jcampconverter 9.5.2 → 9.6.0
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 +5 -5
- package/jcampconverter.mjs +5 -5
- package/package.json +1 -1
package/jcampconverter.cjs
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"use strict";var xe=Object.create;var P=Object.defineProperty;var Ne=Object.getOwnPropertyDescriptor;var Ae=Object.getOwnPropertyNames;var Te=Object.getPrototypeOf,Se=Object.prototype.hasOwnProperty;var ye=(e,i)=>{for(var s in i)P(e,s,{get:i[s],enumerable:!0})},
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"use strict";var xe=Object.create;var P=Object.defineProperty;var Ne=Object.getOwnPropertyDescriptor;var Ae=Object.getOwnPropertyNames;var Te=Object.getPrototypeOf,Se=Object.prototype.hasOwnProperty;var ye=(e,i)=>{for(var s in i)P(e,s,{get:i[s],enumerable:!0})},ae=(e,i,s,a)=>{if(i&&typeof i=="object"||typeof i=="function")for(let n of Ae(i))!Se.call(e,n)&&n!==s&&P(e,n,{get:()=>i[n],enumerable:!(a=Ne(i,n))||a.enumerable});return e};var Xe=(e,i,s)=>(s=e!=null?xe(Te(e)):{},ae(i||!e||!e.__esModule?P(s,"default",{value:e,enumerable:!0}):s,e)),Ce=e=>ae(P({},"__esModule",{value:!0}),e);var $e={};ye($e,{convert:()=>he,createTree:()=>ne,parseJcampCS:()=>de});module.exports=Ce($e);var re=require("ensure-string");var D=/\s*\$\$.*/;function M(e){return e.replace(D,"")}function ne(e,i={}){e=(0,re.ensureString)(e);let{flatten:s=!1}=i;if(typeof e!="string")throw new TypeError("the JCAMP should be a string");let a=e.split(/\r?\n/),n=[],l=[],r=[],t,o=0,p=e.includes("## ");for(let c=0;c<a.length;c++){let d=a[c],u=p?d.replace(/ /g,""):d;if(u.substring(0,9)==="##NTUPLES"&&o++,u.substring(0,7)==="##TITLE"){let f=[u.substring(8).trim()];for(let m=c+1;m<a.length&&!a[m].startsWith("##");m++)f.push(a[m].trim());l.push({title:f.join(`
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`),jcamp:`${d}
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`,children:[]}),t=l[l.length-1],n.push(t)}else if(u.substring(0,5)==="##END"&&o===0){t.jcamp+=`${d}
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`;let f=l.pop();l.length!==0?(t=l[l.length-1],t.children.push(f)):(t=void 0,
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`;let f=u.match(/^##(.*?)=(.+)/);if(f){let m=f[1].replace(/[ _-]/g,"").toUpperCase();m==="DATATYPE"?t.dataType=f[2].trim():m==="DATACLASS"?t.dataClass=f[2].trim():m==="JCAMPDX"?t.jcampDX=M(f[2].trim()):m==="JCAMPCS"&&(t.jcampCS=M(f[2].trim()))}}u.substring(0,5)==="##END"&&o>0&&o--}return s?(n.forEach(c=>{c.children=void 0}),n):a}var me=require("dynamic-typing"),ce=require("ensure-string");var U=["TIC",".RIC","SCANNUMBER"];function oe(e){let i=e.spectra,s=i.length,r={times:new Array(s),series:{ms:{dimension:2,data:new Array(s)}}},n=[];for(let l=0;l<U.length;l++){let a=V(U[l]);i[0][a]&&(n.push(a),r.series[a]={dimension:1,data:new Array(s)})}for(let l=0;l<s;l++){let a=i[l];r.times[l]=a.pageValue;for(let t=0;t<n.length;t++)r.series[n[t]].data[l]=Number(a[n[t]]);a.data&&(r.series.ms.data[l]=[a.data.x,a.data.y])}e.chromatogram=r}function fe(e){return U.indexOf(e)!==-1}function V(e){return e.toLowerCase().replace(/[^a-z0-9]/g,"")}function Y(e){let i=[];for(let s=0;s<e.length;s++)i.push(Number(e[s]));return i}function B(e,i){let s=e.yFactor,r=e.deltaX;e.isXYdata=!0;let n={x:[],y:[]};e.data=n;let l=e.firstX,a=e.firstY,t=!1,o,p=0;for(;p<i.length;p++)if(o=i.charCodeAt(p),o===13||o===10)t=!0;else if(t)break;let c=!0,d=!1,u=!1,f=0,m=!1,h=!1,g=0,A=0,N=!1,y=!1,X=!1,T=0;for(;p<=i.length;p++)if(p===i.length?o=13:o=i.charCodeAt(p),h)(o===13||o===10)&&(c=!0,h=!1);else if(o<=57&&o>=48)y=!0,T>0?g+=(o-48)/10**T++:(g*=10,g+=o-48);else if(o===44||o===46)y=!0,T++;else{if(y){if(c)c=!1,u&&(X=!0);else if(X)X=!1;else{d?