@zakodium/nmrium-core-plugins 0.1.5 → 0.1.7
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 +17 -9
- package/package.json +2 -2
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var Er=Object.defineProperty;var Ft=(e,t)=>{for(var n in t)Er(e,n,{get:t[n],enumerable:!0})};import{NMRiumCore as ns}from"@zakodium/nmrium-core";import{Filters1D as qr,Filters2D as _r}from"nmr-processing";import{getOneIfArray as Tr}from"@zakodium/nmrium-core";function te(e={},t={},n={}){e===null&&(e={}),typeof e=="string"&&(e={pulseSequence:e});let i=Array.isArray(e.pulseSequence)?e.pulseSequence[0]:e.pulseSequence||"";if(typeof i!="string")return e.dimension?`${e.dimension}d`:"";if(i=i.toLowerCase(),i.includes("zg")||i.includes("single_pulse_dec")||i.includes("udeft"))return"1d";if(i.includes("hsqct")||i.includes("invi")&&(i.includes("ml")||i.includes("di")))return"hsqctocsy";if(i.includes("hsqc")||i.includes("invi"))return"hsqc";if(i.includes("hmbc")||i.includes("inv4")&&i.includes("lp"))return"hmbc";if(i.includes("hmqc"))return"hmqc";if(i.includes("cosy"))return"cosy";if(i.includes("jres"))return"jres";if(i.includes("dosy"))return"dosy";if(i.includes("tocsy")||i.includes("mlev")||i.includes("dipsi"))return"tocsy";if(i.includes("noesy"))return"noesy";if(i.includes("roesy"))return"roesy";if(i.includes("dept"))return"dept";if(i.includes("jmod")||i.includes("apt"))return"aptjmod";if(i.includes("inad"))return"inadequate";if(i.includes("adeq"))return"adequate";let{prefix:r=""}=n,o=(Tr(t[`${r}SPECTYP`])||"").replace(/^<(.*)>$/,"$1").toLowerCase();return o.length>0&&o!=="undefined"?o:e.dimension?`${e.dimension}d`:""}import{getOneIfArray as xt}from"@zakodium/nmrium-core";var Or=["no","exponential","modifiedGaussian","sine","qsine","trap","user","sinc","qsinc","traf","trafs"];function Cr(e){return e in Dt}function _e(e,t){let{prefix:n="",index:i=0}=t,r=xt(e[`${n}WDW`],i),o=Or[r?Number(r):0],s={};if(!Cr(o))return s;let a=Dt[o];if(a){let{kind:l,parameters:c}=a,u={};for(let p in c){let g=c[p],{source:d,processor:h}=g;if(d){let f=xt(e[`${n}${d}`],i);if(!f)continue;let b=Number(f);u[p]=h?h(b):b}else g.value!==void 0&&(u[p]=g.value)}s[l]={apply:!0,options:u}}return s}var Dt={exponential:{kind:"exponential",parameters:{lineBroadening:{source:"LB"}}},modifiedGaussian:{kind:"gaussian",parameters:{lineBroadening:{source:"LB"},lineBroadeningCenter:{source:"GB"}}},sine:{kind:"sineBell",parameters:{offset:{source:"SSB",processor:e=>1/e},exponent:{value:1}}},qsine:{kind:"sineSquare",parameters:{offset:{source:"SSB",processor:e=>1/e}}},traf:{kind:"traf",parameters:{lineBroadening:{source:"LB"}}}};var St={sineBell:Nt({offset:0})},Pt={cosy:{...St},hmbc:{...St},hsqc:{sineBell:Nt({offset:.5})}},wr={...Pt};function Be(e="",t=1){let n=vr(e),i={},r=t===1?Pt[n||""]:wr[n||""];return r&&(i=structuredClone(r)),i}function Nt(e){return{apply:!0,options:e}}function vr(e){let n=e.toLowerCase().match(/cosy|hsqc|hmbc/);return n?n[0]:null}function At(e,t={}){let{prefix:n="",experiment:i=te(e)}=t;return e[`${n}WDW`]?{f2:_e(e,{...t,index:0}),f1:_e(e,{...t,index:1})}:{f2:Be(i,1),f1:Be(i,2)}}import{Filters1D as kr}from"nmr-processing";var Ue=["digitalFilter","backwardLinearPrediction","forwardLinearPrediction","apodization","zeroFilling","fft",["shiftX","phaseCorrection","baselineCorrection"]],$={};for(let e=0;e<Ue.length;e++){let t=Ue[e];for(let n of Array.isArray(t)?t:[t])$[n]=e}for(let e of Object.values(kr))e.name in $||($[e.name]=Ue.length);import{Filters2D as Lr}from"nmr-processing";var $e=["digitalFilter2D","blpDimension1","flpDimension1","apodizationDimension1","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","nusDimension2","apodizationDimension2","zeroFillingDimension2","fftDimension2","phaseCorrectionTwoDimensions",["shift2DX","shift2DY","symmetrizeCosyLike"]],j={};for(let e=0;e<$e.length;e++){let t=$e[e];for(let n of Array.isArray(t)?t:[t])j[n]=e}for(let e of Object.values(Lr))e.name in j||(j[e.name]=$e.length);var Br=new Set(["backwardLinearPrediction","forwardLinearPrediction","digitalFilter2D","phaseCorrectionTwoDimensions","blpDimension1","flpDimension1","apodizationDimension1","apodizationDimension2","zeroFillingDimension1","fftDimension1","blpDimension2","flpDimension2","zeroFillingDimension2","fftDimension2","nusDimension2","symmetrizeCosyLike"]);function Ur(e,t){let{filter:n,experimentalFeatures:i=!1}=t,{name:r}=n;({...qr,..._r})[r]&&(e.some(s=>s.name===r)||(i||!Br.has(r))&&e.push({...n,enabled:!0}))}function Mt(e,t={}){let{data:n}=e;if(!n)return;let{autoProcessing:i,experimentalFeatures:r}=t,o=(a,l)=>Ur(a,{...l,experimentalFeatures:r}),{spectra:s}=n;for(let a of s){let{data:l,info:c,meta:u,filters:p}=a,{dimension:g,isFid:d}=c;if(d){if(g===1){let 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D=At(u,{experiment:m});o(p,{filter:{name:"apodizationDimension1",value:D.f2}}),o(p,{filter:{name:"zeroFillingDimension1",value:{nbPoints:y[0]}}}),o(p,{filter:{name:"fftDimension1",value:{}}}),u&&"nuslist"in u&&o(p,{filter:{name:"nusDimension2",value:{}}}),o(p,{filter:{name:"apodizationDimension2",value:D.f1}}),o(p,{filter:{name:"zeroFillingDimension2",value:{nbPoints:y[F?0:1]}}}),F?o(p,{filter:{name:"symmetrizeCosyLike",value:{}}}):o(p,{filter:{name:"phaseCorrectionTwoDimensions",value:{}}}),o(p,{filter:{name:"fftDimension2",value:{}}}),p.sort((N,x)=>j[N.name]-j[x.name])}}}}function $r(e){let{phc0:t=0,phc1:n=0}=e;return It([t,n])?{}:{ph0:t,ph1:n}}function It(e){return Array.isArray(e)?e.every(t=>!t&&t===0):It([e])}var ne=class{id="@zakodium/nmrium-core-plugins#AutoPostProcessingPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onProcessing:this.onPostProcessing.bind(this)}}onPostProcessing(t,n){Mt(t,n)}};function je(){return new ne}import{FileCollection as 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n.info["2D_Y_NUCLEUS"]=h[1],n.info["2D_X_NUCLEUS"]=h[0],n.info["2D_Y_FRECUENCY"]=g[1],n.info["2D_X_FRECUENCY"]=g[0],n.info["2D_Y_OFFSET"]=u,n.info["2D_X_OFFSET"]=c,n.info.twoD=!0,n.twoD=!0,n}async function Ye(e,t={}){let n,i=!1,r=!1;if(["ser","2rr","2ri","2ir","2ii"].some(s=>s in e))i=!0,n=await $t(e,t);else if(e["1r"]||e["1i"]||e.fid)r=!0,n=await Ut(e,t);else throw new RangeError("The current files are invalid");let o={name:e.name,expno:e.expno,isFID:!!e.isFID};for(let s in e){let a=s;(typeof e[a]).match(/number|string|boolean/)&&(o[a]=e[a])}n.source=i?