jcampconverter 9.4.1 → 9.5.0

package/jcampconverter.cjs

@@ -1,8 +1,8 @@
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+`);if(m===-1&&(m=u.indexOf("\r")),m>0){let h=u.substring(0,m).split(/[ ,;\t]+/);z(t,l,h[0]),l.datatable=h[0],h[1]&&h[1].indexOf("PEAKS")>-1?f="PEAKTABLE":h[1]&&(h[1].indexOf("XYDATA")||h[0].indexOf("++")>0)&&(f="XYDATA",l.nbPoints&&(l.deltaX=(l.lastX-l.firstX)/(l.nbPoints-1)))}}if(f==="XYDATA"){i.wantXY&&(E(l),u.match(/.*\+\+.*/)?(l.nbPoints&&(l.deltaX=(l.lastX-l.firstX)/(l.nbPoints-1)),B(l,u,a)):w(l,u,a),t.spectra.push(l),l={});continue}else if(f==="PEAKTABLE"){i.wantXY&&(E(l),w(l,u,a),t.spectra.push(l),l={});continue}if(f==="PEAKASSIGNMENTS"){i.wantXY&&(u.match(/.*([^A-Z]*).*/)&&k(l,u),t.spectra.push(l),l={});continue}if(f==="TITLE"){let m=t;m.children||(m.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},m.children.push(t),r.push(m),s.push(t),t.title=u}else f==="DATATYPE"?(t.dataType=u,u.match(/(^nd|\snd\s)/i)&&(t.twoD=!0)):f==="NTUPLES"?u.match(/(^nd|\snd\s)/i)&&(t.twoD=!0):f==="DATACLASS"?t.dataClass=u:f==="JCAMPDX"?t.jcampDX=F(u):f==="JCAMPCS"?t.jcampCS=F(u):f==="XUNITS"?l.xUnits=u:f==="YUNITS"?l.yUnits=u:f==="FIRSTX"?l.firstX=Number(u):f==="LASTX"?l.lastX=Number(u):f==="FIRSTY"?l.firstY=Number(u):f==="LASTY"?l.lastY=Number(u):f==="NPOINTS"?l.nbPoints=Number(u):f==="XFACTOR"?l.xFactor=Number(u):f==="YFACTOR"?l.yFactor=Number(u):f==="MAXX"?l.maxX=Number(u):f==="MINX"?l.minX=Number(u):f==="MAXY"?l.maxY=Number(u):f==="MINY"?l.minY=Number(u):f==="DELTAX"?l.deltaX=Number(u):f===".OBSERVEFREQUENCY"||f==="$SFO1"?l.observeFrequency||(l.observeFrequency=Number(u)):f===".OBSERVENUCLEUS"?l.xType||(t.xType=u.replace(/[^a-zA-Z0-9]/g,"")):f==="$OFFSET"?(t.shiftOffsetNum=0,l.shiftOffsetVal||(l.shiftOffsetVal=Number(u))):f==="$REFERENCEPOINT"||(f==="VARNAME"?t.ntuples.varname=u.split(M):f==="SYMBOL"?t.ntuples.symbol=u.split(M):f==="VARTYPE"?t.ntuples.vartype=u.split(M):f==="VARFORM"?t.ntuples.varform=u.split(M):f==="VARDIM"?t.ntuples.vardim=Y(u.split(M)):f==="UNITS"?t.ntuples.units=u.split(M):f==="FACTOR"?t.ntuples.factor=Y(u.split(M)):f==="FIRST"?t.ntuples.first=Y(u.split(M)):f==="LAST"?t.ntuples.last=Y(u.split(M)):f==="MIN"?t.ntuples.min=Y(u.split(M)):f==="MAX"?t.ntuples.max=Y(u.split(M)):f===".NUCLEUS"?t.ntuples&&(t.ntuples.nucleus=u.split(M).map(m=>m.replace(/[^a-zA-Z0-9]/g,""))):f==="PAGE"?(l.page=u.trim(),l.pageValue=Number(u.replace(/^.*=/,"")),l.pageSymbol=l.page.replace(/[=].*/,"")):f==="RETENTIONTIME"?l.pageValue=Number(u):fe(f)?l[V(f)]=u:f==="SAMPLEDESCRIPTION"?l.sampleDescription=u:f.startsWith("$NUC")?!t.tmp[f]&&!u.includes("off")&&(t.tmp[f]=u.replace(/[<>]/g,"")):f==="END"&&(t=r.pop()));if(t&&t.info&&t.meta&&f.match(i.keepRecordsRegExp)){let m,h;d.startsWith("$")?