jcampconverter 12.2.2 → 12.2.4

package/dist/jcampconverter.js

@@ -8,4 +8,4 @@ import{ensureString as me}from"ensure-string";var $=/\s*\$\$.*/;function E(e,m=/
 ##`).split(`
 ##`);t.logger?.trace({profiling:!0},"Split to LDRS"),u[0]&&(u[0]=u[0].replace(/^[\r\n ]*##/,""));for(let c of u){let b=c.indexOf("="),p=b>0?c.slice(0,Math.max(0,b)):c,r=b>0?p.match(t.noTrimRegExp)?c.slice(Math.max(0,b+1)):c.slice(Math.max(0,b+1)).trim():"",a=p.replaceAll(/[_ -]/g,"").toUpperCase();if(a==="DATATABLE"){let d=r.indexOf(`
 `);if(d===-1&&(d=r.indexOf("\r")),d>0){let g=r.slice(0,Math.max(0,d)).split(/[ ,;\t]+/);K(n,s,g[0]),s.datatable=g[0],g[1]?.includes("PEAKS")?a="PEAKTABLE":g[1]&&(g[1].indexOf("XYDATA")||g[0].indexOf("++")>0)&&(a="XYDATA",s.nbPoints&&s.lastX!==void 0&&s.firstX!==void 0&&(s.deltaX=(s.lastX-s.firstX)/(s.nbPoints-1)))}}if(a==="XYDATA"){t.wantXY&&(j(s),r.match(/.*\+\+.*/)?(s.nbPoints&&s.lastX!==void 0&&s.firstX!==void 0&&(s.deltaX=(s.lastX-s.firstX)/(s.nbPoints-1)),V(s,r,t)):w(s,r,t),n?.spectra.push(s),s={data:{}});continue}else if(a==="PEAKTABLE"){t.wantXY&&(j(s),w(s,r,t),n?.spectra.push(s),s={data:{}});continue}if(a==="PEAKASSIGNMENTS"){t.wantXY&&(r.match(/.*[^A-Z]*.*/)&&B(s,r),n?.spectra.push(s),s={data:{}});continue}if(t.removeComments&&(r=r.split(/\r?\n/).map(d=>d.replace(/ *\$\$.*$/,"")).join(`
-`)),a==="TITLE"){let d=n;d.children||(d.children=[]),n={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},d.children.push(n),f.push(d),o.push(n),n.title=r}else a==="DATATYPE"?(n.dataType=r,r.match(/^nd|\snd\s/i)&&(n.twoD=!0)):a==="NTUPLES"?r.match(/^nd|\snd\s/i)&&(n.twoD=!0):a==="DATACLASS"?n.dataClass=r:a==="JCAMPDX"?n.jcampDX=E(r):a==="JCAMPCS"?n.jcampCS=E(r):a==="XUNITS"?s.xUnits=r:a==="YUNITS"?s.yUnits=r:a==="FIRSTX"?s.firstX=Number(r):a==="LASTX"?s.lastX=Number(r):a==="FIRSTY"?s.firstY=Number(r):a==="LASTY"?s.lastY=Number(r):a==="NPOINTS"?s.nbPoints=Number(r):a==="XFACTOR"?s.xFactor=Number(r):a==="YFACTOR"?s.yFactor=Number(r):a==="MAXX"?s.maxX=Number(r):a==="MINX"?s.minX=Number(r):a==="MAXY"?s.maxY=Number(r):a==="MINY"?s.minY=Number(r):a==="DELTAX"?s.deltaX=Number(r):a===".OBSERVEFREQUENCY"||a==="$SFO1"?s.observeFrequency||(s.observeFrequency=Number(r)):a===".OBSERVENUCLEUS"?s.xType||(n.xType=r.replaceAll(/[^a-zA-Z0-9]/g,"")):a==="$OFFSET"?(n.shiftOffsetNum=0,s.shiftOffsetVal||(s.shiftOffsetVal=Number(r))):a==="$REFERENCEPOINT"||(a==="VARNAME"?n.ntuples.varname=r.split(R):a==="SYMBOL"?n.ntuples.symbol=r.split(R):a==="VARTYPE"?n.ntuples.vartype=r.split(R):a==="VARFORM"?n.ntuples.varform=r.split(R):a==="VARDIM"?n.ntuples.vardim=O(r.split(R)):a==="UNITS"?n.ntuples.units=r.split(R):a==="FACTOR"?n.ntuples.factor=O(r.split(R)):a==="FIRST"?n.ntuples.first=O(r.split(R)):a==="LAST"?n.ntuples.last=O(r.split(R)):a==="MIN"?n.ntuples.min=O(r.split(R)):a==="MAX"?n.ntuples.max=O(r.split(R)):a===".NUCLEUS"?n.ntuples&&(n.ntuples.nucleus=r.split(R).map(d=>d.replaceAll(/[^a-zA-Z0-9]/g,""))):a==="PAGE"?