{...o,is2D:i}:{...o,is1D:r},t.keepFiles&&(n.source.files=e.fileCollectionItems),n.meta.DATE=Number(n.meta.DATE),n.meta.GRPDLY&&(Ge(n.meta,"DSPFVS",n.meta.DSPFVS),Ge(n.meta,"GRPDLY",n.meta.GRPDLY),Ge(n.meta,"DECIM",n.meta.DECIM));for(let s in n.meta)Array.isArray(n.meta[s])&&(n.meta[s].length===1||typeof n.meta[s][0]=="string"&&n.meta[s][0].includes("(0.."))&&(n.meta[s]=n.meta[s][0]);return n}function Ge(e,t,n){n!==void 0&&(Array.isArray(n)?e[t]=n.slice():e[t]=[n])}var q={};Nt(q,{ECHO_ANTIECHO:()=>qi,QF:()=>Ci,QSEC:()=>wi,STATES:()=>ki,STATES_TPPI:()=>Li,TTPI:()=>vi});var Ci=1,wi=2,vi=3,ki=4,Li=5,qi=6;import{formatSpectra as Gi}from"@zakodium/nmrium-core";function me(e){let t=[];for(let n of e){if(!n)continue;let{groups:{value:i,unit:r}={}}=n.trim().match(/[$$]*\s*(?<value>[\d.]+)\s*(?<unit>[a-zA-Z]+)/)||{};t.push(_i(i,r))}return t}function _i(e,t){switch(t.toLowerCase()){case"s":return Number.parseFloat(e);case"ms":return Number.parseFloat(e)/1e3;case"m":case"min":return Number.parseFloat(e)*60;default:return Number.NaN}}import{isAnyArray as Jt}from"is-any-array";function _(e){if(ji(e))return Bi(e)?e.map(zt):zt(e);if(typeof e=="object"&&e!==null){let t={};for(let n in e)t[n]=_(e[n]);return t}return e}function ji(e){return Jt(e)}function zt(e){return Float64Array.from(e)}function Bi(e){return Jt(e[0])}import{getOneIfArray as K}from"@zakodium/nmrium-core";import{getGyromagneticRatio as Ji}from"gyromagnetic-ratio";import{isAnyArray as Yt}from"is-any-array";import{getFrequency as Wi}from"nmr-processing";import{isAnyArray as W}from"is-any-array";function ue(e){return typeof e=="number"}function pe(e){let{phc0:t,phc1:n}=e;return!W(t)&&!ue(t)||!W(n)&&!ue(n)||W(t)&&!ue(t[0])||W(n)&&!ue(n[0])?{}:(W(n)?n[0]*=-1:n*=-1,W(t)?t[0]*=-1:t*=-1,{phc0:t,phc1:n})}function Vt(e,t,n){if(e>0)return Number(e);if(t>14||t===0)return 0;if(Wt[t]){let i=Wt[t];if(!i[n])throw new Error(`decim ${n} not in lookup table for dspfvs ${t}`);return i[n]}else throw new Error(`dspfvs ${t} not in lookup table`)}var Wt={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}};var Ui=new Map([[String(J.QSIM),"notPhaseSensitive"],["notphasesensitive","notPhaseSensitive"],[String(J.QSEQ),"QSEQ"],["qseq","QSEQ"],[String(q.TTPI),"TPPI"],["tppi","TPPI"],[String(q.STATES),"States"],["states","States"],[String(q.STATES_TPPI),"States-TPPI"],["tppi-states","States-TPPI"],[String(q.ECHO_ANTIECHO),"Echo-antiecho"],["echo-antiecho","Echo-antiecho"]]);function Xt(e){let t=String(e).toLowerCase().replaceAll(" ","");return Ui.get(t)}import{normalizeNucleus as $i}from"nmr-processing";function j(e,t=","){if(e&&typeof e=="string")return e.split(t)}function fe(e,t,n){let i=[];if(e[`${n}AXNUC`]&&(i=e[`${n}AXNUC`],Array.isArray(i)||(i=[i]),i=w(i)),i.length===0&&e[`${n}NUC1`]&&(i=e[`${n}NUC1`],Array.isArray(i)||(i=[i]),i=w(i)),i.length===0&&e[".NUCLEUS"]){let r=j(e[".NUCLEUS"]);if(e[`${n}SYMBOL`]){let o=e[`${n}SYMBOL`].split(","),s=o.findIndex(l=>l.includes("2")),a=o.findIndex(l=>l.includes("1"));s!==-1&&a!==-1&&r?i=w([r[s],r[a]]):i=w(r).reverse()}else i=w(r)}return i.length===0&&e[".OBSERVENUCLEUS"]&&(i=w([e[".OBSERVENUCLEUS"]])),i.length===0&&t.experiment&&(i=w(Ht(t.experiment[0]))),zi(e)&&(i=[e["2D_X_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,""),e["2D_Y_NUCLEUS"].replaceAll(/[^A-Za-z0-9]/g,"")]),t.experiment&&(t.experiment[0].match("jres")||t.experiment[0].match("dosy"))&&(i=Ht(t.experiment[0])),i.map($i)}function zi(e){return e["2D_X_NUCLEUS"]&&!e["2D_X_NUCLEUS"].includes("off")&&e["2D_Y_NUCLEUS"]&&!e["2D_Y_NUCLEUS"].includes("off")}function Ht(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 w(e){if(!e)return[];let t=e.map(i=>String(i).replaceAll(/[^A-Za-z0-9]/g,"").replace("NA","").replace("off","")),n=0;for(let i of t)i||n++;return n===0?t:[]}function S(e,t,n,i=!1){n===void 0||t in e&&!i||(Array.isArray(n)?e[t]=n.map(Gt):e[t]=[Gt(n)])}function Gt(e){return typeof e=="string"&&(e.startsWith("<")&&e.endsWith(">")&&(e=e.slice(1,-1)),e=e.replace(/\$.*/,"").trim()),e}function ge(e,t={}){let{prefix:n="",logger:i}=t,r={dimension:0,nucleus:[],isFid:!1,isFt:!1},o=JSON.stringify(e),s=/\r\n/.exec(o)?`\r
|
|
4
4
|
`:`
|
|
5
|
-
`,{JCAMPDX:a="",ORIGIN:l=""}=e,c=String(a).toLowerCase()+String(l).toLowerCase();"SPECTROMETER/DATASYSTEM"in e&&(c=e["SPECTROMETER/DATASYSTEM"]);let u=(m=[])=>{for(let y of m)if(!(y in r))return!1;return!0};(c.includes("mestre")||c.includes("nova"))&&(c="mnova"),r.creator=c,e.LONGDATE&&
|
|
6
|
-
`}=n;S(e,"spectralWidth",t[`${i}SweepWidth`]/e.originFrequency[0]);let o=t[`${i}.PULSESEQUENCE`].split(r),s=[];t[".OBSERVENUCLEUS"]&&s.push(t[".OBSERVENUCLEUS"]),t.INDIRECTNUCLEUS&&s.push(t.INDIRECTNUCLEUS),e.nucleus=w(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 l=JSON.stringify(a).match(/\$\$SW1=\s*(?<sw>[+-]?(?:[0-9]*[.])?[0-9]+)/);if(l?.groups){let{originFrequency:c}=e,u=Number.parseFloat(l.groups.sw);e.spectralWidth.push(u/c[1])}}return e}function
|
|
7
|
-