(f=N?0-g:g,u=!0,d=!1):m||(A=N?0-g:g);let O=m?g-1:1;for(let v=0;v<O;v++)u?a+=f:a=A,n.x.push(l),n.y.push(a*s),l+=r}N=!1,g=0,T=0,y=!1,m=!1}if(o<74&&o>63)y=!0,u=!1,g=o-64;else if(o>96&&o<106)y=!0,u=!1,g=o-96,N=!0;else if(o===115)y=!0,m=!0,g=9;else if(o>82&&o<91)y=!0,m=!0,g=o-82;else if(o>73&&o<83)y=!0,d=!0,g=o-73;else if(o>105&&o<115)y=!0,d=!0,g=o-105,N=!0;else if(o===36&&i.charCodeAt(p+1)===36)y=!0,h=!0;else if(o===37)y=!0,d=!0,g=0,N=!1;else 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r=i.split(/\r?\n/),n=r[0].replace(/^.*?([A-Z]+).*$/,"$1").split("").map(l=>l.toLowerCase());for(let l=1;l<r.length;l++){let a=r[l].replace(/^\((.*)\)$/,"$1").split(/ *, */);for(let t=0;t<n.length;t++){let o=a[t];switch(n[t]){case"x":case"y":case"w":o=Number.parseFloat(o);break;case"a":o=o.replace(/^<(.*)>$/,"$1");break;case"m":break;default:continue}s[n[t]]||(s[n[t]]=[]),s[n[t]].push(o)}}}var Q=require("dynamic-typing");var j=require("gyromagnetic-ratio"),Z=Xe(require("ml-array-median"));function pe(e){return Array.isArray(e)?e[0]:e}function J(e){let{spectra:i}=e,s=i[0].data.y[0],r=s,n=i.length,l=i[0].data.x.length,a=new Array(n);for(let f=0;f<n;f++){a[f]=i[f].data.y;for(let m=0;m<l;m++){let h=a[f][m];h<s&&(s=h),h>r&&(r=h)}}let t=i[0].data.x[0],o=i[0].data.x[i[0].data.x.length-1],{firstY:p,lastY:c}=Me(e);if(t>o)for(let f of a)f.reverse();p>c&&a.reverse();let d=[];for(let f=0;f<a.length;f++){let m=Float64Array.from(a[f]);for(let h=0;h<m.length;h++)m[h]<0&&(m[h]=-m[h]);d.push((0,Z.default)(m))}let u=(0,Z.default)(d);return{z:a,minX:Math.min(t,o),maxX:Math.max(t,o),minY:Math.min(p,c),maxY:Math.max(p,c),minZ:s,maxZ:r,noise:u}}function Me(e){let{spectra:i,ntuples:s,info:r}=e;if(s)for(let n=0;n<s.length;n++){let{symbol:l,nucleus:a}=s[n];if(l.match(/[F|T]1/)){let t=pe(r[".OBSERVEFREQUENCY"]),{nucleus:o}=s.find(m=>m.symbol.match(/[F|T]2/));if([t,o,a].some(m=>!m))break;let p=(0,j.getGyromagneticRatio)(o),c=(0,j.getGyromagneticRatio)(a),{first:d,last:u}=s[n],f=t*c/p;return{firstY:d/f,lastY:u/f}}}return{firstY:i[0].pageValue,lastY:i[i.length-1].pageValue}}function G(e,i){let s=e.noise,r=e.z,n,l,a,t,o,p,c,d,u=r.length,f=r[0].length,m,h,g,A,N=e.minX,X=(e.maxX-N)/(f-1),T=e.minY,v=(e.maxY-T)/(u-1),ge=e.minZ,W=e.maxZ,ee=i.nbContourLevels*2,te=new Array(ee),x;for(let R=0;R<ee;R++){let I={};te[R]=I;let be=R%2,le=(W-i.noiseMultiplier*s)*Math.exp((R>>1)-i.nbContourLevels);be===0?x=le+i.noiseMultiplier*s:x=0-le-i.noiseMultiplier*s;let b=[];if(I.zValue=x,I.lines=b,!(x<=ge||x>=W))for(let C=0;C<u-1;C++){let se=r[C],ie=r[C+1];for(let S=0;S<f-1;S++)n=se[S],l=se[S+1],a=ie[S],t=ie[S+1],o=n>x,p=l>x,c=a>x,d=t>x,o!==p&&o!==c&&(m=S+(x-n)/(l-n),h=C,g=S,A=C+(x-n)/(a-n),b.push(m*X+N),b.push(h*v+T),b.push(g*X+N),b.push(A*v+T)),d!==p&&d!==c&&(m=S+1,h=C+1-(x-t)/(l-t),g=S+1-(x-t)/(a-t),A=C+1,b.push(m*X+N),b.push(h*v+T),b.push(g*X+N),b.push(A*v+T)),p!==c&&(m=(S+1-(x-l)/(a-l))*X+N,h=(C+(x-l)/(a-l))*v+T,p!==o&&(g=S+1-(x-l)/(n-l),A=C,b.push(m),b.push(h),b.push(g*X+N),b.push(A*v+T)),c!==o&&(g=S,A=C+1-(x-a)/(n-a),b.push(m),b.push(h),b.push(g*X+N),b.push(A*v+T)),p!==d&&(g=S+1,A=C+(x-l)/(t-l),b.push(m),b.push(h),b.push(g*X+N),b.push(A*v+T)),c!==d&&(g=S+(x-a)/(t-a),A=C+1,b.push(m),b.push(h),b.push(g*X+N),b.push(A*v+T)))}}return{minX:e.minX,maxX:e.maxX,minY:e.minY,maxY:e.maxY,segments:te}}function H(e,i){let s=J(e);i.noContour||(e.contourLines=G(s,i),delete s.z),e.minMax=s}var $=require("gyromagnetic-ratio");function q(e,i){for(let s of e){let r=0,n=0;for(let l of s.spectra){if(s.ntuples&&s.ntuples.symbol?