jcampconverter 10.0.0 → 10.0.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/jcampconverter.cjs +6 -6
- package/jcampconverter.d.ts +13 -8
- package/jcampconverter.mjs +6 -6
- package/package.json +2 -1
package/jcampconverter.cjs
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"use strict";var
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"use strict";var de=Object.create;var $=Object.defineProperty;var be=Object.getOwnPropertyDescriptor;var ge=Object.getOwnPropertyNames;var he=Object.getPrototypeOf,xe=Object.prototype.hasOwnProperty;var ye=(e,f)=>{for(var t in f)$(e,t,{get:f[t],enumerable:!0})},se=(e,f,t,o)=>{if(f&&typeof f=="object"||typeof f=="function")for(let a of ge(f))!xe.call(e,a)&&a!==t&&$(e,a,{get:()=>f[a],enumerable:!(o=be(f,a))||o.enumerable});return e};var Ae=(e,f,t)=>(t=e!=null?de(he(e)):{},se(f||!e||!e.__esModule?$(t,"default",{value:e,enumerable:!0}):t,e)),Ce=e=>se($({},"__esModule",{value:!0}),e);var $e={};ye($e,{convert:()=>Me,createTree:()=>Ne,parseJcampCS:()=>Oe});module.exports=Ce($e);var oe=require("ensure-string");var P=/\s*\$\$.*/;function O(e){return e.replace(P,"")}function Ne(e,f={}){e=(0,oe.ensureString)(e);let{flatten:t=!1}=f,o=e.split(/\r?\n/),a=[],i=[],n=[],m={title:"",jcamp:"",children:[]},r=0,p=e.includes("## ");for(let u=0;u<o.length;u++){let b=o[u],h=p?b.replaceAll(" ",""):b;if(h.startsWith("##NTUPLES")&&r++,h.startsWith("##TITLE")){let s=[h.slice(8).trim()];for(let l=u+1;l<o.length&&!o[l].startsWith("##");l++)s.push(o[l].trim());i.push({title:s.join(`
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`),jcamp:`${b}
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`,children:[]}),m=
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`;let s=
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`;let s=h.match(/^##(.*?)=(.+)/);if(s){let l=s[1].replaceAll(/[ _-]/g,"").toUpperCase();l==="DATATYPE"?m.dataType=s[2].trim():l==="DATACLASS"?m.dataClass=s[2].trim():l==="JCAMPDX"?m.jcampDX=O(s[2].trim()):l==="JCAMPCS"&&(m.jcampCS=O(s[2].trim()))}}h.startsWith("##END")&&r>0&&r--}if(t){for(let u of a)u.children=void 0;return a}else return n}var ce=require("dynamic-typing"),pe=require("ensure-string");var ae=["TIC",".RIC","SCANNUMBER"];function le(e){let f=e.spectra,t=f.length,i={times:new Array(t),series:{ms:{dimension:2,data:new Array(t)}}},a=[];for(let o of ae){let n=B(o);f[0][n]&&(a.push(n),i.series[n]={dimension:1,data:new Array(t)})}for(let o=0;o<t;o++){let n=f[o];i.times[o]=n.pageValue;for(let m of a)i.series[m].data[o]=Number(n[m]);n.data&&(i.series.ms.data[o]=[n.data.x,n.data.y])}e.chromatogram=i}function fe(e){return ae.includes(e)}function B(e){return e.toLowerCase().replaceAll(/[^a-z0-9]/g,"")}function E(e){return e.map(Number)}function j(e,f,t){let{logger:i}=t;i&&(e.xFactor||i.info("The xFactor is not defined, it will be set to 1"),e.yFactor||i.info("The yFactor is not defined, it will be set to 1"));let a=e.yFactor??1,o=e.xFactor??1,n=e.deltaX??1,m=Math.abs(n*.1),r=.01;e.isXYdata=!0;let p={x:[],y:[]};e.data=p;let u=e.firstX||0,b=e.firstY||0,h=!1,s,l=0;for(;l<f.length;l++)if(s=f.codePointAt(l),s===13||s===10)h=!0;else if(h)break;let c=0,d=!0,A=!1,y=!1,k=0,N=!1,C=!1,g=0,X=0,M=!1,S=!1,Y=!1,R=0;for(;l<=f.length;l++)if(l===f.length?s=13:s=f.codePointAt(l),C)(s===13||s===10)&&(d=!0,C=!1,c++);else if(s<=57&&s>=48)S=!0,R>0?g+=(s-48)/10**R++:(g*=10,g+=s-48);else if(s===44||s===46)S=!0,R++;else{if(S){if(M&&(g=g*-1,M=!1),d)g*=o,i&&(y?Math.abs(u-n-g)>m&&(Math.abs(u-g)<m?i.trace(`Data line ${c}: After a DIFFERENCE the next line should repeat the last value and this does not seem to be the case: Current value: ${g} - Expected: ${u}.`):Math.abs(u-n-g)>10*m?i.trace(`Data line ${c}: The difference between the first value ${g} and the expected first x value ${u} based on increment after a DIFFERENCE is too high`):i.trace(`Data line ${c}: The difference between the first value ${g} and the expected first x value ${u} based on increment after a DIFFERENCE is too high`)):Math.abs(u-g)>m&&i.trace(`Data line ${c}: The difference between the first value ${g} and the first x value ${u} is too high`)),d=!1,y&&(Y=!0);else if(Y)Y=!1,i&&Math.abs(b-g)>r&&i.trace(`Data line ${c}: After a duplicate the next line should repeat the same value ${g} !== ${b}`),b=g;else{A?(k=M?0-g:g,y=!0,A=!1):N||(X=M?0-g:g);let x=N?g-1:1;for(let F=0;F<x;F++)y?b+=k:b=X,p.x.push(u),p.y.push(b*a),u+=n}M=!1,g=0,R=0,S=!1,N=!1}if(s<74&&s>63)S=!0,y=!1,g=s-64;else if(s>96&&s<106)S=!0,y=!1,g=s-96,M=!0;else if(s===115)S=!0,N=!0,g=9;else if(s>82&&s<91)S=!0,N=!0,g=s-82;else if(s>73&&s<83)S=!0,A=!0,g=s-73;else if(s>105&&s<115)S=!0,A=!0,g=s-105,M=!0;else if(s===36&&f.codePointAt(l+1)===36)S=!0,C=!0;else if(s===37)S=!0,A=!0,g=0,M=!1;else if(s===45){let x=f.codePointAt(l+1);(x!==void 0&&x>=48&&x<=57||x===44||x===46)&&(S=!0,d||(y=!1),M=!0)}else(s===13||s===10)&&(d=!0,C=!1,c++)}i&&y&&i.warn("The last value is a difference, it should be repeated on the next line")}var me=/[,\t ]+/;function w(e,f,t){if(e.isPeaktable=!0,!e.variables||Object.keys(e.variables).length===2?ve(e,f,t):Xe(e,f,t),e.variables)for(let i in e.variables)e.variables[i].data=e.data?.[i]}function ve(e,f,t){let{logger:i}=t,a={x:[],y:[]};e.data=a;let o=f.split(/,? *,?[;\r\n]+ */);for(let n=1;n<o.length;n++){let m=o[n].trim().replace(P,"").split(me);if(m.length%2===0)for(let r=0;r<m.length;r=r+2)e.xFactor!==void 0&&e.yFactor!==void 0&&(a.x.push(Number(m[r])*e.xFactor),a.y.push(Number(m[r+1])*e.yFactor));else i?.warn(`Format error: ${m.toString()}`)}}function Xe(e,f,t){let{logger:i}=t,a={},o=Object.keys(e.variables),n=o.length;for(let r of o)a[r]=[];e.data=a;let m=f.split(/,? *,?[;\r\n]+ */);for(let r=1;r<m.length;r++){let p=m[r].trim().replace(P,"").split(me);if(p.length%n===0)for(let u=0;u<p.length;u++)a[o[u%n]].push(Number(p[u]));else i?.warn(`Wrong number of columns: ${p.toString()}`)}}function Z(e,f){e.isXYAdata=!0;let t={};e.data=t;let i=f.split(/\r?\n/),a=i[0].replace(/^.*?([A-Z]+).*$/,"$1").split("").map(o=>o.toLowerCase());for(let o=1;o<i.length;o++){let n=i[o].replace(/^\((.*)\)$/,"$1").split(/ *, */);for(let m=0;m<a.length;m++){let r=n[m];switch(a[m]){case"x":case"y":case"w":r=Number.parseFloat(r);break;case"a":r=r.replace(/^<(.