jcampconverter 10.0.1 → 10.0.2

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Files changed (4) hide show
  1. package/jcampconverter.cjs +3 -3
  2. package/jcampconverter.d.ts +8 -8
  3. package/jcampconverter.mjs +3 -3
  4. package/package.json +1 -1
package/jcampconverter.cjs CHANGED
@@ -1,9 +1,9 @@
1
- "use strict";var he=Object.create;var $=Object.defineProperty;var xe=Object.getOwnPropertyDescriptor;var ye=Object.getOwnPropertyNames;var Ae=Object.getPrototypeOf,Ce=Object.prototype.hasOwnProperty;var Se=(e,f)=>{for(var t in f)$(e,t,{get:f[t],enumerable:!0})},se=(e,f,t,o)=>{if(f&&typeof f=="object"||typeof f=="function")for(let a of ye(f))!Ce.call(e,a)&&a!==t&&$(e,a,{get:()=>f[a],enumerable:!(o=xe(f,a))||o.enumerable});return e};var Ne=(e,f,t)=>(t=e!=null?he(Ae(e)):{},se(f||!e||!e.__esModule?$(t,"default",{value:e,enumerable:!0}):t,e)),Te=e=>se($({},"__esModule",{value:!0}),e);var $e={};Se($e,{convert:()=>de,createTree:()=>ie,parseJcampCS:()=>be});module.exports=Te($e);var oe=require("ensure-string");var P=/\s*\$\$.*/;function O(e){return e.replace(P,"")}function ie(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(`
1
+ "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($e);var oe=require("ensure-string");var P=/\s*\$\$.*/;function O(e){return e.replace(P,"")}function Ne(e,f={}){e=(0,oe.ensureString)(e);let{flatten:t=!1}=f,o=e.split(/\r?\n/),a=[],i=[],n=[],m={title:"",jcamp:"",children:[]},r=0,p=e.includes("## ");for(let u=0;u<o.length;u++){let b=o[u],h=p?b.replaceAll(" ",""):b;if(h.startsWith("##NTUPLES")&&r++,h.startsWith("##TITLE")){let s=[h.slice(8).trim()];for(let l=u+1;l<o.length&&!o[l].startsWith("##");l++)s.push(o[l].trim());i.push({title:s.join(`
2
2
  `),jcamp:`${b}
3
3
  `,children:[]}),m=i.at(-1),a.push(m)}else if(h.startsWith("##END")&&r===0&&m){m.jcamp+=`${b}
4
4
  `;let s=i.pop();if(!s)throw new Error("Not finished");i.length>0?(m=i.at(-1),m.children?.push(s)):(m=void 0,n.push(s))}else if(m?.jcamp){m.jcamp+=`${b}
5
- `;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,o={times:new Array(t),series:{ms:{dimension:2,data:new Array(t)}}},a=[];for(let i of ae){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 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 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p=m[r].trim().replace(P,"").split(me);if(p.length%n===0)for(let u=0;u<p.length;u++)a[i[u%n]].push(Number(p[u]));else o?.warn(`Wrong number of columns: ${p.toString()}`)}}function Z(e,f){e.isXYAdata=!0;let t={};e.data=t;let o=f.split(/\r?\n/),a=o[0].replace(/^.*?([A-Z]+).*$/,"$1").split("").map(i=>i.toLowerCase());for(let i=1;i<o.length;i++){let n=o[i].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=Ne(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],o=t,a=f.length,i=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<i;l++){let c=n[s][l];c<t&&(t=c),c>o&&(o=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:o,noise:h}}function Le(e){let{spectra:f,ntuples:t,info:o}=e;if(t)for(let a of t){let{symbol:i,nucleus:n,units:m}=a;if(i.match(/[F|T]1/)&&m?.toUpperCase().match("HZ")){let r=ue(o[".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,o=e.z,a,i,n,m,r,p,u,b,h=o.length,s=o[0].length,l,c,d,A,y=e.minX,S=(e.maxX-y)/(s-1),N=e.minY,X=(e.maxY-N)/(h-1),M=e.minZ,C=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=(C-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>=C))for(let v=0;v<h-1;v++){let ne=o[v],re=o[v+1];for(let 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t.spectra){if(t.ntuples?.symbol?(!o&&i.observeFrequency&&(o=i.observeFrequency),!a&&i.shiftOffsetVal&&(a=i.shiftOffsetVal)):(o=i.observeFrequency,a=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 n=0;n<i.data.x.length;n++)i.data.x[n]/=o;if(a&&i.xUnits.toLowerCase().includes("ppm")&&i.firstX!==void 0&&i.lastX!==void 0){let n=i.firstX-a;if(i.firstX=i.firstX-n,i.lastX=i.lastX-n,i.data)for(let m=0;m<i.data.x.length;m++)i.