(s.page=r.trim(),s.pageValue=Number(r.replace(/^.*=/,"")),s.pageSymbol=s.page.replace(/[=].*/,"")):a==="RETENTIONTIME"?s.pageValue=Number(r):re(a)?s[k(a)]=r:a==="SAMPLEDESCRIPTION"?s.sampleDescription=r:a.startsWith("$NUC")?!n.tmp[a]&&!r.includes("off")&&(n.tmp[a]=r.replaceAll(/[<>]/g,"")):a==="END"&&(n=f.pop()));if(n?.info&&n.meta&&a.match(t.keepRecordsRegExp)){let d,g;p.startsWith("$")?(g=t.canonicMetadataLabels?a.slice(1):p.slice(1),d=n.meta):(g=t.canonicDataLabels?a:p,d=n.info),t.dynamicTyping&&(r=be(r)),d[g]?(Array.isArray(d[g])||(d[g]=[d[g]]),d[g].push(r)):d[g]=r}}if(t.logger?.trace({profiling:!0},"Finished parsing"),q(o,l,t),t.logger?.trace({profiling:!0},"Total time"),l.entries=i.children||[],l.flatten=o,t.logger){t.logger.debug("Finished jcamp conversion");for(let c of l.flatten)t.logger.debug(`${c.dataType} - ${c.title}`)}return l}function gt(e,m){let{logger:t,OCL:o}=m;if(!e.info.ATOMLIST||!e.info.BONDLIST){t?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}Te(e,t);let l=xe(e.info.ATOMLIST),i=Ae(e.info.BONDLIST),n=Ne(e.info.CHARGE,t),f=Se(e.info.XYRASTER,t),s=Ce(e.info.STEREOCENTER,t),u=ye(o,{atoms:l,bonds:i,charges:n,xyRasters:f,stereocenters:s},t);return{molecule:u,molfile:u.toMolfile()}}function ye(e,m,t){let{atoms:o,bonds:l,charges:i,xyRasters:n,stereocenters:f}=m,s={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},u={},c=new e.Molecule(o.length,l.length);for(let p of o){let r=e.Molecule.getAtomicNoFromLabel(p.element);r||(t?.error(`Atomic number of ${p.element} could not be determined`),r=e.Molecule.getAtomicNoFromLabel("X")),u[p.atomNumber]=c.addAtom(r),c.setAtomMapNo(u[p.atomNumber],p.atomNumber,!1)}for(let p of l){if(u[p.atomNumber1]===void 0){t?.error(`A bond goes from atomNumber ${p.atomNumber1} that does not exists`);continue}if(u[p.atomNumber2]===void 0){t?.error(`A bond goes to atomNumber ${p.atomNumber2} that does not exists`);continue}let r=c.addBond(u[p.atomNumber1],u[p.atomNumber2]);c.setBondType(r,s[p.bondType])}for(let p of i){if(u[p.atomNumber]===void 0){t?.error(`A charge goes to atomNumber ${p.atomNumber} that does not exists`);continue}c.setAtomCharge(u[p.atomNumber],p.value)}let b=n.length===0||f.length>0;for(let p of n){if(u[p.atomNumber]===void 0){t?.error(`A XYRASTER goes to atomNumber ${p.atomNumber} that does not exists`);continue}c.setAtomX(u[p.atomNumber],p.x),c.setAtomY(u[p.atomNumber],p.y),c.setAtomZ(u[p.atomNumber],p.z)}c.ensureHelperArrays(e.Molecule.cHelperParities);for(let p of f){let{atomNumber:r,type:a}=p,d=u[r];if(d===void 0){t?.error(`A stereocenter goes to atomNumber ${r} that does not exists`);continue}if(!c.isAtomStereoCenter(d)){t?.warn(`Want to set chirality of atom number ${r} but it is not a stereocenter`);continue}if(c.getAtomParity(d)!