y<a&&([a,g]=[y,C])}t=u+Math.sign(u)*d,s=t,i--}t=g-d,s=g+d;let f=5;for(i=5,o=Number.MAX_SAFE_INTEGER;i>0;){o=g;let C=(s-t)/(f-1);for(let y=t;y<=s+1;y+=C){let p=e([u-y*m/c,y]);p<a&&([a,g]=[p,y])}t=g-C,s=g+C,i--}return{ph0:u-g*m/c,ph1:g}}function vg(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:g}=t;for(let H=g-40;H<g+40;H++)for(let S=c-40;S<c+40;S++)l.set(H,S,s.get(H,S)),m.set(H,S,i.get(H,S));let d=wo(l,m,o),u=-15,f=15,C=12,y=0,p=Number.MAX_SAFE_INTEGER,D=Number.MAX_SAFE_INTEGER,h=15;for(;C>0&&y!==p;){p=y;for(let H=u;H<f+1;H+=h){let S=d([H,0]);S<=D&&([D,y]=[S,H])}u=y+Math.sign(y)*h,f=u,C--}u=y-15,f=y+15;let b=5;for(C=5;C>0;){let H=(f-u)/(b-1);for(let S=u;S<=f;S+=H){let P=d([S,0]);P<D&&([D,y]=[P,S])}u=y-H,f=y+H,C--}let O=s.get(g,c),v=i.get(g,c);return O*Math.cos(v+y*T)<0?y-Math.sign(y)*180:y}function Pg(e,n={}){let{re:t,im:s}=e,{transpose:i=!1}=n,o=i?new jo(new _e(t)):new _e(t),a=i?new jo(new _e(s)):new _e(s),{rows:r,columns:l}=o,m=Og({nbRows:r,nbColumns:l});for(let y=0;y<r;y++)for(let p=0;p<l;p++)m[y][p]=Math.hypot(o.get(y,p),a.get(y,p));let{threshold:c=new Hg(m).mean()*2}=n,g=new Ke(m,{threshold:c}),d=new Ke(g.rows,g.columns,{threshold:-1}),u=g.getNonZeros(),{columns:f,rows:C}=u;for(let y=0;y<C.length;y++){let[p,D]=[C[y],f[y]];d.set(p,D,Math.atan2(a.get(p,D),o.get(p,D)))}return{absolute:g,phases:d,threshold:c,nonZeros:u}}function wo(e,n,t){let s=e.columns;return 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Tg={updateXDomain:!1,updateYDomain:!0};function Eg(e,n){let{shift:t}=n,s={...e.data};for(let i in s)s[i].minY+=t,s[i].maxY+=t}function zg(e,n){let{shift:t=0}=e,{shift:s}=n;return{once:!0,reduce:{shift:t+s}}}function Bg(){return!0}var Eo={name:"shift2DY",label:"Shift 2D Y",domainUpdateRules:Tg,apply:Eg,reduce:zg,isApplicable:Bg};import{matrixMinMaxZ as Xg}from"ml-spectra-processing";var qg={updateXDomain:!0,updateYDomain:!0};function Lg(e){if(!Bo(e))throw new Error("Symmetrization is only applicable to square matrices and FT data");let n={...e.data},t=Wg(n.rr.z),s=Xg(t);e.data={rr:{...n.rr,z:t,minZ:s.min,maxZ:s.max}},e.info.isComplex=!1}function Bo(e){if(e.info.isFt&&"rr"in e.data){let n=e.data.rr.z;return n[0].length===n.length}return!1}function Yg(e,n){return{once:!0,reduce:n}}var zo=Math.abs;function Wg(e){let n=e.length,t=e[0].length;for(let s=0;s<n;s++)for(let i=s;i<t;i++){let o=Math.min(zo(e[s][i]),zo(e[i][s]));e[s][i]=o,e[i][s]=o}return e}var 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Qg(e,n,t){let{x:s,y:i}=e;if(n==="origin")return{...e,x:{...s,originalDelta:s.delta-t.x},y:{...i,originalDelta:i.delta-t.y}};if(s.originalDelta===void 0||i.originalDelta===void 0)throw new TypeError('originalDelta must exist when shiftTarget is "current"');return{...e,x:{...s,originalDelta:s.originalDelta,delta:s.originalDelta+t.x},y:{...i,originalDelta:i.originalDelta,delta:i.originalDelta+t.y}}}function ed(e,n,t){let{x:s,y:i}=e;return n==="origin"?{x:{...s,originalFrom:s.from-t.x,originalTo:s.to-t.x},y:{...i,originalFrom:i.from-t.y,originalTo:i.to-t.y}}:{x:{...s,from:(s?.originalFrom||0)+t.x,to:(s?.originalTo||0)+t.x},y:{...i,from:(i?.originalFrom||0)+t.y,to:(i?.originalTo||0)+t.y}}}function td(e,n,t){let{x:s,y:i,originalX:o=0,originalY:a=0}=e;return n==="origin"?