@datagrok/sequence-translator 1.4.5 → 1.4.6

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Files changed (31) hide show
  1. package/CHANGELOG.md +13 -0
  2. package/dist/package-test.js +1 -1
  3. package/dist/package-test.js.map +1 -1
  4. package/dist/package.js +1 -1
  5. package/dist/package.js.map +1 -1
  6. package/files/polytool-rules/rules_example.json +1 -1
  7. package/files/samples/HELM.csv +6 -0
  8. package/files/samples/cyclized.csv +3 -2
  9. package/files/samples/cyclized_MSA.csv +5 -0
  10. package/package.json +5 -5
  11. package/src/apps/common/model/oligo-toolkit-package.ts +11 -4
  12. package/src/consts.ts +12 -0
  13. package/src/global.d.ts +13 -0
  14. package/src/package-test.ts +1 -0
  15. package/src/package.ts +5 -4
  16. package/src/polytool/pt-conversion.ts +222 -70
  17. package/src/polytool/pt-dialog.ts +17 -11
  18. package/src/polytool/pt-enumeration-helm-dialog.ts +63 -25
  19. package/src/polytool/pt-enumeration-helm.ts +9 -6
  20. package/src/polytool/pt-placeholders-breadth-input.ts +4 -4
  21. package/src/polytool/pt-placeholders-input.ts +6 -6
  22. package/src/polytool/pt-unrule-dialog.ts +5 -1
  23. package/src/polytool/pt-unrule.ts +3 -2
  24. package/src/polytool/types.ts +4 -4
  25. package/src/tests/polytool-chain-from-notation-tests.ts +108 -18
  26. package/src/tests/polytool-chain-parse-notation-tests.ts +52 -11
  27. package/src/tests/polytool-convert-tests.ts +102 -25
  28. package/src/tests/polytool-detectors-custom-notation-test.ts +1 -1
  29. package/src/tests/polytool-enumerate-breadth-tests.ts +4 -4
  30. package/src/utils/context-menu.ts +2 -2
  31. package/src/utils/cyclized.ts +6 -8
package/dist/package-test.js CHANGED
@@ -1,3 +1,3 @@
1
1
  /*! For license information please see package-test.js.LICENSE.txt */
2
- var sequencetranslator_test;(()=>{var t={717:(t,e,n)=>{"use strict";n.d(e,{j:()=>o});var r=n(82);async function o(){const t=r.Func.find({package:"Chem",name:"getRdKitModule"});if(0===t.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await t[0].prepare().call()).getOutputParamValue()}},599:(t,e,n)=>{"use strict";n.d(e,{o:()=>r.o});var r=n(869)},124:(t,e,n)=>{"use strict";n.d(e,{b2:()=>i});var r=n(389),o=n(82);async function i(){const t="Helm",e=o.Func.find({package:t,name:"getHelmHelper"});if(0===e.length)throw new Error(`Package '${t}' must be installed for HelmHelper.`);return(await e[0].prepare().call()).getOutputParamValue()}o.JsInputBase,Error,r.input.helmAsync=async function(t,e){return(await i()).createHelmInput(t,e)}},890:(t,e,n)=>{"use strict";n.d(e,{pj:()=>p});var r,o,i,s,a,u,c,l=n(82);n(328);class f{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,r=f._createBuffer(n);if(e)for(let t=0;t<r.length;t++)r[t]=-1;this._data=r,this._length=n}else{if(!(t instanceof Uint32Array))throw new Error("Invalid constructor");this._data=t,this._length=e}}getRawData(){return this._data}assureGoez(t,e){if(t<0)throw new Error(`${e} should be greater than zero`)}assureInRange(t,e,n,r){if(t<e||t>n)throw new Error(`Argument ${r} (${t}) out of range (${e}, ${n})`)}copy(t,e,n){for(let r=0;r<n;r++)e[r]=t[r]}copyFrom(t){if(this._length!=t._length)throw new Error(`Lengths differ (${this._length} != ${t._length})`);this.copy(t._data,this._data,this.lengthInInts),this._version++}get length(){return this._length}get buffer(){return this._data}set buffer(t){this._data=t,this._version++}get version(){return this._version}set version(t){this._version=t}incrementVersion(t=!0){this._version++}get lengthInInts(){return Math.floor((this._length+31)/32)}get versionedName(){return this._version==this._versionedNameVersion?this._versionedName:""}set versionedName(t){this._versionedName=t,this._versionedNameVersion=this._version}get self(){return this}setLength(t){if(t<0)throw new Error("should be >= 0");if(t==this._length)return;const e=Math.floor((t+31)/32);if(e>this._data.length||e+this.SHRINK_THRESHOLD<this._data.length){const t=new Uint32Array(e);this.copy(this._data,t,e>this._data.length?this._data.length:e),this._data=t}t>this._length&&(this._length%32>0&&(this._data[this.lengthInInts-1]&=(1<<(this._length%32&31))-1),this._data.fill(0,this.lengthInInts,e)),this._length=t,this._version++}static fromAnd(t,e){if(t._length!=e._length)throw new Error(`Lengths differ (${t._length} != ${e._length})`);const n=new f(t._length);n._length=t._length,n._data=f._createBuffer(n._length),n._version=0;const r=t.lengthInInts;for(let o=0;o<r;o++)n._data[o]=t._data[o]&e._data[o];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new f(t.length);e._version=0;for(let n=0;n<e._length;n++)t[n]&&(e._data[Math.floor(n/32)]|=1<<(n%32&31));return e}static fromSeq(t,e){const n=new f(t);for(let r=0;r<t;++r)n.setBit(r,e(r));return n._version=0,n}static fromString(t){return f.