because it didn't match the import filters`);continue}s.push(u)}let a=[],l=s.some(Yt),c=s.some(Ht);for(let u of s){if(o!=="both"&&u.dataType!=="LINK"){if(Yt(u)&&(o==="ft"||o==="preferFT"&&c)){i?.warn(`Skipping raw data ${n?`in ${n}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(Ht(u)&&(o==="fid"||o==="preferFID"&&l)){i?.warn(`Skipping FFT data ${n?`in ${n}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}}a.push(u)}return a}function Ht(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function Yt(e){return e.dataType?.toUpperCase().includes("FID")}function Zt(e,t={}){let{logger:n,name:i=""}=t;for(let r of e){if(r.dataType==="LINK"&&Zt(r.children,t))return!0;let{dataType:o=""}=r,s=o.toLowerCase();if(s.length>0){if(s.includes("spectrum")&&!s.includes("nmr"))return n?.warn(`File ${i} was ignored because it is a 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Qt(e,t,n={}){let{spectra:i,info:r,meta:o}=e,s=i[0].data,a=[],l={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:c,name:u,spectraData:p}=n,{CROSSREFERENCE:g}=r,d=typeof g!="string"?g:g.split(/\r?\n/).map(x=>x.trim()).filter(Boolean),h=d.find(x=>x?.toLowerCase().includes("structure"));if(h===void 0)return c&&c.warn(`There is not a structure reference for ${u} file, assignment object could not be completed`),null;let f=Number.parseInt(h?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(f)||f<1)return c&&c.warn(`Structure block_id not found for ${u} file, assignment object could not be completed`),null;let m=p?.molecules?.find(x=>x.blockId===f)?.molfile??"";if(m===""){let x=t.find(A=>A.info.BLOCKID===f),{MOLFILE:P=""}=x?.meta||{};m=P}if(!_i(m))return c&&c.warn(`Empty molfile for ${u} file with structure block_id = ${f}, assignment object could not be completed`),null;let y=Ui(Bi,m),F=fe({...r,...o},{},"");for(let x=0;x<s.x.length;x++){let P={};for(let A in s){let I=s[A][x];typeof I=="string"&&I.startsWith("<")&&I.endsWith(">")&&(I=I.slice(1,-1)),P[l[A]]=I}if("atom"in P){let A=y.map[P.atom-1];F.includes("1H")?A.nbHydrogens>0?(P.diaIDs=A.hydrogenOCLIDs,P.nbHydrogens=A.nbHydrogens):(P.diaIDs=[A.oclID],P.nbHydrogens=A.nbHydrogens):(P.diaIDs=[A.oclID],P.nbHydrogens=1)}a.push(P)}let D={};for(let x of a){let{delta:P,diaIDs:A}=x,I=`${P}_${A.join("_")}`;if(D[I])D[I].atoms.push(x.atom);else{let{atom:gt,...Le}=x;D[I]={...Le,atoms:[x.atom]}}}let N=[];for(let x of d)x.toLowerCase().includes("spectrum")&&N.push(Number(x.toLowerCase().replace(/_/,"").replace(/.*:\s*blockid=(?<blockId>.*)/,"$<blockId>")));if(N.length===0){for(let x of t)if(be(x)){let{BLOCKID:P}=x.info;N.push(Number(P))}N.length>1&&(N=[],c&&c.warn(`There is not a spectral cross-reference for the peak assignment in the ${u} file`))}return{moleculeBlockID:f,spectraBlockIDs:N,assignments:Object.values(D),molecule:y.molecule}}function tn(e,t,n,i){for(let r of e){let{meta:o,dataClass:s="",dataType:a="",info:l}=r,c=Number.parseInt(String(l.BLOCKID),10);o.MOLFILE?Xi(String(o.MOLFILE),t,c):r.jcampCS&&Ji(r,t,c),zi(s,a)&&Wi(t,r,e,i),be(r)&&n.push(r)}}function zi(e,t){return e?.toLowerCase().includes("assignments")&&t?.toLowerCase().includes("assignments")}function Wi(e,t,n,i){let r=Qt(t,n,{spectraData:e,logger:i.logger,name:i.name});if(e.assignmentsByBlocks||(e.assignmentsByBlocks={}),r){let{spectraBlockIDs:o}=r;for(let s of o)e.assignmentsByBlocks[s]=r}}function Ji(e,t,n){t.molecules||(t.molecules=[]);let i=$i(e,{OCL:ji}),r=X(i?.molfile||"");r.length>0&&t.molecules.push({id:en(),blockId:n,...r[0]})}function Xi(e,t,n){t.molecules||(t.molecules=[]);let i=X(String(e));t.molecules.push({id:en(),blockId:n,...i[0]})}import{generateID as gn}from"@zakodium/nmrium-core";import{matrixMinMaxZ as dn,reimPhaseCorrection as ro}from"ml-spectra-processing";import{xyAutoRangesPicking as io}from"nmr-processing";function V(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function H(e){e.sort((t,n)=>t.from-n.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 Zi}from"nmr-processing";import{xMaxValue as Vi}from"ml-spectra-processing";function K(e){return e.trim().slice(1,-1).split(/,\s*/).map(t=>t.trim())}var Hi={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},nn=["I","X","Y","Hs","An","H","C","N","(J)"];function rn(e){let t={headersFromParenthesis:[],headersFromComments:[],comments:[],data:[],multiplets:[]},n=e.split(/\r?\n/).filter(i=>i.trim()!=="");if(n.length===0)return t;if(n[0].startsWith("(")&&!n[0].match(/\d/)){let i=n.shift();t.headersFromParenthesis=K(i)}return t.comments=n.filter(i=>i.startsWith("$$")).map(i=>i.replace(/^\$\$\s*/,"")),t.headersFromComments=Gi(t.comments),t.data=n.filter(i=>!i.startsWith("$$")).map(K),t.multiplets=Yi(t),t}function Yi(e,t={}){let{logger:n}=t,i=e.data[0].map((l,c)=>c).filter(l=>e.data.every(c=>Number.isNaN(c[l])||Number.isNaN(Number(c[l]))));if(n?.trace(`Parsing JCAMP-DX assignment: stringColumnIndexes: ${i.join(",")}`),i.length===0)return n?.warn("Parsing JCAMP-DX assignment: No string columns found. 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Skipping parsing of assignment."),[];return Vi(e.data.map(l=>l.length))>o.length&&n?.warn("Some assignments are containing more values than headers"),e.data.map(l=>{let c={};for(let u=0;u<o.length;u++){let p=o[u];c[Hi[p]||p]=l[u]}return c})}function Gi(e){return e.map(t=>t.split(":")[0].trim()).filter(t=>t.length>0)}function on(e,t={}){let{logger:n}=t,i=rn(e),r={multiplets:[],comments:i.comments};for(let o of i.multiplets){let{id:s,from:a,to:l,delta:c,integration:u,nbAtoms:p,multiplicity:g}=o,d={id:s,js:[],multiplicity:"",...Ki({from:a,to:l,delta:c,integration:u,nbAtoms:p})};if(typeof o.js=="string"){let h=o.js.split(/\s+/).map(Number.parseFloat),f=0,b=Zi(g).map(F=>{let D=(F?.multiplicity||1)-1;return f+=D,{value:F.value,multiplicity:F?.multiplicity,js:h.slice(f-D,f)}}),m=b.reduce((F,D)=>F+(D.multiplicity?D.multiplicity-1:0),0);h.length!==m&&n?.warn(`The number of j values (${h.length}) is not equal to the sum of the multiplicities - 1 (${m})`);let y=[];for(let F of b){if(F.js.every(D=>D===F.js[0])){y.push(F);continue}if(F.multiplicity!==F.js.length+1){y.push(F);continue}for(let D=0;D<F.multiplicity-1;D++)y.push({value:"d",multiplicity:2,js:[F.js[D]]})}y.sort((F,D)=>D.js[0]-F.js[0]),d.js=y.map(F=>({coupling:F.js[0],multiplicity:F.value}))}typeof o.assignment=="string"&&(d.assignment=eo(o.assignment)),typeof o.multiplicity=="string"&&(d.multiplicity=o.multiplicity),r.multiplets.push(d)}return r}function Ki(e){let t={};for(let n in e){let i=e[n],r=typeof i=="number"?i:Number.parseFloat(i);Number.isNaN(r)||(t[n]=r)}return t}var Qi={quot:'"',apos:"'",comma:",",amp:"&",lpar:"(",rpar:")",lt:"<",gt:">",colon:":",semi:";"};function eo(e){return e.replaceAll(/&(\w+);/gi,(t,n)=>Qi[n.toLowerCase()]||t)}function sn(e){let t=e.split(/\r?\n/).filter(i=>i.trim()!