npm - @zakodium/nmrium-core-plugins - Versions diffs - 0.2.0 → 0.3.1 - Mend

@zakodium/nmrium-core-plugins 0.2.0 → 0.3.1

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.

Files changed (3) hide show

package/dist/nmrium-core-plugins.d.ts +6 -0
package/dist/nmrium-core-plugins.js +8 -8
package/package.json +5 -5

package/dist/nmrium-core-plugins.d.ts CHANGED Viewed

@@ -63,6 +63,12 @@ declare interface ParseSDFOptions {
 export declare function processJCAMPDX(text: string, options?: JCAMPDXParsingOptions): NmriumData;
+/**
+ * Load the molecules from a SDF text (could be a molfile as well but a molfile is a SDF without $$$$ at the end)
+ * @param text
+ * @param options
+ * @returns
+ */
 export declare function readSDF(text: string, options?: ParseSDFOptions): StateMolecule[];
 export declare function readSMILES(text: string): StateMolecule[];

package/dist/nmrium-core-plugins.js CHANGED Viewed

@@ -1,20 +1,20 @@
-var ni=Object.defineProperty;var xt=(e,t)=>{for(var r in t)ni(e,r,{get:t[r],enumerable:!0})};import{NMRiumCore as ga}from"@zakodium/nmrium-core";import{defineNMRiumPlugin as yi}from"@zakodium/nmrium-core";import{Filters1D as ui,Filters2D as pi}from"nmr-processing";import{getOneIfArray as ii}from"@zakodium/nmrium-core";function ce(e={},t={},r={}){e===null&&(e={}),typeof e=="string"&&(e={pulseSequence:e});let n=Array.isArray(e.pulseSequence)?e.pulseSequence[0]:e.pulseSequence||"";if(typeof n!="string")return e.dimension?`${e.dimension}d`:"";if(n=n.toLowerCase(),n.includes("zg")||n.includes("single_pulse_dec")||n.includes("udeft"))return"1d";if(n.includes("hsqct")||n.includes("invi")&&(n.includes("ml")||n.includes("di")))return"hsqctocsy";if(n.includes("hsqc")||n.includes("invi"))return"hsqc";if(n.includes("hmbc")||n.includes("inv4")&&n.includes("lp"))return"hmbc";if(n.includes("hmqc"))return"hmqc";if(n.includes("cosy"))return"cosy";if(n.includes("jres"))return"jres";if(n.includes("dosy"))return"dosy";if(n.includes("tocsy")||n.includes("mlev")||n.includes("dipsi"))return"tocsy";if(n.includes("noesy"))return"noesy";if(n.includes("roesy"))return"roesy";if(n.includes("dept"))return"dept";if(n.includes("jmod")||n.includes("apt"))return"aptjmod";if(n.includes("inad"))return"inadequate";if(n.includes("adeq"))return"adequate";let{prefix:i=""}=r,o=(ii(t[`${i}SPECTYP`])||"").replace(/^<(.*)>$/,"$1").toLowerCase();return o.length>0&&o!=="undefined"?o:e.dimension?`${e.dimension}d`:""}import{getOneIfArray as Dt}from"@zakodium/nmrium-core";var oi=["no","exponential","modifiedGaussian","sine","qsine","trap","user","sinc","qsinc","traf","trafs"];function si(e){return e in St}function qe(e,t){let{prefix:r="",index:n=0}=t,i=Dt(e[`${r}WDW`],n),o=oi[i?Number(i):0],s={};if(!si(o))return s;let a=St[o];if(a){let{kind:c,parameters:l}=a,m={};for(let p in l){let f=l[p],{source:g,processor:y}=f;if(g){let u=Dt(e[`${r}${g}`],n);if(!u)continue;let h=Number(u);m[p]=y?y(h):h}else f.value!==void 0&&(m[p]=f.value)}s[c]={apply:!0,options:m}}return s}var St={exponential:{kind:"exponential",parameters:{lineBroadening:{source:"LB"}}},modifiedGaussian:{kind:"gaussian",parameters:{lineBroadening:{source:"LB"},lineBroadeningCenter:{source:"GB"}}},sine:{kind:"sineBell",parameters:{offset:{source:"SSB",processor:e=>1/e},exponent:{value:1}}},qsine:{kind:"sineSquare",parameters:{offset:{source:"SSB",processor:e=>1/e}}},traf:{kind:"traf",parameters:{lineBroadening:{source:"LB"}}}};var At={sineBell:Mt({offset:0})},It={cosy:{...At},hmbc:{...At},hsqc:{sineBell:Mt({offset:.5})}},ai={...It};function je(e="",t=1){let r=ci(e),n={},i=t===1?It[r||""]:ai[r||""];return i&&(n=structuredClone(i)),n}function Mt(e){return{apply:!0,options:e}}function ci(e){let r=e.toLowerCase().match(/cosy|hsqc|hmbc/);return r?r[0]:null}function Nt(e,t={}){let{prefix:r="",experiment:n=ce(e)}=t;return e[`${r}WDW`]?