(!r&&l.observeFrequency&&(r=l.observeFrequency),!n&&l.shiftOffsetVal&&(n=l.shiftOffsetVal)):(r=l.observeFrequency,n=l.shiftOffsetVal),r&&l.xUnits&&l.xUnits.toUpperCase().includes("HZ")){l.xUnits="PPM",l.xFactor=l.xFactor/r,l.firstX=l.firstX/r,l.lastX=l.lastX/r,l.deltaX=l.deltaX/r;for(let a=0;a<l.data.x.length;a++)l.data.x[a]/=r}if(n&&l.xUnits.toLowerCase().includes("ppm")){let a=l.firstX-n;l.firstX=l.firstX-a,l.lastX=l.lastX-a;for(let t=0;t<l.data.x.length;t++)l.data.x[t]-=a}if(s.ntuples&&s.ntuples.nucleus&&s.ntuples.symbol)for(let a=0;a<s.ntuples.nucleus.length;a++){let t=s.ntuples.symbol[a],o=s.ntuples.nucleus[a];if(t.match(/^[F|T]/)&&!o){if(t.match(/[F|T]1/))if(s.tmp.$NUC2)s.ntuples.nucleus[a]=s.tmp.$NUC2;else{let p=s.ntuples.symbol.indexOf(t.replace(/^([F|T]).*/,"$12"));p&&s.ntuples.nucleus[p]&&(s.ntuples.nucleus[a]=s.ntuples.nucleus[p])}t.match(/[F|T]2/)&&(s.ntuples.nucleus[a]=s.tmp.$NUC1)}t.match(/[F|T]2/)&&(s.yType=s.ntuples.nucleus[0],(0,$.getGyromagneticRatio)(s.xType)||(s.xType=s.ntuples.nucleus[1]))}if(r&&s.ntuples&&s.ntuples.symbol&&s.ntuples.nucleus){let a="",t=s.ntuples.symbol.indexOf(l.pageSymbol);if(s.ntuples.units&&s.ntuples.units[t]&&(a=s.ntuples.units[t]),a!=="PPM"){if(t!==0){let u="Not sure about this ntuples format";if(i)i.warn(u);else throw Error(u)}let{nucleus:o}=s.ntuples,p=(0,$.getGyromagneticRatio)(o[0]),c=(0,$.getGyromagneticRatio)(o[1]);if(!p||!c){let u=`Problem with determination of gyromagnetic ratio for ${o.join("-")}`;if(i)i.error(u);else throw Error(u)}let d=p/c*r;l.pageValue/=d}}}}}function L(e,i,s={}){s.logger?.trace(i),e.profiling&&e.profiling.push({action:i,time:Date.now()-s.start})}function K(e){let i=e.spectra[0].data;e.chromatogram={times:i.x.slice(),series:{intensity:{dimension:1,data:i.y.slice()}}}}function _(e,i,s){q(e,s.logger),Le(e,s);for(let r of e){if(Object.keys(r.ntuples).length>0){let n=[],l=Object.keys(r.ntuples);for(let a=0;a<l.length;a++){let t=l[a],o=r.ntuples[t];for(let p=0;p<o.length;p++)n[p]||(n[p]={}),n[p][t]=o[p]}r.ntuples=n}r.twoD&&s.wantXY&&(H(r,s),L(i,"Finished countour plot calculation",s),s.keepSpectra||delete r.spectra),s.chromatogram&&(r.spectra.length>1?oe(r):K(r),L(i,"Finished chromatogram calculation",s)),delete r.tmp}}function Le(e,i){for(let s of e)for(let r in s.meta){let n=s.meta[r];if(typeof n=="string"){if(n[0]==="{"){if(n[n.length-1]==="}"){let l=n.slice(1,-1).split(/[,; ]+/).filter(a=>a);for(let a=0;a<l.length;a++)s.meta[r+String(a)]=i.dynamicTyping?(0,Q.parseString)(l[a]):l[a]}}else if(n[0]==="("){let l=n.split(/\r?\n/),a=/^\((?<from>\d+)\.\.(?<to>\d+)\).*$/;if(a.test(l[0])){let[t,o]=l[0].match(a).slice(1).map(Number),p=l.slice(1).join(" 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e.ntuples)e.ntuples[c][p]&&(i.variables[o][c.replace(/^var/,"")]=e.ntuples[c][p])}}r=e.ntuples.symbol.indexOf(l),n=e.ntuples.symbol.indexOf(a),r===-1&&(r=0),n===-1&&(n=0),e.ntuples.first&&(e.ntuples.first.length>r&&(i.firstX=e.ntuples.first[r]),e.ntuples.first.length>n&&(i.firstY=e.ntuples.first[n])),e.ntuples.last&&(e.ntuples.last.length>r&&(i.lastX=e.ntuples.last[r]),e.ntuples.last.length>n&&(i.lastY=e.ntuples.last[n])),e.ntuples.vardim&&e.ntuples.vardim.length>r&&(i.nbPoints=e.ntuples.vardim[r]),e.ntuples.factor&&(e.ntuples.factor.length>r&&(i.xFactor=e.ntuples.factor[r]),e.ntuples.factor.length>n&&(i.yFactor=e.ntuples.factor[n])),e.ntuples.units&&(e.ntuples.units.length>r&&(e.ntuples.varname&&e.ntuples.varname[r]?i.xUnits=`${e.ntuples.varname[r]} [${e.ntuples.units[r]}]`:i.xUnits=e.ntuples.units[r]),e.ntuples.units.length>n&&(e.ntuples.varname&&e.ntuples.varname[n]?i.yUnits=`${e.ntuples.varname[n]} [${e.ntuples.units[n]}]`:i.yUnits=e.ntuples.units[n]))}function E(e){e.xFactor||(e.xFactor=1),e.yFactor||(e.yFactor=1)}var F=/[ \t]*,[ \t]*/,Ye={keepRecordsRegExp:/^$/,canonicDataLabels:!0,canonicMetadataLabels:!1,dynamicTyping:!0,withoutXY:!1,noTrimRegExp:/^$/,chromatogram:!1,keepSpectra:!1,noContour:!1,nbContourLevels:7,noiseMultiplier:5,profiling:!1};function he(e,i={}){e=(0,ce.ensureString)(e),i={...Ye,...i},i.logger?.debug("Starting jcamp conversion"),i.wantXY=!i.withoutXY,i.start=Date.now();let s=[],r={profiling:i.profiling?