(h=i.canonicMetadataLabels?f.substring(1):d.substring(1),m=t.meta):(h=i.canonicDataLabels?f:d,m=t.info),i.dynamicTyping&&(u=(0,pe.parseString)(u)),m[h]?(Array.isArray(m[h])||(m[h]=[m[h]]),m[h].push(u)):m[h]=u}}if(L(a,"Finished parsing",i),_(s,a,i),L(a,"Total time",i),a.entries=n.children,a.flatten=s,i.logger){i.logger.debug("Finished jcamp conversion");for(let p of a.flatten)i.logger.debug(`${p.dataType} - ${p.title}`)}return a}function he(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}De(e,s);let n=Oe(e.info.ATOMLIST),t=Re(e.info.BONDLIST),r=Pe(e.info.CHARGE,s),l=Ye(a,n,t,r,s);return{molecule:l,molfile:l.toMolfile()}}function Ye(e,i,s,a,n){let t={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},r={},l=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]=l.addAtom(p),l.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=l.addBond(r[o.atomNumber1],r[o.atomNumber2]);l.setBondType(p,t[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}l.setAtomCharge(r[o.atomNumber],o.value)}return l}function Oe(e){let i=e.split(/\r?\n/).map(a=>F(a)).filter(a=>a),s=[];for(let a of i){let[n,t,r]=a.trim().split(/\s+/);s.push({atomNumber:Number(n),element:t,nbImplicitHydrogens:r?.length>0?Number(r):void 0})}return s}function Re(e){let i=e.split(/\r?\n/).map(a=>F(a)).filter(a=>a),s=[];for(let a of i){let[n,t,r]=a.trim().split(/\s+/);s.push({atomNumber1:Number(n),atomNumber2:Number(t),bondType:r})}return s}function Pe(e,i){if(!e)return[];let s=e.split(/\r?\n/).map(n=>F(n)).filter(n=>n),a=[];for(let n of s){let[t,r,l]=n.trim().split(/\s+/);l!==void 0&&i?.warn("Charge on multiple atom is not supported"),a.push({atomNumber:Number(r),value:Number(t)})}return a}function De(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.d.ts

@@ -66,6 +66,8 @@ import { Logger } from 'cheminfo-types';
  * @property {string} [title]
  * @property {string} [dataType]
  * @property {string} [dataClass]
+ * @property {string?} [jcampDX]
+ * @property {string?} [jcampCS]
  * @property {boolean} [twoD]
  * @property {MinMax} [minMax]
  */
@@ -186,6 +188,8 @@ declare type Entry = {
     title?: string | undefined;
     dataType?: string | undefined;
     dataClass?: string | undefined;
+    jcampDX?: string | null | undefined;
+    jcampCS?: string | null | undefined;
     twoD?: boolean | undefined;
     minMax?: MinMax | undefined;
 };
@@ -216,6 +220,28 @@ declare type Ntuples = {
     nucleus?: string[] | undefined;
 };
 
+/**
+ *