{f2:qe(e,{...t,index:0}),f1:qe(e,{...t,index:1})}:{f2:je(n,1),f1:je(n,2)}}import{Filters1D as li}from"nmr-processing";var Be=["digitalFilter","backwardLinearPrediction","forwardLinearPrediction","apodization","zeroFilling","fft",["shiftX","phaseCorrection","baselineCorrection"]],W={};for(let e=0;e<Be.length;e++){let t=Be[e];for(let r of Array.isArray(t)?t:[t])W[r]=e}for(let e of Object.values(li))e.name in W||(W[e.name]=Be.length);import{Filters2D as mi}from"nmr-processing";var Ue=["digitalFilter2D","blpDimension1","flpDimension1","apodizationDimension1","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","nusDimension2","apodizationDimension2","zeroFillingDimension2","fftDimension2","phaseCorrectionTwoDimensions",["shift2DX","shift2DY","symmetrizeCosyLike"]],X={};for(let e=0;e<Ue.length;e++){let t=Ue[e];for(let r of Array.isArray(t)?t:[t])X[r]=e}for(let e of Object.values(mi))e.name in X||(X[e.name]=Ue.length);var fi=new Set([]);function di(e,t){let{filter:r,experimentalFeatures:n=!1}=t,{name:i}=r;({...ui,...pi})[i]&&(e.some(s=>s.name===i)||fi.has(i)&&!n||e.push({...r,enabled:!0}))}function Pt(e,t={}){let{data:r}=e;if(!r)return;let{autoProcessing:n,experimentalFeatures:i}=t,o=(a,c)=>di(a,{...c,experimentalFeatures:i}),{spectra:s}=r;for(let a of s){let{data:c,info:l,meta:m,filters:p}=a,{dimension:f,isFid:g}=l;if(g){if(f===1){let y=c.re.length,{tdOff:u,digitalFilter:h}=l;if(h&&h>0&&o(p,{filter:{name:"digitalFilter",value:{digitalFilterValue:h}}}),!n)continue;u&&Math.abs(u)>0&&o(p,{filter:{name:"backwardLinearPrediction",value:{nbInputs:y/2}}}),o(p,{filter:{name:"apodization",value:{exponential:{apply:!0,options:{lineBroadening:1}}}}}),o(p,{filter:{name:"zeroFilling",value:{nbPoints:2*y}}}),o(p,{filter:{name:"fft",value:{}}}),o(p,{filter:{name:"phaseCorrection",value:gi(l)}}),p.sort((d,b)=>W[d.name]-W[b.name])}else if(f===2){if(!n)continue;let y=c.re.z.length,u=c.re.z[0].length,{tdOff:h,experiment:d=""}=l,b=l.spectrumSize;Array.isArray(b)&&b.length>1?(b[0]<=u&&(b[0]=u*2),b[0]<=y&&(b[0]=y*2)):b=[u*2,2*y];let F=d.toLowerCase().includes("cosy");h&&Math.abs(h[0])>0&&o(p,{filter:{name:"blpDimension1",value:{nbInputs:u/2}}});let S=Nt(m,{experiment:d});o(p,{filter:{name:"apodizationDimension1",value:S.f2}}),o(p,{filter:{name:"zeroFillingDimension1",value:{nbPoints:b[0]}}}),o(p,{filter:{name:"fftDimension1",value:{}}}),m&&"nuslist"in m&&o(p,{filter:{name:"nusDimension2",value:{}}}),o(p,{filter:{name:"apodizationDimension2",value:S.f1}}),o(p,{filter:{name:"zeroFillingDimension2",value:{nbPoints:b[F?0:1]}}}),F?o(p,{filter:{name:"symmetrizeCosyLike",value:{}}}):o(p,{filter:{name:"phaseCorrectionTwoDimensions",value:{}}}),o(p,{filter:{name:"fftDimension2",value:{}}}),p.sort((I,x)=>X[I.name]-X[x.name])}}}}function gi(e){let{phc0:t=0,phc1:r=0}=e;return Et([t,r])?{}:{ph0:t,ph1:r}}function Et(e){return Array.isArray(e)?e.every(t=>!t&&t===0):Et([e])}function $e(){return yi({id:"@zakodium/nmrium-core-plugins#AutoPostProcessingPlugin",version:1,migrations:[],onReadProcess:{onProcessing:Pt}})}import{defineNMRiumPlugin as xo}from"@zakodium/nmrium-core";import{FileCollection as _c}from"file-collection";var Tt=["acqus","acqu2s"],le=["procs","proc2s"];function Ot(e){return e.is1D?hi(e):e.is2D?bi(e):{checked:!1,message:"Multi-dimensional n > 2 is not supported"}}function hi(e){let t=e.isFID?["acqus"]:["acqus","procs"],r=t.every(n=>e[n]);return{checked:r,message:r?"":`File: ${e[e.isFID?"fid":"1r"]?.relativePath} is ignored, files: ${t.join(",")} are required.`}}function bi(e){let t=e.isFID?Tt:Tt.concat(le),r=t.every(n=>e[n]);return r&&e.isFID&&le.some(n=>e[n])&&!le.every(n=>e[n])&&(r=!1,t.push(...le)),{checked:r,message:r?"":`File: ${e.name} is ignored, files: ${t.join(",")} are required.`}}function ze(e,t={}){let{logger:r,processingNumbers:n,experimentNumbers:i,dataSelection:o="both",keep1D:s=!0,keep2D:a=!0,onlyFirstProcessedData:c=!0}=t,l={},m=e.files.map(g=>g.relativePath);for(let g of e){let y,u,h,d=g.relativePath.split("/"),b=d.indexOf("pdata");if(b!