[]:!1,logs:[],entries:[]},n={children:[]},l=n,a=[],t={};if(typeof e!="string")throw new TypeError("the JCAMP should be a string");L(r,"Before split to LDRS",i);let o=e.replace(/[\r\n]+##/g,`
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`;let f=l.pop();l.length!==0?(t=l[l.length-1],t.children.push(f)):(t=void 0,r.push(f))}else if(t&&t.jcamp){t.jcamp+=`${d}
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${p.title}`)}return a}function de(e,i={}){let{logger:s,OCL:a}=i;if(!e.info.ATOMLIST||!e.info.BONDLIST){s?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}we(e,s);let n=Re(e.info.ATOMLIST),l=Pe(e.info.BONDLIST),r=De(e.info.CHARGE,s),t=Oe(a,n,l,r,s);return{molecule:t,molfile:t.toMolfile()}}function Oe(e,i,s,a,n){let l={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},r={},t=new e.Molecule(i.length,s.length);for(let o of i){let p=e.Molecule.getAtomicNoFromLabel(o.element);p||(n?.error(`Atomic number of ${o.element} could not be determined`),p=e.Molecule.getAtomicNoFromLabel("X")),r[o.atomNumber]=t.addAtom(p),t.setAtomMapNo(r[o.atomNumber],o.atomNumber)}for(let o of s){if(r[o.atomNumber1]===void 0){n?.error(`A bond goes to atomNumber ${o.atomNumber1} that does not exists`);continue}if(r[o.atomNumber2]===void 0){n?.error(`A bond goes to atomNumber ${o.atomNumber2} that does not exists`);continue}let p=t.addBond(r[o.atomNumber1],r[o.atomNumber2]);t.setBondType(p,l[o.bondType])}for(let o of a){if(r[o.atomNumber]===void 0){n?.error(`A charge goes to atomNumber ${o.atomNumber1} that does not exists`);continue}t.setAtomCharge(r[o.atomNumber],o.value)}return t}function Re(e){let i=e.split(/\r?\n/).map(a=>M(a)).filter(a=>a),s=[];for(let a of i){let[n,l,r]=a.trim().split(/\s+/);s.push({atomNumber:Number(n),element:l,nbImplicitHydrogens:r?.length>0?Number(r):void 0})}return s}function Pe(e){let i=e.split(/\r?\n/).map(a=>M(a)).filter(a=>a),s=[];for(let a of i){let[n,l,r]=a.trim().split(/\s+/);s.push({atomNumber1:Number(n),atomNumber2:Number(l),bondType:r})}return s}function De(e,i){if(!e)return[];let s=e.split(/\r?\n/).map(n=>M(n)).filter(n=>n),a=[];for(let n of s){let[l,r,t]=n.trim().split(/\s+/);t!==void 0&&i?.warn("Charge on multiple atom is not supported"),a.push({atomNumber:Number(r),value:Number(l)})}return a}function we(e,i){let s=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let a of s)e.info[a]&&i?.warn(`JCAMP-CS parser do not support: ${a}`)}
|
package/jcampconverter.mjs
CHANGED
|
@@ -1,8 +1,8 @@
|
|
|
1
|
-
import{ensureString as ue}from"ensure-string";var P=/\s*\$\$.*/;function M(e){return e.replace(P,"")}function pe(e,
|
|
1
|
+
import{ensureString as ue}from"ensure-string";var P=/\s*\$\$.*/;function M(e){return e.replace(P,"")}function pe(e,a={}){e=ue(e);let{flatten:s=!1}=a;if(typeof e!="string")throw new TypeError("the JCAMP should be a string");let i=e.split(/\r?\n/),o=[],l=[],r=[],t,n=0,p=e.includes("## ");for(let c=0;c<i.length;c++){let d=i[c],u=p?d.replace(/ /g,""):d;if(u.substring(0,9)==="##NTUPLES"&&n++,u.substring(0,7)==="##TITLE"){let f=[u.substring(8).trim()];for(let m=c+1;m<i.length&&!i[m].startsWith("##");m++)f.push(i[m].trim());l.push({title:f.join(`
|
|
2
2
|
`),jcamp:`${d}
|
|
3
3
|