==""),n=[];for(let i of t)if(i.startsWith("(")){let[r,o,s]=K(i).map(Number.parseFloat);n.push({id:r,x:o,y:s})}return n}function an(e,t={}){let n={};if(!e["OBSERVED MULTIPLETS"])return[];let 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D=K(e[`${n}DATE`]),P=Number.parseInt(D,10)*1e3;Number.isNaN(P)?Ke(r,Date.parse(D)):Ke(r,P)}r.solvent||S(r,"solvent",K(e[`${n}SOLVENT`]))}!("baseFrequency"in r)&&"originFrequency"in r&&S(r,"baseFrequency",r.originFrequency);let g=r.dimension<2,h="dataClass"in r&&r.dataClass[0].toUpperCase()==="NTUPLES",p=["LAST","FIRST","VARDIM","SYMBOL"].every(m=>`${n}${m}`in e);if(g&&(h||p)&&(S(r,"last",j(e[`${n}LAST`])),S(r,"first",j(e[`${n}FIRST`])),S(r,"varDim",j(e[`${n}VARDIM`])),S(r,"symbols",j(e[`${n}SYMBOL`])),r.symbols&&Array.isArray(r.symbols))){r.symbols.includes("R")&&r.symbols.includes("I")&&(r.isComplex=!0);let m=r.symbols.findIndex(y=>y.toLowerCase()==="x");if(E(r,"firstX",r.first[m]),E(r,"lastX",r.last[m]),E(r,"numberOfPoints",r.varDim[m]),!("spectralWidth"in r)){let{lastX:y,numberOfPoints:F,firstX:x}=r;S(r,"spectralWidth",r.isFid?F/(2*y):Math.abs(y-x)/r.originFrequency)}}if(`${n}REVERSE`in e){let m=e[`${n}REVERSE`];r.reverse=(Array.isArray(m)?m:[m]).map(y=>typeof y=="string"?y.includes("yes"):y)}let b=e[`${n}REFERENCE_POINT`];if(!("frequencyOffset"in r)&&b&&u(["spectralWidth","baseFrequency"])){let m=typeof b=="number"?b:e[`${n}REFERENCE_POINT`].match(/(?<reference>[+-]?\d+(?:\.\d+)?)\s*.*/),y;if(typeof b=="number"?y=b:(b.match(/(?<reference>[+-]?\d+(?:\.\d+)?)\s*.*/),y=Number(m?.groups?.reference)),!Number.isNaN(y)){let{spectralWidth:F,baseFrequency:x}=r;S(r,"frequencyOffset",.5*F*x-y)}}if(!("frequencyOffset"in r)&&u(["baseFrequency","originFrequency"])){let{baseFrequency:m,originFrequency:y}=r,F=m.map((x,N)=>(y[N]-x)*1e6);S(r,"frequencyOffset",F)}for(let m in r)r[m]&&r[m].length===1&&(r[m]=r[m][0]);return!r.frequencyOffset&&".SHIFTREFERENCE"in e&&Vi(e,r),Array.isArray(r.nucleus)||(r.nucleus=[r.nucleus]),r}function E(e,t,n){n!==void 0&&S(e,t,de(n))}function Ke(e,t){if(!Number.isNaN(t)){e.epoch=t;let n=new Date(t);e.date=n.toUTCString(),e.localeDate=n.toLocaleString()}}function Vi(e,t){let n=e[".SHIFTREFERENCE"],i=n.trim().startsWith("(")?/\((?<data>[^)]+)\)/:/(?<data>[^)]+)/,r=n.match(i);if(r.groups.data){let o=r.groups.data.split(",");if(o.length<4)return;let s=Number.parseInt(t.numberOfPoints,10),{spectralWidth:a,baseFrequency:l}=t,c=Number.parseInt(o[2],10),u=Number.parseFloat(o[3]),f;if(t.isFid){if(["baseFrequency","numberOfPoints","spectralWidth"].some(d=>!(d in t)))return;f=u+(s*.5-c)*a/s}else{let d=Number.parseFloat(t.firstX),g=Number.parseFloat(t.lastX),h=(g+d)/2,p=(g-d)/(s+1),b=p<0?d:g+(c-1)*p;f=(h-b)/l+u}f!==void 0&&!Number.isNaN(f)&&(t.frequencyOffset=f*l)}}function de(e){if(Yt(e)){let t=[];for(let n of e)t.push(typeof n=="string"?Number.parseFloat(n):n);return t}return typeof e=="string"?Number.parseFloat(e):e}function Xi(e,t,n={}){let{prefix:i="",separator:r=`
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`}=n;S(e,"spectralWidth",t[`${i}SweepWidth`]/e.originFrequency[0]);let o=t[`${i}.PULSESEQUENCE`].split(r),s=[];t[".OBSERVENUCLEUS"]&&s.push(t[".OBSERVENUCLEUS"]),t.INDIRECTNUCLEUS&&s.push(t.INDIRECTNUCLEUS),e.nucleus=w(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 l=JSON.stringify(a).match(/\$\$SW1=\s*(?<sw>[+-]?(?:[0-9]*[.])?[0-9]+)/);if(l?.groups){let{originFrequency:c}=e,u=Number.parseFloat(l.groups.sw);e.spectralWidth.push(u/c[1])}}return e}function Hi(e,t){let{T1NUCLEUS:n,T2NUCLEUS:i,PAGE:r}=t;e.pulseSequence=t.EXPERIMENT||t[".PULSESEQUENCE"];let o=[],{dimension:s,isComplex:a}=e;if(s===2&&e.pulseSequence==="T1"){let u=a?2:1;for(let f=0;f<r.length;f+=u){let d=r[f].replace(/T1=/,"");o.push(Number(d))}t.vdlistValues=o}e.nucleus=s>1?[i,n]:i;let{phc0:l,phc1:c}=e;if(l&&c){let u=pe({phc0:l,phc1:c});e={...e,...u}}}var Yi={keepRecordsRegExp:/.*/,keepFiles:!0};async function ye(e,t={}){let n={spectra:[],molecules:[]},{converter:i={},selector:r={},logger:o}=t,s=We(e,{logger:o,...Zi(r)}),a=[];for(let c of s)a.push(Ye(c,{...Yi,...i}).then(u=>Ki(u,t)));let l=await Promise.allSettled(a);for(let c=0;c<l.length;c++){let u=l[c];if(u.status==="fulfilled"){let f=pe(u.value.info);n.spectra.push({...u.value,info:{...u.value.info,...f}})}else if(u.reason){let f=s[c].name;o?.warn(`Bruker data: ${f}, fails with: ${u.reason}`);continue}}return o&&o[n.spectra.length>0?"info":"debug"](`Loaded ${n.spectra.length} spectra from Bruker files`),Gi(n)}function Ki(e,t={}){let{keepSource:n=!1,logger:i}=t,r={...e.info,...e.meta},o=ge(r,{logger:i}),s={},{isFid:a}=o;if(Qi(e)){let g=e.minMax;for(let h in g){let p=g[h];p&&(p.z=_(p.z))}s.components=e.minMax}else o.dimension===1&&(s.components=e.spectra);let{source:l}=e,{expno:c,name:u,files:f}=l;r.vdlist&&(r.vdlistValues=me(r.vdlist));let d={dependentVariables:[s],meta:r,info:{...o,experimentNumber:c,name:u}};return f&&n&&(d.sourceSelector={files:f.map(g=>g.relativePath)}),eo(d,e),d}function Zi(e){let{general:t={},bruker:n={}}=e,{processingNumbers:i,experimentNumbers:r,...o}=n;return{...t,...o,processingNumbers:Kt(i),experimentNumbers:Kt(r)}}function Kt(e){if(e)return e.split(/[^\d]+/).filter(Boolean).map(t=>Number.parseInt(t,10))}function Qi(e){let{info:t}=e;return t.twoD}function eo(e,t){if(!("integrals"in t))return;let{integrals:n=[]}=t;e.integrals={values:n.map(i=>{let{from:r,to:o,integration:s}=i;return{from:r,to:o,integral:s,kind:"signal"}})}}var he=class{id="@zakodium/nmrium-core-plugins#BrukerLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(t,n)=>{let{sourceSelector:i,converter:r,keepSource:o,logger:s}=n??{};return ye(t,{converter:r?.bruker,selector:i,keepSource:o,logger:s})}};function Ze(){return new he}import{formatSpectra as ko}from"@zakodium/nmrium-core";import{createTree as Lo}from"jcampconverter";function Zt(e,t,n={}){let{selector:i={},keepSource:r=!1}=n;if(!r)return e;for(let o=0;o<e.spectra.length;o++){let s=e.spectra[o];s.sourceSelector={files:[t.relativePath],jcamp:{index:o,...i}}}return e}import{convert as to}from"jcampconverter";function Qe(e,t,n){let{dataType:i,children:r}=e,o=i==="LINK"&&r?r:[e];for(let s of o){if(s.dataType==="LINK"){Qe(s,t,n);continue}let a=to(s.jcamp,n);t.push(...a.flatten)}}function tn(e,t={}){let n=[],i=nn(e,t);for(let s of i?e:[])s.dataType==="LINK"?s.children=et(s.children,t):s=et([s],t)[0],n.push(s);let{name:r,logger:o}=t;return e.length===0&&o?.warn(`There is no data ${r?`in ${r}`:"in the JCAMP-DX"}`),n}function et(e=[],t={}){let{name:n,logger:i,tree:r=[],dataSelection:o="both"}=t,s=[];for(let u of e){let{dataType:f,dataClass:d}=u;if(f==="LINK")u.children=et(u.children,t);else if(r.some(g=>{let{dataClass:h=d,dataType:p=f}=g;return d===h&&f===p})){i?.warn(`Skipping ${d} and ${f} ${n?`in ${n}`:"in the JCAMP-DX"},