==-1)y=Number(d[b+1]),u=Number(d[b-1]),h=d.slice(0,-3).join("/");else if(xi(g,m)){let S=d.indexOf(g.name);u=Number(d[S-1]),h=d.slice(0,-1).join("/")}else continue;if(Number.isNaN(u)&&(u=void 0),Number.isNaN(y)&&(y=void 0),i&&!i.includes(u))continue;l[h]||(l[h]={name:h,expno:u,processedData:{},fileCollectionItems:[]});let F=l[h];if(g.name==="vdlist"&&(F.vdlist=g),g.name==="difflist"&&(F.difflist=g),y){F.processedData||(F.processedData={}),F.processedData[y]||(F.processedData[y]={fileCollectionItems:[],name:h,expno:u,procno:y});let S=F.processedData[y];S.fileCollectionItems.push(g),g.name.match(/^(?:1r|1i|2rr|2ir|2ii|2ri|procs|proc2s|title|integrals.txt)$/)&&(S[g.name]=g),g.name==="2rr"&&(S.is2D=!0,S.isFT=!0),g.name==="1r"&&(S.is1D=!0,S.isFT=!0)}else F.fileCollectionItems.push(g),g.name.match(/^(?:ser|fid|acqus|acqu2s|nuslist)$/)&&(F[g.name]=g),g.name==="ser"&&(F.is2D=!0,F.isFID=!0),g.name==="fid"&&(F.is1D=!0,F.isFID=!0);g.name==="QuantFactorSample.xml"&&(F.quantFactorSample=g)}if(n)for(let g in l){let y=l[g].processedData,u={};for(let h in y)n.includes(Number.parseInt(h,10))&&(u[h]=y[h]);l[g].processedData=u}else if(c)for(let g in l){let y=l[g].processedData,u=Object.keys(y??{});u.sort((d,b)=>Number(d)-Number(b));let h=u[0];y&&h!==void 0&&(l[g].processedData={firstProcessedNumber:y[h]})}let p=Di(r),f=[];for(let g in l){let y=l[g],{processedData:u,...h}=y;if(p(y,o)){let b=Object.keys(u??{});if(u&&b.length>0){let F=u[b[0]];F.procs&&(h.fileCollectionItems.push(F.procs),h.procs=F.procs),F.proc2s&&(h.fileCollectionItems.push(F.proc2s),h.proc2s=F.proc2s),F["integrals.txt"]&&(h.integrals=F["integrals.txt"])}f.push(h)}let d="ser"in h||"fid"in h;if(o==="fid"||o==="preferFID"&&d){r?.warn("Skipping FT data because it does not match the import filters");continue}for(let b in u){let F=u[b];(F["1r"]||F["2rr"])&&(h.acqus&&F.fileCollectionItems.push(h.acqus),h.acqu2s&&F.fileCollectionItems.push(h.acqu2s),h.vdlist&&(F.vdlist=h.vdlist),f.push({integrals:F["integrals.txt"],acqus:h.acqus,acqu2s:h.acqu2s,...F}))}}return s||(r?.warn("Skipping 1D data because it does not match the import filters"),f=f.filter(g=>!g.is1D)),a||(r?.warn("Skipping 2D data because it does not match the import filters"),f=f.filter(g=>!g.is2D)),Fi(f,t.logger)}function Fi(e,t){return e.filter(r=>{let{checked:n,message:i}=Ot(r);return n||t?.warn(i),n})}function xi(e,t){return e.name.match(/^(?:ser|acqus|acqu2s|nuslist|vdlist|difflist|QuantFactorSample.xml)$/)||e.name.match(/^fid$/)&&t.includes(e.relativePath.replace(/fid$/,"acqus"))}function Di(e){return(t,r)=>{let{processedData:n}=t,i=Object.keys(n??{}),o=n&&i.length>0&&["1r","1i","2rr"].some(m=>m in n[i[0]]),s="ser"in t||"fid"in t,l=s&&(r!=="ft"&&r!=="preferFT"||r==="preferFT"&&!o);return s&&!l&&e?.warn("Skipping RAW data because it does not match import filters"),l}}function me(e){if(e===void 0||Array.isArray(e)&&e.length===0)return{epoch:null,date:""};let t=e[0]*1e3;return{epoch:t,date:new Date(t).toUTCString()}}function ue(e,t){for(let r in t.meta)e.meta[r]===void 0&&(e.meta[r]=t.meta[r]);for(let r in t.info)e.info[r]===void 0&&(e.info[r]=t.info[r]);for(let r in e.meta)Array.isArray(e.meta[r])||(e.meta[r]=[e.meta[r]])}import{convert as Si}from"jcampconverter";async function _(e,t){if(!e)return Ct();let r=await e.text(),{keepRecordsRegExp:n=/.*/}=t,i=Si(r,{keepRecordsRegExp:n});return 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gr(e,t,r={}){let{spectra:n,info:i,meta:o}=e,s=n[0].data,a=[],c={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:l,name:m,spectraData:p}=r,{CROSSREFERENCE:f}=i,g=typeof f!="string"?f:f.split(/\r?\n/).map(x=>x.trim()).filter(Boolean),y=g.find(x=>x?.toLowerCase().includes("structure"));if(y===void 0)return l&&l.warn(`There is not a structure reference for ${m} file, assignment object could not be completed`),null;let u=Number.parseInt(y?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(u)||u<1)return l&&l.warn(`Structure block_id not found for ${m} file, assignment object could not be completed`),null;let d=p?.molecules?.find(x=>x.blockId===u)?.molfile??"";if(d===""){let x=t.find(M=>M.info.BLOCKID===u),{MOLFILE:A=""}=x?.meta||{};d=A}if(!No(d))return l&&l.warn(`Empty molfile for ${m} file with structure block_id = ${u}, assignment object could not be completed`),null;let 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h){if(F.js.every(S=>S===F.js[0])){b.push(F);continue}if(F.multiplicity!