@zakodium/nmrium-core-plugins 0.6.27 → 0.6.29
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/dist/nmrium-core-plugins.js +12 -12
- package/package.json +3 -3
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var oi=Object.defineProperty;var xt=(e,t)=>{for(var r in t)oi(e,r,{get:t[r],enumerable:!0})};import{NMRiumCore as ha}from"@zakodium/nmrium-core";import{defineNMRiumPlugin as bi}from"@zakodium/nmrium-core";import{Filters1D as fi,Filters2D as di}from"nmr-processing";import{getOneIfArray as si}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?`${e.dimension}d`:"";if(n=n.toLowerCase(),n.includes("zg")||n.includes("single_pulse_dec")||n.includes("udeft"))return"1d";if(n.includes("hsqct")||n.includes("invi")&&(n.includes("ml")||n.includes("di")))return"hsqctocsy";if(n.includes("hsqc")||n.includes("invi"))return"hsqc";if(n.includes("hmbc")||n.includes("inv4")&&n.includes("lp"))return"hmbc";if(n.includes("hmqc"))return"hmqc";if(n.includes("cosy"))return"cosy";if(n.includes("jres"))return"jres";if(n.includes("dosy"))return"dosy";if(n.includes("tocsy")||n.includes("mlev")||n.includes("dipsi"))return"tocsy";if(n.includes("noesy"))return"noesy";if(n.includes("roesy"))return"roesy";if(n.includes("dept"))return"dept";if(n.includes("jmod")||n.includes("apt"))return"aptjmod";if(n.includes("inad"))return"inadequate";if(n.includes("adeq"))return"adequate";let{prefix:i=""}=r,o=(si(t[`${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 ai=["no","exponential","modifiedGaussian","sine","qsine","trap","user","sinc","qsinc","traf","trafs"];function ci(e){return e in At}function qe(e,t){let{prefix:r="",index:n=0}=t,i=Dt(e[`${r}WDW`],n),o=ai[i?Number(i):0],s={};if(!ci(o))return s;let a=At[o];if(a){let{kind:c,parameters:l}=a,m={};for(let u in l){let f=l[u],{source:g,processor:y}=f;if(g){let p=Dt(e[`${r}${g}`],n),h=Number.parseFloat(String(p));if(Number.isNaN(h))continue;m[u]=y?y(h):h}else f.value!==void 0&&(m[u]=f.value)}s[c]={apply:!0,options:m}}return s}var At={exponential:{kind:"exponential",parameters:{lineBroadening:{source:"LB"}}},modifiedGaussian:{kind:"gaussian",parameters:{lineBroadening:{source:"LB"},lineBroadeningCenter:{source:"GB"}}},sine:{kind:"sineBell",parameters:{offset:{source:"SSB",processor:St},exponent:{value:1}}},qsine:{kind:"sineSquare",parameters:{offset:{source:"SSB",processor:St}}},traf:{kind:"traf",parameters:{lineBroadening:{source:"LB"}}}};function St(e){return e===0||e===1?0:1/e}var It={sineBell:Nt({offset:0})},Mt={cosy:{...It},hmbc:{...It},hsqc:{sineBell:Nt({offset:.5})}},li={...Mt};function je(e="",t=1){let r=mi(e),n={},i=t===1?Mt[r||""]:li[r||""];return i&&(n=structuredClone(i)),n}function Nt(e){return{apply:!0,options:e}}function mi(e){let r=e.toLowerCase().match(/cosy|hsqc|hmbc/);return r?r[0]:null}function Pt(e,t={}){let{prefix:r="",experiment:n=ce(e)}=t;return e[`${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 ui}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(ui))e.name in W||(W[e.name]=Be.length);import{Filters2D as pi}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(pi))e.name in X||(X[e.name]=Ue.length);var gi=new Set;function yi(e,t){let{filter:r,experimentalFeatures:n=!1}=t,{name:i}=r;({...fi,...di})[i]&&(e.some(s=>s.name===i)||gi.has(i)&&!n||e.push({...r,enabled:!0}))}function Et(e,t={}){let{data:r}=e;if(!r)return;let{autoProcessing:n,experimentalFeatures:i}=t,o=(a,c)=>yi(a,{...c,experimentalFeatures:i}),{spectra:s}=r;for(let a of s){let{data:c,info:l,meta:m,filters:u}=a,{dimension:f,isFid:g}=l;if(g){if(f===1){let y=c.re.length,{tdOff:p,digitalFilter:h}=l;if(h&&h>0&&o(u,{filter:{name:"digitalFilter",value:{digitalFilterValue:h}}}),!n)continue;p&&Math.abs(p)>0&&o(u,{filter:{name:"backwardLinearPrediction",value:{nbInputs:y/2}}}),o(u,{filter:{name:"apodization",value:{exponential:{apply:!0,options:{lineBroadening:1}}}}}),o(u,{filter:{name:"zeroFilling",value:{nbPoints:2*y}}}),o(u,{filter:{name:"fft",value:{}}}),o(u,{filter:{name:"phaseCorrection",value:hi(l)}}),u.sort((d,b)=>W[d.name]-W[b.name])}else if(f===2){if(!n)continue;let 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Array.isArray(e)?e.every(t=>!t&&t===0):Tt([e])}function $e(){return bi({id:"@zakodium/nmrium-core-plugins#AutoPostProcessingPlugin",version:1,shouldSerialize:!0,migrations:[],onReadProcess:{onProcessing:Et}})}import{defineNMRiumPlugin as So}from"@zakodium/nmrium-core";import{FileCollection as jc}from"file-collection";var Ot=["acqus","acqu2s"],le=["procs","proc2s"];function Ct(e){return e.is1D?Fi(e):e.is2D?xi(e):{checked:!1,message:"Multi-dimensional n > 2 is not supported"}}function Fi(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 xi(e){let t=e.isFID?Ot:Ot.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: ${t.join(",")} are required.`}}function ze(e,t={}){let{logger:r,processingNumbers:n,experimentNumbers:i,dataSelection:o="both",keep1D:s=!0,keep2D:a=!0,onlyFirstProcessedData:c=!0}=t,l={},m=e.files.map(g=>g.relativePath);for(let g of e){let y,p,h,d=g.relativePath.split("/"),b=d.indexOf("pdata");if(b!==-1)y=Number(d[b+1]),p=Number(d[b-1]),h=d.slice(0,-3).join("/");else if(Si(g,m)){let S=d.indexOf(g.name);p=Number(d[S-1]),h=d.slice(0,-1).join("/")}else continue;if(Number.isNaN(p)&&(p=void 0),Number.isNaN(y)&&(y=void 0),i&&!i.includes(p))continue;l[h]||(l[h]={name:h,expno:p,processedData:{},fileCollectionItems:[]});let F=l[h];if(g.name==="vdlist"&&(F.vdlist=g),g.name==="difflist"&&(F.difflist=g),y){F.processedData||(F.processedData={}),F.processedData[y]||(F.processedData[y]={fileCollectionItems:[],name:h,expno:p,procno:y});let 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e.name.match(/^(?:ser|acqus|acqu2s|nuslist|vdlist|difflist|QuantFactorSample.xml)$/)||e.name.match(/^fid$/)&&t.includes(e.relativePath.replace(/fid$/,"acqus"))}function Ai(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 Ii}from"jcampconverter";async function _(e,t){if(!e)return Rt();let r=await e.text(),{keepRecordsRegExp:n=/.