+ * @typedef {object} ParsedCS@typedef {object} ParsedCS
+ * @property {string} molfile
+ * @property {import("openchemlib").OCL} molecule
+ */
+/**
+ *
+ * @param {import("./convert.js").Entry} entry
+ * @param {object} [options={}]
+ * @param {import("fifo-logger").Logger} [options.logger]
+ * @param {import("openchemlib").OCL} [options.OCL]
+ * @returns ParsedCS
+ */
+export declare function parseJcampCS(entry: Entry, options?: {
+    logger?: any;
+    OCL?: any;
+} | undefined): {
+    molecule: any;
+    molfile: any;
+} | undefined;
+
 declare type Spectrum = Record<string, any>;
 
 declare type Tree = {

package/jcampconverter.mjs

@@ -1,8 +1,8 @@
-import{ensureString as fe}from"ensure-string";function ne(e,l={}){e=fe(e);let{flatten:p=!1}=l;if(typeof e!="string")throw new TypeError("the JCAMP should be a string");let a=e.split(/\r?\n/),s=[],t=[],o=[],i,f=0,m=e.includes("## ");for(let c=0;c<a.length;c++){let d=a[c],r=m?d.replace(/ /g,""):d;if(r.substring(0,9)==="##NTUPLES"&&f++,r.substring(0,7)==="##TITLE"){let n=[r.substring(8).trim()];for(let u=c+1;u<a.length&&!a[u].startsWith("##");u++)n.push(a[u].trim());t.push({title:n.join(`
+import{ensureString as fe}from"ensure-string";var P=/\s*\$\$.*/;function F(e){return e.replace(P,"")}function ue(e,a={}){e=fe(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=[],t=[],r=[],l,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());t.push({title:f.join(`
 `),jcamp:`${d}
-`,children:[]}),i=t[t.length-1],s.push(i)}else if(r.substring(0,5)==="##END"&&f===0){i.jcamp+=`${d}
-`;let n=t.pop();t.length!==0?(i=t[t.length-1],i.children.push(n)):(i=void 0,o.push(n))}else if(i&&i.jcamp){i.jcamp+=`${d}
-`;let n=r.match(/^##(.*?)=(.+)/);if(n){let u=n[1].replace(/[ _-]/g,"").toUpperCase();u==="DATATYPE"&&(i.dataType=n[2].trim()),u==="DATACLASS"&&(i.dataClass=n[2].trim())}}r.substring(0,5)==="##END"&&f>0&&f--}return p?(s.forEach(c=>{c.children=void 0}),s):o}import{parseString as me}from"dynamic-typing";import{ensureString as ce}from"ensure-string";var $=["TIC",".RIC","SCANNUMBER"];function J(e){let l=e.spectra,p=l.length,a={times:new Array(p),series:{ms:{dimension:2,data:new Array(p)}}},s=[];for(let t=0;t<$.length;t++){let o=D($[t]);l[0][o]&&(s.push(o),a.series[o]={dimension:1,data:new Array(p)})}for(let t=0;t<p;t++){let o=l[t];a.times[t]=o.pageValue;for(let i=0;i<s.length;i++)a.series[s[i]].data[t]=Number(o[s[i]]);o.data&&(a.series.ms.data[t]=[o.data.x,o.data.y])}e.chromatogram=a}function Q(e){return $.indexOf(e)!