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 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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 o of e){if(Object.keys(o.ntuples).length>0){let a=[],i=Object.keys(o.ntuples);for(let n of i){let m=o.ntuples[n];if(m)for(let r=0;r<m.length;r++)a[r]||(a[r]={}),a[r][n]=m[r]}o.ntuples=a}o.twoD&&t.wantXY&&(q(o,t),t.logger?.trace({profiling:!0},"Finished countour plot calculation"),t.keepSpectra||delete o.spectra),t.chromatogram&&(o.spectra.length>1?le(o):K(o),t.logger?.trace({profiling:!0},"Finished chromatogram calculation")),delete o.tmp}}function Me(e,f){for(let t of e)for(let o in t.meta){let a=t.meta[o];if(typeof a=="string"){if(a.startsWith("{")){if(!a.includes(":")&&a.endsWith("}")){let i=a.slice(1,-1).split(/[,; ]+/).filter(Boolean);for(let n=0;n<i.length;n++)t.meta[o+String(n)]=f.dynamicTyping?(0,Q.parseString)(i[n]):i[n]}}else if(a.startsWith("(")){let 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  `);if(c===-1&&(c=s.indexOf("\r")),c>0){let d=s.slice(0,Math.max(0,c)).split(/[ ,;\t]+/);ee(n,r,d[0]),r.datatable=d[0],d[1]?.includes("PEAKS")?l="PEAKTABLE":d[1]&&(d[1].indexOf("XYDATA")||d[0].indexOf("++")>0)&&(l="XYDATA",r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)))}}if(l==="XYDATA"){t.wantXY&&(U(r),s.match(/.*\+\+.*/)?(r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)),j(r,s,t)):w(r,s,t),n?.spectra.push(r),r={data:{}});continue}else if(l==="PEAKTABLE"){t.wantXY&&(U(r),w(r,s,t),n?.spectra.push(r),r={data:{}});continue}if(l==="PEAKASSIGNMENTS"){t.wantXY&&(s.match(/.*[^A-Z]*.*/)&&Z(r,s),n?.spectra.push(r),r={data:{}});continue}if(t.removeComments&&(s=s.split(/\r?\n/).map(c=>c.replace(/ *\$\$.*$/,"")).join(`
9
- `)),l==="TITLE"){let c=n;c.children||(c.children=[]),n={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},c.children.push(n),m.push(c),o.push(n),n.title=s}else l==="DATATYPE"?(n.dataType=s,s.match(/^nd|\snd\s/i)&&(n.twoD=!0)):l==="NTUPLES"?s.match(/^nd|\snd\s/i)&&(n.twoD=!0):l==="DATACLASS"?n.dataClass=s:l==="JCAMPDX"?n.jcampDX=O(s):l==="JCAMPCS"?n.jcampCS=O(s):l==="XUNITS"?r.xUnits=s:l==="YUNITS"?r.yUnits=s:l==="FIRSTX"?r.firstX=Number(s):l==="LASTX"?r.lastX=Number(s):l==="FIRSTY"?r.firstY=Number(s):l==="LASTY"?r.lastY=Number(s):l==="NPOINTS"?r.nbPoints=Number(s):l==="XFACTOR"?r.xFactor=Number(s):l==="YFACTOR"?r.yFactor=Number(s):l==="MAXX"?r.maxX=Number(s):l==="MINX"?r.minX=Number(s):l==="MAXY"?r.maxY=Number(s):l==="MINY"?r.minY=Number(s):l==="DELTAX"?r.deltaX=Number(s):l===".OBSERVEFREQUENCY"||l==="$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):fe(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,ce.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 be(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: ${o}`)}
9
+ `)),l==="TITLE"){let c=n;c.children||(c.children=[]),n={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},c.children.push(n),m.push(c),o.push(n),n.title=s}else l==="DATATYPE"?(n.dataType=s,s.match(/^nd|\snd\s/i)&&(n.twoD=!0)):l==="NTUPLES"?s.match(/^nd|\snd\s/i)&&(n.twoD=!0):l==="DATACLASS"?n.dataClass=s:l==="JCAMPDX"?n.jcampDX=O(s):l==="JCAMPCS"?n.jcampCS=O(s):l==="XUNITS"?r.xUnits=s:l==="YUNITS"?r.yUnits=s:l==="FIRSTX"?r.firstX=Number(s):l==="LASTX"?r.lastX=Number(s):l==="FIRSTY"?r.firstY=Number(s):l==="LASTY"?r.lastY=Number(s):l==="NPOINTS"?r.nbPoints=Number(s):l==="XFACTOR"?r.xFactor=Number(s):l==="YFACTOR"?r.yFactor=Number(s):l==="MAXX"?r.maxX=Number(s):l==="MINX"?r.minX=Number(s):l==="MAXY"?r.maxY=Number(s):l==="MINY"?r.minY=Number(s):l==="DELTAX"?r.deltaX=Number(s):l===".OBSERVEFREQUENCY"||l==="$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 +41,7 @@ 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
45
  /**
46
46
  * If it is true, anywhere out of XYDATA, PEAKTABLE n PEAKASSIGNMENTS the comments are removed
47
47
  * @default false
@@ -93,7 +93,7 @@ declare interface ConvertOptions extends Partial<Add2DOptions> {
93
93
  fastParse?: boolean;
94
94
  }
95
95
 