*/}=t,i=Ii(r,{keepRecordsRegExp:n});return 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Xt(e,t,r){let{prefix:n=""}=r,i=t[`${n}.ACQUISITIONSCHEME`]||t[`${n}FnMODE`];i&&D(e,"acquisitionScheme",zt(eo(i,1))),D(e,"acquisitionMode",t[`${n}.ACQUISITIONMODE`]),P(e,"lpNumberOfCoefficients",t[`${n}NCOEF`]),P(e,"linearPredictionBin",t[`${n}LPBIN`]),P(e,"tdOff",t[`${n}TDoff`])}import{getOneIfArray as ao}from"@zakodium/nmrium-core";import{UTCDate as to}from"@date-fns/utc";import{getOneIfArray as ro}from"@zakodium/nmrium-core";import{getTime as Ht,isValid as Gt,parse as no,parseISO as io}from"date-fns";import{removeComment as oo}from"jcampconverter";function Vt(e,t){if(t!==null&&Number.isInteger(t)){e.epoch=t;let r=new Date(t);e.date=r.toISOString(),e.localeDate=r.toLocaleString()}}function Yt(e,t,r={}){let n=t.LONGDATE??ro(t.DATE);if(!n)return;let{separator:i}=r,o=Number(n)*1e3;Vt(e,o||so(n,i))}function so(e,t){let r=oo(e,t),n=io(r,{});if(Gt(n)){let o=n.getTimezoneOffset()*60*1e3;return Ht(n)-o}let i=["dd/MM/yyyy HH:mm:ss","EEE MMM dd HH:mm:ss yyyy","dd/MM/yyyy HH:mm:ss","yyyy/MM/dd 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s=e.type[0].toUpperCase();s.includes("FID")?(e.isFid=!0,e.isComplex=!0):s.includes("SPECTRUM")&&(e.isFt=!0)}if(D(e,"firstX",t[`${n}FIRSTX`]),D(e,"lastX",t[`${n}LASTX`]),D(e,"numberOfPoints",t[`${n}NPOINTS`]),`${n}REVERSE`in t){let s=t[`${n}REVERSE`];e.reverse=(Array.isArray(s)?s:[s]).map(a=>typeof a=="string"?a.includes("yes"):a)}}function Zt(e){let{JCAMPDX:t="",ORIGIN:r=""}=e,n=String(t).toLowerCase()+String(r).toLowerCase();return"SPECTROMETER/DATASYSTEM"in e&&(n=e["SPECTROMETER/DATASYSTEM"]),(n.includes("mestre")||n.includes("nova"))&&(n="mnova"),n}import{isAnyArray as co}from"is-any-array";import{calculateRelativeFrequency as lo}from"nmr-processing";function Qt(e,t,r){let{prefix:n=""}=r;if(P(e,"originFrequency",t[`${n}SFO1`]),e.dimension===1&&P(e,"originFrequency",t[".OBSERVEFREQUENCY"]),!e.originFrequency&&e.dimension===2&&".OBSERVEFREQUENCY"in t){let i=G(t[".OBSERVEFREQUENCY"]);if(co(i)&&i.length>1){let o=t[`${n}SYMBOL`].split(","),s=o.findIndex(c=>c.includes("2")),a=o.findIndex(c=>c.includes("1"));s!==-1&&a!==-1?e.originFrequency=[i[s],i[a]]:e.originFrequency=i.slice()}else typeof i=="number"&&(e.originFrequency=lo(e.nucleus,i))}(!e.originFrequency||e.originFrequency.some(i=>Number.isNaN(i)||i===0))&&(e.originFrequency=e.dimension>1?[400,400]:[400],r.logger?.warn("Frequency could not be determined, set to 400 MHz"))}function C(e,t,r=""){return e.every(n=>`${r}${n}`in t)}import{matrixTranspose as mo}from"ml-spectra-processing";function ne(e,t){return mo(e).map(t)}function er(e,t,r){let{prefix:n=""}=r,i=t[`${n}REFERENCE_POINT`];if(!("baseFrequency"in e)&&"originFrequency"in e&&D(e,"baseFrequency",e.originFrequency),!("frequencyOffset"in e)&&i&&C(["spectralWidth","baseFrequency"],e)){let o=typeof i=="number"?i:Number(t[`${n}REFERENCE_POINT`].match(/(?<reference>[+-]?\d+(?:\.\d+)?)\s*.*/)?.groups?.reference);if(!Number.isNaN(o)){let{spectralWidth:s,baseFrequency:a}=e;D(e,"frequencyOffset",.5*s[0]*a[0]-o)}}if(!("frequencyOffset"in e)&&C(["baseFrequency","originFrequency"],e)){let{baseFrequency:o,originFrequency:s}=e;D(e,"frequencyOffset",ne([s,o],a=>(a[0]-a[1])*1e6))}!e.frequencyOffset[0]&&".SHIFTREFERENCE"in t&&uo(t,e)}function uo(e,t){let r=e[".SHIFTREFERENCE"],n=r.trim().startsWith("(")?/\((?<data>[^)]+)\)/:/(?<data>[^)]+)/,i=r.match(n);if(i.groups.data){let o=i.groups.data.split(",");if(o.length<4)return;let s=Number.parseInt(t.numberOfPoints,10),{spectralWidth:a,baseFrequency:c}=t,l=Number.parseInt(o[2],10),m=Number.parseFloat(o[3]),u;if(t.isFid){if(!C(["numberOfPoints","spectralWidth"],t))return;u=m+(s*.5-l)*a/s}else if(C(["firstX","lastX","numberOfPoints"],t)){let f=Number.parseFloat(t.firstX),g=Number.parseFloat(t.lastX),y=(g+f)/2,p=(g-f)/(s+1),h=p<0?f:g+(l-1)*p;u=(y-h)/c+m}u!==void 0&&!Number.isNaN(u)&&(t.frequencyOffset=u*c)}}import{isAnyArray as Y}from"is-any-array";function he(e){return typeof e=="number"}function be(e){let{phc0:t,phc1:r}=e;return!Y(t)&&!he(t)||!Y(r)&&!he(r)||Y(t)&&!he(t[0])||Y(r)&&!he(r[0])?{}:(Y(r)?r[0]*=-1:r*=-1,Y(t)?t[0]*=-1:t*=-1,{phc0:t,phc1:r})}function tr(e,t){let{T1NUCLEUS:r,T2NUCLEUS:n,PAGE:i}=t;e.pulseSequence=t.EXPERIMENT||t[".PULSESEQUENCE"];let o=[],{dimension:s,isComplex:a}=e;if(s===2&&e.pulseSequence==="T1"){let m=a?2:1;for(let u=0;u<i.length;u+=m){let f=i[u].replace(/T1=/,"");o.push(Number(f))}t.vdlistValues=o}e.nucleus=s>1?[n,r]:[n];let{phc0:c,phc1:l}=e;if(c&&l){let m=be({phc0:c,phc1:l});e={...e,...m}}}import{getOneIfArray as ir}from"@zakodium/nmrium-core";import{getGyromagneticRatio as po}from"gyromagnetic-ratio";function nr(e,t,r){if(e>0)return e;if(t>14||t===0)return 0;if(rr[t]){let n=rr[t];if(!n[r])throw new Error(`decim ${r} not in lookup table for dspfvs ${t}`);return n[r]}else throw new Error(`dspfvs ${t} not in lookup table`)}var rr={10:{2:44.75,3:33.5,4:66.625,6:59.08333333333333,8:68.5625,12:60.375,16:69.53125,24:61.02083333333333,32:70.015625,48:61.34375,64:70.2578125,96:61.50520833333333,128:70.37890625,192:61.5859375,256:70.439453125,384:61.62630208333333,512:70.4697265625,768:61.646484375,1024:70.48486328125,1536:61.65657552083333,2048:70.492431640625},11:{2:46,3:36.5,4:48,6:50.16666666666667,8:53.25,12:69.5,16:72.25,24:70.16666666666667,32:72.75,48:70.5,64:73,96:70.66666666666667,128:72.5,192:71.33333333333333,256:72.25,384:71.66666666666667,512:72.125,768:71.83333333333333,1024:72.0625,1536:71.91666666666667,2048:72.03125},12:{2:46,3:36.5,4:48,6:50.16666666666667,8:53.25,12:69.5,16:71.625,24:70.16666666666667,32:72.125,48:70.5,64:72.375,96:70.66666666666666,128:72.5,192:71.333333333,256:72.25,384:71.66666666666667,512:72.125,768:71.83333333333333,1024:72.0625,1536:71.91666666666667,2048:72.03125},13:{2:2.75,3:2.833333333333333,4:2.875,6:2.916666666666667,8:2.9375,12:2.958333333333333,16:2.96875,24:2.979166666666667,32:2.984375,48:2.989583333333333,64:2.9921875,96:2.994791666666667}};function or(e,t,r){let{prefix:n=""}=r,i=e.nucleus[0],o=po(i);if(D(e,"probeName",t[`${n}PROBHD`]),D(e,"baseFrequency",t[`${n}BF1`]||t[`${n}SF`]),P(e,"scaleFactor",t[`${n}NC_proc`]),"scaleFactor"in e&&(e.scaleFactor=e.scaleFactor.map(a=>2**a)),!("baseFrequency"in e)&&"originFrequency"in e?D(e,"baseFrequency",e.originFrequency):e.baseFrequency=G(e.baseFrequency),o&&C(["baseFrequency","originFrequency"],e)){let a=2*Math.PI*(e.baseFrequency[0]/o)*1e6;D(e,"fieldStrength",a)}if(P(e,"spectralWidth",t[`${n}SW`]||t[`${n}QM_SPECTRAL_WIDTH`]),e.dimension===1&&t[`${n}SweepWidth`]&&e.originFrequency&&P(e,"spectralWidth",t[`${n}SweepWidth`]/e.originFrequency[0]),D(e,"numberOfPoints",t[`${n}TD`],!0),D(e,"spectrumSize",t[`${n}SI`]??e.numberOfPoints),D(e,"sampleName",t[`${n}NAME`]),t[`${n}FNTYPE`]!==void 0&&D(e,"acquisitionMode",Number.parseInt(t[`${n}FNTYPE`],10)),t[`${n}VARNAME`]?.split(",")[0]==="TIME"){let a=typeof t.LAST=="string"?t.LAST.replace(" ","").split(",")[0]:t.LAST;P(e,"acquisitionTime",a)}if(!e.acquisitionTime&&C(["numberOfPoints","spectralWidth"],e)){let{spectralWidth:a,originFrequency:c,numberOfPoints:l}=e;D(e,"acquisitionTime",(l[0]-1)/(2*a[0]*c[0]))}if(t[`${n}P`]){let a=1e6/(ir(t[`${n}P`]).split(r.separator||`