==-1}function D(e){return e.toLowerCase().replace(/[^a-z0-9]/g,"")}function Y(e){let l=[];for(let p=0;p<e.length;p++)l.push(Number(e[p]));return l}function U(e,l){let p=e.yFactor,a=e.deltaX;e.isXYdata=!0;let s={x:[],y:[]};e.data=s;let t=e.firstX,o=e.firstY,i=!1,f,m=0;for(;m<l.length;m++)if(f=l.charCodeAt(m),f===13||f===10)i=!0;else if(i)break;let c=!0,d=!1,r=!1,n=0,u=!1,h=!1,g=0,T=0,A=!1,y=!1,N=!1,S=0;for(;m<=l.length;m++)if(m===l.length?f=13:f=l.charCodeAt(m),h)(f===13||f===10)&&(c=!0,h=!1);else if(f<=57&&f>=48)y=!0,S>0?g+=(f-48)/Math.pow(10,S++):(g*=10,g+=f-48);else if(f===44||f===46)y=!0,S++;else{if(y){if(c)c=!1,r&&(N=!0);else if(N)N=!1;else{d?(n=A?0-g:g,r=!0,d=!1):u||(T=A?0-g:g);let O=u?g-1:1;for(let F=0;F<O;F++)r?o+=n:o=T,s.x.push(t),s.y.push(o*p),t+=a}A=!1,g=0,S=0,y=!1,u=!1}if(f<74&&f>63)y=!0,r=!1,g=f-64;else if(f>96&&f<106)y=!0,r=!1,g=f-96,A=!0;else if(f===115)y=!0,u=!0,g=9;else if(f>82&&f<91)y=!0,u=!0,g=f-82;else if(f>73&&f<83)y=!0,d=!0,g=f-73;else if(f>105&&f<115)y=!0,d=!0,g=f-105,A=!0;else if(f===36&&l.charCodeAt(m+1)===36)y=!0,h=!0;else if(f===37)y=!0,d=!0,g=0,A=!1;else if(f===45){let O=l.charCodeAt(m+1);(O>=48&&O<=57||O===44||O===46)&&(y=!0,c||(r=!1),A=!0)}else(f===13||f===10)&&(c=!0,h=!1)}}var ee=/\$\$.*/,te=/[,\t ]+/;function P(e,l,p){if(e.isPeaktable=!0,!e.variables||Object.keys(e.variables)===2?oe(e,l,p):pe(e,l,p),e.variables)for(let a in e.variables)e.variables[a].data=e.data[a]}function oe(e,l,p){let a={x:[],y:[]};e.data=a;let s=l.split(/,? *,?[;\r\n]+ */);for(let t=1;t<s.length;t++){let o=s[t].trim().replace(ee,"").split(te);if(o.length%2===0)for(let i=0;i<o.length;i=i+2)a.x.push(Number(o[i])*e.xFactor),a.y.push(Number(o[i+1])*e.yFactor);else p.logs.push(`Format error: ${o}`)}}function pe(e,l,p){let a={},s=Object.keys(e.variables),t=s.length;s.forEach(i=>a[i]=[]),e.data=a;let o=l.split(/,? *,?[;\r\n]+ */);for(let i=1;i<o.length;i++){let f=o[i].trim().replace(ee,"").split(te);if(f.length%t===0)for(let m=0;m<f.length;m++)a[s[m%t]].push(Number(f[m]));else p.logs.push(`Format error: ${f}`)}}function V(e,l){e.isXYAdata=!0;let p={};e.data=p;let a=l.split(/\r?\n/),s=a[0].replace(/^.*?([A-Z]+).*$/,"$1").split("").map(t=>t.toLowerCase());for(let t=1;t<a.length;t++){let o=a[t].replace(/^\((.*)\)$/,"$1").split(/ *, */);for(let i=0;i<s.length;i++){let f=o[i];switch(s[i]){case"x":case"y":case"w":f=Number.parseFloat(f);break;case"a":f=f.replace(/^<(.