*)>$/,"$1");break;case"m":break;default:continue}t[a[m]]||(t[a[m]]=[]),t[a[m]].push(r)}}}var Q=require("dynamic-typing");var G=require("gyromagnetic-ratio"),W=Ce(require("ml-array-median"));function ue(e){return Array.isArray(e)?e[0]:e}function H(e){let{spectra:f}=e,t=f[0].data.y[0],i=t,a=f.length,o=f[0].data.x.length||0,n=new Array(a);for(let s=0;s<a;s++){n[s]=f[s].data.y;for(let l=0;l<o;l++){let c=n[s][l];c<t&&(t=c),c>i&&(i=c)}}let m=f[0].data.x[0],r=f[0].data.x.at(-1),{firstY:p,lastY:u}=Le(e);if(m>r)for(let s of n)s.reverse();p>u&&n.reverse();let b=[];for(let s of n){let l=Float64Array.from(s);for(let c=0;c<l.length;c++)l[c]<0&&(l[c]=-l[c]);b.push((0,W.default)(l))}let h=(0,W.default)(b);return{z:n,minX:Math.min(m,r),maxX:Math.max(m,r),minY:Math.min(p,u),maxY:Math.max(p,u),minZ:t,maxZ:i,noise:h}}function Le(e){let{spectra:f,ntuples:t,info:i}=e;if(t)for(let a of t){let{symbol:o,nucleus:n,units:m}=a;if(o.match(/[F|T]1/)&&m?.toUpperCase().match("HZ")){let r=ue(i[".OBSERVEFREQUENCY"]),{nucleus:p}=t.find(c=>c.symbol.match(/[F|T]2/));if([r,p,n].some(c=>!c))break;let u=(0,G.getGyromagneticRatio)(p),b=(0,G.getGyromagneticRatio)(n),{first:h,last:s}=a,l=b!==null&&u!==null?r*b/u:r;return{firstY:h/l,lastY:s/l}}}return{firstY:f[0].pageValue,lastY:f.at(-1).pageValue}}function J(e,f){let t=e.noise,i=e.z,a,o,n,m,r,p,u,b,h=i.length,s=i[0].length,l,c,d,A,y=e.minX,N=(e.maxX-y)/(s-1),C=e.minY,X=(e.maxY-C)/(h-1),M=e.minZ,S=e.maxZ,Y=f.nbContourLevels*2,R=new Array(Y),x;for(let F=0;F<Y;F++){let V={};R[F]=V;let ge=F%2,te=(S-f.noiseMultiplier*t)*Math.exp((F>>1)-f.nbContourLevels);ge===0?x=te+f.noiseMultiplier*t:x=0-te-f.noiseMultiplier*t;let D=[];if(V.zValue=x,V.lines=D,!(x<=M||x>=S))for(let v=0;v<h-1;v++){let ne=i[v],re=i[v+1];for(let T=0;T<s-1;T++)a=ne[T],o=ne[T+1],n=re[T],m=re[T+1],r=a>x,p=o>x,u=n>x,b=m>x,r!==p&&r!==u&&(l=T+(x-a)/(o-a),c=v,d=T,A=v+(x-a)/(n-a),D.push(l*N+y,c*X+C,d*N+y,A*X+C)),b!==p&&b!==u&&(l=T+1,c=v+1-(x-m)/(o-m),d=T+1-(x-m)/(n-m),A=v+1,D.push(l*N+y,c*X+C,d*N+y,A*X+C)),p!==u&&(l=(T+1-(x-o)/(n-o))*N+y,c=(v+(x-o)/(n-o))*X+C,p!==r&&(d=T+1-(x-o)/(a-o),A=v,D.push(l,c,d*N+y,A*X+C)),u!==r&&(d=T,A=v+1-(x-n)/(a-n),D.push(l,c,d*N+y,A*X+C)),p!==b&&(d=T+1,A=v+(x-o)/(m-o),D.push(l,c,d*N+y,A*X+C)),u!==b&&(d=T+(x-n)/(m-n),A=v+1,D.push(l,c,d*N+y,A*X+C)))}}return{minX:e.minX,maxX:e.maxX,minY:e.minY,maxY:e.maxY,segments:R}}function q(e,f){let t=H(e);f.noContour||(e.contourLines=J(t,f),delete t.z),e.minMax=t}var I=require("gyromagnetic-ratio");function z(e,f){for(let t of e){let i=0,a=0;for(let o of t.spectra){if(t.ntuples?.symbol?(!i&&o.observeFrequency&&(i=o.observeFrequency),!a&&o.shiftOffsetVal&&(a=o.shiftOffsetVal)):(i=o.observeFrequency,a=o.shiftOffsetVal),i&&o.xUnits?.toUpperCase().includes("HZ")&&(o.xUnits="PPM",o.xFactor=o.xFactor!==void 0?o.xFactor/i:void 0,o.firstX=o.firstX!==void 0?o.firstX/i:void 0,o.lastX=o.lastX!==void 0?o.lastX/i:void 0,o.deltaX=o.deltaX!==void 0?o.deltaX/i:void 0,o.data))for(let n=0;n<o.data.x.length;n++)o.data.x[n]/=i;if(a&&o.xUnits.toLowerCase().includes("ppm")&&o.firstX!==void 0&&o.lastX!==void 0){let n=o.firstX-a;if(o.firstX=o.firstX-n,o.lastX=o.lastX-n,o.data)for(let m=0;m<o.data.x.length;m++)o.data.x[m]-=n}if(t.ntuples?.nucleus&&t.ntuples.symbol)for(let n=0;n<t.ntuples.nucleus.length;n++){let m=t.ntuples.symbol[n],r=t.ntuples.nucleus[n];if(m.match(/^[F|T]/)&&!r){if(m.match(/[F|T]1/))if(t.tmp.$NUC2&&typeof t.tmp.$NUC2=="string")t.ntuples.nucleus[n]=t.tmp.$NUC2;else{let p=t.ntuples.symbol.indexOf(m.replace(/^([F|T]).*/,"$12"));p&&t.ntuples.nucleus[p]&&(t.ntuples.nucleus[n]=t.ntuples.nucleus[p])}m.match(/[F|T]2/)&&typeof t.tmp.$NUC1=="string"&&(t.ntuples.nucleus[n]=t.tmp.$NUC1)}m.match(/[F|T]2/)&&(t.yType=t.ntuples.nucleus[0],t.xType&&!(0,I.getGyromagneticRatio)(t.xType)&&(t.xType=t.ntuples.nucleus[1]))}if(i&&t.ntuples?.symbol&&t.ntuples.nucleus){let n="",m=t.ntuples.symbol.indexOf(o.pageSymbol);t.ntuples.units?.[m]&&(n=t.ntuples.units[m]);let{nucleus:r}=t.ntuples;if(!n.toLowerCase().match(/(ppm|seconds)/)&&r.length>1){if(m!==0){let h="Not sure about this ntuples format";if(f){f.warn(h);continue}else throw new Error(h)}let{nucleus:p}=t.ntuples,u=(0,I.getGyromagneticRatio)(p[0]),b=(0,I.getGyromagneticRatio)(p[1]);if(!u||!b){let h=`Problem with determination of gyromagnetic ratio for ${p.join("-")}`;if(f)f.error(h);else throw new Error(h)}else{let h=u/b*i;o.pageValue/=h}}}}}}function K(e){let f=e.spectra[0].data;e.chromatogram={times:f.x.slice(),series:{intensity:{dimension:1,data:f.y.slice()}}}}function _(e,f,t){z(e,t.logger),Me(e,t);for(let i of e){if(Object.keys(i.ntuples).length>0){let a=[],o=Object.keys(i.ntuples);for(let n of o){let m=i.ntuples[n];if(m)for(let r=0;r<m.length;r++)a[r]||(a[r]={}),a[r][n]=m[r]}i.ntuples=a}i.twoD&&t.wantXY&&(q(i,t),t.logger?.trace({profiling:!0},"Finished countour plot calculation"),t.keepSpectra||delete i.spectra),t.chromatogram&&(i.spectra.length>1?le(i):K(i),t.logger?.trace({profiling:!0},"Finished chromatogram calculation")),delete i.tmp}}function Me(e,f){for(let t of e)for(let i in t.meta){let a=t.meta[i];if(typeof a=="string"){if(a.startsWith("{")){if(!a.includes(":")&&a.endsWith("}")){let o=a.slice(1,-1).split(/[,; ]+/).filter(Boolean);for(let n=0;n<o.length;n++)t.meta[i+String(n)]=f.dynamicTyping?(0,Q.parseString)(o[n]):o[n]}}else if(a.startsWith("(")){let o=a.split(/\r?\n/),n=/^\((?<from>\d+)\.\.(?<to>\d+)\).*$/;if(n.test(o[0])){let[m,r]=o[0].match(n)?.slice(1).map(Number)??[],p=o.slice(1).join(" ").split(/[,; ]+/).filter(Boolean);for(let u=m;u<=r;u++)f.dynamicTyping&&typeof p[u-m]=="string"?t.meta[i+String(u)]=(0,Q.parseString)(p[u-m]):t.meta[i+String(u)]=p[u-m]}}}}}function ee(e,f,t){let i=-1,a=-1,o="",n="";if(t.indexOf("++")>0)o=t.replace(/.*\(([a-zA-Z0-9]+)\+\+.*/,"$1"),n=t.replace(/.*\.\.([a-zA-Z0-9]+).*/,"$1");else{t=t.replaceAll(/[^a-zA-Z%]/g,""),o=t.charAt(0),n=t.charAt(1),f.variables={};for(let m of t){let r=m.toLowerCase(),p=e.ntuples.symbol?.indexOf(m)||0;if(p===-1)throw new Error(`Symbol undefined: ${m}`);f.variables[r]={};for(let u in e.ntuples)e.ntuples[u]?.[p]&&(f.variables[r][u.replace(/^var/,"")]=e.ntuples[u]?.[p])}}i=e.ntuples.symbol?.indexOf(o)??-1,a=e.ntuples.symbol?.indexOf(n)??-1,i===-1&&(i=0),a===-1&&(a=0),e.ntuples.first&&(e.ntuples.first.length>i&&(f.firstX=e.ntuples.first[i]),e.ntuples.first.length>a&&(f.firstY=e.ntuples.first[a])),e.ntuples.last&&(e.ntuples.last.length>i&&(f.lastX=e.ntuples.last[i]),e.ntuples.last.length>a&&(f.lastY=e.ntuples.last[a])),e.ntuples.vardim&&e.ntuples.vardim.length>i&&(f.nbPoints=e.ntuples.vardim[i]),e.ntuples.factor&&(e.ntuples.factor.length>i&&(f.xFactor=e.ntuples.factor[i]),e.ntuples.factor.length>a&&(f.yFactor=e.ntuples.factor[a])),e.ntuples.units&&(e.ntuples.units.length>i&&(e.ntuples.varname?.[i]?f.xUnits=`${e.ntuples.varname[i]} [${e.ntuples.units[i]}]`:f.xUnits=e.ntuples.units[i]),e.ntuples.units.length>a&&(e.ntuples.varname?.[a]?f.yUnits=`${e.ntuples.varname[a]} [${e.ntuples.units[a]}]`:f.yUnits=e.ntuples.units[a]))}function U(e){e.xFactor||(e.xFactor=1),e.yFactor||(e.yFactor=1)}var L=/[ \t]*,[ \t]*/,Oe={keepRecordsRegExp:/^$/,canonicDataLabels:!0,canonicMetadataLabels:!1,dynamicTyping:!0,withoutXY:!1,noTrimRegExp:/^$/,chromatogram:!1,keepSpectra:!1,noContour:!1,nbContourLevels:7,noiseMultiplier:5};function de(e,f={}){e=(0,pe.ensureString)(e);let t={...Oe,...f};t.logger?.debug("Starting jcamp conversion"),t.wantXY=!t.withoutXY,t.start=Date.now();let i=[],a={entries:[],flatten:[]},o={children:[],spectra:[],ntuples:{},info:{},meta:{},tmp:{}},n=o,m=[],r={data:{}};t.logger?.trace({profiling:!0},"Before split to LDRS");let p=e.replaceAll(/[\r\n]+##/g,`