==e.Molecule.cAtomParityUnknown){t?.debug(`Atom number ${r} already has a parity defined based on 3D coordinates`);continue}let x=a==="P"?e.Molecule.cAtomParity1:e.Molecule.cAtomParity2;c.setAtomParity(u[r],x,!1)}return c.ensureHelperArrays(e.Molecule.cHelperParities),b&&c.inventCoordinates(),c}function xe(e){let m=P(e),t=[];for(let o of m){let[l,i,n]=o.trim().split(/\s+/);t.push({atomNumber:Number(l),element:i,nbImplicitHydrogens:n?.length>0?Number(n):void 0})}return t}function Ae(e){let m=P(e),t=[];for(let o of m){let[l,i,n]=o.trim().split(/\s+/);t.push({atomNumber1:Number(l),atomNumber2:Number(i),bondType:n})}return t}function Ne(e,m){if(!e)return[];let t=P(e),o=[];for(let l of t){let[i,n,f]=l.trim().split(/\s+/);f!==void 0&&m?.warn("Charge on multiple atom is not supported"),o.push({atomNumber:Number(n),value:Number(i)})}return o}function Se(e,m){if(!e)return[];let t=P(e),o=[];for(let l of t){let[i,n,f,s]=l.trim().split(/\s+/);if(i===void 0){m?.warn("XYRASTER without atom number is not supported");continue}o.push({atomNumber:Number(i),x:Number(n),y:Number(f),z:s!==void 0?Number(s):0})}return o}function Ce(e,m){if(!e)return[];let t=P(e),o=[];for(let l of t){let[i,n]=l.trim().split(/\s+/);if(!["P","M"].includes(n)){m?.warn(`Stereocenter type ${n} is not supported`);continue}o.push({atomNumber:Number(i),type:n})}return o}function P(e){return e.split(/\r?\n/).map(m=>E(m)).filter(Boolean)}function Te(e,m){let t=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let o of t)e.info[o]&&m?.warn(`JCAMP-CS parser do not support: ${o}`)}export{pt as convert,Le as createTree,gt as parseJcampCS,E as removeComment,$ as removeCommentRegExp};
+`)),a==="TITLE"){let d=n;d.children||(d.children=[]),n={spectra:[],ntuples:{},info:{},meta:{},tmp:{}},d.children.push(n),f.push(d),o.push(n),n.title=r}else a==="DATATYPE"?(n.dataType=r,r.match(/^nd|\snd\s/i)&&(n.twoD=!0)):a==="NTUPLES"?r.match(/^nd|\snd\s/i)&&(n.twoD=!0):a==="DATACLASS"?n.dataClass=r:a==="JCAMPDX"?n.jcampDX=E(r):a==="JCAMPCS"?n.jcampCS=E(r):a==="XUNITS"?s.xUnits=r:a==="YUNITS"?s.yUnits=r:a==="FIRSTX"?s.firstX=Number(r):a==="LASTX"?s.lastX=Number(r):a==="FIRSTY"?s.firstY=Number(r):a==="LASTY"?s.lastY=Number(r):a==="NPOINTS"?s.nbPoints=Number(r):a==="XFACTOR"?s.xFactor=Number(r):a==="YFACTOR"?s.yFactor=Number(r):a==="MAXX"?s.maxX=Number(r):a==="MINX"?s.minX=Number(r):a==="MAXY"?s.maxY=Number(r):a==="MINY"?s.minY=Number(r):a==="DELTAX"?s.deltaX=Number(r):a===".OBSERVEFREQUENCY"||a==="$SFO1"?s.observeFrequency||(s.observeFrequency=Number(r)):a===".OBSERVENUCLEUS"?s.xType||(n.xType=r.replaceAll(/[^a-zA-Z0-9]/g,"")):a==="$OFFSET"?