*)>$/,"$1");break;case"m":break;default:continue}p[s[i]]||(p[s[i]]=[]),p[s[i]].push(f)}}}import{parseString as se}from"dynamic-typing";import le from"ml-array-median";function I(e){let l=e[0].data.y[0],p=l,a=e.length,s=e[0].data.x.length,t=new Array(a);for(let r=0;r<a;r++){t[r]=e[r].data.y;for(let n=0;n<s;n++){let u=t[r][n];u<l&&(l=u),u>p&&(p=u)}}let o=e[0].data.x[0],i=e[0].data.x[e[0].data.x.length-1],f=e[0].pageValue,m=e[a-1].pageValue;if(o>i)for(let r of t)r.reverse();f>m&&t.reverse();let c=[];for(let r=0;r<t.length;r++){let n=Float64Array.from(t[r]);for(let u=0;u<n.length;u++)n[u]<0&&(n[u]=-n[u]);c.push(le(n))}let d=le(c);return{z:t,minX:Math.min(o,i),maxX:Math.max(o,i),minY:Math.min(f,m),maxY:Math.max(f,m),minZ:l,maxZ:p,noise:d}}function E(e,l){let p=e.noise,a=e.z,s,t,o,i,f,m,c,d,r=a.length,n=a[0].length,u,h,g,T,A=e.minX,N=(e.maxX-A)/(n-1),S=e.minY,F=(e.maxY-S)/(r-1),ae=e.minZ,H=e.maxZ,G=l.nbContourLevels*2,K=new Array(G),x;for(let M=0;M<G;M++){let R={};K[M]=R;let re=M%2,_=(H-l.noiseMultiplier*p)*Math.exp((M>>1)-l.nbContourLevels);re===0?x=_+l.noiseMultiplier*p:x=0-_-l.noiseMultiplier*p;let b=[];if(R.zValue=x,R.lines=b,!(x<=ae||x>=H))for(let v=0;v<r-1;v++){let z=a[v],W=a[v+1];for(let 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w(e){e.xFactor||(e.xFactor=1),e.yFactor||(e.yFactor=1)}var M=/[ \t]*,[ \t]*/,be={keepRecordsRegExp:/^$/,canonicDataLabels:!0,canonicMetadataLabels:!1,dynamicTyping:!0,withoutXY:!1,noTrimRegExp:/^$/,chromatogram:!1,keepSpectra:!1,noContour:!1,nbContourLevels:7,noiseMultiplier:5,profiling:!1};function xe(e,a={}){e=ge(e),a={...be,...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:[]},t=o,r=[],l={};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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-##`);L(a,"Split to LDRS",l),f[0]&&(f[0]=f[0].replace(/^[\r\n ]*##/,""));for(let m of f){let c=m.indexOf("="),d=c>0?m.substring(0,c):m,r=c>0?d.match(l.noTrimRegExp)?m.substring(c+1):m.substring(c+1).trim():"",n=d.replace(/[_ -]/g,"").toUpperCase();if(n==="DATATABLE"){let u=r.indexOf(`
-`);if(u===-1&&(u=r.indexOf("\r")),u>0){let h=r.substring(0,u).split(/[ ,;\t]+/);q(t,i,h[0]),i.datatable=h[0],h[1]&&h[1].indexOf("PEAKS")>-1?n="PEAKTABLE":h[1]&&(h[1].indexOf("XYDATA")||h[0].indexOf("++")>0)&&(n="XYDATA",i.nbPoints&&(i.deltaX=(i.lastX-i.firstX)/(i.nbPoints-1)))}}if(n==="XYDATA"){l.wantXY&&(w(i),r.match(/.*\+\+.*/)?(i.nbPoints&&(i.deltaX=(i.lastX-i.firstX)/(i.nbPoints-1)),U(i,r,a)):P(i,r,a),t.spectra.push(i),i={});continue}else if(n==="PEAKTABLE"){l.wantXY&&(w(i),P(i,r,a),t.spectra.push(i),i={});continue}if(n==="PEAKASSIGNMENTS"){l.wantXY&&(r.match(/.*([^A-Z]*).*/)&&V(i,r),t.spectra.push(i),i={});continue}if(n==="TITLE"){let u=t;u.children||(u.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},u.children.push(t),o.push(u),p.push(t),t.title=r}else n==="DATATYPE"?