|
|
4
|
+
`)[1].split(" ")[1]*4);D(e,"pulseStrength90",a)}if(t[`${n}D`]){let a=ir(t[`${n}D`]).split(r.separator||`
|
|
5
|
+
`)[1].split(" ")[1];P(e,"relaxationTime",a)}if(P(e,"numberOfScans",t[`${n}NS`]||t[`${n}QM_NSCANS`]),D(e,"groupDelay",t[`${n}GRPDLY`]),D(e,"dspfvs",t[`${n}DSPFVS`]),D(e,"decim",t[`${n}DECIM`]),e.isFid&&("groupDelay"in e||C(["dspfvs","decim"],e))){let{groupDelay:a,dspfvs:c,decim:l}=e,m=nr(a?.[0]??0,c?.[0],l?.[0]);D(e,"digitalFilter",m)}if(C(["numberOfPoints","spectralWidth"],e)){let{spectralWidth:a,numberOfPoints:c}=e,l=c.map((m,u)=>e.isFid?e.acquisitionTime[0]/(m-1):a[u]/(m-1));D(e,"increment",l)}}function $(e,t=","){if(e&&typeof e=="string")return e.split(t)}function sr(e,t,r){let{prefix:n=""}=r,i=e.dimension<2,o=e.dataClass?.[0].toUpperCase()==="NTUPLES",s=C(["LAST","FIRST","VARDIM","SYMBOL"],t,n);if(i&&(o||s)&&(D(e,"last",$(t[`${n}LAST`])),D(e,"first",$(t[`${n}FIRST`])),D(e,"varDim",$(t[`${n}VARDIM`])),D(e,"symbols",$(t[`${n}SYMBOL`])),e.symbols&&Array.isArray(e.symbols))){e.symbols.includes("R")&&e.symbols.includes("I")&&(e.isComplex=!0);let a=e.symbols.findIndex(c=>c.toLowerCase()==="x");if(P(e,"firstX",e.first[a]),P(e,"lastX",e.last[a]),P(e,"numberOfPoints",e.varDim[a]),!("spectralWidth"in e)){let{lastX:c,numberOfPoints:l,firstX:m,originFrequency:u}=e;D(e,"spectralWidth",e.isFid?ne([l,c],f=>f[0]/(2*f[1])):ne([c,m,u],f=>Math.abs(f[0]-f[1])/f[2]))}}}import{normalizeNucleus as fo}from"nmr-processing";function Fe(e,t,r){let n=[];if(e[`${r}AXNUC`]&&(n=e[`${r}AXNUC`],Array.isArray(n)||(n=[n]),n=v(n)),n.length===0&&e[`${r}NUC1`]&&(n=e[`${r}NUC1`],Array.isArray(n)||(n=[n]),n=v(n)),n.length===0&&e[".NUCLEUS"]){let s=$(e[".NUCLEUS"]);if(e[`${r}SYMBOL`]){let a=e[`${r}SYMBOL`].split(","),c=a.findIndex(m=>m.includes("2")),l=a.findIndex(m=>m.includes("1"));c!==-1&&l!==-1&&s?n=v([s[c],s[l]]):n=v(s).toReversed()}else n=v(s)}n.length===0&&e[".OBSERVENUCLEUS"]&&(n=v([e[".OBSERVENUCLEUS"]])),n.length===0&&t.experiment&&(n=v(ar(t.experiment[0]))),go(e)&&(n=[e["2D_X_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,""),e["2D_Y_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,"")]);let{pulseSequence:i=[""],experiment:o}=t;return!i[0].toLowerCase().match("1d")&&o&&(o[0].match("jres")||o[0].match("dosy"))&&(n=ar(t.experiment[0])),n.map(fo)}function go(e){return e["2D_X_NUCLEUS"]&&!e["2D_X_NUCLEUS"].includes("off")&&e["2D_Y_NUCLEUS"]&&!e["2D_Y_NUCLEUS"].includes("off")}function ar(e){return typeof e!="string"?[]:(e=e.toLowerCase(),e.includes("jres")?["1H","Hz"]:e.includes("dosy")?["1H","D"]:e.includes("hmbc")||e.includes("hsqc")?["1H","13C"]:e.includes("cosy")||e.includes("tocsy")?["1H","1H"]:[])}function v(e){if(!e)return[];let t=e.map(n=>String(n).replaceAll(/[^A-Za-z0-9]/g,"").replace("NA","").replace("off","")),r=0;for(let n of t)n||r++;return r===0?t:[]}function cr(e,t,r){let{logger:n,prefix:i=""}=r;if(e.nucleus=Fe(t,e,i),e.nucleus.length===0)if(n)n.warn("No nucleus detected, assuming 1H"),e.nucleus=["1H"];else throw new Error("No nucleus detected");e.dimension=e.nucleus.length}function lr(e,t,r={}){let{prefix:n="",separator:i=`
|
|
6
|
+
`}=r;D(e,"spectralWidth",t[`${n}SweepWidth`]/e.originFrequency[0]);let o=t[`${n}.PULSESEQUENCE`].split(i),s=[];t[".OBSERVENUCLEUS"]&&s.push(t[".OBSERVENUCLEUS"]),t.INDIRECTNUCLEUS&&s.push(t.INDIRECTNUCLEUS),e.nucleus=v(s),e.pulseSequence=o[0];let a=o.slice(2,-1);if(s.length>1)if(s[0]===s[1])e.spectralWidth.push(e.spectralWidth[0]);else{let c=JSON.stringify(a).match(/\$\$SW1=\s*(?<sw>[+-]?(?:[0-9]*[.])?[0-9]+)/);if(c?.groups){let{originFrequency:l}=e,m=Number.parseFloat(c.groups.sw);e.spectralWidth.push(m/l[1])}}}function xe(e,t={}){let{prefix:r="",logger:n}=t,i={creator:Zt(e),dimension:0,nucleus:[],isFid:!1,isFt:!1},o=JSON.stringify(e),s=/\r\n/.exec(o)?`\r
|
|
7
7
|
`:`
|
|
8
|
-
`,a=[
|
|
9
|
-
because it didn't match the import filters`);continue}s.push(m)}let a=[],c=s.some(pr),l=s.some(ur);for(let m of s){if(o!=="both"&&m.dataType!=="LINK"){if(pr(m)&&(o==="ft"||o==="preferFT"&&l)){n?.warn(`Skipping raw data ${r?`in ${r}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(ur(m)&&(o==="fid"||o==="preferFID"&&c)){n?.warn(`Skipping FFT data ${r?`in ${r}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}}a.push(m)}return a}function ur(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function pr(e){return e.dataType?.toUpperCase().includes("FID")}function dr(e,t={}){let{logger:r,name:n=""}=t;for(let i of e){if(i.dataType==="LINK"&&dr(i.children,t))return!0;let{dataType:o=""}=i,s=o.toLowerCase();if(s.length>0){if(s.includes("spectrum")&&!s.includes("nmr"))return r?.warn(`File ${n} was ignored because it is a ${o}`),!1;if(s.includes("nmr"))return!0}}return!1}import{generateID as br}from"@zakodium/nmrium-core";import{parseJcampCS as Oo}from"jcampconverter";import*as Co from"openchemlib";import{isMolfileNotEmpty as Mo}from"nmr-processing";import*as gr from"openchemlib";async function yr(e,t={}){let{logger:r,selector:n}=t;if(n?.files&&!n.files.includes(e.relativePath))return{molecules:[],spectra:[]};let i=await e.text(),o=K(i),s={molecules:o,spectra:[]};return o.length===0&&r?.debug(`${e.name} is an empty molfile`),s}function K(e){let t=[];if(!Mo(e))return[];let n=gr.Molecule.fromMolfile(e,{customLabelPosition:"superscript"}).toMolfileV3();return t.push({molfile:n}),t}import{isMolfileNotEmpty as Po}from"nmr-processing";import*as Eo from"openchemlib";import{getDiastereotopicAtomIDsFromMolfile as To}from"openchemlib-utils";var No=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function Se(e){let{dataType:t="",dataClass:r=""}=e,n=t.replaceAll(/\s/g,"").toLowerCase(),i=r.replaceAll(/\s/g,"").toLowerCase();return No.has(n)&&i!