npm - @datagrok/sequence-translator - Versions diffs - 1.2.5 → 1.2.7 - Mend

@datagrok/sequence-translator 1.2.5 → 1.2.7

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Files changed (10) hide show

package/CHANGELOG.md +12 -0
package/dist/package-test.js +1 -1
package/dist/package-test.js.map +1 -1
package/dist/package.js +1 -1
package/dist/package.js.map +1 -1
package/package.json +2 -2
package/src/model/structure-app/mol-transformations.ts +2 -2
package/src/model/structure-app/sequence-to-molfile.ts +1 -1
package/src/view/apps/oligo-translator.ts +334 -17
package/src/view/const/oligo-translator.ts +2 -0

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,17 @@
 # Sequence Translator changelog
+## 1.2.7 (2024-01-29)
+### Features
+* Bulk translation for formats
+## 1.2.6 (2024-01-29)
+### Bug fixes
+* Fixed column input in Pattern
+* Fixed whitespaces in molfiles
 ## 1.2.0 (2023-10-27)
 ### Features

package/dist/package-test.js CHANGED Viewed

@@ -1,2 +1,2 @@
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n?[n.get(e),e,o,4]:[this.undefinedColor,r,o,4]}return[this.undefinedColor,r,o,0]}}L.SemType="Aminoacids",L.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",L.undefinedColor="rgb(100,100,100)",L.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},L.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},L.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},L.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class H{}H.SemType="Nucleotides",H.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",H.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class I{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class G{}class U extends G{static buildPalette(){return[].concat(...Object.values(k.colourPalette))}get(t){const e=I.hashCode(t)%U.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=r.Color.fromHtml(t),n=r.Color.g(e),o=r.Color.r(e),a=r.Color.b(e),s=Math.sqrt(Math.pow(0-o,2)+Math.pow(0-n,2)+Math.pow(0-a,2));return s>210?`rgb(${o/s*210},${n/s*210},${a/s*210})`:r.Color.toRgb(e)}(U.palette[e])}}U.palette=U.buildPalette();new Uint32Array(65536);var P,_;(_=P||(P={})).HAMMING="Hamming",_.LEVENSHTEIN="Levenshtein",_.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",P.HAMMING,P.LEVENSHTEIN,P.NEEDLEMANN_WUNSCH,new 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getPalette(t="grok"){switch(t){case"grok":return u.GrokGroups;case"lesk":return u.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",r="";for(const o of t)"("==o?e++:")"==o?e--:e?n+=o:r+=o;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[r,o]=this.getInnerOuter(t);if(r=r.length>6?`${r.slice(0,3)}...`:r,o=o.length>6?`${o.slice(0,3)}...`:o,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,o,1]:[this.undefinedColor,r,o,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,o,2]:[this.undefinedColor,r,o,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,o,3]:[this.undefinedColor,r,o,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,o,4]:[this.undefinedColor,r,o,4]}return[this.undefinedColor,r,o,0]}}p.SemType="Aminoacids",p.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",p.undefinedColor="rgb(100,100,100)",p.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},p.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},p.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},p.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class d{}d.SemType="Nucleotides",d.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",d.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class g{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class h{}class m extends h{static buildPalette(){return[].concat(...Object.values(c.colourPalette))}get(t){const e=g.hashCode(t)%m.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=r.Color.fromHtml(t),n=r.Color.g(e),o=r.Color.r(e),a=r.Color.b(e),s=Math.sqrt(Math.pow(0-o,2)+Math.pow(0-n,2)+Math.pow(0-a,2));return s>210?`rgb(${o/s*210},${n/s*210},${a/s*210})`:r.Color.toRgb(e)}(m.palette[e])}}m.palette=m.buildPalette();new Uint32Array(65536);var f,A;(A=f||(f={})).HAMMING="Hamming",A.LEVENSHTEIN="Levenshtein",A.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",f.HAMMING,f.LEVENSHTEIN,f.NEEDLEMANN_WUNSCH,new class{constructor(){this.uhTemp=`units-handler.${r.SEMTYPE.MACROMOLECULE}`}},o.FASTA,o.SEPARATOR,o.HELM,rxjs;var C=n(379),b=n.n(C),v=n(795),w=n.n(v),E=n(569),y=n.n(E),x=n(565),B=n.n(x),O=n(216),N=n.n(O),S=n(589),T=n.n(S),M=n(602),R={};R.styleTagTransform=T(),R.setAttributes=B(),R.insert=y().bind(null,"head"),R.domAPI=w(),R.insertStyleElement=N(),b()(M.Z,R),M.Z&&M.Z.locals&&M.Z.locals,n(947);var k=n(88);n(29),n(559),n(996),$;var F,L,H=n(490),I={};I.styleTagTransform=T(),I.setAttributes=B(),I.insert=y().bind(null,"head"),I.domAPI=w(),I.insertStyleElement=N(),b()(H.Z,I),H.Z&&H.Z.locals&&H.Z.locals,n(864),(L=F||(F={})).HEADER="V2000",L[L.