(n.shiftOffsetNum=0,s.shiftOffsetVal||(s.shiftOffsetVal=Number(r))):a==="$REFERENCEPOINT"||(a==="VARNAME"?n.ntuples.varname=r.split(R):a==="SYMBOL"?n.ntuples.symbol=r.split(R):a==="VARTYPE"?n.ntuples.vartype=r.split(R):a==="VARFORM"?n.ntuples.varform=r.split(R):a==="VARDIM"?n.ntuples.vardim=O(r.split(R)):a==="UNITS"?n.ntuples.units=r.split(R):a==="FACTOR"?n.ntuples.factor=O(r.split(R)):a==="FIRST"?n.ntuples.first=O(r.split(R)):a==="LAST"?n.ntuples.last=O(r.split(R)):a==="MIN"?n.ntuples.min=O(r.split(R)):a==="MAX"?n.ntuples.max=O(r.split(R)):a===".NUCLEUS"?n.ntuples&&(n.ntuples.nucleus=r.split(R).map(d=>d.replaceAll(/[^a-zA-Z0-9]/g,""))):a==="PAGE"?(s.page=r.trim(),s.pageValue=Number(r.replace(/^.*=/,"")),s.pageSymbol=s.page.replace(/[=].*/,"")):a==="RETENTIONTIME"?s.pageValue=Number(r):re(a)?s[k(a)]=r:a==="SAMPLEDESCRIPTION"?s.sampleDescription=r:a.startsWith("$NUC")?!n.tmp[a]&&!r.includes("off")&&(n.tmp[a]=r.replaceAll(/[<>]/g,"")):a==="END"&&(n=f.pop()));if(n?.info&&n.meta&&a.match(t.keepRecordsRegExp)){let d,g;p.startsWith("$")?(g=t.canonicMetadataLabels?a.slice(1):p.slice(1),d=n.meta):(g=t.canonicDataLabels?a:p,d=n.info),t.dynamicTyping&&(r=be(r)),d[g]?(Array.isArray(d[g])||(d[g]=[d[g]]),d[g].push(r)):d[g]=r}}if(t.logger?.trace({profiling:!0},"Finished parsing"),q(o,l,t),t.logger?.trace({profiling:!0},"Total time"),l.entries=i.children||[],l.flatten=o,t.logger){t.logger.debug("Finished jcamp conversion");for(let c of l.flatten)t.logger.debug(`${c.dataType} - ${c.title}`)}return l}function gt(e,m){let{logger:t,OCL:o}=m;if(!e.info.ATOMLIST||!e.info.BONDLIST){t?.warn("No ATOMLIST or BONDLIST in the JCAMP-CS entry");return}Te(e,t);let l=xe(e.info.ATOMLIST),i=Ae(e.info.BONDLIST),n=Ne(e.info.CHARGE,t),f=Se(e.info.XYRASTER,t),s=Ce(e.info.STEREOCENTER,t),u=ye(o,{atoms:l,bonds:i,charges:n,xyRasters:f,stereocenters:s},t);return{molecule:u,molfile:u.toMolfile()}}function ye(e,m,t){let{atoms:o,bonds:l,charges:i,xyRasters:n,stereocenters:f}=m,s={S:e.Molecule.cBondTypeSingle,D:e.Molecule.cBondTypeDouble,T:e.Molecule.cBondTypeTriple,Q:e.Molecule.cBondTypeQuadruple},u={},c=new e.Molecule(o.length,l.length);for(let p of o){let r=e.Molecule.getAtomicNoFromLabel(p.element);r||(t?.error(`Atomic number of ${p.element} could not be determined`),r=e.Molecule.getAtomicNoFromLabel("X")),u[p.atomNumber]=c.addAtom(r),c.setAtomMapNo(u[p.atomNumber],p.atomNumber,!1)}for(let p of l){if(u[p.atomNumber1]===void 0){t?.error(`A bond goes from atomNumber ${p.atomNumber1} that does not exists`);continue}if(u[p.atomNumber2]===void 0){t?.error(`A bond goes to atomNumber ${p.atomNumber2} that does not exists`);continue}let r=c.addBond(u[p.atomNumber1],u[p.atomNumber2]);c.setBondType(r,s[p.bondType])}for(let p of i){if(u[p.atomNumber]===void 0){t?.error(`A charge goes to atomNumber ${p.atomNumber} that does not exists`);continue}c.setAtomCharge(u[p.atomNumber],p.value)}let b=n.length===0||f.length>0;for(let p of n){if(u[p.atomNumber]===void 0){t?.error(`A XYRASTER goes to atomNumber ${p.atomNumber} that does not exists`);continue}c.setAtomX(u[p.atomNumber],p.x),c.setAtomY(u[p.atomNumber],p.y),c.setAtomZ(u[p.atomNumber],p.z)}c.ensureHelperArrays(e.Molecule.cHelperParities);for(let p of f){let{atomNumber:r,type:a}=p,d=u[r];if(d===void 0){t?.error(`A stereocenter goes to atomNumber ${r} that does not exists`);continue}if(!c.isAtomStereoCenter(d)){t?.warn(`Want to set chirality of atom number ${r} but it is not a stereocenter`);continue}if(c.getAtomParity(d)!