=="peaktable"}function hr(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:u}=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 ${m} file, assignment object could not be completed`),null;let p=Number.parseInt(y?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(p)||p<1)return l&&l.warn(`Structure block_id not found for ${m} file, assignment object could not be completed`),null;let d=u?.molecules?.find(x=>x.blockId===p)?.molfile??"";if(d===""){let x=t.find(M=>M.info.BLOCKID===p),{MOLFILE:A=""}=x?.meta||{};d=A}if(!Po(d))return l&&l.warn(`Empty molfile for ${m} file with structure block_id = ${p}, assignment object could not be completed`),null;let b=To(Eo,d),F=Fe({...i,...o},{},"");for(let x=0;x<s.x.length;x++){let A={};for(let M in s){let T=s[M][x];typeof T=="string"&&T.startsWith("<")&&T.endsWith(">")&&(T=T.slice(1,-1)),A[c[M]]=T}if("atom"in A){let M=b.map[A.atom-1];F.includes("1H")?M.nbHydrogens>0?(A.diaIDs=M.hydrogenOCLIDs,A.nbHydrogens=M.nbHydrogens):(A.diaIDs=[M.oclID],A.nbHydrogens=M.nbHydrogens):(A.diaIDs=[M.oclID],A.nbHydrogens=1)}a.push(A)}let S={};for(let x of a){let{delta:A,diaIDs:M}=x,T=`${A}_${M.join("_")}`;if(S[T])S[T].atoms.push(x.atom);else{let{atom:j,...re}=x;S[T]={...re,atoms:[x.atom]}}}let I=[];for(let x of g)x.toLowerCase().includes("spectrum")&&I.push(Number(x.toLowerCase().replace(/_/,"").replace(/.*:\s*blockid=(?<blockId>.*)/,"$<blockId>")));if(I.length===0){for(let x of t)if(Se(x)){let{BLOCKID:A}=x.info;I.push(Number(A))}I.length>1&&(I=[],l&&l.warn(`There is not a spectral cross-reference for the peak assignment in the ${m} file`))}return{moleculeBlockID:p,spectraBlockIDs:I,assignments:Object.values(S),molecule:b.molecule}}function Fr(e,t,r,n){for(let i of e){let{meta:o,dataClass:s="",dataType:a="",info:c}=i,l=Number.parseInt(String(c.BLOCKID),10);o.MOLFILE?Lo(String(o.MOLFILE),t,l):i.jcampCS&&vo(i,t,l),Ro(s,a)&&wo(t,i,e,n),Se(i)&&r.push(i)}}function Ro(e,t){return e?.toLowerCase().includes("assignments")&&t?.toLowerCase().includes("assignments")}function wo(e,t,r,n){let i=hr(t,r,{spectraData:e,logger:n.logger,name:n.name});if(e.assignmentsByBlocks||(e.assignmentsByBlocks={}),i){let{spectraBlockIDs:o}=i;for(let s of o)e.assignmentsByBlocks[s]=i}}function vo(e,t,r){t.molecules||(t.molecules=[]);let n=Oo(e,{OCL:Co}),i=K(n?.molfile||"");i.length>0&&t.molecules.push({id:br(),blockId:r,...i[0]})}function Lo(e,t,r){t.molecules||(t.molecules=[]);let n=K(e);t.molecules.push({id:br(),blockId:r,...n[0]})}import{generateID as Rr}from"@zakodium/nmrium-core";import{matrixMinMaxZ as Cr,reimPhaseCorrection as Xo}from"ml-spectra-processing";import{xyAutoRangesPicking as Vo}from"nmr-processing";function Z(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function Q(e){e.sort((t,r)=>t.from-r.from);for(let t=0;t<e.length-1;t++)e[t].to>e[t+1].from&&(e[t].to=Math.max(e[t+1].to,e[t].to),e[t].signals=e[t].signals.concat(e[t+1].signals),e[t].integration+=e[t+1].integration,e.splice(t+1,1),t--);return e}import{splitPatterns as Bo}from"nmr-processing";import{xMaxValue as ko}from"ml-spectra-processing";function ie(e){return e.trim().slice(1,-1).split(/,\s*/).map(t=>t.trim())}var _o={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},xr=["I","X","Y","Hs","An","H","C","N","(J)"];function Dr(e){let 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n.dataFormat==="Two_D"&&(s.push(w(i,"y_domain")?.value),l.push(E(i,"y_acq_time")),m.push(E(i,"y_sweep")),f.push(E(i,"y_resolution")),g.push(E(i,"y_freq")),y.push(E(i,"y_offset")),p.push(n.dataUnits[1].base)),{info:{sampleName:w(i,"sample_id")?.value,creationTime:n.creationTime,revisionTime:n.revisionTime,author:n.author,comment:n.comment,solvent:w(i,"solvent")?.value,temperature:E(i,"temp_get"),probeName:w(i,"probe_id")?.value,fieldStrength:E(i,"field_strength"),experiment:w(i,"experiment")?.value,dimension:n.dataDimensionNumber,nucleus:s,date:a,epoch:c,pulseStrength90:E(i,"x90"),numberOfScans:w(i,"scans")?.value,relaxationTime:E(i,"relaxation_delay"),dataPoints:n.dataPoints.slice(0,n.dataDimensionNumber),dataOffsetStart:n.dataOffsetStart,dataOffsetStop:n.dataOffsetStop,dataUnits:p,dataSections:o?Object.keys(o):void 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8
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`,a=[Kt,cr,Xt,Qt],{creator:c=""}=i;c.includes("nanalysis")?a.push(tr):c.toLocaleLowerCase().includes("oxford instruments")&&a.push(lr),c!=="mnova"&&c!=="mestre"&&a.push(or),a.push(sr,er);for(let l of a)l(i,e,{prefix:r,logger:n,separator:s});return ho(i)}function ho(e){return e.dimension===1&&(e.nucleus=[e.nucleus]),Object.fromEntries(Object.entries(e).map(([t,r])=>[t,yo(r)&&r.length===1?r[0]:r]))}var Fo={keepRecordsRegExp:/.*/,keepFiles:!0};async function De(e,t={}){let r={spectra:[],molecules:[]},{converter:n={},selector:i={},logger:o}=t,s=ze(e,{logger:o,...Do(i)}),a=[];for(let l of s)a.push(He(l,{...Fo,...n,keepFiles:!0}).then(m=>xo(m,t)));let c=await Promise.allSettled(a);for(let l=0;l<c.length;l++){let m=c[l];if(m.status==="fulfilled"){let u=be(m.value.info);r.spectra.push({...m.value,info:{...m.value.info,...u}})}else if(m.reason){let u=s[l].name;o?.warn(`Bruker data: ${u}, fails with: ${m.reason}`);continue}}return o&&o[r.spectra.length>0?"info":"debug"](`Loaded ${r.spectra.length} spectra from Bruker files`),bo(r)}function xo(e,t={}){let{logger:r}=t,n={...e.info,...e.meta},i=xe(n,{logger:r}),o={},{isFid:s}=i;if(So(e)){let f=e.minMax;for(let g in f){let y=f[g];y&&(y.z=U(y.z))}o.components=e.minMax}else i.dimension===1&&(o.components=e.spectra);let{source:a}=e,{expno:c,name:l,files:m}=a;n.vdlist&&(n.vdlistValues=ye(n.vdlist));let u={dependentVariables:[o],meta:n,info:{...i,experimentNumber:c,name:l}};return m&&(u.selector={files:m.map(f=>f.relativePath)}),Ao(u,e),u}function Do(e){let{general:t={},bruker:r={}}=e,{processingNumbers:n,experimentNumbers:i,...o}=r;return{...t,...o,processingNumbers:mr(n),experimentNumbers:mr(i)}}function mr(e){if(e)return e.split(/[^\d]+/).filter(Boolean).map(t=>Number.parseInt(t,10))}function So(e){let{info:t}=e;return t.twoD}function Ao(e,t){if(!