`,children:[]}),t=l[l.length-1],o.push(t)}else if(u.substring(0,5)==="##END"&&n===0){t.jcamp+=`${d}
|
|
4
|
-
`;let f=l.pop();l.length!==0?(t=l[l.length-1],t.children.push(f)):(t=void 0,
|
|
5
|
-
`;let f=u.match(/^##(.*?)=(.+)/);if(f){let m=f[1].replace(/[ _-]/g,"").toUpperCase();m==="DATATYPE"?t.dataType=f[2].trim():m==="DATACLASS"?t.dataClass=f[2].trim():m==="JCAMPDX"?t.jcampDX=M(f[2].trim()):m==="JCAMPCS"&&(t.jcampCS=M(f[2].trim()))}}u.substring(0,5)==="##END"&&n>0&&n--}return s?(o.forEach(c=>{c.children=void 0}),o):a}import{parseString as ge}from"dynamic-typing";import{ensureString as be}from"ensure-string";var E=["TIC",".RIC","SCANNUMBER"];function te(e){let r=e.spectra,s=r.length,i={times:new Array(s),series:{ms:{dimension:2,data:new Array(s)}}},o=[];for(let l=0;l<E.length;l++){let a=I(E[l]);r[0][a]&&(o.push(a),i.series[a]={dimension:1,data:new Array(s)})}for(let l=0;l<s;l++){let a=r[l];i.times[l]=a.pageValue;for(let t=0;t<o.length;t++)i.series[o[t]].data[l]=Number(a[o[t]]);a.data&&(i.series.ms.data[l]=[a.data.x,a.data.y])}e.chromatogram=i}function le(e){return E.indexOf(e)!==-1}function I(e){return e.toLowerCase().replace(/[^a-z0-9]/g,"")}function Y(e){let r=[];for(let s=0;s<e.length;s++)r.push(Number(e[s]));return r}function U(e,r){let s=e.yFactor,i=e.deltaX;e.isXYdata=!0;let o={x:[],y:[]};e.data=o;let l=e.firstX,a=e.firstY,t=!1,n,p=0;for(;p<r.length;p++)if(n=r.charCodeAt(p),n===13||n===10)t=!0;else if(t)break;let c=!0,d=!1,u=!1,f=0,m=!1,h=!1,g=0,A=0,N=!1,y=!1,X=!1,T=0;for(;p<=r.length;p++)if(p===r.length?n=13:n=r.charCodeAt(p),h)(n===13||n===10)&&(c=!0,h=!1);else if(n<=57&&n>=48)y=!0,T>0?g+=(n-48)/10**T++:(g*=10,g+=n-48);else if(n===44||n===46)y=!0,T++;else{if(y){if(c)c=!1,u&&(X=!0);else if(X)X=!1;else{d?(f=N?0-g:g,u=!0,d=!1):m||(A=N?0-g:g);let O=m?g-1:1;for(let v=0;v<O;v++)u?a+=f:a=A,o.x.push(l),o.y.push(a*s),l+=i}N=!1,g=0,T=0,y=!1,m=!1}if(n<74&&n>63)y=!0,u=!1,g=n-64;else if(n>96&&n<106)y=!0,u=!1,g=n-96,N=!0;else if(n===115)y=!0,m=!0,g=9;else if(n>82&&n<91)y=!0,m=!0,g=n-82;else if(n>73&&n<83)y=!0,d=!0,g=n-73;else if(n>105&&n<115)y=!0,d=!0,g=n-105,N=!0;else if(n===36&&r.charCodeAt(p+1)===36)y=!0,h=!0;else if(n===37)y=!0,d=!0,g=0,N=!1;else 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e.ntuples)e.ntuples[c][p]&&(r.variables[n][c.replace(/^var/,"")]=e.ntuples[c][p])}}i=e.ntuples.symbol.indexOf(l),o=e.ntuples.symbol.indexOf(a),i===-1&&(i=0),o===-1&&(o=0),e.ntuples.first&&(e.ntuples.first.length>i&&(r.firstX=e.ntuples.first[i]),e.ntuples.first.length>o&&(r.firstY=e.ntuples.first[o])),e.ntuples.last&&(e.ntuples.last.length>i&&(r.lastX=e.ntuples.last[i]),e.ntuples.last.length>o&&(r.lastY=e.ntuples.last[o])),e.ntuples.vardim&&e.ntuples.vardim.length>i&&(r.nbPoints=e.ntuples.vardim[i]),e.ntuples.factor&&(e.ntuples.factor.length>i&&(r.xFactor=e.ntuples.factor[i]),e.ntuples.factor.length>o&&(r.yFactor=e.ntuples.factor[o])),e.ntuples.units&&(e.ntuples.units.length>i&&(e.ntuples.varname&&e.ntuples.varname[i]?r.xUnits=`${e.ntuples.varname[i]} [${e.ntuples.units[i]}]`:r.xUnits=e.ntuples.units[i]),e.ntuples.units.length>o&&(e.ntuples.varname&&e.ntuples.varname[o]?r.yUnits=`${e.ntuples.varname[o]} [${e.ntuples.units[o]}]`:r.yUnits=e.ntuples.units[o]))}function 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|
|
4
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+
`;let f=l.pop();l.length!==0?(t=l[l.length-1],t.children.push(f)):(t=void 0,r.push(f))}else if(t&&t.jcamp){t.jcamp+=`${d}
|
|
5