==e.Molecule.cAtomParityUnknown){t?.debug(`Atom number ${r} already has a parity defined based on 3D coordinates`);continue}let x=a==="P"?e.Molecule.cAtomParity1:e.Molecule.cAtomParity2;c.setAtomParity(u[r],x,!1)}return c.ensureHelperArrays(e.Molecule.cHelperParities),b&&c.inventCoordinates({keepHydrogens:!0}),c}function xe(e){let m=P(e),t=[];for(let o of m){let[l,i,n]=o.trim().split(/\s+/);t.push({atomNumber:Number(l),element:i,nbImplicitHydrogens:n?.length>0?Number(n):void 0})}return t}function Ae(e){let m=P(e),t=[];for(let o of m){let[l,i,n]=o.trim().split(/\s+/);t.push({atomNumber1:Number(l),atomNumber2:Number(i),bondType:n})}return t}function Ne(e,m){if(!e)return[];let t=P(e),o=[];for(let l of t){let[i,n,f]=l.trim().split(/\s+/);f!==void 0&&m?.warn("Charge on multiple atom is not supported"),o.push({atomNumber:Number(n),value:Number(i)})}return o}function Se(e,m){if(!e)return[];let t=P(e),o=[];for(let l of t){let[i,n,f,s]=l.trim().split(/\s+/);if(i===void 0){m?.warn("XYRASTER without atom number is not supported");continue}o.push({atomNumber:Number(i),x:Number(n),y:Number(f),z:s!==void 0?Number(s):0})}return o}function Ce(e,m){if(!e)return[];let t=P(e),o=[];for(let l of t){let[i,n]=l.trim().split(/\s+/);if(!["P","M"].includes(n)){m?.warn(`Stereocenter type ${n} is not supported`);continue}o.push({atomNumber:Number(i),type:n})}return o}function P(e){return e.split(/\r?\n/).map(m=>E(m)).filter(Boolean)}function Te(e,m){let t=["STEREOPAIR","STEREOCENTER","RADICAL","STEREOMOLECULE"];for(let o of t)e.info[o]&&m?.warn(`JCAMP-CS parser do not support: ${o}`)}export{pt as convert,Le as createTree,gt as parseJcampCS,E as removeComment,$ as removeCommentRegExp};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jcampconverter",
-  "version": "12.2.2",
+  "version": "12.2.4",
   "description": "Parse and convert JCAMP-DX data",
   "license": "CC-BY-NC-SA-4.0",
   "type": "module",
@@ -45,18 +45,18 @@
     "ml-spectra-processing": "^14.22.0",
     "rimraf": "^6.1.3",
     "typescript": "~5.9.3",
-    "vitest": "^4.0.18"
+    "vitest": "^4.1.1"
   },
   "dependencies": {
     "cheminfo-types": "^1.10.0",
-    "dynamic-typing": "^1.0.1",
+    "dynamic-typing": "^2.0.0",
     "ensure-string": "^2.0.0",
     "gyromagnetic-ratio": "^2.0.0",
     "ml-array-median": "^1.1.6",
-    "openchemlib": "^9.20.0"
+    "openchemlib": "^9.22.0"
   },
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "e3b53eca637c956b6cf7ff043f45dfe5737693be"
+  "gitHead": "d195e40bc01b2ea8e99bb4782902bc85a7b128b4"
 }