96
- declare interface ConvertResult {
96
+ export declare interface ConvertResult {
97
97
  entries: Entry[];
98
98
  flatten: Entry[];
99
99
  }
@@ -106,11 +106,11 @@ declare interface ConvertResult {
106
106
  */
107
107
  export declare function createTree(jcamp: string | ArrayBuffer | Uint8Array, options?: CreateTreeOptions): Stack[];
108
108
 
109
- declare interface CreateTreeOptions {
109
+ export declare interface CreateTreeOptions {
110
110
  flatten?: boolean;
111
111
  }
112
112
 
113
- declare interface Entry {
113
+ export declare interface Entry {
114
114
  spectra: Spectrum[];
115
115
  ntuples: Ntuples;
116
116
  meta: Record<string, string | string[] | number | number[] | boolean | boolean[] | undefined>;
@@ -145,7 +145,7 @@ declare interface GenerateContourLinesOptions {
145
145
  noiseMultiplier: number;
146
146
  }
147
147
 
148
- declare interface MinMax {
148
+ export declare interface MinMax {
149
149
  z: number[][];
150
150
  minX: number;
151
151
  maxX: number;
@@ -157,7 +157,7 @@ declare interface MinMax {
157
157
  noice?: number;
158
158
  }
159
159
 
160
- declare interface Ntuples {
160
+ export declare interface Ntuples {
161
161
  varname?: string[];
162
162
  symbol?: string[];
163
163
  vartype?: string[];
@@ -188,12 +188,12 @@ declare interface ParsedCS {
188
188
  */
189
189
  export declare function parseJcampCS(entry: Entry, options: ParseJcampCSOptions): ParsedCS | undefined;
190
190
 
191
- declare interface ParseJcampCSOptions {
191
+ export declare interface ParseJcampCSOptions {
192
192
  OCL: OCL;
193
193
  logger?: Logger;
194
194
  }
195
195
 