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`,children:[]}),m=i.at(-1),a.push(m)}else if(h.startsWith("##END")&&r===0&&m){m.jcamp+=`${b}
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`;let s=i.pop();if(!s)throw new Error("Not finished");i.length>0?(m=i.at(-1),m.children?.push(s)):(m=void 0,n.push(s))}else if(m?.jcamp){m.jcamp+=`${b}
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`;let s=h.match(/^##(.*?)=(.+)/);if(s){let l=s[1].replaceAll(/[ _-]/g,"").toUpperCase();l==="DATATYPE"?m.dataType=s[2].trim():l==="DATACLASS"?m.dataClass=s[2].trim():l==="JCAMPDX"?m.jcampDX=O(s[2].trim()):l==="JCAMPCS"&&(m.jcampCS=O(s[2].trim()))}}h.startsWith("##END")&&r>0&&r--}if(t){for(let u of a)u.children=void 0;return a}else return n}var ue=require("dynamic-typing"),ce=require("ensure-string");var ie=["TIC",".RIC","SCANNUMBER"];function ae(e){let f=e.spectra,t=f.length,o={times:new Array(t),series:{ms:{dimension:2,data:new Array(t)}}},a=[];for(let i of ie){let n=B(i);f[0][n]&&(a.push(n),o.series[n]={dimension:1,data:new Array(t)})}for(let i=0;i<t;i++){let n=f[i];o.times[i]=n.pageValue;for(let m of a)o.series[m].data[i]=Number(n[m]);n.data&&(o.series.ms.data[i]=[n.data.x,n.data.y])}e.chromatogram=o}function le(e){return ie.includes(e)}function B(e){return e.toLowerCase().replaceAll(/[^a-z0-9]/g,"")}function E(e){return e.map(Number)}function 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|
+
`)),l==="TITLE"){let c=n;c.children||(c.children=[]),n={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},c.children.push(n),m.push(c),o.push(n),n.title=s}else l==="DATATYPE"?(n.dataType=s,s.match(/^nd|\snd\s/i)&&(n.twoD=!0)):l==="NTUPLES"?s.match(/^nd|\snd\s/i)&&(n.twoD=!0):l==="DATACLASS"?n.dataClass=s:l==="JCAMPDX"?n.jcampDX=O(s):l==="JCAMPCS"?n.jcampCS=O(s):l==="XUNITS"?r.xUnits=s:l==="YUNITS"?r.yUnits=s:l==="FIRSTX"?r.firstX=Number(s):l==="LASTX"?r.lastX=Number(s):l==="FIRSTY"?r.firstY=Number(s):l==="LASTY"?r.lastY=Number(s):l==="NPOINTS"?r.nbPoints=Number(s):l==="XFACTOR"?r.xFactor=Number(s):l==="YFACTOR"?r.yFactor=Number(s):l==="MAXX"?r.maxX=Number(s):l==="MINX"?r.minX=Number(s):l==="MAXY"?r.maxY=Number(s):l==="MINY"?r.minY=Number(s):l==="DELTAX"?r.deltaX=Number(s):l===".OBSERVEFREQUENCY"||l==="$SFO1"?r.observeFrequency||(r.observeFrequency=Number(s)):l===".OBSERVENUCLEUS"?r.xType||(n.xType=s.replaceAll(/[^a-zA-Z0-9]/g,"")):l==="$OFFSET"?(n.shiftOffsetNum=0,r.shiftOffsetVal||(r.shiftOffsetVal=Number(s))):l==="$REFERENCEPOINT"||(l==="VARNAME"?n.ntuples.varname=s.split(L):l==="SYMBOL"?n.ntuples.symbol=s.split(L):l==="VARTYPE"?n.ntuples.vartype=s.split(L):l==="VARFORM"?n.ntuples.varform=s.split(L):l==="VARDIM"?n.ntuples.vardim=E(s.split(L)):l==="UNITS"?n.ntuples.units=s.split(L):l==="FACTOR"?n.ntuples.factor=E(s.split(L)):l==="FIRST"?n.ntuples.first=E(s.split(L)):l==="LAST"?n.ntuples.last=E(s.split(L)):l==="MIN"?n.ntuples.min=E(s.split(L)):l==="MAX"?n.ntuples.max=E(s.split(L)):l===".NUCLEUS"?n.ntuples&&(n.ntuples.nucleus=s.split(L).map(c=>c.replaceAll(/[^a-zA-Z0-9]/g,""))):l==="PAGE"?(r.page=s.trim(),r.pageValue=Number(s.replace(/^.*=/,"")),r.pageSymbol=r.page.replace(/[=].*/,"")):l==="RETENTIONTIME"?r.pageValue=Number(s):le(l)?r[B(l)]=s:l==="SAMPLEDESCRIPTION"?r.sampleDescription=s:l.startsWith("$NUC")?!n.tmp[l]&&!s.includes("off")&&(n.tmp[l]=s.replaceAll(/[<>]/g,"")):l==="END"&&(n=m.pop()));if(n?.info&&n.meta&&l.match(t.keepRecordsRegExp)){let c,d;h.startsWith("$")?(d=t.canonicMetadataLabels?l.slice(1):h.slice(1),c=n.meta):(d=t.canonicDataLabels?l:h,c=n.info),t.dynamicTyping&&(s=(0,ue.parseString)(s)),c[d]?(Array.isArray(c[d])||(c[d]=[c[d]]),c[d].push(s)):c[d]=s}}if(t.logger?.trace({profiling:!0},"Finished parsing"),_(o,a,t),t.logger?.trace({profiling:!0},"Total time"),a.entries=i.children||[],a.flatten=o,t.logger){t.logger.debug("Finished jcamp conversion");for(let u of a.flatten)t.logger.debug(`${u.dataType} - ${u.title}`)}return a}function Oe(e,f){let{logger:t,OCL:o}=f;if(!e.info.ATOMLIST||!e.info.BONDLIST){t?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}Ye(e,t);let a=Ee(e.info.ATOMLIST),i=Re(e.info.BONDLIST),n=De(e.info.CHARGE,t),m=Fe(o,a,i,n,t);return{molecule:m,molfile:m.toMolfile()}}function Fe(e,f,t,o,a){let i={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},n={},m=new e.Molecule(f.length,t.length);for(let r of f){let p=e.Molecule.getAtomicNoFromLabel(r.element);p||(a?.error(`Atomic number of ${r.element} could not be determined`),p=e.Molecule.getAtomicNoFromLabel("X")),n[r.atomNumber]=m.addAtom(p),m.setAtomMapNo(n[r.atomNumber],r.atomNumber,!1)}for(let r of t){if(n[r.atomNumber1]===void 0){a?.error(`A bond goes to atomNumber ${r.atomNumber1} that does not exists`);continue}if(n[r.atomNumber2]===void 0){a?.error(`A bond goes to atomNumber ${r.atomNumber2} that does not exists`);continue}let p=m.addBond(n[r.atomNumber1],n[r.atomNumber2]);m.setBondType(p,i[r.bondType])}for(let r of o){if(n[r.atomNumber]===void 0){a?.error(`A charge goes to atomNumber ${r.atomNumber} that does not exists`);continue}m.setAtomCharge(n[r.atomNumber],r.value)}return m}function Ee(e){let f=e.split(/\r?\n/).map(o=>O(o)).filter(Boolean),t=[];for(let o of f){let[a,i,n]=o.trim().split(/\s+/);t.push({atomNumber:Number(a),element:i,nbImplicitHydrogens:n?.length>0?Number(n):void 0})}return t}function Re(e){let f=e.split(/\r?\n/).map(o=>O(o)).filter(Boolean),t=[];for(let o of f){let[a,i,n]=o.trim().split(/\s+/);t.push({atomNumber1:Number(a),atomNumber2:Number(i),bondType:n})}return t}function De(e,f){if(!e)return[];let t=e.split(/\r?\n/).map(a=>O(a)).filter(Boolean),o=[];for(let a of t){let[i,n,m]=a.trim().split(/\s+/);m!==void 0&&f?.warn("Charge on multiple atom is not supported"),o.push({atomNumber:Number(n),value:Number(i)})}return o}function Ye(e,f){let t=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let o of t)e.info[o]&&f?.warn(`JCAMP-CS parser do not support: ${o}`)}
|
package/jcampconverter.d.ts
CHANGED
|
@@ -41,7 +41,12 @@ export declare function convert(jcamp: string | ArrayBuffer | Uint8Array, option
|
|
|
41
41
|
/**
|
|
42
42
|
* Conversion options.
