jcampconverter 11.0.3 → 11.0.5

package/dist/jcampconverter.d.ts

@@ -192,6 +192,10 @@ export declare interface ParseJcampCSOptions {
     logger?: Logger;
 }
 
+export declare function removeComment(value: string, separator?: string): string;
+
+export declare const removeCommentRegExp: RegExp;
+
 export declare interface Spectrum {
     [key: string]: any;
     data: Record<string, number[]>;

package/dist/jcampconverter.js

@@ -1,4 +1,6 @@
-import{ensureString as fe}from"ensure-string";var $=/\s*\$\$.*/;function M(e){return e.replace($,"")}function Te(e,m={}){e=fe(e);let{flatten:n=!1}=m,s=e.split(/\r?\n/),f=[],i=[],t=[],l={title:"",jcamp:"",children:[]},r=0,p=e.includes("## ");for(let c=0;c<s.length;c++){let b=s[c],h=p?b.replaceAll(" ",""):b;if(h.startsWith("##NTUPLES")&&r++,h.startsWith("##TITLE")){let o=[h.slice(8).trim()];for(let a=c+1;a<s.length&&!s[a].startsWith("##");a++)o.push(s[a].trim());i.push({title:o.join(`
+import{ensureString as fe}from"ensure-string";var $=/\s*\$\$.*/;function M(e,m=/\r\n/.exec(e)?`\r
+`:`
+`){return e.split(m).map(s=>s.replace($,"")).filter(Boolean).join(m).trim()}function Te(e,m={}){e=fe(e);let{flatten:n=!1}=m,s=e.split(/\r?\n/),f=[],i=[],t=[],l={title:"",jcamp:"",children:[]},r=0,p=e.includes("## ");for(let c=0;c<s.length;c++){let b=s[c],h=p?b.replaceAll(" ",""):b;if(h.startsWith("##NTUPLES")&&r++,h.startsWith("##TITLE")){let o=[h.slice(8).trim()];for(let a=c+1;a<s.length&&!s[a].startsWith("##");a++)o.push(s[a].trim());i.push({title:o.join(`
 `),jcamp:`${b}
 `,children:[]}),l=i.at(-1),f.push(l)}else if(h.startsWith("##END")&&r===0&&l){l.jcamp+=`${b}
 `;let o=i.pop();if(!o)throw new Error("Not finished");i.length>0?(l=i.at(-1),l.children?.push(o)):(l=void 0,t.push(o))}else if(l?.jcamp){l.jcamp+=`${b}
@@ -6,4 +8,4 @@ import{ensureString as fe}from"ensure-string";var $=/\s*\$\$.*/;function M(e){re
 ##`).split(`
 ##`);n.logger?.trace({profiling:!0},"Split to LDRS"),p[0]&&(p[0]=p[0].replace(/^[\r\n ]*##/,""));for(let c of p){let b=c.indexOf("="),h=b>0?c.slice(0,Math.max(0,b)):c,o=b>0?h.match(n.noTrimRegExp)?c.slice(Math.max(0,b+1)):c.slice(Math.max(0,b+1)).trim():"",a=h.replaceAll(/[_ -]/g,"").toUpperCase();if(a==="DATATABLE"){let u=o.indexOf(`
 `);if(u===-1&&(u=o.indexOf("\r")),u>0){let d=o.slice(0,Math.max(0,u)).split(/[ ,;\t]+/);z(t,r,d[0]),r.datatable=d[0],d[1]?.includes("PEAKS")?a="PEAKTABLE":d[1]&&(d[1].indexOf("XYDATA")||d[0].indexOf("++")>0)&&(a="XYDATA",r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)))}}if(a==="XYDATA"){n.wantXY&&(w(r),o.match(/.*\+\+.*/)?(r.nbPoints&&r.lastX!==void 0&&r.firstX!==void 0&&(r.deltaX=(r.lastX-r.firstX)/(r.nbPoints-1)),k(r,o,n)):P(r,o,n),t?.spectra.push(r),r={data:{}});continue}else if(a==="PEAKTABLE"){n.wantXY&&(w(r),P(r,o,n),t?.spectra.push(r),r={data:{}});continue}if(a==="PEAKASSIGNMENTS"){n.wantXY&&(o.match(/.*[^A-Z]*.*/)&&V(r,o),t?.spectra.push(r),r={data:{}});continue}if(n.removeComments&&(o=o.split(/\r?\n/).map(u=>u.replace(/ *\$\$.*$/,"")).join(`