{...e,originalX:s-t.x,originalY:i-t.y}:{...e,x:o+t.x,y:a+t.y}}function _o(e,n,t={}){let{checkIsExisting:s=!0,shiftTarget:i="origin"}=t,o=$o(n),a=Go(n);return 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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 va}from"gyromagnetic-ratio";function G8(e){if(e in va)return e;if(e.toLowerCase()==="proton")return"1H";let n=e.replaceAll(/[^0-9]/g,"");if(!n)return e;for(let t in va)if(t.includes(n))return t;return e}function K8(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 hu(s),bu(s,n),t?.info(`Found: ${s.ranges.length} ranges`),s}function bu(e,n={}){let{logger:t}=n;for(let s of e.parts)if(s.toLowerCase().includes("nmr"))Du(e,s);else{e.info.frequency||(e.info.frequency=400,t?.warn("Frequency not defined, assuming 400 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ye(e,n,t={}){let{solvent:s,symRatio:i=1.5,integrationSum:o=100,joinOverlapRanges:a=!0,clean:r=.4,compile:l=!1,integralType:m="sum",frequency:c=400,frequencyCluster:g=16,keepPeaks:d=!1,nucleus:u="1H"}=t,f={solvent:s,integrationSum:o,integralType:m,frequencyCluster:g,frequency:c,nucleus:u};if(n.length===0)return[];e.x[0]>e.x[1]&&(e.x=e.x.toReversed(),e.y=e.y.toReversed());let{peaks:C,solventSignals:y}=$u(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,b;for(let O=0;O<p.length;O++){p[O]=Ta.compilePattern(p[O],{symRatio:i});let v=p[O];if(v.maskPattern&&v.multiplicity!=="m"&&v.multiplicity!==""){Ju(v),h=0,b=0;let x=[];for(let H=v.maskPattern.length-1;H>=0;H--)if(b+=Se(v.peaks[H],c),!v.maskPattern[H]){let 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V7(e,n){let{from:t,to:s}=n.peakPicking,{fromIndex:i,toIndex:o}=gf(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:df(e,{fromIndex:i,toIndex:o}).x,multiplicity:"",js:[]}]}];let{ranges:r={}}=n,{nucleus:l=""}=r;switch(l){case"1H":return La(e,n);case"13C":return Ba(e,n);default:return Xa(e,n)}}import{BaseRegression as uf}from"ml-regression-base";import{SimpleLinearRegression as ff}from"ml-regression-simple-linear";import{xyCheck as pf}from"ml-spectra-processing";function K7(e,n){pf(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 ff(l,r),{slope:c,intercept:g}=m.toJSON(),d=-c/a/(i*o)**2,u=Math.exp(g);return{regression:new _t(d,u,n),coefficient:d,signalAbsenseDiffussion:u}}var _t=class extends uf{coefficient;signalAbsenseDiffussion;gyromagneticRatio;gradientPulseDuration;timeCorrection;constructor(n,t,s){let{gyromagneticRatio:i,gradientPulseDuration:o,timeCorrection:a}=s;super(),this.coefficient=n,this.signalAbsenseDiffussion=t,this.gyromagneticRatio=i,this.gradientPulseDuration=o,this.timeCorrection=a}_predict(n){return this.signalAbsenseDiffussion*Math.exp(-this.timeCorrection*this.coefficient*(n*this.gyromagneticRatio*this.gradientPulseDuration)**2)}};import{levenbergMarquardt as Cf}from"ml-levenberg-marquardt";import{BaseRegression as yf}from"ml-regression-base";import{xyCheck as bf}from"ml-spectra-processing";var Df={damping:1.5,maxIterations:100,errorTolerance:1e-8};function 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