("integrals"in t))return;let{integrals:r=[]}=t;e.integrals={values:r.map(n=>{let{from:i,to:o,integration:s}=n;return{from:i,to:o,integral:s,kind:"signal"}})}}function Mo(e,t){let{selector:r,converter:n,logger:i}=t??{};return De(e,{converter:n?.bruker,selector:r,logger:i})}function Ge(){return Io({id:"@zakodium/nmrium-core-plugins#BrukerLoaderPlugin",version:1,shouldSerialize:!0,migrations:[],onReadProcess:{onFiles:Mo}})}import{defineNMRiumPlugin as cs}from"@zakodium/nmrium-core";import{formatSpectra as is}from"@zakodium/nmrium-core";import{createTree as os}from"jcampconverter";function ur(e,t,r={}){let{selector:n={}}=r;for(let i=0;i<e.spectra.length;i++){let o=e.spectra[i];o.selector={files:[t.relativePath],jcamp:{index:i,...n}}}return e}import{convert as No}from"jcampconverter";function Ye(e,t,r){let{dataType:n,children:i}=e,o=n==="LINK"&&i?i:[e];for(let s of o){if(s.dataType==="LINK"){Ye(s,t,r);continue}let a=No(s.jcamp,r);t.push(...a.flatten)}}function dr(e,t={}){let r=[],n=gr(e,t);for(let s of n?e:[])s.dataType==="LINK"?s.children=Ke(s.children,t):s=Ke([s],t)[0],r.push(s);let{name:i,logger:o}=t;return e.length===0&&o?.warn(`There is no data ${i?`in ${i}`:"in the JCAMP-DX"}`),r}function Ke(e=[],t={}){let{name:r,logger:n,tree:i=[],dataSelection:o="both"}=t,s=[];for(let m of e){let{dataType:u,dataClass:f}=m;if(u==="LINK")m.children=Ke(m.children,t);else if(i.some(g=>{let{dataClass:y=f,dataType:p=u}=g;return f===y&&u===p})){n?.warn(`Skipping ${f} and ${u} ${r?`in ${r}`:"in the JCAMP-DX"},
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because it didn't match the import filters`);continue}s.push(m)}let a=[],c=s.some(fr),l=s.some(pr);for(let m of s){if(o!=="both"&&m.dataType!=="LINK"){if(fr(m)&&(o==="ft"||o==="preferFT"&&l)){n?.warn(`Skipping raw data ${r?`in ${r}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(pr(m)&&(o==="fid"||o==="preferFID"&&c)){n?.warn(`Skipping FFT data ${r?`in ${r}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}}a.push(m)}return a}function pr(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function fr(e){return e.dataType?.toUpperCase().includes("FID")}function gr(e,t={}){let{logger:r,name:n=""}=t;for(let i of e){if(i.dataType==="LINK"&&gr(i.children,t))return!0;let{dataType:o=""}=i,s=o.toLowerCase();if(s.length>0){if(s.includes("spectrum")&&!s.includes("nmr"))return r?.warn(`File ${n} was ignored because it is a ${o}`),!1;if(s.includes("nmr"))return!0}}return!1}import{generateID as Fr}from"@zakodium/nmrium-core";import{parseJcampCS as Ro}from"jcampconverter";import*as wo from"openchemlib";import{isMolfileNotEmpty as Po}from"nmr-processing";import*as yr from"openchemlib";async function hr(e,t={}){let{logger:r,selector:n}=t;if(n?.files&&!n.files.includes(e.relativePath))return{molecules:[],spectra:[]};let i=await e.text(),o=K(i),s={molecules:o,spectra:[]};return o.length===0&&r?.debug(`${e.name} is an empty molfile`),s}function K(e){let t=[];if(!Po(e))return[];let n=yr.Molecule.fromMolfile(e,{customLabelPosition:"superscript"}).toMolfileV3();return t.push({molfile:n}),t}import{isMolfileNotEmpty as To}from"nmr-processing";import*as Oo from"openchemlib";import{getDiastereotopicAtomIDsFromMolfile as Co}from"openchemlib-utils";var Eo=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function Se(e){let{dataType:t="",dataClass:r=""}=e,n=t.replaceAll(/\s/g,"").toLowerCase(),i=r.replaceAll(/\s/g,"").toLowerCase();return Eo.has(n)&&i!=="peaktable"}function br(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:u}=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 ${m} file, assignment object could not be completed`),null;let p=Number.parseInt(y?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(p)||p<1)return l&&l.warn(`Structure block_id not found for ${m} file, assignment object could not be completed`),null;let d=u?.molecules?.find(x=>x.blockId===p)?.molfile??"";if(d===""){let x=t.find(M=>M.info.BLOCKID===p),{MOLFILE:A=""}=x?.meta||{};d=A}if(!To(d))return l&&l.warn(`Empty molfile for ${m} file with structure block_id = ${p}, assignment object could not be completed`),null;let b=Co(Oo,d),F=Fe({...i,...o},{},"");for(let x=0;x<s.x.length;x++){let A={};for(let M in s){let T=s[M][x];typeof T=="string"&&T.startsWith("<")&&T.endsWith(">")&&(T=T.slice(1,-1)),A[c[M]]=T}if("atom"in A){let M=b.map[A.atom-1];F.includes("1H")?M.nbHydrogens>0?(A.diaIDs=M.hydrogenOCLIDs,A.nbHydrogens=M.nbHydrogens):(A.diaIDs=[M.oclID],A.nbHydrogens=M.nbHydrogens):(A.diaIDs=[M.oclID],A.nbHydrogens=1)}a.push(A)}let S={};for(let x of a){let{delta:A,diaIDs:M}=x,T=`${A}_${M.join("_")}`;if(S[T])S[T].atoms.push(x.atom);else{let{atom:j,...re}=x;S[T]={...re,atoms:[x.atom]}}}let I=[];for(let x of g)x.toLowerCase().includes("spectrum")&&I.push(Number(x.toLowerCase().replace(/_/,"").replace(/.*:\s*blockid=(?<blockId>.*)/,"$<blockId>")));if(I.length===0){for(let x of t)if(Se(x)){let{BLOCKID:A}=x.info;I.push(Number(A))}I.length>1&&(I=[],l&&l.warn(`There is not a spectral cross-reference for the peak assignment in the ${m} file`))}return{moleculeBlockID:p,spectraBlockIDs:I,assignments:Object.values(S),molecule:b.molecule}}function xr(e,t,r,n){for(let i of e){let{meta:o,dataClass:s="",dataType:a="",info:c}=i,l=Number.parseInt(String(c.BLOCKID),10);o.MOLFILE?_o(String(o.MOLFILE),t,l):i.jcampCS&&ko(i,t,l),vo(s,a)&&Lo(t,i,e,n),Se(i)&&r.push(i)}}function vo(e,t){return e?.toLowerCase().includes("assignments")&&t?.toLowerCase().includes("assignments")}function Lo(e,t,r,n){let i=br(t,r,{spectraData:e,logger:n.logger,name:n.name});if(e.assignmentsByBlocks||(e.assignmentsByBlocks={}),i){let{spectraBlockIDs:o}=i;for(let s of o)e.assignmentsByBlocks[s]=i}}function ko(e,t,r){t.molecules||(t.molecules=[]);let n=Ro(e,{OCL:wo}),i=K(n?.molfile||"");i.length>0&&t.molecules.push({id:Fr(),blockId:r,...i[0]})}function _o(e,t,r){t.molecules||(t.molecules=[]);let n=K(e);t.molecules.push({id:Fr(),blockId:r,...n[0]})}import{generateID as wr}from"@zakodium/nmrium-core";import{matrixMinMaxZ as Rr,reimPhaseCorrection as Ho}from"ml-spectra-processing";import{xyAutoRangesPicking as Go}from"nmr-processing";function Z(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function Q(e){e.sort((t,r)=>t.from-r.from);for(let t=0;t<e.length-1;t++)e[t].to>e[t+1].from&&(e[t].to=Math.max(e[t+1].to,e[t].to),e[t].signals=e[t].signals.concat(e[t+1].signals),e[t].integration+=e[t+1].integration,e.splice(t+1,1),t--);return e}import{splitPatterns as $o}from"nmr-processing";import{xMaxValue as qo}from"ml-spectra-processing";function ie(e){return e.trim().slice(1,-1).split(/,\s*/).map(t=>t.trim())}var jo={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},Dr=["I","X","Y","Hs","An","H","C","N","(J)"];function Sr(e){let t={headersFromParenthesis:[],headersFromComments:[],comments:[],data:[],multiplets:[]},r=e.split(/\r?