-`)),a==="TITLE"){let u=t;u.children||(u.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},u.children.push(t),l.push(u),s.push(t),t.title=o}else a==="DATATYPE"?(t.dataType=o,o.match(/^nd|\snd\s/i)&&(t.twoD=!0)):a==="NTUPLES"?o.match(/^nd|\snd\s/i)&&(t.twoD=!0):a==="DATACLASS"?t.dataClass=o:a==="JCAMPDX"?t.jcampDX=M(o):a==="JCAMPCS"?t.jcampCS=M(o):a==="XUNITS"?r.xUnits=o:a==="YUNITS"?r.yUnits=o:a==="FIRSTX"?r.firstX=Number(o):a==="LASTX"?r.lastX=Number(o):a==="FIRSTY"?r.firstY=Number(o):a==="LASTY"?r.lastY=Number(o):a==="NPOINTS"?r.nbPoints=Number(o):a==="XFACTOR"?r.xFactor=Number(o):a==="YFACTOR"?r.yFactor=Number(o):a==="MAXX"?r.maxX=Number(o):a==="MINX"?r.minX=Number(o):a==="MAXY"?r.maxY=Number(o):a==="MINY"?r.minY=Number(o):a==="DELTAX"?r.deltaX=Number(o):a===".OBSERVEFREQUENCY"||a==="$SFO1"?r.observeFrequency||(r.observeFrequency=Number(o)):a===".OBSERVENUCLEUS"?r.xType||(t.xType=o.replaceAll(/[^a-zA-Z0-9]/g,"")):a==="$OFFSET"?(t.shiftOffsetNum=0,r.shiftOffsetVal||(r.shiftOffsetVal=Number(o))):a==="$REFERENCEPOINT"||(a==="VARNAME"?t.ntuples.varname=o.split(L):a==="SYMBOL"?t.ntuples.symbol=o.split(L):a==="VARTYPE"?t.ntuples.vartype=o.split(L):a==="VARFORM"?t.ntuples.varform=o.split(L):a==="VARDIM"?t.ntuples.vardim=E(o.split(L)):a==="UNITS"?t.ntuples.units=o.split(L):a==="FACTOR"?t.ntuples.factor=E(o.split(L)):a==="FIRST"?t.ntuples.first=E(o.split(L)):a==="LAST"?t.ntuples.last=E(o.split(L)):a==="MIN"?t.ntuples.min=E(o.split(L)):a==="MAX"?t.ntuples.max=E(o.split(L)):a===".NUCLEUS"?t.ntuples&&(t.ntuples.nucleus=o.split(L).map(u=>u.replaceAll(/[^a-zA-Z0-9]/g,""))):a==="PAGE"?(r.page=o.trim(),r.pageValue=Number(o.replace(/^.*=/,"")),r.pageSymbol=r.page.replace(/[=].*/,"")):a==="RETENTIONTIME"?r.pageValue=Number(o):ne(a)?r[U(a)]=o:a==="SAMPLEDESCRIPTION"?r.sampleDescription=o:a.startsWith("$NUC")?!t.tmp[a]&&!o.includes("off")&&(t.tmp[a]=o.replaceAll(/[<>]/g,"")):a==="END"&&(t=l.pop()));if(t?.info&&t.meta&&a.match(n.keepRecordsRegExp)){let u,d;h.startsWith("$")?(d=n.canonicMetadataLabels?a.slice(1):h.slice(1),u=t.meta):(d=n.canonicDataLabels?a:h,u=t.info),n.dynamicTyping&&(o=de(o)),u[d]?(Array.isArray(u[d])||(u[d]=[u[d]]),u[d].push(o)):u[d]=o}}if(n.logger?.trace({profiling:!0},"Finished parsing"),q(s,f,n),n.logger?.trace({profiling:!0},"Total time"),f.entries=i.children||[],f.flatten=s,n.logger){n.logger.debug("Finished jcamp conversion");for(let c of f.flatten)n.logger.debug(`${c.dataType} - ${c.title}`)}return f}function pt(e,m){let{logger:n,OCL:s}=m;if(!e.info.ATOMLIST||!e.info.BONDLIST){n?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}Ae(e,n);let f=ye(e.info.ATOMLIST),i=xe(e.info.BONDLIST),t=Ce(e.info.CHARGE,n),l=he(s,f,i,t,n);return{molecule:l,molfile:l.toMolfile()}}function he(e,m,n,s,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 s){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 ye(e){let m=e.split(/\r?