196
- declare interface Spectrum {
196
+ export declare interface Spectrum {
197
197
  [key: string]: any;
198
198
  data: Record<string, number[]>;
199
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 me(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(`
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:`${b}
3
3
  `,children:[]}),l=i.at(-1),f.push(l)}else if(h.startsWith("##END")&&r===0&&l){l.jcamp+=`${b}
4
4
  `;let s=i.pop();if(!s)throw new Error("Not finished");i.length>0?(l=i.at(-1),l.children?.push(s)):(l=void 0,t.push(s))}else if(l?.jcamp){l.jcamp+=`${b}
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,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,S=!1,N=!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),N)(s===13||s===10)&&(d=!0,N=!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 the expected first x value ${u} based on increment after a DIFFERENCE is too high`):o.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&&o.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,o&&Math.abs(b-g)>r&&o.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):S||(X=M?0-g:g);let x=S?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,C=!1,S=!1}if(s<74&&s>63)C=!0,y=!1,g=s-64;else if(s>96&&s<106)C=!0,y=!1,g=s-96,M=!0;else if(s===115)C=!0,S=!0,g=9;else if(s>82&&s<91)C=!0,S=!0,g=s-82;else if(s>73&&s<83)C=!0,A=!0,g=s-73;else if(s>105&&s<115)C=!0,A=!0,g=s-105,M=!0;else if(s===36&&m.codePointAt(a+1)===36)C=!0,N=!0;else if(s===37)C=!0,A=!0,g=0,M=!1;else if(s===45){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*S+y,c*X+N,d*S+y,A*X+N)),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*S+y,c*X+N,d*S+y,A*X+N)),p!==u&&(a=(T+1-(x-i)/(t-i))*S+y,c=(v+(x-i)/(t-i))*X+N,p!==r&&(d=T+1-(x-i)/(f-i),A=v,D.push(a,c,d*S+y,A*X+N)),u!==r&&(d=T,A=v+1-(x-t)/(f-t),D.push(a,c,d*S+y,A*X+N)),p!==b&&(d=T+1,A=v+(x-i)/(l-i),D.push(a,c,d*S+y,A*X+N)),u!==b&&(d=T+(x-t)/(l-t),A=v+1,D.push(a,c,d*S+y,A*X+N)))}}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 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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 ${p.join("-")}`;if(m)m.error(h);else throw new Error(h)}else{let h=u/b*o;i.pageValue/=h}}}}}}function J(e){let m=e.spectra[0].data;e.chromatogram={times:m.x.slice(),series:{intensity:{dimension:1,data:m.y.slice()}}}}function 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  ##`);n.logger?.trace({profiling:!0},"Split to LDRS"),p[0]&&(p[0]=p[0].replace(/^[\r\n ]*##/,""));for(let u of p){let b=u.indexOf("="),h=b>0?u.slice(0,Math.max(0,b)):u,s=b>0?h.match(n.noTrimRegExp)?u.slice(Math.max(0,b+1)):u.slice(Math.max(0,b+1)).trim():"",a=h.replaceAll(/[_ -]/g,"").toUpperCase();if(a==="DATATABLE"){let c=s.indexOf(`
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9
- `)),a==="TITLE"){let c=t;c.children||(c.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},c.children.push(t),l.push(c),o.push(t),t.title=s}else a==="DATATYPE"?(t.dataType=s,s.match(/^nd|\snd\s/i)&&(t.twoD=!0)):a==="NTUPLES"?s.match(/^nd|\snd\s/i)&&(t.twoD=!0):a==="DATACLASS"?t.dataClass=s:a==="JCAMPDX"?t.jcampDX=O(s):a==="JCAMPCS"?t.jcampCS=O(s):a==="XUNITS"?r.xUnits=s:a==="YUNITS"?r.yUnits=s:a==="FIRSTX"?r.firstX=Number(s):a==="LASTX"?r.lastX=Number(s):a==="FIRSTY"?r.firstY=Number(s):a==="LASTY"?r.lastY=Number(s):a==="NPOINTS"?r.nbPoints=Number(s):a==="XFACTOR"?r.xFactor=Number(s):a==="YFACTOR"?r.yFactor=Number(s):a==="MAXX"?r.maxX=Number(s):a==="MINX"?r.minX=Number(s):a==="MAXY"?r.maxY=Number(s):a==="MINY"?r.minY=Number(s):a==="DELTAX"?r.deltaX=Number(s):a===".OBSERVEFREQUENCY"||a==="$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=be(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 ye(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}Te(e,n);let f=Ce(e.info.ATOMLIST),i=Se(e.info.BONDLIST),t=Ne(e.info.CHARGE,n),l=Ae(o,f,i,t,n);return{molecule:l,molfile:l.toMolfile()}}function Ae(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 Ce(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 Se(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 Ne(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 Te(e,m){let n=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let o of n)e.info[o]&&m?.warn(`JCAMP-CS parser do not support: ${o}`)}export{xe as convert,me as createTree,ye as parseJcampCS};
9
+ `)),a==="TITLE"){let c=t;c.children||(c.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},c.children.push(t),l.push(c),o.push(t),t.title=s}else a==="DATATYPE"?(t.dataType=s,s.match(/^nd|\snd\s/i)&&(t.twoD=!0)):a==="NTUPLES"?s.match(/^nd|\snd\s/i)&&(t.twoD=!0):a==="DATACLASS"?t.dataClass=s:a==="JCAMPDX"?t.jcampDX=O(s):a==="JCAMPCS"?t.jcampCS=O(s):a==="XUNITS"?r.xUnits=s:a==="YUNITS"?r.yUnits=s:a==="FIRSTX"?r.firstX=Number(s):a==="LASTX"?r.lastX=Number(s):a==="FIRSTY"?r.firstY=Number(s):a==="LASTY"?r.lastY=Number(s):a==="NPOINTS"?r.nbPoints=Number(s):a==="XFACTOR"?r.xFactor=Number(s):a==="YFACTOR"?r.yFactor=Number(s):a==="MAXX"?r.maxX=Number(s):a==="MINX"?r.minX=Number(s):a==="MAXY"?r.maxY=Number(s):a==="MINY"?r.minY=Number(s):a==="DELTAX"?r.deltaX=Number(s):a===".OBSERVEFREQUENCY"||a==="$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": "10.0.1",
3
+ "version": "10.0.2",
4
4
  "description": "Parse and convert JCAMP data",
5
5
  "keywords": [
6
6
  "jcamp",