|
|
43
43
|
*/
|
|
44
|
-
declare interface ConvertOptions extends Partial<Add2DOptions> {
|
|
44
|
+
export declare interface ConvertOptions extends Partial<Add2DOptions> {
|
|
45
|
+
/**
|
|
46
|
+
* If it is true, anywhere out of XYDATA, PEAKTABLE n PEAKASSIGNMENTS the comments are removed
|
|
47
|
+
* @default false
|
|
48
|
+
*/
|
|
49
|
+
removeComments?: boolean;
|
|
45
50
|
/**
|
|
46
51
|
* By default we don't keep meta information.
|
|
47
52
|
* @default `/^$/`
|
|
@@ -88,7 +93,7 @@ declare interface ConvertOptions extends Partial<Add2DOptions> {
|
|
|
88
93
|
fastParse?: boolean;
|
|
89
94
|
}
|
|
90
95
|
|
|
91
|
-
declare interface ConvertResult {
|
|
96
|
+
export declare interface ConvertResult {
|
|
92
97
|
entries: Entry[];
|
|
93
98
|
flatten: Entry[];
|
|
94
99
|
}
|
|
@@ -101,11 +106,11 @@ declare interface ConvertResult {
|
|
|
101
106
|
*/
|
|
102
107
|
export declare function createTree(jcamp: string | ArrayBuffer | Uint8Array, options?: CreateTreeOptions): Stack[];
|
|
103
108
|
|
|
104
|
-
declare interface CreateTreeOptions {
|
|
109
|
+
export declare interface CreateTreeOptions {
|
|
105
110
|
flatten?: boolean;
|
|
106
111
|
}
|
|
107
112
|
|
|
108
|
-
declare interface Entry {
|
|
113
|
+
export declare interface Entry {
|
|
109
114
|
spectra: Spectrum[];
|
|
110
115
|
ntuples: Ntuples;
|
|
111
116
|
meta: Record<string, string | string[] | number | number[] | boolean | boolean[] | undefined>;
|
|
@@ -140,7 +145,7 @@ declare interface GenerateContourLinesOptions {
|
|
|
140
145
|
noiseMultiplier: number;
|
|
141
146
|
}
|
|
142
147
|
|
|
143
|
-
declare interface MinMax {
|
|
148
|
+
export declare interface MinMax {
|
|
144
149
|
z: number[][];
|
|
145
150
|
minX: number;
|
|
146
151
|
maxX: number;
|
|
@@ -152,7 +157,7 @@ declare interface MinMax {
|
|
|
152
157
|
noice?: number;
|
|
153
158
|
}
|
|
154
159
|
|
|
155
|
-
declare interface Ntuples {
|
|
160
|
+
export declare interface Ntuples {
|
|
156
161
|
varname?: string[];
|
|
157
162
|
symbol?: string[];
|
|
158
163
|
vartype?: string[];
|
|
@@ -183,12 +188,12 @@ declare interface ParsedCS {
|
|
|
183
188
|
*/
|
|
184
189
|
export declare function parseJcampCS(entry: Entry, options: ParseJcampCSOptions): ParsedCS | undefined;
|
|
185
190
|
|
|
186
|
-
declare interface ParseJcampCSOptions {
|
|
191
|
+
export declare interface ParseJcampCSOptions {
|
|
187
192
|
OCL: OCL;
|
|
188
193
|
logger?: Logger;
|
|
189
194
|
}
|
|
190
195
|
|
|
191
|
-
declare interface Spectrum {
|
|
196
|
+
export declare interface Spectrum {
|
|
192
197
|
[key: string]: any;
|
|
193
198
|
data: Record<string, number[]>;
|
|
194
199
|
firstX?: number;
|
package/jcampconverter.mjs
CHANGED
|
@@ -1,9 +1,9 @@
|
|
|
1
|
-
import{ensureString as fe}from"ensure-string";var $=/\s*\$\$.*/;function O(e){return e.replace($,"")}function
|
|
1
|
+
import{ensureString as fe}from"ensure-string";var $=/\s*\$\$.*/;function O(e){return e.replace($,"")}function ve(e,m={}){e=fe(e);let{flatten:n=!1}=m,o=e.split(/\r?\n/),f=[],i=[],t=[],l={title:"",jcamp:"",children:[]},r=0,p=e.includes("## ");for(let u=0;u<o.length;u++){let b=o[u],h=p?b.replaceAll(" ",""):b;if(h.startsWith("##NTUPLES")&&r++,h.startsWith("##TITLE")){let s=[h.slice(8).trim()];for(let a=u+1;a<o.length&&!o[a].startsWith("##");a++)s.push(o[a].trim());i.push({title:s.join(`
|
|
2
2
|
`),jcamp:`${b}
|
|
3
|
-
`,children:[]}),l=
|
|
4
|
-
`;let s=
|
|
5
|
-
`;let s=h.match(/^##(.*?)=(.+)/);if(s){let a=s[1].replaceAll(/[ _-]/g,"").toUpperCase();a==="DATATYPE"?l.dataType=s[2].trim():a==="DATACLASS"?l.dataClass=s[2].trim():a==="JCAMPDX"?l.jcampDX=O(s[2].trim()):a==="JCAMPCS"&&(l.jcampCS=O(s[2].trim()))}}h.startsWith("##END")&&r>0&&r--}if(n){for(let u of f)u.children=void 0;return f}else return t}import{parseString as be}from"dynamic-typing";import{ensureString as ge}from"ensure-string";var ee=["TIC",".RIC","SCANNUMBER"];function te(e){let m=e.spectra,n=m.length,i={times:new Array(n),series:{ms:{dimension:2,data:new Array(n)}}},f=[];for(let o of ee){let t=k(o);m[0][t]&&(f.push(t),i.series[t]={dimension:1,data:new Array(n)})}for(let o=0;o<n;o++){let t=m[o];i.times[o]=t.pageValue;for(let l of f)i.series[l].data[o]=Number(t[l]);t.data&&(i.series.ms.data[o]=[t.data.x,t.data.y])}e.chromatogram=i}function ne(e){return ee.includes(e)}function k(e){return e.toLowerCase().replaceAll(/[^a-z0-9]/g,"")}function E(e){return e.map(Number)}function V(e,m,n){let{logger:i}=n;i&&(e.xFactor||i.info("The xFactor is not defined, it will be set to 1"),e.yFactor||i.info("The yFactor is not defined, it will be set to 1"));let f=e.yFactor??1,o=e.xFactor??1,t=e.deltaX??1,l=Math.abs(t*.1),r=.01;e.isXYdata=!0;let p={x:[],y:[]};e.data=p;let u=e.firstX||0,b=e.firstY||0,h=!1,s,a=0;for(;a<m.length;a++)if(s=m.codePointAt(a),s===13||s===10)h=!0;else if(h)break;let c=0,d=!0,A=!1,y=!1,I=0,N=!1,C=!1,g=0,X=0,M=!1,S=!1,Y=!1,R=0;for(;a<=m.length;a++)if(a===m.length?s=13:s=m.codePointAt(a),C)(s===13||s===10)&&(d=!0,C=!1,c++);else if(s<=57&&s>=48)S=!0,R>0?g+=(s-48)/10**R++:(g*=10,g+=s-48);else if(s===44||s===46)S=!0,R++;else{if(S){if(M&&(g=g*-1,M=!1),d)g*=o,i&&(y?Math.abs(u-t-g)>l&&(Math.abs(u-g)<l?i.trace(`Data line ${c}: After a DIFFERENCE the next line should repeat the last value and this does not seem to be the case: Current value: ${g} - Expected: ${u}.`):Math.abs(u-t-g)>10*l?i.trace(`Data line ${c}: The difference between the first value ${g} and the expected first x value ${u} based on increment after a DIFFERENCE is too high`):i.trace(`Data line ${c}: The difference between the first value ${g} and the expected first x value ${u} based on increment after a DIFFERENCE is too high`)):Math.abs(u-g)>l&&i.trace(`Data line ${c}: The difference between the first value ${g} and the first x value ${u} is too high`)),d=!1,y&&(Y=!0);else if(Y)Y=!1,i&&Math.abs(b-g)>r&&i.trace(`Data line ${c}: After a duplicate the next line should repeat the same value ${g} !== ${b}`),b=g;else{A?(I=M?0-g:g,y=!0,A=!1):N||(X=M?0-g:g);let x=N?g-1:1;for(let F=0;F<x;F++)y?b+=I:b=X,p.x.push(u),p.y.push(b*f),u+=t}M=!1,g=0,R=0,S=!1,N=!1}if(s<74&&s>63)S=!0,y=!1,g=s-64;else if(s>96&&s<106)S=!0,y=!1,g=s-96,M=!0;else if(s===115)S=!0,N=!0,g=9;else if(s>82&&s<91)S=!0,N=!0,g=s-82;else if(s>73&&s<83)S=!0,A=!0,g=s-73;else if(s>105&&s<115)S=!0,A=!0,g=s-105,M=!0;else if(s===36&&m.codePointAt(a+1)===36)S=!0,C=!0;else if(s===37)S=!0,A=!0,g=0,M=!1;else if(s===45){let x=m.codePointAt(a+1);(x!