\n/).filter(n=>n.trim()!=="");if(r.length===0)return t;if(r[0].startsWith("(")&&!r[0].match(/\d/)){let n=r.shift();t.headersFromParenthesis=ie(n)}return t.comments=r.filter(n=>n.startsWith("$$")).map(n=>n.replace(/^\$\$\s*/,"")),t.headersFromComments=Uo(t.comments),t.data=r.filter(n=>!n.startsWith("$$")).map(ie),t.multiplets=Bo(t),t}function Bo(e,t={}){let{logger:r}=t,n=e.data[0].map((c,l)=>l).filter(c=>e.data.every(l=>Number.isNaN(l[c])||Number.isNaN(Number(l[c]))));if(r?.trace(`Parsing JCAMP-DX assignment: stringColumnIndexes: ${n.join(",")}`),n.length===0)return r?.warn("Parsing JCAMP-DX assignment: No string columns found. 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h){if(F.js.every(S=>S===F.js[0])){b.push(F);continue}if(F.multiplicity!==F.js.length+1){b.push(F);continue}for(let S=0;S<F.multiplicity-1;S++)b.push({value:"d",multiplicity:2,js:[F.js[S]]})}b.sort((F,S)=>S.js[0]-F.js[0]),g.js=b.map(F=>({coupling:F.js[0],multiplicity:F.value}))}typeof o.assignment=="string"&&(g.assignment=Wo(o.assignment)),typeof o.multiplicity=="string"&&(g.multiplicity=o.multiplicity),i.multiplets.push(g)}return i}function zo(e){let t={};for(let r in e){let n=e[r],i=typeof n=="number"?n:Number.parseFloat(n);Number.isNaN(i)||(t[r]=i)}return t}var Jo={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function Wo(e){return e.replaceAll(/&(\w+);/gi,(t,r)=>Jo[r.toLowerCase()]||t)}function Ir(e){let t=e.split(/\r?\n/).filter(n=>n.trim()!==""),r=[];for(let n of t)if(n.startsWith("(")){let[i,o,s]=ie(n).map(Number.parseFloat);r.push({id:i,x:o,y:s})}return r}function Mr(e,t={}){let r={};if(!e["OBSERVED MULTIPLETS"])return[];let n=Ar(e["OBSERVED MULTIPLETS"],t);if(!n)return[];let{multiplets:i}=n;for(let o of i){let{id:s,from:a,to:c,integration:l=0,...m}=o;r[s]={from:a,to:c,integration:l,signals:[{id:s,...m}]}}if(e["OBSERVED MULTIPLETS PEAKS"]){let o=Ir(e["OBSERVED MULTIPLETS PEAKS"]),s={};for(let a of o){let{id:c,x:l,y:m}=a;s[c]||(s[c]=[]),s[c].push({x:l,y:m,width:.05})}for(let a in r)s[a]&&(r[a].signals[0].peaks=s[a])}return Q(Object.values(r))}function Nr(e,t){let n=[...e.getMolecularFormula().formula.matchAll(/(?<element>[A-Z][a-z]?)(?<count>\d*)/g)].map(o=>({element:o?.groups?.element,count:o?.groups?.count?Number(o.groups.count):1})),i=[...t.nucleus[0].matchAll(/[0-9]*(?<element>[A-Z][a-z]?)/g,"$element")][0].groups.element;return n.find(o=>o.element===i)?.count||100}function Pr(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 Er}from"@zakodium/nmrium-core";function Tr(e,t,r){for(let n=0;n<e.length;n++){if(t.includes(n))continue;let{delta:i,multiplicity:o="",diaIDs:s}=e[n],a=i-.01,c=i+.01;r.push({from:a,to:c,integration:1,id:Er(),signals:[{id:Er(),delta:i,multiplicity:o,diaIDs:s}]})}}import{linearSumAssignment as Xo}from"linear-sum-assignment";import{xCostMatrix as Vo}from"ml-spectra-processing";function Or(e,t){let r=e.map(s=>s.delta),n=t.map(s=>s.delta),i=Vo(n,r,{fct:(s,a)=>Math.abs(s-a)}),{rowAssignments:o}=Xo(i,{maximaze:!1});return Array.from(o)}function Cr(e,t){let{assignments:r,ranges:n}=t;r?.sort((s,a)=>a.delta-s.delta);let i=[],o=[];for(let s of n){let a=0,{from:c,to:l}=s,m=[];for(let u=a;u<r.length;u++){let{delta:f}=r[u];f<=l&&f>=c?(m.push(r[u]),o.push(u)):f>l&&(a=u)}if(m.length>0){let u=s.signals,f=[],g=m.length>1&&u.length>1?Or(u,m):[0];for(let y=0;y<m.length;y++){let p=g[y],{delta:h,multiplicity:d,diaIDs:b}=m[y];p>-1?f.push({...u[p],diaIDs:b}):f.push({delta:h,multiplicity:d,diaIDs:b})}s.signals=f,i.push(s)}}Tr(r,o,i),i.sort((s,a)=>s.from-a.from),e.ranges={values:Q(i).map(s=>{let{integration:a,...c}=s;return c}),options:{sum:t.integrationSum,isSumConstant:!0,sumAuto:!0}},e.ranges.options.moleculeId=String(t.moleculeId)}function vr(e,t,r,n,i){let{logger:o}=i,s={components:Lr(e)?Zo(e,r.isFid):Ko(e)},{name:a=r.title||`jcamp_${wr()}`}=i,c={dependentVariables:[s],meta:t,info:{...r,name:Z(a)}};return Yo(e)&&Qo(c,n,t,e,r,{logger:o}),c}function Lr(e){return"minMax"in e}function Yo(e){return!Lr(e)}function Ko(e){return e.spectra.map(t=>{let r=U(t.data);return{...t,data:r}})}function Zo(e,t){let r={...e.minMax,z:U(e.minMax?.z)};return t?es(r):{rr:r}}function Qo(e,t,r,n,i,o){let{assignmentsByBlocks:s}=t,a=Pr(r);Ze(a)&&ts(e,a);let c=String(n.info.BLOCKID);if(s?.[c]){let{molecule:l,assignments:m,moleculeBlockID:u}=s[c],f=Nr(l,i),g=U(n.spectra[0].data);if(g.x[0]>g.x[1])for(let d of n.spectra)d.data.x.reverse(),d.data.y.reverse();if(Ze(a)&&n.spectra.length>1){let{re:d}=rs(n,a);g.y=d}let{x:y,y:p}=g,h=Mr(r,o)??Go({x:y,y:p},{peakPicking:{frequency:i.originFrequency},ranges:{frequency:i.originFrequency,integrationSum:f}});Cr(e,{moleculeId:u,ranges:h,assignments:m,integrationSum:f})}}function es(e){let{z:t,...r}=e,n=[],i=[];for(let a=0;a<t.length;a+=2)n.push(t[a].slice()),i.push(t[a+1].slice());let o=Rr(n),s=Rr(i);return{re:{...r,z:n,minZ:o.min,maxZ:o.max},im:{...r,z:i,minZ:s.min,maxZ:s.max}}}function ts(e,t){let{ph0:r,ph1:n}=t;e.filters||(e.filters=[]),e.filters.push({id:wr(),name:"phaseCorrection",value:{ph0:r,ph1:n,absolute:!1},enabled:!0})}function rs(e,t){let{ph0:r,ph1:n}=t,{re:i,im:o}=Ho({re:e.spectra[0].data.y,im:e.spectra[1].data.y},r*Math.PI/180,n*Math.PI/180);return{re:i,im:o}}function kr(e,t,r){let{logger:n}=r,i=[];for(let o of e)if(o.spectra&&o.spectra.length>0||o.minMax){ns(o);let s={...o.info,...o.meta},a=xe(s,{logger:n});if(a.experiment==="wobble_curve")continue;i.push(vr(o,s,a,t,r))}return i}function ns(e){let t=e.meta["BRUKER FILE EXP"];if(!t)return;let n=(Array.isArray(t)?t:[t]).find(o=>o.slice(0,10).includes("vdlist"));if(!n)return;let i=n.split(`
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10