==F.js.length+1){b.push(F);continue}for(let S=0;S<F.multiplicity-1;S++)b.push({value:"d",multiplicity:2,js:[F.js[S]]})}b.sort((F,S)=>S.js[0]-F.js[0]),g.js=b.map(F=>({coupling:F.js[0],multiplicity:F.value}))}typeof o.assignment=="string"&&(g.assignment=$o(o.assignment)),typeof o.multiplicity=="string"&&(g.multiplicity=o.multiplicity),i.multiplets.push(g)}return i}function Bo(e){let t={};for(let r in e){let n=e[r],i=typeof n=="number"?n:Number.parseFloat(n);Number.isNaN(i)||(t[r]=i)}return t}var Uo={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function $o(e){return e.replaceAll(/&(\w+);/gi,(t,r)=>Uo[r.toLowerCase()]||t)}function Dr(e){let t=e.split(/\r?\n/).filter(n=>n.trim()!==""),r=[];for(let n of t)if(n.startsWith("(")){let[i,o,s]=ie(n).map(Number.parseFloat);r.push({id:i,x:o,y:s})}return r}function Sr(e,t={}){let r={};if(!e["OBSERVED MULTIPLETS"])return[];let n=xr(e["OBSERVED MULTIPLETS"],t);if(!n)return[];let{multiplets:i}=n;for(let o of i){let{id:s,from:a,to:c,integration:l=0,...m}=o;r[s]={from:a,to:c,integration:l,signals:[{id:s,...m}]}}if(e["OBSERVED MULTIPLETS PEAKS"]){let o=Dr(e["OBSERVED MULTIPLETS PEAKS"]),s={};for(let a of o){let{id:c,x:l,y:m}=a;s[c]||(s[c]=[]),s[c].push({x:l,y:m,width:.05})}for(let a in r)s[a]&&(r[a].signals[0].peaks=s[a])}return Q(Object.values(r))}function Ar(e,t){let n=[...e.getMolecularFormula().formula.matchAll(/(?<element>[A-Z][a-z]?)(?<count>\d*)/g)].map(o=>({element:o?.groups?.element,count:o?.groups?.count?Number(o.groups.count):1})),i=[...t.nucleus[0].matchAll(/[0-9]*(?<element>[A-Z][a-z]?)/g,"$element")][0].groups.element;return n.find(o=>o.element===i)?.count||100}function Ir(e){let t={};return".PHASE0"in e&&(t.ph0=Number.parseFloat(e[".PHASE0"]),t.ph1=Number.parseFloat(e[".PHASE1"])),t}function Ze(e){let{ph0:t,ph1:r}=e;return Number.isFinite(t)&&Number.isFinite(r)}import{generateID as 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n={spectra:[],molecules:[]},i=await Ys(e,t,r);if(i.spectra.length>0){let{spectra:o,molecules:s,usedFiles:a}=i;n.spectra.push(...o),n.molecules.push(...s);let c=e.files.length;for(let l=c-1;l>=0;l--){let m=e.files[l].relativePath;!m.match(/acqu.*/s)&&a.includes(m)&&e.files.splice(l,1)}}return n}async function Ys(e,t,r){let n=[],i=await lt(e),o={spectra:[],molecules:[]};if(i.length===0)return{...o,usedFiles:n};let s=[];for(let c of i){let l=bn({sdf:c,fileCollection:e}).then(m=>{let{spectra:p,molecules:f=[]}=m;return n.push(c.root+c.filename),o.molecules.push(...f),Ks(p,t,r)});s.push(l)}let a=await Promise.allSettled(s);for(let c of a)c.status==="fulfilled"?(o.spectra.push(...c.value.spectra),n.push(...c.value.usedFiles)):c.reason&&r?.logger?.error(c.reason);return{...o,usedFiles:n}}async function Ks(e,t,r){let n=[],i=[],o={spectra:[],molecules:[]};for(let s of e){let a=Zs(s.source,t,r).then(c=>{let{spectra:l,files:m}=c;n.push(...m);for(let p of l)Mn(p)?In(s.signals,p):Sn(s.signals,p);o.spectra.push(...l)});i.push(a)}return await Promise.allSettled(i),{...o,usedFiles:n}}async function Zs(e,t,r={}){let{file:n,jcampURL:i}=e,{converter:o}=r;if(i){let c=await Qs(i,t,o?.jcamp);if(c)return{...c,files:[]}}let s=[];for(let c of n||[])s.push(ea(c,r).then(l=>({...l,files:c.fileCollection.files.map(m=>m.relativePath)})));let a=await Promise.allSettled(s);for(let c of a){if(c.status==="fulfilled")return c.value;c.reason&&r?.logger?.error(c.reason)}return{spectra:[],molecules:[],files:[]}}async function Qs(e,t,r={}){let n={entries:[{relativePath:e}]},i={name:Z(e||""),xy:!0,noContours:!0,...r},{data:o}=await t.readFromWebSource(n,i);return o}async function ea(e,t={}){let{converter:r,sourceSelector:n}=t;switch(e.type){case"jcamp":return Ae(e.fileCollection.files[0],{name:e?.fileCollection.files[0].name||"",converter:r?.jcamp,selector:n?.jcamp,logger:t.logger,keepSource:t.keepSource});case"brukerFiles":return De(e.fileCollection,{converter:r?.bruker,selector:n});default:throw new Error("There is not a supported source")}}function ut(e){return ta({id:"@zakodium/nmrium-core-plugins#NMReDATALoaderPlugin",version:1,migrations:[],onReadProcess:{onFiles(t,r){return Nn(t,e,r)}}})}import{defineNMRiumPlugin as na}from"@zakodium/nmrium-core";import{parse as ra}from"sdf-parser";function Pn(e,t={}){let{mixedEOL:r}=t,{molecules:n}=ra(e,{mixedEOL:r}),i=[];for(let{molfile:o}of n){let s=K(o);i.push(...s)}return i}async function En(e,t={}){let{logger:r,mixedEOL:n}=t,i=await e.text(),o=Pn(i,{mixedEOL:n}),s={molecules:o,spectra:[]};return r&&r[o.length>0?"info":"debug"](`Loaded ${s.molecules.length} molecules from the ${e.name} file`),s}function ia(e,t={}){let{logger:r}=t;return r?.debug(`Reading sdf file: ${e.name}`),En(e,{logger:r})}function pt(){return na({id:"@zakodium/nmrium-core-plugins#SDFLoaderPlugin",version:1,migrations:[],onReadProcess:{supportedExtensions:["sdf"],onFile:ia}})}import{defineNMRiumPlugin as sa}from"@zakodium/nmrium-core";import{Molecule as oa}from"openchemlib";function Tn(e){let t=[],r=e.split(/\r?