\n/).map(s=>M(s)).filter(Boolean),n=[];for(let s of m){let[f,i,t]=s.trim().split(/\s+/);n.push({atomNumber:Number(f),element:i,nbImplicitHydrogens:t?.length>0?Number(t):void 0})}return n}function xe(e){let m=e.split(/\r?\n/).map(s=>M(s)).filter(Boolean),n=[];for(let s of m){let[f,i,t]=s.trim().split(/\s+/);n.push({atomNumber1:Number(f),atomNumber2:Number(i),bondType:t})}return n}function Ce(e,m){if(!e)return[];let n=e.split(/\r?\n/).map(f=>M(f)).filter(Boolean),s=[];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"),s.push({atomNumber:Number(t),value:Number(i)})}return s}function Ae(e,m){let n=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let s of n)e.info[s]&&m?.warn(`JCAMP-CS parser do not support: ${s}`)}export{mt as convert,Te as createTree,pt as parseJcampCS};
+`)),a==="TITLE"){let u=t;u.children||(u.children=[]),t={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},u.children.push(t),l.push(u),s.push(t),t.title=o}else a==="DATATYPE"?(t.dataType=o,o.match(/^nd|\snd\s/i)&&(t.twoD=!0)):a==="NTUPLES"?o.match(/^nd|\snd\s/i)&&(t.twoD=!0):a==="DATACLASS"?t.dataClass=o:a==="JCAMPDX"?t.jcampDX=M(o):a==="JCAMPCS"?t.jcampCS=M(o):a==="XUNITS"?r.xUnits=o:a==="YUNITS"?r.yUnits=o:a==="FIRSTX"?r.firstX=Number(o):a==="LASTX"?r.lastX=Number(o):a==="FIRSTY"?r.firstY=Number(o):a==="LASTY"?r.lastY=Number(o):a==="NPOINTS"?r.nbPoints=Number(o):a==="XFACTOR"?r.xFactor=Number(o):a==="YFACTOR"?r.yFactor=Number(o):a==="MAXX"?r.maxX=Number(o):a==="MINX"?r.minX=Number(o):a==="MAXY"?r.maxY=Number(o):a==="MINY"?r.minY=Number(o):a==="DELTAX"?r.deltaX=Number(o):a===".OBSERVEFREQUENCY"||a==="$SFO1"?r.observeFrequency||(r.observeFrequency=Number(o)):a===".OBSERVENUCLEUS"?r.xType||(t.xType=o.replaceAll(/[^a-zA-Z0-9]/g,"")):a==="$OFFSET"?(t.shiftOffsetNum=0,r.shiftOffsetVal||(r.shiftOffsetVal=Number(o))):a==="$REFERENCEPOINT"||(a==="VARNAME"?t.ntuples.varname=o.split(L):a==="SYMBOL"?t.ntuples.symbol=o.split(L):a==="VARTYPE"?t.ntuples.vartype=o.split(L):a==="VARFORM"?t.ntuples.varform=o.split(L):a==="VARDIM"?t.ntuples.vardim=E(o.split(L)):a==="UNITS"?t.ntuples.units=o.split(L):a==="FACTOR"?t.ntuples.factor=E(o.split(L)):a==="FIRST"?t.ntuples.first=E(o.split(L)):a==="LAST"?t.ntuples.last=E(o.split(L)):a==="MIN"?t.ntuples.min=E(o.split(L)):a==="MAX"?t.ntuples.max=E(o.split(L)):a===".NUCLEUS"?t.ntuples&&(t.ntuples.nucleus=o.split(L).map(u=>u.replaceAll(/[^a-zA-Z0-9]/g,""))):a==="PAGE"?(r.page=o.trim(),r.pageValue=Number(o.replace(/^.*=/,"")),r.pageSymbol=r.page.replace(/[=].*/,"")):a==="RETENTIONTIME"?r.pageValue=Number(o):ne(a)?r[U(a)]=o:a==="SAMPLEDESCRIPTION"?r.sampleDescription=o:a.startsWith("$NUC")?!t.tmp[a]&&!o.includes("off")&&(t.tmp[a]=o.replaceAll(/[<>]/g,"")):a==="END"&&(t=l.pop()));if(t?.info&&t.meta&&a.match(n.keepRecordsRegExp)){let u,d;h.startsWith("$")?