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`).slice(1);e.info.vdlistValues=ye(i)}async function Ae(e,t={}){let r=await e.text(),n=_r(r,{name:e.name,...t});return ur(n,e,t)}function _r(e,t={}){let r={spectra:[],molecules:[]},{name:n,converter:i={},selector:o={},logger:s}=t,{keepRecordsRegExp:a=/.*/}=i,c={keepSpectra:!0,noContour:!0,noTrimRegExp:/\$MOLFILE/,keepRecordsRegExp:a,logger:s},l=dr(os(e),{name:n,...o,logger:s});for(let m of l)ss(m,r,c,n);if(as(r,o),r.spectra.length===0&&l.length>0){let m=r.molecules.length===0?" nor molecule":"";s?.warn(`No spectra${m} data was loaded from file ${n}`)}return is(r)}function ss(e,t,r,n){let i=[],o=[],s={molecules:[]},{logger:a}=r,c={name:n,logger:a};Ye(e,o,r),xr(o,s,i,c),t.spectra.push(...kr(i,s,c)),t.molecules.push(...s.molecules)}function as(e,t){t.index!==void 0&&(e.spectra=e.spectra.slice(t.index,t.index+1))}function ls(e,t={}){let{selector:r={},converter:n,logger:i}=t;return i?.debug(`Reading JCAMP-DX file: ${e.name}`),Ae(e,{selector:ms(r),converter:n?.jcamp,logger:i})}function 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n={spectra:[],molecules:[]},i=await Zs(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 Zs(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=Dn({sdf:c,fileCollection:e}).then(m=>{let{spectra:u,molecules:f=[]}=m;return n.push(c.root+c.filename),o.molecules.push(...f),Qs(u,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 Qs(e,t,r){let n=[],i=[],o={spectra:[],molecules:[]};for(let s of e){let a=ea(s.source,t,r).then(c=>{let{spectra:l,files:m}=c;n.push(...m);for(let u of l)En(u)?Pn(s.signals,u):Mn(s.signals,u);o.spectra.push(...l)});i.push(a)}return await Promise.allSettled(i),{...o,usedFiles:n}}async function ea(e,t,r={}){let{file:n,jcampURL:i}=e,{converter:o}=r;if(i){let c=await ta(i,t,o?.jcamp);if(c)return{...c,files:[]}}let s=[];for(let c of n||[])s.push(ra(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 ta(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 ra(e,t={}){let{converter:r,selector: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});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 na({id:"@zakodium/nmrium-core-plugins#NMReDATALoaderPlugin",version:1,shouldSerialize:!0,migrations:[],onReadProcess:{onFiles(t,r){return Tn(t,e,r)}}})}import{defineNMRiumPlugin as sa}from"@zakodium/nmrium-core";import{parse as ia}from"sdf-parser";function On(e,t={}){let{mixedEOL:r}=t,{molecules:n}=ia(e,{mixedEOL:r}),i=[];for(let[o,{molfile:s}]of n.entries()){let a=K(s).entries();for(let[c,l]of a)l.selector={sdfIndex:o,molfileIndex:c},i.push(l)}return i}async function Cn(e,t={}){let{logger:r,mixedEOL:n,selector:i}=t;if(i?.files&&!i.files.includes(e.relativePath))return{molecules:[],spectra:[]};let o=await e.text(),s=On(o,{mixedEOL:n,selector:i});for(let c of s)c.selector={...c.selector,files:[e.relativePath]};let a={molecules:oa(s,i),spectra:[]};return r&&r[s.length>0?"info":"debug"](`Loaded ${a.molecules.length} molecules from the ${e.name} file`),a}function oa(e,t){if(!t)return e;let{sdfIndex:r,molfileIndex:n}=t;return e.filter(i=>(typeof r=="number"?r===i.selector?.sdfIndex:!0)&&(typeof n=="number"?n===i.selector?.molfileIndex:!0))}function aa(e,t={}){let{logger:r,selector:n}=t;return r?.debug(`Reading sdf file: ${e.name}`),Cn(e,{logger:r,selector:n})}function pt(){return sa({id:"@zakodium/nmrium-core-plugins#SDFLoaderPlugin",version:1,shouldSerialize:!0,migrations:[],onReadProcess:{supportedExtensions:["sdf"],onFile:aa}})}import{defineNMRiumPlugin as la}from"@zakodium/nmrium-core";import{Molecule as ca}from"openchemlib";function Rn(e,t){let r=t?.smilesIndex,n=[],i=e.split(/\r?\n/).filter(Boolean);for(let[o,s]of i.entries()){if(typeof r=="number"&&r!==o)continue;let c=ca.fromSmiles(s).toMolfile();n.push({molfile:c,selector:{smilesIndex:o}})}return n}async function wn(e,t={}){let{logger:r,selector:n}=t;if(n?.files&&!n.files.includes(e.relativePath))return{molecules:[],spectra:[]};let i=await e.text(),o=Rn(i,n);for(let a of o)a.selector={...a.selector,files:[e.relativePath]};let s={molecules:o,spectra:[]};return r?.info(`Found ${o.length} molecules from the ${e.name} file`),s}function ft(){return la({id:"@zakodium/nmrium-core-plugins#SMILESLoaderPlugin",version:1,shouldSerialize:!0,migrations:[],onReadProcess:{supportedExtensions:["smi","smiles"],onFile:wn}})}import{defineNMRiumPlugin as ha}from"@zakodium/nmrium-core";import{formatSpectra as da}from"@zakodium/nmrium-core";import{createFromToArray as ua}from"ml-spectra-processing/utils";function vn(e){e.setLittleEndian();let t=e.offset,r=96;e.offset=r/8;let n=e.readInt32(),i=[2,4],o=[2**25,2**26];if(!i.includes(n))if(o.includes(n))e.setBigEndian();else throw new Error(`Unexpected value of eBytes (${n}). Expect one of
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19
19
|
${i.concat(o).join(",")}`);return e.offset=t,e.isBigEndian()?"BE":"LE"}var Pe=class{storesData;isSpectrum;isInt32;isFloat32;isComplex;isHypercomplex;isBaselineCorrected;constructor(t){if(this.storesData=(t&1)!==0,!this.storesData)throw new Error("No data stored in file. Exiting...");if(this.isSpectrum=(t&2)!==0,this.isSpectrum)throw new Error("Script only analyzes FIDs. Found spectrum.");if(this.isInt32=(t&4)!==0,this.isFloat32=(t&8)!==0,this.isComplex=(t&16)!==0,this.isHypercomplex=(t&32)!==0,this.isHypercomplex)throw new Error("Script does not analyze hypercomplex data (yet).");this.isBaselineCorrected=(t&64)!==0}},Ee=class extends Pe{moreBlocks;npComplex;nfComplex;niComplex;ni2Complex;constructor(t){super(t),this.moreBlocks=(t&128)!==0,this.npComplex=(t&256)!==0,this.nfComplex=(t&512)!==0,this.niComplex=(t&1024)!==0,this.ni2Complex=(t&2048)!==0}},Te=class extends Pe{isAcqPar;isSecondFT;isTransformed;is3D;isNp;isNf;isNi;isNi2;constructor(t){super(t),this.isAcqPar=(t&128)!==0,this.isSecondFT=(t&256)!==0,this.isTransformed=(t&512)!==0,this.is3D=(t&1024)!==0,this.isNp=(t&2048)!==0,this.isNf=(t&4096)!==0,this.isNi=(t&8192)!==0,this.isNi2=(t&16384)!==0}},Oe=class{lines;length;index;eol;constructor(t,r={}){let{eol:n=`
|
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20
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-
`,index:i=0}=r;this.eol=n,this.index=i,this.lines=t.split(this.eol),this.length=this.lines.length}readLine(){if(this.index>=this.length)throw new Error(`Last index is ${this.length-1}. 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=