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+
because it didn't match the import filters`);continue}s.push(u)}let a=[],l=s.some(en),c=s.some(Qt);for(let u of s){if(o!=="both"&&u.dataType!=="LINK"){if(en(u)&&(o==="ft"||o==="preferFT"&&c)){i?.warn(`Skipping raw data ${n?`in ${n}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}if(Qt(u)&&(o==="fid"||o==="preferFID"&&l)){i?.warn(`Skipping FFT data ${n?`in ${n}`:"in the JCAMP-DX"} because it didn't match the import filters`);continue}}a.push(u)}return a}function Qt(e){return e.dataType?.toUpperCase().includes("SPECTRUM")&&e.dataClass&&!e.dataClass.toUpperCase().includes("PEAK")}function en(e){return e.dataType?.toUpperCase().includes("FID")}function nn(e,t={}){let{logger:n,name:i=""}=t;for(let r of e){if(r.dataType==="LINK"&&nn(r.children,t))return!0;let{dataType:o=""}=r,s=o.toLowerCase();if(s.length>0){if(s.includes("spectrum")&&!s.includes("nmr"))return n?.warn(`File ${i} was ignored because it is a ${o}`),!1;if(s.includes("nmr"))return!0}}return!1}import{generateID as sn}from"@zakodium/nmrium-core";import{parseJcampCS as co}from"jcampconverter";import*as lo from"openchemlib";import{isMolfileNotEmpty as no}from"nmr-processing";import{Molecule as ro}from"openchemlib";async function rn(e,t={}){let n=await e.text(),i=V(n),r={molecules:i,spectra:[]};return i.length===0&&t.logger?.debug(`${e.name} is an empty molfile`),r}function V(e){let t=[];if(!no(e))return[];let i=ro.fromMolfile(e).toMolfile();return t.push({molfile:i}),t}import{isMolfileNotEmpty as oo}from"nmr-processing";import*as so from"openchemlib";import{getDiastereotopicAtomIDsFromMolfile as ao}from"openchemlib-utils";var io=new Set(["ndnmrspectrum","ndnmrfid","nmrspectrum","nmrfid"]);function be(e){let{dataType:t="",dataClass:n=""}=e,i=t.replaceAll(/\s/g,"").toLowerCase(),r=n.replaceAll(/\s/g,"").toLowerCase();return io.has(i)&&r!=="peaktable"}function on(e,t,n={}){let{spectra:i,info:r,meta:o}=e,s=i[0].data,a=[],l={x:"delta",y:"intensity",w:"width",m:"multiplicity",a:"atom"},{logger:c,name:u,spectraData:f}=n,{CROSSREFERENCE:d}=r,g=typeof d!="string"?d:d.split(/\r?\n/).map(D=>D.trim()).filter(Boolean),h=g.find(D=>D?.toLowerCase().includes("structure"));if(h===void 0)return c&&c.warn(`There is not a structure reference for ${u} file, assignment object could not be completed`),null;let p=Number.parseInt(h?.toLowerCase().replace(/_/,"").replace(/structure:\s*blockid\s*=\s*(?<blockId>.*)/,"$<blockId>"),10);if(Number.isNaN(p)||p<1)return c&&c.warn(`Structure block_id not found for ${u} file, assignment object could not be completed`),null;let m=f?.molecules?.find(D=>D.blockId===p)?.molfile??"";if(m===""){let D=t.find(A=>A.info.BLOCKID===p),{MOLFILE:P=""}=D?.meta||{};m=P}if(!oo(m))return c&&c.warn(`Empty molfile for ${u} file with structure block_id = ${p}, assignment object could not be completed`),null;let y=ao(so,m),F=fe({...r,...o},{},"");for(let D=0;D<s.x.length;D++){let P={};for(let A in s){let I=s[A][D];typeof I=="string"&&I.startsWith("<")&&I.endsWith(">")&&(I=I.slice(1,-1)),P[l[A]]=I}if("atom"in P){let A=y.map[P.atom-1];F.includes("1H")?A.nbHydrogens>0?(P.diaIDs=A.hydrogenOCLIDs,P.nbHydrogens=A.nbHydrogens):(P.diaIDs=[A.oclID],P.nbHydrogens=A.nbHydrogens):(P.diaIDs=[A.oclID],P.nbHydrogens=1)}a.push(P)}let x={};for(let D of a){let{delta:P,diaIDs:A}=D,I=`${P}_${A.join("_")}`;if(x[I])x[I].atoms.push(D.atom);else{let{atom:Dt,..._e}=D;x[I]={..._e,atoms:[D.atom]}}}let N=[];for(let D of g)D.toLowerCase().includes("spectrum")&&N.push(Number(D.toLowerCase().replace(/_/,"").replace(/.*:\s*blockid=(?<blockId>.*)/,"$<blockId>")));if(N.length===0){for(let D of t)if(be(D)){let{BLOCKID:P}=D.info;N.push(Number(P))}N.length>1&&(N=[],c&&c.warn(`There is not a spectral cross-reference for the peak assignment in the ${u} file`))}return{moleculeBlockID:p,spectraBlockIDs:N,assignments:Object.values(x),molecule:y.molecule}}function an(e,t,n,i){for(let r of e){let{meta:o,dataClass:s="",dataType:a="",info:l}=r,c=Number.parseInt(String(l.BLOCKID),10);o.MOLFILE?fo(String(o.MOLFILE),t,c):r.jcampCS&&po(r,t,c),mo(s,a)&&uo(t,r,e,i),be(r)&&n.push(r)}}function mo(e,t){return e?.toLowerCase().includes("assignments")&&t?.toLowerCase().includes("assignments")}function uo(e,t,n,i){let r=on(t,n,{spectraData:e,logger:i.logger,name:i.name});if(e.assignmentsByBlocks||(e.assignmentsByBlocks={}),r){let{spectraBlockIDs:o}=r;for(let s of o)e.assignmentsByBlocks[s]=r}}function po(e,t,n){t.molecules||(t.molecules=[]);let i=co(e,{OCL:lo}),r=V(i?.molfile||"");r.length>0&&t.molecules.push({id:sn(),blockId:n,...r[0]})}function fo(e,t,n){t.molecules||(t.molecules=[]);let i=V(String(e));t.molecules.push({id:sn(),blockId:n,...i[0]})}import{generateID as Dn}from"@zakodium/nmrium-core";import{matrixMinMaxZ as Fn,reimPhaseCorrection as Ao}from"ml-spectra-processing";import{xyAutoRangesPicking as Mo}from"nmr-processing";function X(e){return e.slice(0,Math.max(0,e.lastIndexOf(".")))}function H(e){e.sort((t,n)=>t.from-n.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 Fo}from"nmr-processing";import{xMaxValue as go}from"ml-spectra-processing";function Z(e){return e.trim().slice(1,-1).split(/,\s*/).map(t=>t.trim())}var yo={I:"id",X:"from",Y:"to",Hs:"delta",An:"integration",H:"nbAtoms",C:"multiplicity",N:"assignment","(J)":"js"},cn=["I","X","Y","Hs","An","H","C","N","(J)"];function ln(e){let t={headersFromParenthesis:[],headersFromComments:[],comments:[],data:[],multiplets:[]},n=e.split(/\r?\n/).filter(i=>i.trim()!