==void 0&&x>=48&&x<=57||x===44||x===46)&&(S=!0,d||(y=!1),M=!0)}else(s===13||s===10)&&(d=!0,C=!1,c++)}i&&y&&i.warn("The last value is a difference, it should be repeated on the next line")}var re=/[,\t ]+/;function P(e,m,n){if(e.isPeaktable=!0,!e.variables||Object.keys(e.variables).length===2?ue(e,m,n):ce(e,m,n),e.variables)for(let i in e.variables)e.variables[i].data=e.data?.[i]}function ue(e,m,n){let{logger:i}=n,f={x:[],y:[]};e.data=f;let o=m.split(/,? *,?[;\r\n]+ */);for(let t=1;t<o.length;t++){let l=o[t].trim().replace($,"").split(re);if(l.length%2===0)for(let r=0;r<l.length;r=r+2)e.xFactor!==void 0&&e.yFactor!==void 0&&(f.x.push(Number(l[r])*e.xFactor),f.y.push(Number(l[r+1])*e.yFactor));else i?.warn(`Format error: ${l.toString()}`)}}function ce(e,m,n){let{logger:i}=n,f={},o=Object.keys(e.variables),t=o.length;for(let r of o)f[r]=[];e.data=f;let l=m.split(/,? *,?[;\r\n]+ */);for(let r=1;r<l.length;r++){let p=l[r].trim().replace($,"").split(re);if(p.length%t===0)for(let u=0;u<p.length;u++)f[o[u%t]].push(Number(p[u]));else i?.warn(`Wrong number of columns: ${p.toString()}`)}}function B(e,m){e.isXYAdata=!0;let n={};e.data=n;let i=m.split(/\r?\n/),f=i[0].replace(/^.*?([A-Z]+).*$/,"$1").split("").map(o=>o.toLowerCase());for(let o=1;o<i.length;o++){let t=i[o].replace(/^\((.*)\)$/,"$1").split(/ *, */);for(let l=0;l<f.length;l++){let r=t[l];switch(f[l]){case"x":case"y":case"w":r=Number.parseFloat(r);break;case"a":r=r.replace(/^<(.*)>$/,"$1");break;case"m":break;default:continue}n[f[l]]||(n[f[l]]=[]),n[f[l]].push(r)}}}import{parseString as ae}from"dynamic-typing";import{getGyromagneticRatio as ie}from"gyromagnetic-ratio";import oe from"ml-array-median";function se(e){return Array.isArray(e)?e[0]:e}function j(e){let{spectra:m}=e,n=m[0].data.y[0],i=n,f=m.length,o=m[0].data.x.length||0,t=new Array(f);for(let s=0;s<f;s++){t[s]=m[s].data.y;for(let a=0;a<o;a++){let c=t[s][a];c<n&&(n=c),c>i&&(i=c)}}let l=m[0].data.x[0],r=m[0].data.x.at(-1),{firstY:p,lastY:u}=pe(e);if(l>r)for(let s of t)s.reverse();p>u&&t.reverse();let b=[];for(let s of t){let a=Float64Array.from(s);for(let c=0;c<a.length;c++)a[c]<0&&(a[c]=-a[c]);b.push(oe(a))}let h=oe(b);return{z:t,minX:Math.min(l,r),maxX:Math.max(l,r),minY:Math.min(p,u),maxY:Math.max(p,u),minZ:n,maxZ:i,noise:h}}function pe(e){let{spectra:m,ntuples:n,info:i}=e;if(n)for(let f of n){let{symbol:o,nucleus:t,units:l}=f;if(o.match(/[F|T]1/)&&l?.toUpperCase().match("HZ")){let r=se(i[".OBSERVEFREQUENCY"]),{nucleus:p}=n.find(c=>c.symbol.match(/[F|T]2/));if([r,p,t].some(c=>!c))break;let u=ie(p),b=ie(t),{first:h,last:s}=f,a=b!==null&&u!==null?r*b/u:r;return{firstY:h/a,lastY:s/a}}}return{firstY:m[0].pageValue,lastY:m.at(-1).pageValue}}function Z(e,m){let n=e.noise,i=e.z,f,o,t,l,r,p,u,b,h=i.length,s=i[0].length,a,c,d,A,y=e.minX,N=(e.maxX-y)/(s-1),C=e.minY,X=(e.maxY-C)/(h-1),M=e.minZ,S=e.maxZ,Y=m.nbContourLevels*2,R=new Array(Y),x;for(let F=0;F<Y;F++){let U={};R[F]=U;let le=F%2,K=(S-m.noiseMultiplier*n)*Math.exp((F>>1)-m.nbContourLevels);le===0?x=K+m.noiseMultiplier*n:x=0-K-m.noiseMultiplier*n;let D=[];if(U.zValue=x,U.lines=D,!(x<=M||x>=S))for(let v=0;v<h-1;v++){let Q=i[v],_=i[v+1];for(let T=0;T<s-1;T++)f=Q[T],o=Q[T+1],t=_[T],l=_[T+1],r=f>x,p=o>x,u=t>x,b=l>x,r!==p&&r!==u&&(a=T+(x-f)/(o-f),c=v,d=T,A=v+(x-f)/(t-f),D.push(a*N+y,c*X+C,d*N+y,A*X+C)),b!==p&&b!==u&&(a=T+1,c=v+1-(x-l)/(o-l),d=T+1-(x-l)/(t-l),A=v+1,D.push(a*N+y,c*X+C,d*N+y,A*X+C)),p!==u&&(a=(T+1-(x-o)/(t-o))*N+y,c=(v+(x-o)/(t-o))*X+C,p!==r&&(d=T+1-(x-o)/(f-o),A=v,D.push(a,c,d*N+y,A*X+C)),u!==r&&(d=T,A=v+1-(x-t)/(f-t),D.push(a,c,d*N+y,A*X+C)),p!==b&&(d=T+1,A=v+(x-o)/(l-o),D.push(a,c,d*N+y,A*X+C)),u!==b&&(d=T+(x-t)/(l-t),A=v+1,D.push(a,c,d*N+y,A*X+C)))}}return{minX:e.minX,maxX:e.maxX,minY:e.minY,maxY:e.maxY,segments:R}}function G(e,m){let n=j(e);m.noContour||(e.contourLines=Z(n,m),delete n.z),e.minMax=n}import{getGyromagneticRatio as W}from"gyromagnetic-ratio";function H(e,m){for(let n of e){let i=0,f=0;for(let o of n.spectra){if(n.ntuples?.symbol?(!i&&o.observeFrequency&&(i=o.observeFrequency),!f&&o.shiftOffsetVal&&(f=o.shiftOffsetVal)):(i=o.observeFrequency,f=o.shiftOffsetVal),i&&o.xUnits?.toUpperCase().includes("HZ")&&(o.xUnits="PPM",o.xFactor=o.xFactor!==void 0?o.xFactor/i:void 0,o.firstX=o.firstX!==void 0?o.firstX/i:void 0,o.lastX=o.lastX!==void 0?o.lastX/i:void 0,o.deltaX=o.deltaX!==void 0?o.deltaX/i:void 0,o.data))for(let t=0;t<o.data.x.length;t++)o.data.x[t]/=i;if(f&&o.xUnits.toLowerCase().includes("ppm")&&o.firstX!==void 0&&o.lastX!==void 0){let t=o.firstX-f;if(o.firstX=o.firstX-t,o.lastX=o.lastX-t,o.data)for(let l=0;l<o.data.x.length;l++)o.data.x[l]-=t}if(n.ntuples?.nucleus&&n.ntuples.symbol)for(let t=0;t<n.ntuples.nucleus.length;t++){let l=n.ntuples.symbol[t],r=n.ntuples.nucleus[t];if(l.match(/^[F|T]/)&&!r){if(l.match(/[F|T]1/))if(n.tmp.$NUC2&&typeof n.tmp.$NUC2=="string")n.ntuples.nucleus[t]=n.tmp.$NUC2;else{let p=n.ntuples.symbol.indexOf(l.replace(/^([F|T]).*/,"$12"));p&&n.ntuples.nucleus[p]&&(n.ntuples.nucleus[t]=n.ntuples.nucleus[p])}l.match(/[F|T]2/)&&typeof n.tmp.$NUC1=="string"&&(n.ntuples.nucleus[t]=n.tmp.$NUC1)}l.match(/[F|T]2/)&&(n.yType=n.ntuples.nucleus[0],n.xType&&!W(n.xType)&&(n.xType=n.ntuples.nucleus[1]))}if(i&&n.ntuples?.symbol&&n.ntuples.nucleus){let t="",l=n.ntuples.symbol.indexOf(o.pageSymbol);n.ntuples.units?.[l]&&(t=n.ntuples.units[l]);let{nucleus:r}=n.ntuples;if(!t.toLowerCase().match(/(ppm|seconds)/)&&r.length>1){if(l!==0){let h="Not sure about this ntuples format";if(m){m.warn(h);continue}else throw new Error(h)}let{nucleus:p}=n.ntuples,u=W(p[0]),b=W(p[1]);if(!u||!b){let h=`Problem with determination of gyromagnetic ratio for ${p.join("-")}`;if(m)m.error(h);else throw new Error(h)}else{let h=u/b*i;o.pageValue/=h}}}}}}function J(e){let m=e.spectra[0].data;e.chromatogram={times:m.x.slice(),series:{intensity:{dimension:1,data:m.y.slice()}}}}function q(e,m,n){H(e,n.logger),de(e,n);for(let i of e){if(Object.keys(i.ntuples).length>0){let f=[],o=Object.keys(i.ntuples);for(let t of o){let l=i.ntuples[t];if(l)for(let r=0;r<l.length;r++)f[r]||(f[r]={}),f[r][t]=l[r]}i.ntuples=f}i.twoD&&n.wantXY&&(G(i,n),n.logger?.trace({profiling:!0},"Finished countour plot calculation"),n.keepSpectra||delete i.spectra),n.chromatogram&&(i.spectra.length>1?te(i):J(i),n.logger?.trace({profiling:!0},"Finished chromatogram calculation")),delete i.tmp}}function de(e,m){for(let n of e)for(let i in n.meta){let f=n.meta[i];if(typeof f=="string"){if(f.startsWith("{")){if(!f.includes(":")&&f.endsWith("}")){let o=f.slice(1,-1).split(/[,; ]+/).filter(Boolean);for(let t=0;t<o.length;t++)n.meta[i+String(t)]=m.dynamicTyping?ae(o[t]):o[t]}}else if(f.startsWith("(")){let o=f.split(/\r?