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`;let f=u.match(/^##(.*?)=(.+)/);if(f){let m=f[1].replace(/[ _-]/g,"").toUpperCase();m==="DATATYPE"?t.dataType=f[2].trim():m==="DATACLASS"?t.dataClass=f[2].trim():m==="JCAMPDX"?t.jcampDX=M(f[2].trim()):m==="JCAMPCS"&&(t.jcampCS=M(f[2].trim()))}}u.substring(0,5)==="##END"&&n>0&&n--}return s?(o.forEach(c=>{c.children=void 0}),o):r}import{parseString as ge}from"dynamic-typing";import{ensureString as be}from"ensure-string";var E=["TIC",".RIC","SCANNUMBER"];function te(e){let a=e.spectra,s=a.length,i={times:new Array(s),series:{ms:{dimension:2,data:new Array(s)}}},o=[];for(let l=0;l<E.length;l++){let r=I(E[l]);a[0][r]&&(o.push(r),i.series[r]={dimension:1,data:new Array(s)})}for(let l=0;l<s;l++){let r=a[l];i.times[l]=r.pageValue;for(let t=0;t<o.length;t++)i.series[o[t]].data[l]=Number(r[o[t]]);r.data&&(i.series.ms.data[l]=[r.data.x,r.data.y])}e.chromatogram=i}function le(e){return E.indexOf(e)!==-1}function I(e){return e.toLowerCase().replace(/[^a-z0-9]/g,"")}function Y(e){let a=[];for(let 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p=s.ntuples.symbol.indexOf(t.replace(/^([F|T]).*/,"$12"));p&&s.ntuples.nucleus[p]&&(s.ntuples.nucleus[r]=s.ntuples.nucleus[p])}t.match(/[F|T]2/)&&(s.ntuples.nucleus[r]=s.tmp.$NUC1)}t.match(/[F|T]2/)&&(s.yType=s.ntuples.nucleus[0],Z(s.xType)||(s.xType=s.ntuples.nucleus[1]))}if(i&&s.ntuples&&s.ntuples.symbol&&s.ntuples.nucleus){let r="",t=s.ntuples.symbol.indexOf(l.pageSymbol);if(s.ntuples.units&&s.ntuples.units[t]&&(r=s.ntuples.units[t]),r!=="PPM"){if(t!==0){let u="Not sure about this ntuples format";if(a)a.warn(u);else throw Error(u)}let{nucleus:n}=s.ntuples,p=Z(n[0]),c=Z(n[1]);if(!p||!c){let u=`Problem with determination of gyromagnetic ratio for ${n.join("-")}`;if(a)a.error(u);else throw Error(u)}let d=p/c*i;l.pageValue/=d}}}}}function L(e,a,s={}){s.logger?.trace(a),e.profiling&&e.profiling.push({action:a,time:Date.now()-s.start})}function G(e){let a=e.spectra[0].data;e.chromatogram={times:a.x.slice(),series:{intensity:{dimension:1,data:a.y.slice()}}}}function H(e,a,s){J(e,s.logger),de(e,s);for(let i of e){if(Object.keys(i.ntuples).length>0){let o=[],l=Object.keys(i.ntuples);for(let r=0;r<l.length;r++){let t=l[r],n=i.ntuples[t];for(let p=0;p<n.length;p++)o[p]||(o[p]={}),o[p][t]=n[p]}i.ntuples=o}i.twoD&&s.wantXY&&(j(i,s),L(a,"Finished countour plot calculation",s),s.keepSpectra||delete i.spectra),s.chromatogram&&(i.spectra.length>1?te(i):G(i),L(a,"Finished chromatogram calculation",s)),delete i.tmp}}function de(e,a){for(let s of e)for(let i in s.meta){let o=s.meta[i];if(typeof o=="string"){if(o[0]==="{"){if(o[o.length-1]==="}"){let l=o.slice(1,-1).split(/[,; ]+/).filter(r=>r);for(let r=0;r<l.length;r++)s.meta[i+String(r)]=a.dynamicTyping?ne(l[r]):l[r]}}else if(o[0]==="("){let l=o.split(/\r?\n/),r=/^\((?<from>\d+)\.\.(?<to>\d+)\).*$/;if(r.test(l[0])){let[t,n]=l[0].match(r).slice(1).map(Number),p=l.slice(1).join(" ").split(/[,; ]+/).filter(c=>c);for(let c=t;c<=n;c++)a.dynamicTyping&&typeof p[c-t]=="string"?s.meta[i+String(c)]=ne(p[c-t]):s.meta[i+String(c)]=p[c-t]}}}}}function q(e,a,s){let i=-1,o=-1,l="",r="";if(s.indexOf("++")>0)l=s.replace(/.*\(([a-zA-Z0-9]+)\+\+.*/,"$1"),r=s.replace(/.*\.\.([a-zA-Z0-9]+).*/,"$1");else{s=s.replace(/[^a-zA-Z%]/g,""),l=s.charAt(0),r=s.charAt(1),a.variables={};for(let t of s){let n=t.toLowerCase(),p=e.ntuples.symbol.indexOf(t);if(p===-1)throw Error(`Symbol undefined: ${t}`);a.variables[n]={};for(let c in