(t.dataType=r,r.match(/(^nd|\snd\s)/i)&&(t.twoD=!0)):n==="NTUPLES"?r.match(/(^nd|\snd\s)/i)&&(t.twoD=!0):n==="DATACLASS"?t.dataClass=r:n==="XUNITS"?i.xUnits=r:n==="YUNITS"?i.yUnits=r:n==="FIRSTX"?i.firstX=Number(r):n==="LASTX"?i.lastX=Number(r):n==="FIRSTY"?i.firstY=Number(r):n==="LASTY"?i.lastY=Number(r):n==="NPOINTS"?i.nbPoints=Number(r):n==="XFACTOR"?i.xFactor=Number(r):n==="YFACTOR"?i.yFactor=Number(r):n==="MAXX"?i.maxX=Number(r):n==="MINX"?i.minX=Number(r):n==="MAXY"?i.maxY=Number(r):n==="MINY"?i.minY=Number(r):n==="DELTAX"?i.deltaX=Number(r):n===".OBSERVEFREQUENCY"||n==="$SFO1"?i.observeFrequency||(i.observeFrequency=Number(r)):n===".OBSERVENUCLEUS"?i.xType||(t.xType=r.replace(/[^a-zA-Z0-9]/g,"")):n==="$OFFSET"?(t.shiftOffsetNum=0,i.shiftOffsetVal||(i.shiftOffsetVal=Number(r))):n==="$REFERENCEPOINT"||(n==="VARNAME"?t.ntuples.varname=r.split(C):n==="SYMBOL"?t.ntuples.symbol=r.split(C):n==="VARTYPE"?t.ntuples.vartype=r.split(C):n==="VARFORM"?t.ntuples.varform=r.split(C):n==="VARDIM"?t.ntuples.vardim=Y(r.split(C)):n==="UNITS"?t.ntuples.units=r.split(C):n==="FACTOR"?t.ntuples.factor=Y(r.split(C)):n==="FIRST"?t.ntuples.first=Y(r.split(C)):n==="LAST"?t.ntuples.last=Y(r.split(C)):n==="MIN"?t.ntuples.min=Y(r.split(C)):n==="MAX"?t.ntuples.max=Y(r.split(C)):n===".NUCLEUS"?t.ntuples&&(t.ntuples.nucleus=r.split(C).map(u=>u.replace(/[^a-zA-Z0-9]/g,""))):n==="PAGE"?(i.page=r.trim(),i.pageValue=Number(r.replace(/^.*=/,"")),i.pageSymbol=i.page.replace(/[=].*/,"")):n==="RETENTIONTIME"?i.pageValue=Number(r):Q(n)?i[D(n)]=r:n==="SAMPLEDESCRIPTION"?i.sampleDescription=r:n.startsWith("$NUC")?!t.tmp[n]&&!r.includes("off")&&(t.tmp[n]=r.replace(/[<>]/g,"")):n==="END"&&(t=o.pop()));if(t&&t.info&&t.meta&&n.match(l.keepRecordsRegExp)){let u,h;d.startsWith("$")?(h=l.canonicMetadataLabels?n.substring(1):d.substring(1),u=t.meta):(h=l.canonicDataLabels?n:d,u=t.info),l.dynamicTyping&&(r=me(r)),u[h]?(Array.isArray(u[h])||(u[h]=[u[h]]),u[h].push(r)):u[h]=r}}if(L(a,"Finished parsing",l),B(p,a,l),L(a,"Total time",l),a.entries=s.children,a.flatten=p,l.logger){l.logger.debug("Finished jcamp conversion");for(let m of a.flatten)l.logger.debug(`${m.dataType} - ${m.title}`)}return a}export{ge as convert,ne as createTree};
+##`);L(i,"Split to LDRS",a),n[0]&&(n[0]=n[0].replace(/^[\r\n ]*##/,""));for(let p of n){let c=p.indexOf("="),d=c>0?p.substring(0,c):p,u=c>0?d.match(a.noTrimRegExp)?p.substring(c+1):p.substring(c+1).trim():"",f=d.replace(/[_ -]/g,"").toUpperCase();if(f==="DATATABLE"){let m=u.indexOf(`