\n/),t=/^\((?<from>\d+)\.\.(?<to>\d+)\).*$/;if(t.test(o[0])){let[l,r]=o[0].match(t)?.slice(1).map(Number)??[],p=o.slice(1).join(" ").split(/[,; ]+/).filter(Boolean);for(let u=l;u<=r;u++)m.dynamicTyping&&typeof p[u-l]=="string"?n.meta[i+String(u)]=ae(p[u-l]):n.meta[i+String(u)]=p[u-l]}}}}}function z(e,m,n){let i=-1,f=-1,o="",t="";if(n.indexOf("++")>0)o=n.replace(/.*\(([a-zA-Z0-9]+)\+\+.*/,"$1"),t=n.replace(/.*\.\.([a-zA-Z0-9]+).*/,"$1");else{n=n.replaceAll(/[^a-zA-Z%]/g,""),o=n.charAt(0),t=n.charAt(1),m.variables={};for(let l of n){let r=l.toLowerCase(),p=e.ntuples.symbol?.indexOf(l)||0;if(p===-1)throw new Error(`Symbol undefined: ${l}`);m.variables[r]={};for(let u in e.ntuples)e.ntuples[u]?.[p]&&(m.variables[r][u.replace(/^var/,"")]=e.ntuples[u]?.[p])}}i=e.ntuples.symbol?.indexOf(o)??-1,f=e.ntuples.symbol?.indexOf(t)??-1,i===-1&&(i=0),f===-1&&(f=0),e.ntuples.first&&(e.ntuples.first.length>i&&(m.firstX=e.ntuples.first[i]),e.ntuples.first.length>f&&(m.firstY=e.ntuples.first[f])),e.ntuples.last&&(e.ntuples.last.length>i&&(m.lastX=e.ntuples.last[i]),e.ntuples.last.length>f&&(m.lastY=e.ntuples.last[f])),e.ntuples.vardim&&e.ntuples.vardim.length>i&&(m.nbPoints=e.ntuples.vardim[i]),e.ntuples.factor&&(e.ntuples.factor.length>i&&(m.xFactor=e.ntuples.factor[i]),e.ntuples.factor.length>f&&(m.yFactor=e.ntuples.factor[f])),e.ntuples.units&&(e.ntuples.units.length>i&&(e.ntuples.varname?.[i]?m.xUnits=`${e.ntuples.varname[i]} [${e.ntuples.units[i]}]`:m.xUnits=e.ntuples.units[i]),e.ntuples.units.length>f&&(e.ntuples.varname?.[f]?m.yUnits=`${e.ntuples.varname[f]} [${e.ntuples.units[f]}]`:m.yUnits=e.ntuples.units[f]))}function w(e){e.xFactor||(e.xFactor=1),e.yFactor||(e.yFactor=1)}var L=/[ \t]*,[ \t]*/,he={keepRecordsRegExp:/^$/,canonicDataLabels:!0,canonicMetadataLabels:!1,dynamicTyping:!0,withoutXY:!1,noTrimRegExp:/^$/,chromatogram:!1,keepSpectra:!1,noContour:!1,nbContourLevels:7,noiseMultiplier:5};function xe(e,m={}){e=ge(e);let n={...he,...m};n.logger?.debug("Starting jcamp conversion"),n.wantXY=!n.withoutXY,n.start=Date.now();let i=[],f={entries:[],flatten:[]},o={children:[],spectra:[],ntuples:{},info:{},meta:{},tmp:{}},t=o,l=[],r={data:{}};n.logger?.trace({profiling:!0},"Before split to LDRS");let p=e.replaceAll(/[\r\n]+##/g,`
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3
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4
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5
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`;let s=h.match(/^##(.*?)=(.+)/);if(s){let a=s[1].replaceAll(/[ _-]/g,"").toUpperCase();a==="DATATYPE"?l.dataType=s[2].trim():a==="DATACLASS"?l.dataClass=s[2].trim():a==="JCAMPDX"?l.jcampDX=O(s[2].trim()):a==="JCAMPCS"&&(l.jcampCS=O(s[2].trim()))}}h.startsWith("##END")&&r>0&&r--}if(n){for(let u of f)u.children=void 0;return f}else return t}import{parseString as de}from"dynamic-typing";import{ensureString as be}from"ensure-string";var ee=["TIC",".RIC","SCANNUMBER"];function te(e){let m=e.spectra,n=m.length,o={times:new Array(n),series:{ms:{dimension:2,data:new Array(n)}}},f=[];for(let i of ee){let t=k(i);m[0][t]&&(f.push(t),o.series[t]={dimension:1,data:new Array(n)})}for(let i=0;i<n;i++){let t=m[i];o.times[i]=t.pageValue;for(let l of f)o.series[l].data[i]=Number(t[l]);t.data&&(o.series.ms.data[i]=[t.data.x,t.data.y])}e.chromatogram=o}function ne(e){return ee.includes(e)}function k(e){return e.toLowerCase().replaceAll(/[^a-z0-9]/g,"")}function E(e){return e.map(Number)}function V(e,m,n){let{logger:o}=n;o&&(e.xFactor||o.info("The xFactor is not defined, it will be set to 1"),e.yFactor||o.info("The yFactor is not defined, it will be set to 1"));let f=e.yFactor??1,i=e.xFactor??1,t=e.deltaX??1,l=Math.abs(t*.1),r=.01;e.isXYdata=!0;let p={x:[],y:[]};e.data=p;let u=e.firstX||0,b=e.firstY||0,h=!1,s,a=0;for(;a<m.length;a++)if(s=m.codePointAt(a),s===13||s===10)h=!0;else if(h)break;let c=0,d=!0,A=!1,y=!1,I=0,N=!1,S=!1,g=0,X=0,M=!1,C=!1,Y=!1,R=0;for(;a<=m.length;a++)if(a===m.length?s=13:s=m.codePointAt(a),S)(s===13||s===10)&&(d=!0,S=!1,c++);else if(s<=57&&s>=48)C=!0,R>0?g+=(s-48)/10**R++:(g*=10,g+=s-48);else if(s===44||s===46)C=!0,R++;else{if(C){if(M&&(g=g*-1,M=!1),d)g*=i,o&&(y?Math.abs(u-t-g)>l&&(Math.abs(u-g)<l?o.trace(`Data line ${c}: After a DIFFERENCE the next line should repeat the last value and this does not seem to be the case: Current value: ${g} - Expected: ${u}.`):Math.abs(u-t-g)>10*l?o.trace(`Data line ${c}: The difference between the first value ${g} and 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x=m.codePointAt(a+1);(x!==void 0&&x>=48&&x<=57||x===44||x===46)&&(C=!0,d||(y=!1),M=!0)}else(s===13||s===10)&&(d=!0,S=!1,c++)}o&&y&&o.warn("The last value is a difference, it should be repeated on the next line")}var re=/[,\t ]+/;function P(e,m,n){if(e.isPeaktable=!0,!e.variables||Object.keys(e.variables).length===2?me(e,m,n):ue(e,m,n),e.variables)for(let o in e.variables)e.variables[o].data=e.data?.[o]}function me(e,m,n){let{logger:o}=n,f={x:[],y:[]};e.data=f;let i=m.split(/,? *,?[;\r\n]+ */);for(let t=1;t<i.length;t++){let l=i[t].trim().replace($,"").split(re);if(l.length%2===0)for(let r=0;r<l.length;r=r+2)e.xFactor!==void 0&&e.yFactor!==void 0&&(f.x.push(Number(l[r])*e.xFactor),f.y.push(Number(l[r+1])*e.yFactor));else o?.warn(`Format error: ${l.toString()}`)}}function ue(e,m,n){let{logger:o}=n,f={},i=Object.keys(e.variables),t=i.length;for(let r of i)f[r]=[];e.data=f;let l=m.split(/,? *,?[;\r\n]+ */);for(let r=1;r<l.length;r++){let 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U={};R[F]=U;let le=F%2,K=(C-m.noiseMultiplier*n)*Math.exp((F>>1)-m.nbContourLevels);le===0?x=K+m.noiseMultiplier*n:x=0-K-m.noiseMultiplier*n;let D=[];if(U.zValue=x,U.lines=D,!(x<=M||x>=C))for(let v=0;v<h-1;v++){let Q=o[v],_=o[v+1];for(let T=0;T<s-1;T++)f=Q[T],i=Q[T+1],t=_[T],l=_[T+1],r=f>x,p=i>x,u=t>x,b=l>x,r!==p&&r!==u&&(a=T+(x-f)/(i-f),c=v,d=T,A=v+(x-f)/(t-f),D.push(a*N+y,c*X+S,d*N+y,A*X+S)),b!