\n/).filter(Boolean);for(let n of r){let o=oa.fromSmiles(n).toMolfile();t.push({molfile:o})}return t}async function On(e,t={}){let r=await e.text(),n=Tn(r),i={molecules:n,spectra:[]};return t.logger?.info(`Found ${n.length} molecules from the ${e.name} file`),i}function ft(){return sa({id:"@zakodium/nmrium-core-plugins#SMILESLoaderPlugin",version:1,migrations:[],onReadProcess:{supportedExtensions:["smi","smiles"],onFile:On}})}import{defineNMRiumPlugin as da}from"@zakodium/nmrium-core";import{formatSpectra as ua}from"@zakodium/nmrium-core";import{createFromToArray as ca}from"ml-spectra-processing/utils";function Cn(e){e.setLittleEndian();let t=e.offset,r=96;e.offset=r/8;let n=e.readInt32(),i=[2,4],o=[2**25,2**26];if(!i.includes(n))if(o.includes(n))e.setBigEndian();else throw new Error(`Unexpected value of eBytes (${n}). 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this.index+=t,r}},Ce=class{softwareVersion;typeOfFile;vendorIdStatus;constructor(t){this.softwareVersion=t&2**6-1,this.typeOfFile={fidFile:(t&64)!==0,dataFile:(t&128)!==0,data3DFile:(t&256)!==0},this.vendorIdStatus={isVar:(t&0)!==0,isQOne:(t&2048)!==0,isMakeFid:(t&4096)!==0,isJeol:(t&8192)!==0,isBru:(t&16384)!==0,isMag:(t&6144)!==0,isOx:(t&10240)!==0,ipVers:(t&63)!==0,ipFileId:(t&1984)!==0,ipVendorId:(t&30720)!==0}}},Re=class{npPhMode;npAvMode;npPwrMode;nfPhMode;nfAvMode;nfPwrMode;niPhMode;niAvMode;niPwrMode;ni2PhMode;ni2AvMode;ni2PwrMode;niPaMode;ni2PaMode;constructor(t){this.npPhMode=(t&1)!==0,this.npAvMode=(t&2)!==0,this.npPwrMode=(t&4)!==0,this.nfPhMode=(t&16)!==0,this.nfAvMode=(t&32)!==0,this.nfPwrMode=(t&64)!==0,this.niPhMode=(t&256)!==0,this.niAvMode=(t&512)!==0,this.niPwrMode=(t&1024)!==0,this.ni2PhMode=(t&8)!==0,this.ni2AvMode=(t&256)!==0,this.ni2PwrMode=(t&8192)!==0,this.niPaMode=(t&16384)!==0,this.ni2PaMode=(t&32768)!==0}};var 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ve=class{nBlocks;nTraces;np;eBytes;tBytes;bBytes;version;status;nBlockHeaders;constructor(t){t.offset=0,this.nBlocks=t.readInt32(),this.nTraces=t.readInt32(),this.np=t.readInt32(),this.eBytes=t.readInt32(),this.tBytes=t.readInt32(),this.bBytes=t.readInt32(),this.version=new Ce(t.readInt16()),this.status=new Te(t.readInt16()),this.nBlockHeaders=t.readInt32()}};var gt=class{name;subType;basicType;maxValue;minValue;stepSize;gGroup;dGroup;protection;active;intptr;constructor(t){let r=t.split(" ");this.name=r[0],this.subType=Number.parseInt(r[1],10),this.basicType=Number.parseInt(r[2],10),this.maxValue=Number.parseFloat(r[3]),this.minValue=Number.parseFloat(r[4]),this.stepSize=Number.parseFloat(r[5]),this.gGroup=Number.parseInt(r[6],10),this.dGroup=Number.parseInt(r[7],10),this.protection=Number.parseInt(r[8],10),this.active=Number.parseInt(r[9],10),this.intptr=Number.parseInt(r[10],10)}};function Rn(e){let t=[],r=new Oe(e.readChars(e.length));for(;r.index<r.length-1;){let n=[],i=[],o=new 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c of s)if(c.name==="at"){a=c.values[0];break}if(typeof a!="number")throw new Error("acquisition time parameter must exist and be a number.");{let c=aa({from:0,to:a,length:o.np/2,distribution:"uniform"}),l=new we(i,o);return{meta:o,fid:l,procpar:s,x:c}}}import{isAnyArray as ua}from"is-any-array";import{xMultiply as pa}from"ml-spectra-processing";import{normalizeNucleus as ca}from"nmr-processing";function vn(e,t){let{meta:r,procpar:n}=e,i={};for(let b of n)i[b.name]=b.values;let o={},s={},{np:a,solvent:c,sfrq:l,reffrq:m,temp:p,rp:f,sw:g,rfl:y,rfp:u}=i;D(o,"numberOfPoints",a&&Number(q(a))/2),D(o,"solvent",q(c)),D(o,"originFrequency",q(l)),D(o,"baseFrequency",q(m)),(Number.isNaN(o.originFrequency)||o.originFrequency===0)&&(o.originFrequency=400,t?.warn("The frequency could not be determined and was set to 400MHz")),D(o,"temperature",q(p)),D(o,"phc0",f&&Number(f[0])),D(s,"rfl",y&&Number(q(y))),D(s,"rfp",u&&Number(q(u))),D(s,"sw",g&&Number(q(g)));for(let b in s){let 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s.spectra.length>0&&n?.info(`Loaded ${s.spectra.length}  spectra from Varian files`),ma(s)}function da(e,t){let{keepSource:r,logger:n}=t??