=="");if(n.length===0)return t;if(n[0].startsWith("(")&&!n[0].match(/\d/)){let i=n.shift();t.headersFromParenthesis=Z(i)}return t.comments=n.filter(i=>i.startsWith("$$")).map(i=>i.replace(/^\$\$\s*/,"")),t.headersFromComments=bo(t.comments),t.data=n.filter(i=>!i.startsWith("$$")).map(Z),t.multiplets=ho(t),t}function ho(e,t={}){let{logger:n}=t,i=e.data[0].map((l,c)=>c).filter(l=>e.data.every(c=>Number.isNaN(c[l])||Number.isNaN(Number(c[l]))));if(n?.trace(`Parsing JCAMP-DX assignment: stringColumnIndexes: ${i.join(",")}`),i.length===0)return n?.warn("Parsing JCAMP-DX assignment: No string columns found. 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`),i[o]=s}return i}function ft(e,t={}){if(typeof e=="string"){let{filename:n="nmredata.sdf",root:i=""}=t;return{...Ne(e,{mixedEOL:!0}),root:i,filename:n}}return e}import{generateID as mr}from"@zakodium/nmrium-core";import{generateID as cr}from"@zakodium/nmrium-core";import{xyIntegration as hs}from"ml-spectra-processing";function lr(e,t){let{x:n,re:i}=t.data;return e.map(r=>{let o=hs({x:n,y:i},{from:r.from,to:r.to}),s=[];for(let a of r.signals||[]){let{kind:l=null,id:c,js:u=[],diaIDs:f=[],...d}=a;s.push({...d,kind:l||"signal",js:u,id:c||cr(),diaIDs:f})}return{...r,id:r.id||cr(),kind:s?.[0].kind||"signal",absolute:o,signals:s}})}function ur(e,t){let n=[],{baseFrequency:i=500}=t.info;for(let r of e){let{delta:o,diaIDs:s=[],multiplicity:a="",integration:l=0}=r,c=r.jCoupling||[],u=bs({delta:o,js:c,frequency:i});if(c&&a&&c.length===a.length){c.sort((f,d)=>d.coupling-f.coupling);for(let f=0;f<c.length;f++)c[f].multiplicity=a[f]}n.push({id:mr(),...u,integration:l,signals:[{id:mr(),js:c,delta:o,diaIDs:s,multiplicity:a}]})}t.ranges.values=lr(H(n),t)}function bs(e){let{delta:t,js:n=[],frequency:i}=e,r=.5;for(let o of n)r+=o.coupling;return r/=i,{from:t-r,to:t+r}}import{generateID as pr}from"@zakodium/nmrium-core";var Fs=["x","y"],Ds={x:0,y:0};function fr(e,t,n={}){let i=[],{shift:r=Ds}=n,{originFrequency:o=[400,400]}=t.info,s={x:o[0],y:o[1]};for(let a of e){let l={x:{},y:{},id:pr(),kind:"signal"},c={id:pr(),kind:"signal",peaks:[]},u={x:10,y:10};for(let f of Fs){let{coupling:d=[],delta:g,diaIDs:h=[]}=a[f];for(let p of d)u[f]+=p.coupling;if(a.activeCoupling){let{activeCoupling:p=[]}=a;for(let b of p)u[f]+=b.coupling}u[f]/=s[f],l[f]={from:g-u[f],to:g+u[f]},c[f]={delta:g,diaIDs:h,originalDelta:g-r[f]}}i.push({...l,signals:[c]})}t.zones.values=i}function dr(e){return xs(e.data)}function xs(e){return"rr"in e||!("x"in e)&&"re"in e}async function gr(e,t,n={}){let i={spectra:[],molecules:[]},r=await Ss(e,t,n);if(r.spectra.length>0){let{spectra:o,molecules:s,usedFiles:a}=r;i.spectra.push(...o),i.molecules.push(...s);let l=e.files.length;for(let c=l-1;c>=0;c--){let u=e.files[c].relativePath;!u.match(/acqu.*/s)&&a.includes(u)&&e.files.splice(c,1)}}return i}async function Ss(e,t,n){let i=[],r=await pt(e),o={spectra:[],molecules:[]};if(r.length===0)return{...o,usedFiles:i};let s=[];for(let l of r){let c=ar({sdf:l,fileCollection:e}).then(u=>{let{spectra:f,molecules:d=[]}=u;return i.push(l.root+l.filename),o.molecules.push(...d),Ps(f,t,n)});s.push(c)}let a=await Promise.allSettled(s);for(let l of a)l.status==="fulfilled"?(o.spectra.push(...l.value.spectra),i.push(...l.value.usedFiles)):l.reason&&n?.logger?.error(l.reason);return{...o,usedFiles:i}}async function Ps(e,t,n){let i=[],r=[],o={spectra:[],molecules:[]};for(let s of e){let a=Ns(s.source,t,n).then(l=>{let{spectra:c,files:u}=l;i.push(...u);for(let f of c)dr(f)?fr(s.signals,f):ur(s.signals,f);o.spectra.push(...c)});r.push(a)}return await Promise.allSettled(r),{...o,usedFiles:i}}async function Ns(e,t,n={}){let{file:i,jcampURL:r}=e,{converter:o}=n;if(r){let l=await As(r,t,o?.jcamp);if(l)return{...l,files:[]}}let s=[];for(let l of i||[])s.push(Ms(l,n).then(c=>({...c,files:l.fileCollection.files.map(u=>u.relativePath)})));let a=await Promise.allSettled(s);for(let l of a){if(l.status==="fulfilled")return l.value;l.reason&&n?.logger?.error(l.reason)}return{spectra:[],molecules:[],files:[]}}async function As(e,t,n={}){let i={entries:[{relativePath:e}]},r={name:X(e||""),xy:!0,noContours:!0,...n},{data:o}=await t.readFromWebSource(i,r);return o}async function Ms(e,t={}){let{converter:n,sourceSelector:i}=t;switch(e.type){case"jcamp":return Fe(e.fileCollection.files[0],{name:e?.fileCollection.files[0].name||"",converter:n?.jcamp,selector:i?.jcamp,logger:t.logger,keepSource:t.keepSource});case"brukerFiles":return ye(e.fileCollection,{converter:n?.bruker,selector:i});default:throw new Error("There is not a supported source")}}var Me=class{id="@zakodium/nmrium-core-plugins#NMReDATALoaderPlugin";version=1;migrations=[];onReadProcess;#e;constructor(t){this.#e=t,this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(t,n)=>gr(t,this.#e,n)};function dt(e){return new Me(e)}import{parse as Is}from"sdf-parser";function yr(e,t={}){let{mixedEOL:n}=t,{molecules:i}=Is(e,{mixedEOL:n}),r=[];for(let{molfile:o}of i){let s=V(o);r.push(...s)}return r}async function hr(e,t={}){let{logger:n,mixedEOL:i}=t,r=await e.text(),o=yr(r,{mixedEOL:i}),s={molecules:o,spectra:[]};return n&&n[o.length>0?"info":"debug"](`Loaded ${s.molecules.length} molecules from the ${e.name} file`),s}var Ie=class{id="@zakodium/nmrium-core-plugins#SDFLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={supportedExtensions:["sdf"],onFile:this.onReadProcessFile.bind(this)}}onReadProcessFile(t,n={}){let{logger:i}=n;return i?.debug(`Reading sdf file: ${t.name}`),hr(t,{logger:i})}};function gt(){return new Ie}import{Molecule as Rs}from"openchemlib";function br(e){let t=[],n=e.split(/\r?\n/).filter(Boolean);for(let i of n){let o=Rs.fromSmiles(i).toMolfile();t.push({molfile:o})}return t}async function Fr(e,t={}){let n=await e.text(),i=br(n),r={molecules:i,spectra:[]};return t.logger?.info(`Found ${i.length} molecules from the ${e.name} file`),r}var Re=class{id="@zakodium/nmrium-core-plugins#SMILESLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={supportedExtensions:["smi","smiles"],onFile:this.onReadProcessFile.bind(this)}}onReadProcessFile(t,n={}){let{logger:i}=n;return Fr(t,{logger:i})}};function yt(){return new Re}import{formatSpectra as ws}from"@zakodium/nmrium-core";import{createFromToArray as Ts}from"ml-spectra-processing/utils";function Dr(e){e.setLittleEndian();let t=e.offset,n=32*3;e.offset=n/8;let i=e.readInt32(),r=[2,4],o=[2**25,2**26];if(!r.includes(i))if(o.includes(i))e.setBigEndian();else throw new Error(`Unexpected value of eBytes (${i}). Expect one of