==p&&b!==u&&(a=T+1,c=v+1-(x-l)/(i-l),d=T+1-(x-l)/(t-l),A=v+1,D.push(a*N+y,c*X+S,d*N+y,A*X+S)),p!==u&&(a=(T+1-(x-i)/(t-i))*N+y,c=(v+(x-i)/(t-i))*X+S,p!==r&&(d=T+1-(x-i)/(f-i),A=v,D.push(a,c,d*N+y,A*X+S)),u!==r&&(d=T,A=v+1-(x-t)/(f-t),D.push(a,c,d*N+y,A*X+S)),p!==b&&(d=T+1,A=v+(x-i)/(l-i),D.push(a,c,d*N+y,A*X+S)),u!==b&&(d=T+(x-t)/(l-t),A=v+1,D.push(a,c,d*N+y,A*X+S)))}}return{minX:e.minX,maxX:e.maxX,minY:e.minY,maxY:e.maxY,segments:R}}function G(e,m){let n=j(e);m.noContour||(e.contourLines=Z(n,m),delete n.z),e.minMax=n}import{getGyromagneticRatio as W}from"gyromagnetic-ratio";function H(e,m){for(let n of e){let o=0,f=0;for(let i of n.spectra){if(n.ntuples?.symbol?(!o&&i.observeFrequency&&(o=i.observeFrequency),!f&&i.shiftOffsetVal&&(f=i.shiftOffsetVal)):(o=i.observeFrequency,f=i.shiftOffsetVal),o&&i.xUnits?.toUpperCase().includes("HZ")&&(i.xUnits="PPM",i.xFactor=i.xFactor!==void 0?i.xFactor/o:void 0,i.firstX=i.firstX!==void 0?i.firstX/o:void 0,i.lastX=i.lastX!==void 0?i.lastX/o:void 0,i.deltaX=i.deltaX!==void 0?i.deltaX/o:void 0,i.data))for(let t=0;t<i.data.x.length;t++)i.data.x[t]/=o;if(f&&i.xUnits.toLowerCase().includes("ppm")&&i.firstX!==void 0&&i.lastX!==void 0){let t=i.firstX-f;if(i.firstX=i.firstX-t,i.lastX=i.lastX-t,i.data)for(let l=0;l<i.data.x.length;l++)i.data.x[l]-=t}if(n.ntuples?.nucleus&&n.ntuples.symbol)for(let t=0;t<n.ntuples.nucleus.length;t++){let l=n.ntuples.symbol[t],r=n.ntuples.nucleus[t];if(l.match(/^[F|T]/)&&!r){if(l.match(/[F|T]1/))if(n.tmp.$NUC2&&typeof n.tmp.$NUC2=="string")n.ntuples.nucleus[t]=n.tmp.$NUC2;else{let p=n.ntuples.symbol.indexOf(l.replace(/^([F|T]).*/,"$12"));p&&n.ntuples.nucleus[p]&&(n.ntuples.nucleus[t]=n.ntuples.nucleus[p])}l.match(/[F|T]2/)&&typeof n.tmp.$NUC1=="string"&&(n.ntuples.nucleus[t]=n.tmp.$NUC1)}l.match(/[F|T]2/)&&(n.yType=n.ntuples.nucleus[0],n.xType&&!W(n.xType)&&(n.xType=n.ntuples.nucleus[1]))}if(o&&n.ntuples?.symbol&&n.ntuples.nucleus){let t="",l=n.ntuples.symbol.indexOf(i.pageSymbol);n.ntuples.units?.[l]&&(t=n.ntuples.units[l]);let{nucleus:r}=n.ntuples;if(!t.toLowerCase().match(/(ppm|seconds)/)&&r.length>1){if(l!==0){let h="Not sure about this ntuples format";if(m){m.warn(h);continue}else throw new Error(h)}let{nucleus:p}=n.ntuples,u=W(p[0]),b=W(p[1]);if(!u||!b){let h=`Problem with determination of gyromagnetic ratio for ${p.join("-")}`;if(m)m.error(h);else throw new Error(h)}else{let h=u/b*o;i.pageValue/=h}}}}}}function J(e){let m=e.spectra[0].data;e.chromatogram={times:m.x.slice(),series:{intensity:{dimension:1,data:m.y.slice()}}}}function q(e,m,n){H(e,n.logger),pe(e,n);for(let o of e){if(Object.keys(o.ntuples).length>0){let f=[],i=Object.keys(o.ntuples);for(let t of i){let l=o.ntuples[t];if(l)for(let r=0;r<l.length;r++)f[r]||(f[r]={}),f[r][t]=l[r]}o.ntuples=f}o.twoD&&n.wantXY&&(G(o,n),n.logger?.trace({profiling:!0},"Finished countour plot calculation"),n.keepSpectra||delete o.spectra),n.chromatogram&&(o.spectra.length>1?te(o):J(o),n.logger?.trace({profiling:!0},"Finished chromatogram calculation")),delete o.tmp}}function pe(e,m){for(let n of e)for(let o in n.meta){let f=n.meta[o];if(typeof f=="string"){if(f.startsWith("{")){if(!f.includes(":")&&f.endsWith("}")){let i=f.slice(1,-1).split(/[,; ]+/).filter(Boolean);for(let t=0;t<i.length;t++)n.meta[o+String(t)]=m.dynamicTyping?ae(i[t]):i[t]}}else if(f.startsWith("(")){let i=f.split(/\r?\n/),t=/^\((?<from>\d+)\.\.(?<to>\d+)\).*$/;if(t.test(i[0])){let[l,r]=i[0].match(t)?.slice(1).map(Number)??[],p=i.slice(1).join(" ").split(/[,; ]+/).filter(Boolean);for(let u=l;u<=r;u++)m.dynamicTyping&&typeof p[u-l]=="string"?n.meta[o+String(u)]=ae(p[u-l]):n.meta[o+String(u)]=p[u-l]}}}}}function z(e,m,n){let o=-1,f=-1,i="",t="";if(n.indexOf("++")>0)i=n.replace(/.*\(([a-zA-Z0-9]+)\+\+.*/,"$1"),t=n.replace(/.*\.\.([a-zA-Z0-9]+).*/,"$1");else{n=n.replaceAll(/[^a-zA-Z%]/g,""),i=n.charAt(0),t=n.charAt(1),m.variables={};for(let l of n){let r=l.toLowerCase(),p=e.ntuples.symbol?.indexOf(l)||0;if(p===-1)throw new Error(`Symbol undefined: ${l}`);m.variables[r]={};for(let u in e.ntuples)e.ntuples[u]?.[p]&&(m.variables[r][u.replace(/^var/,"")]=e.ntuples[u]?.[p])}}o=e.ntuples.symbol?.indexOf(i)??-1,f=e.ntuples.symbol?.indexOf(t)??-1,o===-1&&(o=0),f===-1&&(f=0),e.ntuples.first&&(e.ntuples.first.length>o&&(m.firstX=e.ntuples.first[o]),e.ntuples.first.length>f&&(m.firstY=e.ntuples.first[f])),e.ntuples.last&&(e.ntuples.last.length>o&&(m.lastX=e.ntuples.last[o]),e.ntuples.last.length>f&&(m.lastY=e.ntuples.last[f])),e.ntuples.vardim&&e.ntuples.vardim.length>o&&(m.nbPoints=e.ntuples.vardim[o]),e.ntuples.factor&&(e.ntuples.factor.length>o&&(m.xFactor=e.ntuples.factor[o]),e.ntuples.factor.length>f&&(m.yFactor=e.ntuples.factor[f])),e.ntuples.units&&(e.ntuples.units.length>o&&(e.ntuples.varname?.[o]?m.xUnits=`${e.ntuples.varname[o]} [${e.ntuples.units[o]}]`:m.xUnits=e.ntuples.units[o]),e.ntuples.units.length>f&&(e.ntuples.varname?.[f]?m.yUnits=`${e.ntuples.varname[f]} [${e.ntuples.units[f]}]`:m.yUnits=e.ntuples.units[f]))}function w(e){e.xFactor||(e.xFactor=1),e.yFactor||(e.yFactor=1)}var L=/[ \t]*,[ \t]*/,ge={removeComments:!1,keepRecordsRegExp:/^$/,canonicDataLabels:!0,canonicMetadataLabels:!1,dynamicTyping:!0,withoutXY:!1,noTrimRegExp:/^$/,chromatogram:!1,keepSpectra:!1,noContour:!1,nbContourLevels:7,noiseMultiplier:5};function pt(e,m={}){e=be(e);let n={...ge,...m};n.logger?.debug("Starting jcamp conversion"),n.wantXY=!n.withoutXY,n.start=Date.now();let o=[],f={entries:[],flatten:[]},i={children:[],spectra:[],ntuples:{},info:{},meta:{},tmp:{}},t=i,l=[],r={data:{}};n.logger?.trace({profiling:!0},"Before split to LDRS");let p=e.replaceAll(/[\r\n]+##/g,`
|
|
6
6
|
##`).split(`
|
|
7
7
|
##`);n.logger?.trace({profiling:!0},"Split to LDRS"),p[0]&&(p[0]=p[0].replace(/^[\r\n ]*##/,""));for(let u of p){let b=u.indexOf("="),h=b>0?u.slice(0,Math.max(0,b)):u,s=b>0?h.match(n.noTrimRegExp)?u.slice(Math.max(0,b+1)):u.slice(Math.max(0,b+1)).trim():"",a=h.replaceAll(/[_ -]/g,"").toUpperCase();if(a==="DATATABLE"){let c=s.indexOf(`
|
|
8
|
-