e.ntuples)e.ntuples[c][p]&&(a.variables[n][c.replace(/^var/,"")]=e.ntuples[c][p])}}i=e.ntuples.symbol.indexOf(l),o=e.ntuples.symbol.indexOf(r),i===-1&&(i=0),o===-1&&(o=0),e.ntuples.first&&(e.ntuples.first.length>i&&(a.firstX=e.ntuples.first[i]),e.ntuples.first.length>o&&(a.firstY=e.ntuples.first[o])),e.ntuples.last&&(e.ntuples.last.length>i&&(a.lastX=e.ntuples.last[i]),e.ntuples.last.length>o&&(a.lastY=e.ntuples.last[o])),e.ntuples.vardim&&e.ntuples.vardim.length>i&&(a.nbPoints=e.ntuples.vardim[i]),e.ntuples.factor&&(e.ntuples.factor.length>i&&(a.xFactor=e.ntuples.factor[i]),e.ntuples.factor.length>o&&(a.yFactor=e.ntuples.factor[o])),e.ntuples.units&&(e.ntuples.units.length>i&&(e.ntuples.varname&&e.ntuples.varname[i]?a.xUnits=`${e.ntuples.varname[i]} [${e.ntuples.units[i]}]`:a.xUnits=e.ntuples.units[i]),e.ntuples.units.length>o&&(e.ntuples.varname&&e.ntuples.varname[o]?a.yUnits=`${e.ntuples.varname[o]} [${e.ntuples.units[o]}]`:a.yUnits=e.ntuples.units[o]))}function w(e){e.xFactor||(e.xFactor=1),e.yFactor||(e.yFactor=1)}var F=/[ \t]*,[ \t]*/,xe={keepRecordsRegExp:/^$/,canonicDataLabels:!0,canonicMetadataLabels:!1,dynamicTyping:!0,withoutXY:!1,noTrimRegExp:/^$/,chromatogram:!1,keepSpectra:!1,noContour:!1,nbContourLevels:7,noiseMultiplier:5,profiling:!1};function Ne(e,a={}){e=be(e),a={...xe,...a},a.logger?.debug("Starting jcamp conversion"),a.wantXY=!a.withoutXY,a.start=Date.now();let s=[],i={profiling:a.profiling?[]:!1,logs:[],entries:[]},o={children:[]},l=o,r=[],t={};if(typeof e!="string")throw new TypeError("the JCAMP should be a string");L(i,"Before split to LDRS",a);let n=e.replace(/[\r\n]+##/g,`
|
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6
6
|
##`).split(`
|
|
7
|
-
##`);L(i,"Split to LDRS",
|
|
8
|
-
`);if(m===-1&&(m=u.indexOf("\r")),m>0){let h=u.substring(0,m).split(/[ ,;\t]+/);q(l,t,h[0]),t.datatable=h[0],h[1]&&h[1].indexOf("PEAKS")>-1?f="PEAKTABLE":h[1]&&(h[1].indexOf("XYDATA")||h[0].indexOf("++")>0)&&(f="XYDATA",t.nbPoints&&(t.deltaX=(t.lastX-t.firstX)/(t.nbPoints-1)))}}if(f==="XYDATA"){
|
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7
|
+
##`);L(i,"Split to LDRS",a),n[0]&&(n[0]=n[0].replace(/^[\r\n ]*##/,""));for(let p of n){let c=p.indexOf("="),d=c>0?p.substring(0,c):p,u=c>0?d.match(a.noTrimRegExp)?p.substring(c+1):p.substring(c+1).trim():"",f=d.replace(/[_ -]/g,"").toUpperCase();if(f==="DATATABLE"){let m=u.indexOf(`
|
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8
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+
`);if(m===-1&&(m=u.indexOf("\r")),m>0){let h=u.substring(0,m).split(/[ ,;\t]+/);q(l,t,h[0]),t.datatable=h[0],h[1]&&h[1].indexOf("PEAKS")>-1?f="PEAKTABLE":h[1]&&(h[1].indexOf("XYDATA")||h[0].indexOf("++")>0)&&(f="XYDATA",t.nbPoints&&(t.deltaX=(t.lastX-t.firstX)/(t.nbPoints-1)))}}if(f==="XYDATA"){a.wantXY&&(w(t),u.match(/.*\+\+.*/)?(t.nbPoints&&(t.deltaX=(t.lastX-t.firstX)/(t.nbPoints-1)),U(t,u,i)):D(t,u,i),l.spectra.push(t),t={});continue}else if(f==="PEAKTABLE"){a.wantXY&&(w(t),D(t,u,i),l.spectra.push(t),t={});continue}if(f==="PEAKASSIGNMENTS"){a.wantXY&&(u.match(/.*([^A-Z]*).*/)&&V(t,u),l.spectra.push(t),t={});continue}if(f==="TITLE"){let m=l;m.children||(m.children=[]),l={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},m.children.push(l),r.push(m),s.push(l),l.title=u}else f==="DATATYPE"?(l.dataType=u,u.match(/(^nd|\snd\s)/i)&&(l.twoD=!0)):f==="NTUPLES"?u.match(/(^nd|\snd\s)/i)&&(l.twoD=!0):f==="DATACLASS"?l.dataClass=u:f==="JCAMPDX"?l.jcampDX=M(u):f==="JCAMPCS"?l.jcampCS=M(u):f==="XUNITS"?t.xUnits=u:f==="YUNITS"?t.yUnits=u:f==="FIRSTX"?t.firstX=Number(u):f==="LASTX"?t.lastX=Number(u):f==="FIRSTY"?t.firstY=Number(u):f==="LASTY"?t.lastY=Number(u):f==="NPOINTS"?t.nbPoints=Number(u):f==="XFACTOR"?t.xFactor=Number(u):f==="YFACTOR"?t.yFactor=Number(u):f==="MAXX"?t.maxX=Number(u):f==="MINX"?t.minX=Number(u):f==="MAXY"?t.maxY=Number(u):f==="MINY"?t.minY=Number(u):f==="DELTAX"?t.deltaX=Number(u):f===".OBSERVEFREQUENCY"||f==="$SFO1"?t.observeFrequency||(t.observeFrequency=Number(u)):f===".OBSERVENUCLEUS"?t.xType||(l.xType=u.replace(/[^a-zA-Z0-9]/g,"")):f==="$OFFSET"?