+`);if(m===-1&&(m=u.indexOf("\r")),m>0){let h=u.substring(0,m).split(/[ ,;\t]+/);q(t,l,h[0]),l.datatable=h[0],h[1]&&h[1].indexOf("PEAKS")>-1?f="PEAKTABLE":h[1]&&(h[1].indexOf("XYDATA")||h[0].indexOf("++")>0)&&(f="XYDATA",l.nbPoints&&(l.deltaX=(l.lastX-l.firstX)/(l.nbPoints-1)))}}if(f==="XYDATA"){a.wantXY&&(w(l),u.match(/.*\+\+.*/)?(l.nbPoints&&(l.deltaX=(l.lastX-l.firstX)/(l.nbPoints-1)),U(l,u,i)):D(l,u,i),t.spectra.push(l),l={});continue}else if(f==="PEAKTABLE"){a.wantXY&&(w(l),D(l,u,i),t.spectra.push(l),l={});continue}if(f==="PEAKASSIGNMENTS"){a.wantXY&&(u.match(/.*([^A-Z]*).*/)&&V(l,u),t.spectra.push(l),l={});continue}if(f==="TITLE"){let m=t;m.children||(m.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},m.children.push(t),r.push(m),s.push(t),t.title=u}else f==="DATATYPE"?(t.dataType=u,u.match(/(^nd|\snd\s)/i)&&(t.twoD=!0)):f==="NTUPLES"?u.match(/(^nd|\snd\s)/i)&&(t.twoD=!0):f==="DATACLASS"?t.dataClass=u:f==="JCAMPDX"?t.jcampDX=F(u):f==="JCAMPCS"?t.jcampCS=F(u):f==="XUNITS"?l.xUnits=u:f==="YUNITS"?l.yUnits=u:f==="FIRSTX"?l.firstX=Number(u):f==="LASTX"?l.lastX=Number(u):f==="FIRSTY"?l.firstY=Number(u):f==="LASTY"?l.lastY=Number(u):f==="NPOINTS"?l.nbPoints=Number(u):f==="XFACTOR"?l.xFactor=Number(u):f==="YFACTOR"?l.yFactor=Number(u):f==="MAXX"?l.maxX=Number(u):f==="MINX"?l.minX=Number(u):f==="MAXY"?l.maxY=Number(u):f==="MINY"?l.minY=Number(u):f==="DELTAX"?l.deltaX=Number(u):f===".OBSERVEFREQUENCY"||f==="$SFO1"?l.observeFrequency||(l.observeFrequency=Number(u)):f===".OBSERVENUCLEUS"?l.xType||(t.xType=u.replace(/[^a-zA-Z0-9]/g,"")):f==="$OFFSET"?(t.shiftOffsetNum=0,l.shiftOffsetVal||(l.shiftOffsetVal=Number(u))):f==="$REFERENCEPOINT"||(f==="VARNAME"?t.ntuples.varname=u.split(M):f==="SYMBOL"?t.ntuples.symbol=u.split(M):f==="VARTYPE"?t.ntuples.vartype=u.split(M):f==="VARFORM"?t.ntuples.varform=u.split(M):f==="VARDIM"?t.ntuples.vardim=Y(u.split(M)):f==="UNITS"?t.ntuples.units=u.split(M):f==="FACTOR"?t.ntuples.factor=Y(u.split(M)):f==="FIRST"?t.ntuples.first=Y(u.split(M)):f==="LAST"?t.ntuples.last=Y(u.split(M)):f==="MIN"?t.ntuples.min=Y(u.split(M)):f==="MAX"?t.ntuples.max=Y(u.split(M)):f===".NUCLEUS"?t.ntuples&&(t.ntuples.nucleus=u.split(M).map(m=>m.replace(/[^a-zA-Z0-9]/g,""))):f==="PAGE"?(l.page=u.trim(),l.pageValue=Number(u.replace(/^.*=/,"")),l.pageSymbol=l.page.replace(/[=].*/,"")):f==="RETENTIONTIME"?l.pageValue=Number(u):le(f)?l[I(f)]=u:f==="SAMPLEDESCRIPTION"?l.sampleDescription=u:f.startsWith("$NUC")?!t.tmp[f]&&!u.includes("off")&&(t.tmp[f]=u.replace(/[<>]/g,"")):f==="END"&&(t=r.pop()));if(t&&t.info&&t.meta&&f.match(a.keepRecordsRegExp)){let m,h;d.startsWith("$")?