|
|
17
|
+
${r.concat(o).join(",")}`);return e.offset=t,e.isBigEndian()?"BE":"LE"}var Ee=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}},Te=class extends Ee{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}},Oe=class extends Ee{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}},Ce=class{lines;length;index;eol;constructor(t,n={}){let{eol:i=`
|
|
18
|
+
`,index:r=0}=n;this.eol=i,this.index=r,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 n=this.lines.slice(this.index,this.index+t);return this.index+=t,n}},we=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}}},ve=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 ke=class{scale;status;index;mode;ctCount;lpVal;rpVal;lvl;tlt;data;constructor(t,n,i){i&&(t.offset=i),this.scale=t.readInt16(),this.status=new Te(t.readInt16()),this.index=t.readInt16(),this.mode=new ve(t.readInt16()),this.ctCount=t.readInt32(),this.lpVal=t.readFloat32(),this.rpVal=t.readFloat32(),this.lvl=t.readFloat32(),this.tlt=t.readFloat32(),this.data=Es(t,n)}};function Es(e,t){let{np:n,nTraces:i,status:{isFloat32:r,isInt32:o}}=t;return r?ht(e,i,n,"readFloat32"):o?ht(e,i,n,"readInt32"):ht(e,i,n,"readInt16")}function ht(e,t,n,i){let r=[],o;i==="readFloat32"?o={re:new Float32Array(n/2),im:new Float32Array(n/2)}:i==="readInt32"?o={re:new Int32Array(n/2),im:new Int32Array(n/2)}:o={re:new Int16Array(n/2),im:new Int16Array(n/2)};for(let s=0;s<t;s++){for(let a=0;a<n;a+=2)o.re[a>>>1]=e[i](),o.im[a>>>1]=e[i]();r[s]=o}return r}var Le=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 we(t.readInt16()),this.status=new Oe(t.readInt16()),this.nBlockHeaders=t.readInt32()}};var bt=class{name;subType;basicType;maxValue;minValue;stepSize;gGroup;dGroup;protection;active;intptr;constructor(t){let n=t.split(" ");this.name=n[0],this.subType=Number.parseInt(n[1],10),this.basicType=Number.parseInt(n[2],10),this.maxValue=Number.parseFloat(n[3]),this.minValue=Number.parseFloat(n[4]),this.stepSize=Number.parseFloat(n[5]),this.gGroup=Number.parseInt(n[6],10),this.dGroup=Number.parseInt(n[7],10),this.protection=Number.parseInt(n[8],10),this.active=Number.parseInt(n[9],10),this.intptr=Number.parseInt(n[10],10)}};function xr(e){let t=[],n=new Ce(e.readChars(e.length));for(;n.index<n.length-1;){let i=[],r=[],o=new bt(n.readLine()),s=n.readLine();if(o.basicType!==0){if(o.basicType===1)i=s.split(" ").slice(1).map(u=>Number.parseFloat(u));else if(o.basicType===2){i=s.split('"').slice(1,2);let c=Number.parseInt(s.split(" ")[0],10);for(;c>1;)i.push(n.readLine().split('"')[1]),c--}}let a=n.readLine(),l=Number.parseInt(a.split(" ")[0],10);l!==0&&(o.basicType===1?r=a.split(" ").slice(1):o.basicType===2&&(r=a.split('"').filter((c,u)=>u%2===1))),t.push({...o,values:i,enumerable:l,enumerables:r})}return t}async function Sr(e){let t={};function n(l,c){return l.then(u=>{t[c]=u})}let i=[];for(let l of e)switch(l.name.toLowerCase()){case"fid":{i.push(n(l.arrayBuffer(),"fidB"));break}case"procpar":{i.push(n(l.arrayBuffer(),"procparB"));break}default:break}if(await Promise.all(i),!t.fidB||!t.procparB)throw new RangeError("fid and procpar must exist.");let r=new O(t.fidB);Dr(r);let o=new Le(r);if(o.nBlocks!==1)throw new Error("We currently do not support 2D varian spectra ");let s=xr(new O(t.procparB)),a;for(let l of s)if(l.name==="at"){a=l.values[0];break}if(typeof a!="number")throw new Error("acquisition time parameter must exist and be a number.");{let l=Ts({from:0,to:a,length:o.np/2,distribution:"uniform"}),c=new ke(r,o);return{meta:o,fid:c,procpar:s,x:l}}}import{isAnyArray as vs}from"is-any-array";import{xMultiply as ks}from"ml-spectra-processing";import{normalizeNucleus as Os}from"nmr-processing";function Pr(e,t){let{meta:n,procpar:i}=e,r={};for(let y of i)r[y.name]=y.values;let o={},s={},{np:a,solvent:l,sfrq:c,reffrq:u,temp:f,rp:d,sw:g,rfl:h,rfp:p}=r;S(o,"numberOfPoints",a&&Number(L(a))/2),S(o,"solvent",L(l)),S(o,"originFrequency",L(c)),S(o,"baseFrequency",L(u)),(Number.isNaN(o.originFrequency)||o.originFrequency===0)&&(o.originFrequency=400,t?.warn("The frequency could not be determined and was set to 400MHz")),S(o,"temperature",L(f)),S(o,"phc0",d&&Number(d[0])),S(s,"rfl",h&&Number(L(h))),S(s,"rfp",p&&Number(L(p))),S(s,"sw",g&&Number(L(g)));for(let y in s){let F=s[y];Array.isArray(F)&&F.length===1&&(s[y]=F[0])}if(!("baseFrequency"in o)&&"originFrequency"in o){let y=Number.parseFloat(o.originFrequency);if(["sw","rfl","rfp"].every(F=>F in s)){let{sw:F=1,rfl:x=1,rfp:N=1}=Cs(s,["sw","rfl","rfp"]);S(o,"baseFrequency",y-(F/2-x+N)/1e6)}else S(o,"baseFrequency",y)}let{baseFrequency:b,originFrequency:m}=o;S(o,"frequencyOffset",(m-b)*1e6),S(o,"spectralWidth",g&&Number(g[0])/o.baseFrequency);for(let y in o)o[y].length===1&&(o[y]=o[y][0]);return r.tn&&(o.nucleus=r.tn.map(Os)),o.dimension=1,o.isFid=!n.status.isSpectrum,{info:o,meta:{...s,...Nr(n),...r}}}function L(e){return e&&(Array.isArray(e)?e[0]:e)}function Cs(e,t){let n={};for(let i of t){let r=e[i];r&&typeof r=="number"&&(n[i]=r)}return n}function Nr(e){let t={};for(let n of Object.keys(e)){let i=e[n];typeof i=="object"&&i!==null&&i.constructor&&i.constructor!