{};return _n(e,{keepSource:r,logger:n})}function yt(){return fa({id:"@zakodium/nmrium-core-plugins#VarianLoaderPlugin",version:1,migrations:[],onReadProcess:{onFiles:da}})}function ya(e,t=[]){return[ut(e),yt(),Ge(),Qe(),at(),pt(),ft(),st(),$e()].concat(t)}function ha(e=[]){let t=new ga;return t.registerPlugins(ya(t,e)),t}import{getOneIfArray as jn}from"@zakodium/nmrium-core";import{from1DNMRVariables as ba}from"convert-to-jcamp";function qn(e,t){return e.filters.find(r=>r.name===t)}function Fa(e,t={}){let{onlyReal:r=!1}=t,{info:n,meta:i,data:o}=e,{owner:s,title:a,isFid:c,spectralWidth:l,baseFrequency:m,originFrequency:p,nucleus:f,solvent:g,scaleFactor:y,frequencyOffset:u,decim:h,dspfvs:d,digitalFilter:b}=n,F=jn(m||p),{x:S,re:I,im:x}=o,A=new Float64Array(I),M=!r&&x?new Float64Array(x):void 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Bn=["title","decim","dspfvs","grpdly","bf1","sw","offset",".solvent","owner","firsty","page","vardim","symbol","symbols","varform","vartype","datatype","dataclass",".observefrequency",".observenucleus","ncproc"];function xa(e,t=Bn){let r=new Set(t);return Object.fromEntries(Object.entries(e).filter(([n])=>!r.has(n.toLocaleLowerCase().replaceAll(/[\s|_]*/g,""))))}export{$e as autoPostProcessing,Ge as brukerLoader,ha as default,ha as init,Qe as jcampDXLoader,st as jeolLoader,at as molfileLoader,ut as nmreDATALoader,vr as processJCAMPDX,Pn as readSDF,Tn as readSMILES,ya as recommended,pt as sdfLoader,ft as smilesLoader,Fa as spectrum1DToJCAMPDX,yt as varianLoader};
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Current index ${this.index}.`);return this.lines[this.index++]}readLines(t){let r=this.lines.slice(this.index,this.index+t);return this.index+=t,r}},Ce=class{softwareVersion;typeOfFile;vendorIdStatus;constructor(t){this.softwareVersion=t&2**6-1,this.typeOfFile={fidFile:(t&64)!==0,dataFile:(t&128)!==0,data3DFile:(t&256)!==0},this.vendorIdStatus={isVar:(t&0)!==0,isQOne:(t&2048)!==0,isMakeFid:(t&4096)!==0,isJeol:(t&8192)!==0,isBru:(t&16384)!==0,isMag:(t&6144)!==0,isOx:(t&10240)!==0,ipVers:(t&63)!==0,ipFileId:(t&1984)!==0,ipVendorId:(t&30720)!==0}}},Re=class{npPhMode;npAvMode;npPwrMode;nfPhMode;nfAvMode;nfPwrMode;niPhMode;niAvMode;niPwrMode;ni2PhMode;ni2AvMode;ni2PwrMode;niPaMode;ni2PaMode;constructor(t){this.npPhMode=(t&1)!==0,this.npAvMode=(t&2)!==0,this.npPwrMode=(t&4)!==0,this.nfPhMode=(t&16)!==0,this.nfAvMode=(t&32)!==0,this.nfPwrMode=(t&64)!==0,this.niPhMode=(t&256)!==0,this.niAvMode=(t&512)!==0,this.niPwrMode=(t&1024)!==0,this.ni2PhMode=(t&8)!==0,this.ni2AvMode=(t&256)!==0,this.ni2PwrMode=(t&8192)!==0,this.niPaMode=(t&16384)!==0,this.ni2PaMode=(t&32768)!==0}};var we=class{scale;status;index;mode;ctCount;lpVal;rpVal;lvl;tlt;data;constructor(t,r,n){n&&(t.offset=n),this.scale=t.readInt16(),this.status=new Ee(t.readInt16()),this.index=t.readInt16(),this.mode=new Re(t.readInt16()),this.ctCount=t.readInt32(),this.lpVal=t.readFloat32(),this.rpVal=t.readFloat32(),this.lvl=t.readFloat32(),this.tlt=t.readFloat32(),this.data=aa(t,r)}};function aa(e,t){let{np:r,nTraces:n,status:{isFloat32:i,isInt32:o}}=t;return i?dt(e,n,r,"readFloat32"):o?dt(e,n,r,"readInt32"):dt(e,n,r,"readInt16")}function dt(e,t,r,n){let i=[],o;n==="readFloat32"?o={re:new Float32Array(r/2),im:new Float32Array(r/2)}:n==="readInt32"?o={re:new Int32Array(r/2),im:new Int32Array(r/2)}:o={re:new Int16Array(r/2),im:new Int16Array(r/2)};for(let s=0;s<t;s++){for(let a=0;a<r;a+=2)o.re[a>>>1]=e[n](),o.im[a>>>1]=e[n]();i[s]=o}return i}var