(l.shiftOffsetNum=0,t.shiftOffsetVal||(t.shiftOffsetVal=Number(u))):f==="$REFERENCEPOINT"||(f==="VARNAME"?l.ntuples.varname=u.split(F):f==="SYMBOL"?l.ntuples.symbol=u.split(F):f==="VARTYPE"?l.ntuples.vartype=u.split(F):f==="VARFORM"?l.ntuples.varform=u.split(F):f==="VARDIM"?l.ntuples.vardim=Y(u.split(F)):f==="UNITS"?l.ntuples.units=u.split(F):f==="FACTOR"?l.ntuples.factor=Y(u.split(F)):f==="FIRST"?l.ntuples.first=Y(u.split(F)):f==="LAST"?l.ntuples.last=Y(u.split(F)):f==="MIN"?l.ntuples.min=Y(u.split(F)):f==="MAX"?l.ntuples.max=Y(u.split(F)):f===".NUCLEUS"?l.ntuples&&(l.ntuples.nucleus=u.split(F).map(m=>m.replace(/[^a-zA-Z0-9]/g,""))):f==="PAGE"?(t.page=u.trim(),t.pageValue=Number(u.replace(/^.*=/,"")),t.pageSymbol=t.page.replace(/[=].*/,"")):f==="RETENTIONTIME"?t.pageValue=Number(u):le(f)?t[I(f)]=u:f==="SAMPLEDESCRIPTION"?t.sampleDescription=u:f.startsWith("$NUC")?!l.tmp[f]&&!u.includes("off")&&(l.tmp[f]=u.replace(/[<>]/g,"")):f==="END"&&(l=r.pop()));if(l&&l.info&&l.meta&&f.match(a.keepRecordsRegExp)){let m,h;d.startsWith("$")?(h=a.canonicMetadataLabels?f.substring(1):d.substring(1),m=l.meta):(h=a.canonicDataLabels?f:d,m=l.info),a.dynamicTyping&&(u=ge(u)),m[h]?(Array.isArray(m[h])||(m[h]=[m[h]]),m[h].push(u)):m[h]=u}}if(L(i,"Finished parsing",a),H(s,i,a),L(i,"Total time",a),i.entries=o.children,i.flatten=s,a.logger){a.logger.debug("Finished jcamp conversion");for(let p of i.flatten)a.logger.debug(`${p.dataType} - ${p.title}`)}return i}function Ae(e,a={}){let{logger:s,OCL:i}=a;if(!e.info.ATOMLIST||!e.info.BONDLIST){s?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}Ce(e,s);let o=Se(e.info.ATOMLIST),l=ye(e.info.BONDLIST),r=Xe(e.info.CHARGE,s),t=Te(i,o,l,r,s);return{molecule:t,molfile:t.toMolfile()}}function Te(e,a,s,i,o){let l={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},r={},t=new e.Molecule(a.length,s.length);for(let n of a){let p=e.Molecule.getAtomicNoFromLabel(n.element);p||(o?.error(`Atomic number of ${n.element} could not be determined`),p=e.Molecule.getAtomicNoFromLabel("X")),r[n.atomNumber]=t.addAtom(p),t.setAtomMapNo(r[n.atomNumber],n.atomNumber)}for(let n of s){if(r[n.atomNumber1]===void 0){o?.error(`A bond goes to atomNumber ${n.atomNumber1} that does not exists`);continue}if(r[n.atomNumber2]===void 0){o?.error(`A bond goes to atomNumber ${n.atomNumber2} that does not exists`);continue}let p=t.addBond(r[n.atomNumber1],r[n.atomNumber2]);t.setBondType(p,l[n.bondType])}for(let n of i){if(r[n.atomNumber]===void 0){o?.error(`A charge goes to atomNumber ${n.atomNumber1} that does not exists`);continue}t.setAtomCharge(r[n.atomNumber],n.value)}return t}function Se(e){let a=e.split(/\r?\n/).map(i=>M(i)).filter(i=>i),s=[];for(let i of a){let[o,l,r]=i.trim().split(/\s+/);s.push({atomNumber:Number(o),element:l,nbImplicitHydrogens:r?.length>0?Number(r):void 0})}return s}function ye(e){let a=e.split(/\r?\n/).map(i=>M(i)).filter(i=>i),s=[];for(let i of a){let[o,l,r]=i.trim().split(/\s+/);s.push({atomNumber1:Number(o),atomNumber2:Number(l),bondType:r})}return s}function Xe(e,a){if(!e)return[];let s=e.split(/\r?\n/).map(o=>M(o)).filter(o=>o),i=[];for(let o of s){let[l,r,t]=o.trim().split(/\s+/);t!==void 0&&a?.warn("Charge on multiple atom is not supported"),i.push({atomNumber:Number(r),value:Number(l)})}return i}function Ce(e,a){let s=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let i of s)e.info[i]&&a?.warn(`JCAMP-CS parser do not support: ${i}`)}export{Ne as convert,pe as createTree,Ae as parseJcampCS};
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