==Object?t[n]=Nr(i):t[n]=i}return t}function Ar(e){let t={},n=new Set(e.files.map(i=>i.relativePath));for(let i of e){let r=i.name.toLowerCase();if(r.match(/^(?:fid|procpar|text|log)$/)){if(r.match(/^(?:fid|text|log)$/)){let a=i.relativePath.replace(/(?:fid|text|log)$/,"procpar");if(!n.has(a))continue}let o=i.relativePath.split("/"),s=o.slice(0,-1).join("/");t[s]||(t[s]={name:o.at(-2),files:[]}),t[s].files.push(i)}}return Object.values(t)}async function Mr(e,t={}){let{keepSource:n,logger:i}=t,r=Ar(e);i&&i.debug(`Found ${Object.keys(r).length} varian experiments`);let o=[],s={spectra:[],molecules:[]};for(let l of r){let{name:c,files:u}=l,f=Sr(u).then(d=>{let{info:g,meta:h}=Pr(d),p=d.fid.data[0],b=vs(p.im),m={data:{...p,x:d.x},meta:h,info:{isComplex:b,name:c,...g},display:{name:c}};if(g.isFid&&b){let{im:y}=m.data;ks(y,-1,{output:y})}u&&n&&(m.sourceSelector={files:u.map(y=>y.relativePath)}),s.spectra.push(m)});o.push(f)}let a=await Promise.allSettled(o);for(let l=0;l<a.length;l++){let c=a[l];if(c.status==="rejected"&&c.reason){let u=r[l].name;i?.warn(`Varian data: ${u}, fails with: ${c.reason}`)}}return s.spectra.length>0&&i?.info(`Loaded ${s.spectra.length} spectra from Varian files`),ws(s)}var qe=class{id="@zakodium/nmrium-core-plugins#VarianLoaderPlugin";version=1;migrations=[];onReadProcess;constructor(){this.onReadProcess={onFiles:this.onReadProcessFiles}}onReadProcessFiles=(t,n)=>{let{keepSource:i,logger:r}=n??{};return Mr(t,{keepSource:i,logger:r})}};function Ft(){return new qe}function qs(e,t=[]){return[dt(e),Ft(),Ze(),nt(),mt(),gt(),yt(),lt(),Je()].concat(t)}function _s(){let e=new Ls;return e.registerPlugins(qs(e)),e}import{getOneIfArray as Rr}from"@zakodium/nmrium-core";import{from1DNMRVariables as js}from"convert-to-jcamp";function Ir(e,t){return e.filters.find(n=>n.name===t)}function Bs(e,t={}){let{info:n,meta:i,data:r}=e,{onlyReal:o=!1}=t,{isFid:s,spectralWidth:a}=n,l=Rr(n.baseFrequency||n.originFrequency),{x:c,re:u,im:f}=r,d=new Float64Array(u),g=!o&&f?new Float64Array(f):void 0,h={};Q(h,"SW",a),Q(h,"BF1",l);let p=Ir(e,"fft")?.enabled,b={originFrequency:n.originFrequency,dataType:!n.isFid||p?"NMR SPECTRUM":"NMR FID",dataClass:!o&&f?"NTUPLES":"XYDATA"};if(s){let F=e.filters.find(x=>x.name==="digitalFilter");if(F&&!p){let{value:{digitalFilterValue:x},enabled:N}=F;if(N){let D=Math.floor(x);d.set(u.slice(u.length-D)),d.set(u.slice(0,u.length-D),D),f&&g&&(g.set(f.slice(f.length-D)),g.set(f.slice(0,f.length-D),D))}}Q(b,"decim",n.decim),Q(b,"dspfvs",n.dspfvs),Q(b,"digitalFilter",n.digitalFilter)}let m={xyEncoding:"DIFDUP",info:{...n,...b},meta:{...i,...h}},y={x:{data:c,label:n.isFid?"TIME":"FREQUENCY",units:n.isFid?"second":"HZ",symbol:"X"},r:{data:d,label:`${n.isFid?"FID":"SPECTRUM"}/REAL`,units:"ARBITRARY UNITS",symbol:"R"}};return g&&(y.i={data:g,label:`${n.isFid?"FID":"SPECTRUM"}/IMAG`,units:"ARBITRARY UNITS",symbol:"I"}),js(y,m)}function Q(e,t,n){n!==void 0&&(e[t]=Rr(n))}export{ne as AutoPostProcessingPlugin,he as BrukerLoaderPlugin,De as JCAMPDXLoaderPlugin,Se as JEOLLoaderPlugin,Pe as MolfileLoaderPlugin,Me as NMReDATALoaderPlugin,Ie as SDFLoaderPlugin,Re as SMILESLoaderPlugin,qe as VarianLoaderPlugin,Je as autoPostProcessing,Ze as brukerLoader,_s as default,_s as init,nt as jcampDXLoader,lt as jeolLoader,mt as molfileLoader,dt as nmreDATALoader,Nn as processJCAMPDX,yr as readSDF,br as readSMILES,qs as recommended,gt as sdfLoader,yt as smilesLoader,Bs as spectrum1DToJCAMPDX,Ft as varianLoader};
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package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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1
1
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{
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2
2
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"name": "@zakodium/nmrium-core-plugins",
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3
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-
"version": "0.1.
|
|
3
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+
"version": "0.1.7",
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4
4
|
"description": "Recommended plugins for NMRium, loaders of common formats like bruker or jcamp, and some post-processing plugins",
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5
5
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"author": "Zakodium Sàrl",
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6
6
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"license": "CC-BY-NC-SA-4.0",
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@@ -31,6 +31,7 @@
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31
31
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"@zakodium/bruker-parser": "^0.0.0",
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32
32
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"@zakodium/jeol-parser": "^0.0.0",
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33
33
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"@zakodium/nmr-types": "^0.1.0",
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34
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+
"@zakodium/nmredata": "^0.0.0",
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34
35
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"@zakodium/varian-parser": "^0.0.0",
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35
36
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"bruker-data-test": "^1.0.0",
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36
37
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"esbuild": "^0.25.5",
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@@ -44,7 +45,6 @@
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44
45
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"vitest": "^3.2.4"
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45
46
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},
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46
47
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"dependencies": {
|
|
47
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-
"@zakodium/nmredata": "^0.0.0",
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48
48
|
"@zakodium/nmrium-core": "^0.1.4",
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49
49
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"cheminfo-types": "^1.8.1",
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50
50
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"convert-to-jcamp": "^5.4.11",
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