|
|
20
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+
`,index:i=0}=r;this.eol=n,this.index=i,this.lines=t.split(this.eol),this.length=this.lines.length}readLine(){if(this.index>=this.length)throw new Error(`Last index is ${this.length-1}. 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=ma(t,r)}};function ma(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 Ln(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 kn(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);vn(i);let o=new ve(i);if(o.nBlocks!==1)throw new Error("We currently do not support 2D varian spectra ");let s=Ln(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=ua({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 ga}from"is-any-array";import{xMultiply as ya}from"ml-spectra-processing";import{normalizeNucleus as pa}from"nmr-processing";function _n(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:u,rp:f,sw:g,rfl:y,rfp:p}=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(u)),D(o,"phc0",f&&Number(f[0])),D(s,"rfl",y&&Number(q(y))),D(s,"rfp",p&&Number(q(p))),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}=fa(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(pa)),o.dimension=1,o.isFid=!r.status.isSpectrum,{info:o,meta:{...s,...qn(r),...i}}}function q(e){return e&&(Array.isArray(e)?e[0]:e)}function fa(e,t){let r={};for(let n of t){let i=e[n];i&&typeof i=="number"&&(r[n]=i)}return r}function qn(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]=qn(n):t[r]=n}return t}function jn(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 Bn(e,t={}){let{logger:r,selector:n}=t,i=jn(e);r&&r.debug(`Found ${Object.keys(i).length} varian experiments`);let o=[],s={spectra:[],molecules:[]};e:for(let c of i){let{name:l,files:m}=c;if(n?.files){let f=m;if(f.length===0)continue;let g=new Set(n.files);for(let y of f)if(!g.has(y.relativePath))continue e}let u=kn(m).then(f=>{let{info:g,meta:y}=_n(f),p=f.fid.data[0],h=ga(p.im),d={data:{...p,x:f.x},meta:y,info:{isComplex:h,name:l,...g},display:{name:l}};if(g.isFid&&h){let{im:b}=d.data;ya(b,-1,{output:b})}d.selector={files:m.map(b=>b.relativePath)},s.spectra.push(d)});o.push(u)}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;r?.warn(`Varian data: ${m}, fails with: ${l.reason}`)}}return s.spectra.length>0&&r?.info(`Loaded ${s.spectra.length} spectra from Varian files`),da(s)}function ba(e,t){let{logger:r}=t??{};return Bn(e,{logger:r})}function yt(){return ha({id:"@zakodium/nmrium-core-plugins#VarianLoaderPlugin",version:1,shouldSerialize:!0,migrations:[],onReadProcess:{onFiles:ba}})}function xa(e,t=[]){return[ut(e),yt(),Ge(),Qe(),at(),pt(),ft(),st(),$e()].concat(t)}function Da(e=[]){let t=new Fa;return t.registerPlugins(xa(t,e)),t}import{getOneIfArray as $n}from"@zakodium/nmrium-core";import{from1DNMRVariables as Sa}from"convert-to-jcamp";function Un(e,t){return e.filters.find(r=>r.name===t)}function Aa(e,t={}){let{onlyReal:r=!1}=t,{info:n,meta:i,data:o}=e,{owner:s,title:a,isFid:c,spectralWidth:l,baseFrequency:m,originFrequency:u,nucleus:f,solvent:g,scaleFactor:y,frequencyOffset:p,decim:h,dspfvs:d,digitalFilter:b}=n,F=$n(m||u),{x:S,re:I,im:x}=o,A=new Float64Array(I),M=!r&&x?new Float64Array(x):void 0,T=Un(e,"fft")?.enabled,j={owner:s,isFid:c,title:a,nucleus:f,solvent:g,scaleFactor:y,spectralWidth:l,frequencyOffset:p,originFrequency:u,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=Ia(i,zn),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"}),Sa(oe,Le)}function ht(e,t,r){r!==void 0&&(e[t]=$n(r))}var zn=["title","decim","dspfvs","grpdly","bf1","sw","offset",".solvent","owner","firsty","page","vardim","symbol","symbols","varform","vartype","datatype","dataclass",".observefrequency",".observenucleus","ncproc"];function Ia(e,t=zn){let r=new Set(t);return Object.fromEntries(Object.entries(e).filter(([n])=>!r.has(n.toLocaleLowerCase().replaceAll(/[\s|_]*/g,""))))}export{$e as autoPostProcessing,Ge as brukerLoader,Da as default,Da as init,Qe as jcampDXLoader,st as jeolLoader,at as molfileLoader,ut as nmreDATALoader,_r as processJCAMPDX,On as readSDF,Rn as readSMILES,xa as recommended,pt as sdfLoader,ft as smilesLoader,Aa as spectrum1DToJCAMPDX,yt as varianLoader};
|
package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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{
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"name": "@zakodium/nmrium-core-plugins",
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"version": "0.6.
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+
"version": "0.6.29",
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"description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
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"author": "Zakodium Sàrl",
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"license": "CC-BY-NC-SA-4.0",
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@@ -47,7 +47,7 @@
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},
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"dependencies": {
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"@date-fns/utc": "^2.1.1",
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"@zakodium/nmrium-core": "^0.
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+
"@zakodium/nmrium-core": "^0.6.0",
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"cheminfo-types": "^1.8.1",
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"convert-to-jcamp": "^6.0.0",
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"date-fns": "^4.1.0",
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@@ -66,5 +66,5 @@
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"volta": {
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"extends": "../../../package.json"
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},
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69
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"gitHead": "
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69
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+
"gitHead": "3279db28ba465d2b3d4893c3c582b218569aee8d"
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