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",L[L.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",L[L.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",L[L.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",L[L.BOND_TYPE_COL=3]="BOND_TYPE_COL",L[L.RGP_SHIFT=8]="RGP_SHIFT",L.RGP_LINE="M  RGP",L.A_LINE="A  ",L.END="M  END",Error,n(456);var G=n(753),U={};function P(t,e){const n=document.createElement("canvas").getContext("2d");return n.font=String(e),2*n.measureText(t).width}U.styleTagTransform=T(),U.setAttributes=B(),U.insert=y().bind(null,"head"),U.domAPI=w(),U.insertStyleElement=N(),b()(G.Z,U),G.Z&&G.Z.locals&&G.Z.locals;Math.max(P("SS: 5'",17),P("AS: 3'",17)),Math.max(P("3'",17),P("5'",17)),n(803);var _=n(895);n(61);class D extends r.Package{_monomerLib;get monomerLib(){if(!this._monomerLib)throw new Error("Monomer lib not loaded");return this._monomerLib}async initMonomerLib(){if(void 0!==this._monomerLib)return;const t=r.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");await(0,k.Y3)((async()=>{const t=await async function(){const t=r.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}();this._monomerLib=await t.readLibrary(_.BX,_.a_)}),(()=>t.close()))}}const j=new D},976:t=>{t.exports=DG},469:t=>{t.exports=grok}},e={};function n(r){var o=e[r];if(void 0!==o)return o.exports;var a=e[r]={id:r,exports:{}};return t[r](a,a.exports,n),a.exports}n.n=t=>{var e=t&&t.__esModule?()=>t.default:()=>t;return n.d(e,{a:e}),e},n.d=(t,e)=>{for(var r in e)n.o(e,r)&&!n.o(t,r)&&Object.defineProperty(t,r,{enumerable:!0,get:e[r]})},n.o=(t,e)=>Object.prototype.hasOwnProperty.call(t,e),n.r=t=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},n.nc=void 0;var r={};(()=>{n.r(r),n.d(r,{_package:()=>f,test:()=>A,tests:()=>e.QK});var t=n(976),e=n(61),o=n(29),a=n(456),s=n(996);const i={Axolabs:{UfAfsCfsGfuacg:"RNA1{[fR](U)p.[fR](A)[sp].[fR](C)[sp].[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$"},BioSpring:{"AT*GC*123456789":"RNA1{r(A)p.r(T)[sp].r(G)p.r(C)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)p.d([m5C])}$$$$"},Mermade12:{hefglijkLIJKHEFG:"RNA1{[25r](U)[sp].[25r](A)[sp].[25r](C)[sp].[25r](G)[sp].[fR](U)[sp].[fR](A)[sp].[fR](C)[sp].[fR](G)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$"}},l={"RNA1{[fR](U)p.[fR](A)[sp].[fR](C)[sp].[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$":"UACGUACG","RNA1{r(A)p.r(T)[sp].r(G)p.r(C)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)p.d([m5C])}$$$$":"ATGCUACGUACGC","RNA1{[25r](U)[sp].[25r](A)[sp].[25r](C)[sp].[25r](G)[sp].[fR](U)[sp].[fR](A)[sp].[fR](C)[sp].[fR](G)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$":"UACGUACGUACGUACG"};var c=n(669);function u(t,e){return new a.I(t,e).convertTo(o.NI.HELM)}function p(t,e){return new a.I(t,o.NI.HELM).convertTo(e)}(0,e.W3)("Formats to HELM",(()=>{(0,e.bb)((async()=>{await(0,s.VO)(),await c._package.initMonomerLib()}));for(const t of Object.keys(i))for(const[n,r]of Object.entries(i[t]))(0,e.Bu)(`${t} to HELM`,(async()=>{const o=r,a=u(n,t);(0,e.l_)(a,o)}))})),(0,e.W3)("HELM to Formats",(()=>{(0,e.bb)((async()=>{await(0,s.VO)(),await c._package.initMonomerLib()}));for(const t of Object.keys(i))for(const[n,r]of Object.entries(i[t]))(0,e.Bu)(`${t} to HELM`,(async()=>{const o=n,a=p(r,t);(0,e.l_)(a,o)}))}));var d=n(864),g=n(559);(0,e.W3)("HELM to Nucleotides",(()=>{(0,e.bb)((async()=>{await(0,s.VO)(),await c._package.initMonomerLib()})),Object.entries(l).forEach((([t,n],r)=>{(0,e.Bu)(`Sequence ${r+1} to nucleotides`,(async()=>{const r=n,o=(0,d.C)(t,g.A.getInstance());(0,e.l_)(o,r)}))}))}));var h=n(947);const m={[o.NI.AXOLABS]:"Afcgacsu",[o.NI.HELM]:"RNA1{[fR](A)p.[25r](C)p.[25r](G)p.[25r](A)p.[25r](C)[sp].[25r](U)}$$$$"};(0,e.W3)("Formats support",(()=>{(0,e.bb)((async()=>{await(0,s.VO)(),await c._package.initMonomerLib()})),Object.entries(m).forEach((([t,n])=>{(0,e.Bu)(`All formats for ${t}`,(async()=>{const r=function(t,e){const n=new h.b(t).getInvalidCodeIndex(e);return(0,d.D)(t,n,e)}(n,t),o=Object.keys(r).length,a=Object.keys(i).length+1;(0,e.l_)(!0,a<=o)}))}))}));const f=new t.Package;async function A(n,r,o){const a=await(0,e.ci)({category:n,test:r,testContext:o});return t.DataFrame.fromObjects(a)}})(),sequencetranslator_test=r})();
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