`);if(c===-1&&(c=s.indexOf("\r")),c>0){let d=s.slice(0,Math.max(0,c)).split(/[ ,;\t]+/);z(t,r,d[0]),r.datatable=d[0],d[1]?.includes("PEAKS")?a="PEAKTABLE":d[1]&&(d[1].indexOf("XYDATA")||d[0].indexOf("++")>0)&&(a="XYDATA",r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)))}}if(a==="XYDATA"){n.wantXY&&(w(r),s.match(/.*\+\+.*/)?(r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)),V(r,s,n)):P(r,s,n),t?.spectra.push(r),r={data:{}});continue}else if(a==="PEAKTABLE"){n.wantXY&&(w(r),P(r,s,n),t?.spectra.push(r),r={data:{}});continue}if(a==="PEAKASSIGNMENTS"){n.wantXY&&(s.match(/.*[^A-Z]*.*/)&&B(r,s),t?.spectra.push(r),r={data:{}});continue}if(s=s.split(/\r?\n/).map(c=>c.replace(/ *\$\$.*$/,"")).join(`
|
|
9
|
-
`),a==="TITLE"){let c=t;c.children||(c.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},c.children.push(t),l.push(c),
|
|
8
|
+
`);if(c===-1&&(c=s.indexOf("\r")),c>0){let d=s.slice(0,Math.max(0,c)).split(/[ ,;\t]+/);z(t,r,d[0]),r.datatable=d[0],d[1]?.includes("PEAKS")?a="PEAKTABLE":d[1]&&(d[1].indexOf("XYDATA")||d[0].indexOf("++")>0)&&(a="XYDATA",r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)))}}if(a==="XYDATA"){n.wantXY&&(w(r),s.match(/.*\+\+.*/)?(r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)),V(r,s,n)):P(r,s,n),t?.spectra.push(r),r={data:{}});continue}else if(a==="PEAKTABLE"){n.wantXY&&(w(r),P(r,s,n),t?.spectra.push(r),r={data:{}});continue}if(a==="PEAKASSIGNMENTS"){n.wantXY&&(s.match(/.*[^A-Z]*.*/)&&B(r,s),t?.spectra.push(r),r={data:{}});continue}if(n.removeComments&&(s=s.split(/\r?\n/).map(c=>c.replace(/ *\$\$.*$/,"")).join(`
|
|
9
|
+
`)),a==="TITLE"){let c=t;c.children||(c.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},c.children.push(t),l.push(c),o.push(t),t.title=s}else a==="DATATYPE"?(t.dataType=s,s.match(/^nd|\snd\s/i)&&(t.twoD=!0)):a==="NTUPLES"?s.match(/^nd|\snd\s/i)&&(t.twoD=!0):a==="DATACLASS"?t.dataClass=s:a==="JCAMPDX"?t.jcampDX=O(s):a==="JCAMPCS"?t.jcampCS=O(s):a==="XUNITS"?r.xUnits=s:a==="YUNITS"?r.yUnits=s:a==="FIRSTX"?r.firstX=Number(s):a==="LASTX"?r.lastX=Number(s):a==="FIRSTY"?r.firstY=Number(s):a==="LASTY"?r.lastY=Number(s):a==="NPOINTS"?r.nbPoints=Number(s):a==="XFACTOR"?r.xFactor=Number(s):a==="YFACTOR"?r.yFactor=Number(s):a==="MAXX"?r.maxX=Number(s):a==="MINX"?r.minX=Number(s):a==="MAXY"?r.maxY=Number(s):a==="MINY"?r.minY=Number(s):a==="DELTAX"?r.deltaX=Number(s):a===".OBSERVEFREQUENCY"||a==="$SFO1"?r.observeFrequency||(r.observeFrequency=Number(s)):a===".OBSERVENUCLEUS"?r.xType||(t.xType=s.replaceAll(/[^a-zA-Z0-9]/g,"")):a==="$OFFSET"?(t.shiftOffsetNum=0,r.shiftOffsetVal||(r.shiftOffsetVal=Number(s))):a==="$REFERENCEPOINT"||(a==="VARNAME"?t.ntuples.varname=s.split(L):a==="SYMBOL"?t.ntuples.symbol=s.split(L):a==="VARTYPE"?t.ntuples.vartype=s.split(L):a==="VARFORM"?t.ntuples.varform=s.split(L):a==="VARDIM"?t.ntuples.vardim=E(s.split(L)):a==="UNITS"?t.ntuples.units=s.split(L):a==="FACTOR"?t.ntuples.factor=E(s.split(L)):a==="FIRST"?t.ntuples.first=E(s.split(L)):a==="LAST"?t.ntuples.last=E(s.split(L)):a==="MIN"?t.ntuples.min=E(s.split(L)):a==="MAX"?t.ntuples.max=E(s.split(L)):a===".NUCLEUS"?t.ntuples&&(t.ntuples.nucleus=s.split(L).map(c=>c.replaceAll(/[^a-zA-Z0-9]/g,""))):a==="PAGE"?(r.page=s.trim(),r.pageValue=Number(s.replace(/^.*=/,"")),r.pageSymbol=r.page.replace(/[=].*/,"")):a==="RETENTIONTIME"?r.pageValue=Number(s):ne(a)?r[k(a)]=s:a==="SAMPLEDESCRIPTION"?r.sampleDescription=s:a.startsWith("$NUC")?!t.tmp[a]&&!s.includes("off")&&(t.tmp[a]=s.replaceAll(/[<>]/g,"")):a==="END"&&(t=l.pop()));if(t?.info&&t.meta&&a.match(n.keepRecordsRegExp)){let c,d;h.startsWith("$")?(d=n.canonicMetadataLabels?a.slice(1):h.slice(1),c=t.meta):(d=n.canonicDataLabels?a:h,c=t.info),n.dynamicTyping&&(s=de(s)),c[d]?(Array.isArray(c[d])||(c[d]=[c[d]]),c[d].push(s)):c[d]=s}}if(n.logger?.trace({profiling:!0},"Finished parsing"),q(o,f,n),n.logger?.trace({profiling:!0},"Total time"),f.entries=i.children||[],f.flatten=o,n.logger){n.logger.debug("Finished jcamp conversion");for(let u of f.flatten)n.logger.debug(`${u.dataType} - ${u.title}`)}return f}function gt(e,m){let{logger:n,OCL:o}=m;if(!e.info.ATOMLIST||!e.info.BONDLIST){n?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}Ce(e,n);let f=xe(e.info.ATOMLIST),i=ye(e.info.BONDLIST),t=Ae(e.info.CHARGE,n),l=he(o,f,i,t,n);return{molecule:l,molfile:l.toMolfile()}}function he(e,m,n,o,f){let i={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},t={},l=new e.Molecule(m.length,n.length);for(let r of m){let p=e.Molecule.getAtomicNoFromLabel(r.element);p||(f?.error(`Atomic number of ${r.element} could not be determined`),p=e.Molecule.getAtomicNoFromLabel("X")),t[r.atomNumber]=l.addAtom(p),l.setAtomMapNo(t[r.atomNumber],r.atomNumber,!1)}for(let r of n){if(t[r.atomNumber1]===void 0){f?.error(`A bond goes to atomNumber ${r.atomNumber1} that does not exists`);continue}if(t[r.atomNumber2]===void 0){f?.error(`A bond goes to atomNumber ${r.atomNumber2} that does not exists`);continue}let p=l.addBond(t[r.atomNumber1],t[r.atomNumber2]);l.setBondType(p,i[r.bondType])}for(let r of o){if(t[r.atomNumber]===void 0){f?.error(`A charge goes to atomNumber ${r.atomNumber} that does not exists`);continue}l.setAtomCharge(t[r.atomNumber],r.value)}return l}function xe(e){let m=e.split(/\r?\n/).map(o=>O(o)).filter(Boolean),n=[];for(let o of m){let[f,i,t]=o.trim().split(/\s+/);n.push({atomNumber:Number(f),element:i,nbImplicitHydrogens:t?.length>0?Number(t):void 0})}return n}function ye(e){let m=e.split(/\r?\n/).map(o=>O(o)).filter(Boolean),n=[];for(let o of m){let[f,i,t]=o.trim().split(/\s+/);n.push({atomNumber1:Number(f),atomNumber2:Number(i),bondType:t})}return n}function Ae(e,m){if(!e)return[];let n=e.split(/\r?\n/).map(f=>O(f)).filter(Boolean),o=[];for(let f of n){let[i,t,l]=f.trim().split(/\s+/);l!==void 0&&m?.warn("Charge on multiple atom is not supported"),o.push({atomNumber:Number(t),value:Number(i)})}return o}function Ce(e,m){let n=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let o of n)e.info[o]&&m?.warn(`JCAMP-CS parser do not support: ${o}`)}export{pt as convert,ve as createTree,gt as parseJcampCS};
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "jcampconverter",
|
|
3
|
-
"version": "10.0.
|
|
3
|
+
"version": "10.0.2",
|
|
4
4
|
"description": "Parse and convert JCAMP data",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jcamp",
|
|
@@ -58,6 +58,7 @@
|
|
|
58
58
|
"eslint": "^9.12.0",
|
|
59
59
|
"eslint-config-cheminfo-typescript": "^16.0.0",
|
|
60
60
|
"fifo-logger": "^1.0.0",
|
|
61
|
+
"jcamp-data-test": "^0.8.1",
|
|
61
62
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
62
63
|
"jscpd": "^4.0.5",
|
|
63
64
|
"ml-spectra-processing": "^14.6.0",
|