(h=a.canonicMetadataLabels?f.substring(1):d.substring(1),m=t.meta):(h=a.canonicDataLabels?f:d,m=t.info),a.dynamicTyping&&(u=de(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 Ne(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}Xe(e,s);let o=Ae(e.info.ATOMLIST),t=Se(e.info.BONDLIST),r=ye(e.info.CHARGE,s),l=Te(i,o,t,r,s);return{molecule:l,molfile:l.toMolfile()}}function Te(e,a,s,i,o){let t={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},r={},l=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]=l.addAtom(p),l.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=l.addBond(r[n.atomNumber1],r[n.atomNumber2]);l.setBondType(p,t[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}l.setAtomCharge(r[n.atomNumber],n.value)}return l}function Ae(e){let a=e.split(/\r?\n/).map(i=>F(i)).filter(i=>i),s=[];for(let i of a){let[o,t,r]=i.trim().split(/\s+/);s.push({atomNumber:Number(o),element:t,nbImplicitHydrogens:r?.length>0?Number(r):void 0})}return s}function Se(e){let a=e.split(/\r?\n/).map(i=>F(i)).filter(i=>i),s=[];for(let i of a){let[o,t,r]=i.trim().split(/\s+/);s.push({atomNumber1:Number(o),atomNumber2:Number(t),bondType:r})}return s}function ye(e,a){if(!e)return[];let s=e.split(/\r?\n/).map(o=>F(o)).filter(o=>o),i=[];for(let o of s){let[t,r,l]=o.trim().split(/\s+/);l!==void 0&&a?.warn("Charge on multiple atom is not supported"),i.push({atomNumber:Number(r),value:Number(t)})}return i}function Xe(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{xe as convert,ue as createTree,Ne as parseJcampCS};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jcampconverter",
-  "version": "9.4.1",
+  "version": "9.5.0",
   "description": "Parse and convert JCAMP data",
   "types": "jcampconverter.d.ts",
   "main": "jcampconverter.cjs",
@@ -51,30 +51,31 @@
   },
   "devDependencies": {
     "@microsoft/api-extractor": "^7.38.3",
-    "@types/jest": "^29.5.8",
+    "@types/jest": "^29.5.10",
     "@types/pino": "^7.0.5",
     "@vitest/coverage-v8": "^0.34.6",
     "benchmark": "^2.1.4",
     "c8": "^8.0.1",
     "cheminfo-build": "^1.2.0",
-    "esbuild": "^0.19.5",
-    "eslint": "^8.53.0",
+    "esbuild": "^0.19.7",
+    "eslint": "^8.54.0",
     "eslint-config-cheminfo-typescript": "^12.0.4",
     "esm": "^3.2.25",
     "fifo-logger": "^0.6.1",
     "jest-matcher-deep-close-to": "^3.0.2",
     "jscpd": "^3.5.10",
     "ml-spectra-processing": "^12.6.0",
+    "openchemlib": "^8.7.2",
     "prettier": "^3.1.0",
     "rimraf": "^5.0.5",
-    "typescript": "^5.2.2",
+    "typescript": "^5.3.2",
     "vitest": "^0.34.6"
   },
   "dependencies": {
     "cheminfo-types": "^1.7.2",
     "dynamic-typing": "^1.0.0",
     "ensure-string": "^1.2.0",
-    "gyromagnetic-ratio": "^1.0.0",
+    "gyromagnetic-ratio": "^1.1.1",
     "ml-array-median": "^1.1.6"
   }
 }