ve=class{nBlocks;nTraces;np;eBytes;tBytes;bBytes;version;status;nBlockHeaders;constructor(t){t.offset=0,this.nBlocks=t.readInt32(),this.nTraces=t.readInt32(),this.np=t.readInt32(),this.eBytes=t.readInt32(),this.tBytes=t.readInt32(),this.bBytes=t.readInt32(),this.version=new Ce(t.readInt16()),this.status=new Te(t.readInt16()),this.nBlockHeaders=t.readInt32()}};var gt=class{name;subType;basicType;maxValue;minValue;stepSize;gGroup;dGroup;protection;active;intptr;constructor(t){let r=t.split(" ");this.name=r[0],this.subType=Number.parseInt(r[1],10),this.basicType=Number.parseInt(r[2],10),this.maxValue=Number.parseFloat(r[3]),this.minValue=Number.parseFloat(r[4]),this.stepSize=Number.parseFloat(r[5]),this.gGroup=Number.parseInt(r[6],10),this.dGroup=Number.parseInt(r[7],10),this.protection=Number.parseInt(r[8],10),this.active=Number.parseInt(r[9],10),this.intptr=Number.parseInt(r[10],10)}};function Rn(e){let t=[],r=new Oe(e.readChars(e.length));for(;r.index<r.length-1;){let n=[],i=[],o=new gt(r.readLine()),s=r.readLine();if(o.basicType!==0){if(o.basicType===1)n=s.split(" ").slice(1).map(m=>Number.parseFloat(m));else if(o.basicType===2){n=s.split('"').slice(1,2);let l=Number.parseInt(s.split(" ")[0],10);for(;l>1;)n.push(r.readLine().split('"')[1]),l--}}let a=r.readLine(),c=Number.parseInt(a.split(" ")[0],10);c!==0&&(o.basicType===1?i=a.split(" ").slice(1):o.basicType===2&&(i=a.split('"').filter((l,m)=>m%2===1))),t.push({...o,values:n,enumerable:c,enumerables:i})}return t}async function wn(e){let t={};function r(c,l){return c.then(m=>{t[l]=m})}let n=[];for(let c of e)switch(c.name.toLowerCase()){case"fid":{n.push(r(c.arrayBuffer(),"fidB"));break}case"procpar":{n.push(r(c.arrayBuffer(),"procparB"));break}default:break}if(await Promise.all(n),!t.fidB||!t.procparB)throw new RangeError("fid and procpar must exist.");let i=new R(t.fidB);Cn(i);let o=new ve(i);if(o.nBlocks!==1)throw new Error("We currently do not support 2D varian spectra ");let s=Rn(new R(t.procparB)),a;for(let c of s)if(c.name==="at"){a=c.values[0];break}if(typeof a!="number")throw new Error("acquisition time parameter must exist and be a number.");{let c=ca({from:0,to:a,length:o.np/2,distribution:"uniform"}),l=new we(i,o);return{meta:o,fid:l,procpar:s,x:c}}}import{isAnyArray as pa}from"is-any-array";import{xMultiply as fa}from"ml-spectra-processing";import{normalizeNucleus as la}from"nmr-processing";function vn(e,t){let{meta:r,procpar:n}=e,i={};for(let b of n)i[b.name]=b.values;let o={},s={},{np:a,solvent:c,sfrq:l,reffrq:m,temp:p,rp:f,sw:g,rfl:y,rfp:u}=i;D(o,"numberOfPoints",a&&Number(q(a))/2),D(o,"solvent",q(c)),D(o,"originFrequency",q(l)),D(o,"baseFrequency",q(m)),(Number.isNaN(o.originFrequency)||o.originFrequency===0)&&(o.originFrequency=400,t?.warn("The frequency could not be determined and was set to 400MHz")),D(o,"temperature",q(p)),D(o,"phc0",f&&Number(f[0])),D(s,"rfl",y&&Number(q(y))),D(s,"rfp",u&&Number(q(u))),D(s,"sw",g&&Number(q(g)));for(let b in s){let F=s[b];Array.isArray(F)&&F.length===1&&(s[b]=F[0])}if(!("baseFrequency"in o)&&"originFrequency"in o){let b=Number.parseFloat(o.originFrequency);if(["sw","rfl","rfp"].every(F=>F in s)){let{sw:F=1,rfl:S=1,rfp:I=1}=ma(s,["sw","rfl","rfp"]);D(o,"baseFrequency",b-(F/2-S+I)/1e6)}else D(o,"baseFrequency",b)}let{baseFrequency:h,originFrequency:d}=o;D(o,"frequencyOffset",(d-h)*1e6),D(o,"spectralWidth",g&&Number(g[0])/o.baseFrequency);for(let b in o)o[b].length===1&&(o[b]=o[b][0]);return i.tn&&(o.nucleus=i.tn.map(la)),o.dimension=1,o.isFid=!r.status.isSpectrum,{info:o,meta:{...s,...Ln(r),...i}}}function q(e){return e&&(Array.isArray(e)?e[0]:e)}function ma(e,t){let r={};for(let n of t){let i=e[n];i&&typeof i=="number"&&(r[n]=i)}return r}function Ln(e){let t={};for(let r of Object.keys(e)){let n=e[r];typeof n=="object"&&n!==null&&n.constructor&&n.constructor!