(d=n.canonicMetadataLabels?a.slice(1):h.slice(1),u=t.meta):(d=n.canonicDataLabels?a:h,u=t.info),n.dynamicTyping&&(o=de(o)),u[d]?(Array.isArray(u[d])||(u[d]=[u[d]]),u[d].push(o)):u[d]=o}}if(n.logger?.trace({profiling:!0},"Finished parsing"),q(s,f,n),n.logger?.trace({profiling:!0},"Total time"),f.entries=i.children||[],f.flatten=s,n.logger){n.logger.debug("Finished jcamp conversion");for(let c of f.flatten)n.logger.debug(`${c.dataType} - ${c.title}`)}return f}function pt(e,m){let{logger:n,OCL:s}=m;if(!e.info.ATOMLIST||!e.info.BONDLIST){n?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}Ae(e,n);let f=ye(e.info.ATOMLIST),i=xe(e.info.BONDLIST),t=Ce(e.info.CHARGE,n),l=he(s,f,i,t,n);return{molecule:l,molfile:l.toMolfile()}}function he(e,m,n,s,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 s){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 ye(e){let m=e.split(/\r?\n/).map(s=>M(s)).filter(Boolean),n=[];for(let s of m){let[f,i,t]=s.trim().split(/\s+/);n.push({atomNumber:Number(f),element:i,nbImplicitHydrogens:t?.length>0?Number(t):void 0})}return n}function xe(e){let m=e.split(/\r?\n/).map(s=>M(s)).filter(Boolean),n=[];for(let s of m){let[f,i,t]=s.trim().split(/\s+/);n.push({atomNumber1:Number(f),atomNumber2:Number(i),bondType:t})}return n}function Ce(e,m){if(!e)return[];let n=e.split(/\r?\n/).map(f=>M(f)).filter(Boolean),s=[];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"),s.push({atomNumber:Number(t),value:Number(i)})}return s}function Ae(e,m){let n=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let s of n)e.info[s]&&m?.warn(`JCAMP-CS parser do not support: ${s}`)}export{mt as convert,Te as createTree,pt as parseJcampCS,M as removeComment,$ as removeCommentRegExp};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jcampconverter",
-  "version": "11.0.3",
+  "version": "11.0.5",
   "description": "Parse and convert JCAMP-DX data",
   "license": "CC-BY-NC-SA-4.0",
   "type": "module",
@@ -37,14 +37,14 @@
   "devDependencies": {
     "benchmark": "^2.1.4",
     "cheminfo-build": "^1.2.1",
-    "esbuild": "^0.25.5",
-    "fifo-logger": "^1.0.0",
-    "jcamp-data-test": "^1.0.0",
+    "esbuild": "^0.25.8",
+    "fifo-logger": "^2.0.0",
+    "jcamp-data-test": "^2.1.0",
     "jest-matcher-deep-close-to": "^3.0.2",
     "jscpd": "^4.0.5",
-    "ml-spectra-processing": "^14.12.0",
+    "ml-spectra-processing": "^14.14.1",
     "rimraf": "^6.0.1",
-    "vitest": "^3.1.4"
+    "vitest": "^3.2.4"
   },
   "dependencies": {
     "cheminfo-types": "^1.8.1",
@@ -52,7 +52,7 @@
     "ensure-string": "^1.2.0",
     "gyromagnetic-ratio": "^2.0.0",
     "ml-array-median": "^1.1.6",
-    "openchemlib": "^9.2.0"
+    "openchemlib": "^9.6.0"
   },
   "volta": {
     "extends": "../../../package.json"