==Object?t[r]=Ln(n):t[r]=n}return t}function kn(e){let t={},r=new Set(e.files.map(n=>n.relativePath));for(let n of e){let i=n.name.toLowerCase();if(i.match(/^(?:fid|procpar|text|log)$/)){if(i.match(/^(?:fid|text|log)$/)){let a=n.relativePath.replace(/(?:fid|text|log)$/,"procpar");if(!r.has(a))continue}let o=n.relativePath.split("/"),s=o.slice(0,-1).join("/");t[s]||(t[s]={name:o.at(-2),files:[]}),t[s].files.push(n)}}return Object.values(t)}async function _n(e,t={}){let{keepSource:r,logger:n}=t,i=kn(e);n&&n.debug(`Found ${Object.keys(i).length} varian experiments`);let o=[],s={spectra:[],molecules:[]};for(let c of i){let{name:l,files:m}=c,p=wn(m).then(f=>{let{info:g,meta:y}=vn(f),u=f.fid.data[0],h=pa(u.im),d={data:{...u,x:f.x},meta:y,info:{isComplex:h,name:l,...g},display:{name:l}};if(g.isFid&&h){let{im:b}=d.data;fa(b,-1,{output:b})}m&&r&&(d.sourceSelector={files:m.map(b=>b.relativePath)}),s.spectra.push(d)});o.push(p)}let a=await Promise.allSettled(o);for(let c=0;c<a.length;c++){let l=a[c];if(l.status==="rejected"&&l.reason){let m=i[c].name;n?.warn(`Varian data: ${m}, fails with: ${l.reason}`)}}return s.spectra.length>0&&n?.info(`Loaded ${s.spectra.length}  spectra from Varian files`),ua(s)}function ga(e,t){let{keepSource:r,logger:n}=t??{};return _n(e,{keepSource:r,logger:n})}function yt(){return da({id:"@zakodium/nmrium-core-plugins#VarianLoaderPlugin",version:1,migrations:[],onReadProcess:{onFiles:ga}})}function ha(e,t=[]){return[ut(e),yt(),Ge(),Qe(),at(),pt(),ft(),st(),$e()].concat(t)}function ba(e=[]){let t=new ya;return t.registerPlugins(ha(t,e)),t}import{getOneIfArray as jn}from"@zakodium/nmrium-core";import{from1DNMRVariables as Fa}from"convert-to-jcamp";function qn(e,t){return e.filters.find(r=>r.name===t)}function xa(e,t={}){let{onlyReal:r=!1}=t,{info:n,meta:i,data:o}=e,{owner:s,title:a,isFid:c,spectralWidth:l,baseFrequency:m,originFrequency:p,nucleus:f,solvent:g,scaleFactor:y,frequencyOffset:u,decim:h,dspfvs:d,digitalFilter:b}=n,F=jn(m||p),{x:S,re:I,im:x}=o,A=new Float64Array(I),M=!r&&x?new Float64Array(x):void 0,T=qn(e,"fft")?.enabled,j={owner:s,isFid:c,title:a,nucleus:f,solvent:g,scaleFactor:y,spectralWidth:l,frequencyOffset:u,originFrequency:p,baseFrequency:F,dataType:!c||T?"NMR SPECTRUM":"NMR FID",dataClass:!r&&x?"NTUPLES":"XYDATA"};if(c){let se=e.filters.find(J=>J.name==="digitalFilter");if(se&&!T){let{value:{digitalFilterValue:J},enabled:ke}=se;if(ke){let k=Math.floor(J);A.set(I.slice(I.length-k)),A.set(I.slice(0,I.length-k),k),x&&M&&(M.set(x.slice(x.length-k)),M.set(x.slice(0,x.length-k),k))}}ht(j,"decim",h),ht(j,"dspfvs",d),ht(j,"digitalFilter",b)}let re=Da(i,Bn),Le={xyEncoding:"DIFDUP",nmrInfo:j,meta:re},oe={x:{data:S,label:n.isFid?"TIME":"FREQUENCY",units:n.isFid?"second":"HZ",symbol:"X"},r:{data:A,label:`${n.isFid?"FID":"SPECTRUM"}/REAL`,units:"ARBITRARY UNITS",symbol:"R"}};return M&&(oe.i={data:M,label:`${n.isFid?"FID":"SPECTRUM"}/IMAG`,units:"ARBITRARY UNITS",symbol:"I"}),Fa(oe,Le)}function ht(e,t,r){r!==void 0&&(e[t]=jn(r))}var Bn=["title","decim","dspfvs","grpdly","bf1","sw","offset",".solvent","owner","firsty","page","vardim","symbol","symbols","varform","vartype","datatype","dataclass",".observefrequency",".observenucleus","ncproc"];function Da(e,t=Bn){let r=new Set(t);return Object.fromEntries(Object.entries(e).filter(([n])=>!r.has(n.toLocaleLowerCase().replaceAll(/[\s|_]*/g,""))))}export{$e as autoPostProcessing,Ge as brukerLoader,ba as default,ba as init,Qe as jcampDXLoader,st as jeolLoader,at as molfileLoader,ut as nmreDATALoader,vr as processJCAMPDX,Pn as readSDF,Tn as readSMILES,ha as recommended,pt as sdfLoader,ft as smilesLoader,xa as spectrum1DToJCAMPDX,yt as varianLoader};

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core-plugins",
-  "version": "0.2.0",
+  "version": "0.3.1",
   "description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -46,7 +46,7 @@
   },
   "dependencies": {
     "@date-fns/utc": "^2.1.1",
-    "@zakodium/nmrium-core": "^0.2.0",
+    "@zakodium/nmrium-core": "^0.2.1",
     "cheminfo-types": "^1.8.1",
     "convert-to-jcamp": "^6.0.0",
     "date-fns": "^4.1.0",
@@ -57,13 +57,13 @@
     "linear-sum-assignment": "^1.0.7",
     "lodash.merge": "^4.6.2",
     "ml-spectra-processing": "^14.17.1",
-    "nmr-processing": "^19.2.0",
+    "nmr-processing": "^19.3.0",
     "openchemlib": "^9.8.0",
-    "openchemlib-utils": "^8.3.1",
+    "openchemlib-utils": "^8.5.0",
     "sdf-parser": "^7.0.4"
   },
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "1fe1f91e225b5c3140ff63df99a74ad8e88d87b8"
+  "gitHead": "3ae265679edc9e722d29dc66f3338d9fb8ab2062"
 }