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new f(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new f(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let r=0,o=0;for(;e-o>=4;)n._data[r++]=255&t[o]|(255&t[o+1])<<8|(255&t[o+2])<<16|(255&t[o+3])<<24,o+=4;return e-o==3&&(n._data[r]=(255&t[o+2])<<16),e-o==2&&(n._data[r]|=(255&t[o+1])<<8),e-o==1&&(n._data[r]|=255&t[o]),n._version=0,n}toString(){return`${this._length} bits, ${this.countBits(!0)} set`}equals(t){if(this==t)return!0;if(null==t)return!1;if(this._length!=t._length)return!1;if(0==this._length)return!0;for(let e=0;e<this._data.length-1;e++)if(this._data[e]!=t._data[e])return!1;for(let e=8*(this._data.length-1);e<this._length;e++)if(this.getBit(e)!=t.getBit(e))return!1;return!0}clone(){const t=new f(0,!1);return t._data=Uint32Array.from(this._data),t._length=this._length,t._version=this._version,t}init(t,e){this.setAll(!1,!1);for(let e=0;e<this._length;e++)t(e)&&(this._data[Math.floor(e/32)]|=1<<(e%32&31));return this.incrementVersion(e),this}invert(t=!0){for(let t=0;t<this._data.length;t++)this._data[t]^=-1;this.incrementVersion(t)}setAll(t,e=!1){const n=t?-1:0,r=this.lengthInInts;for(let t=0;t<r;t++)this._data[t]=n;this.incrementVersion(e)}setIndexes(t,e=!0,n=!0,r=!0){n&&this.setAll(!e,!1);for(const n of t)this.setFast(n,e);this.incrementVersion(r)}everyIndex(t,e=!0){for(const n of t)if(this.getBit(n)!=e)return!1;return!0}anyIndex(t,e=!0){for(const n of t)if(this.getBit(n)==e)return!0;return!1}setWhere(t,e=!0,n=!0,r=!0,o=!0){if(n&&o&&this.setAll(!e,!1),o)for(let n=0;n<this._length;n++)t(n)&&this.setFast(n,e);else for(let n=0;n<this._length;n++)this.setFast(n,t(n)?e:!e);this.incrementVersion(r)}getRange(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let r=t;r<e;++r)n.push(this.getBit(r));return f.fromValues(n)}getRangeAsList(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let r=t;r<e;++r)n.push(this.getBit(r));return n}setRange(t,e,n,r=!0){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length-1,"to");const o=Math.min(t,e),i=Math.max(t,e);if(n)for(let t=o;t<=i;t++)this.setTrue(t);else for(let t=o;t<=i;t++)this.setFalse(t);return this.incrementVersion(r),this}setRandom(t,e,n=!0){if(t<0||t>this._length)throw new Error("n must be >= 0 && <= Count");t>this._length/2&&this.setRandom(this._length-t,!e),this.setAll(!e);for(let n=0;n<t;){const t=Math.floor(Math.random()*this._length);this.getBit(t)!=e&&(this.setFast(t,e),n++)}this.incrementVersion(n)}and(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]&=t._data[e];return this.incrementVersion(e),this}andNot(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");const n=this.lengthInInts;for(let e=0;e<n;e++)this._data[e]&=~t._data[e];return this.incrementVersion(e),this}notAnd(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]=~this._data[e]&t._data[e];return this.incrementVersion(e),this}not(t=!0){for(let t=0,e=this.lengthInInts;t<e;t++)this._data[t]=~this._data[t];return this.incrementVersion(t),this}or(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]|=t._data[e];return this.incrementVersion(e),this}xor(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]^=t._data[e];return this.incrementVersion(e),this}insertAt(t,e,n=!1){if(this.assureInRange(t,0,this._length,"pos"),0==e)return;const r=this._length;this.setLength(this._length+e);for(let n=r-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let r=t;r<t+e;r++)this.setBit(r,n)}removeAt(t,e=1){if(e<0)throw new Error("n cannot be negative");if(this.assureInRange(t,0,this._length-e,"pos"),this.contains(!0))for(let n=t;n<this._length-e;n++)this.setBit(n,this.getBit(n+e));this.setLength(this._length-e)}removeByMask(t,e=!0){if(this._length!=t.length)throw new Error("length != mask.length");if(t==this)this.setLength(t.countBits(!e)),this.setAll(!e);else{let n=0;for(let r=-1;-1!=(r=t.findNext(r,!e));)this.setFast(n++,this.getBit(r));this._length=n,this._version++}return this}getBit(t){return!!(this._data[Math.floor(t/32)]&1<<(31&t))}setBit(t,e,n=!0){this.setFast(t,e),this._version++}setFast(t,e){e?this._data[Math.floor(t/32)]|=1<<(31&t):this._data[Math.floor(t/32)]&=~(1<<(31&t))}setTrue(t){this._data[Math.floor(t/32)]|=1<<(31&t)}setFalse(t){this._data[Math.floor(t/32)]&=~(1<<(31&t))}trueCount(){return this.countBits(!0)}falseCount(){return this.countBits(!1)}countBits(t){if(0==this._length)return 0;if(this._selectedCountVersion!=this._version){this._selectedCount=0;const t=this.lengthInInts;let e=0;for(;e<t-1;e++)for(let t=this._data[e];0!=t;t>>>=8)this._selectedCount+=f._onBitCount[255&t];let n=this._data[e];const r=31&this._length;for(0!=r&&(n&=~(4294967295<<r));0!=n;n>>>=8)this._selectedCount+=f._onBitCount[255&n];this._selectedCountVersion=this._version}return t?this._selectedCount:this._length-this._selectedCount}countWhere(t){let e=0;if(this.trueCount()==this._length)for(let n=0;n<this._length;n++)e+=t(n)?1:0;else for(let n=-1;-1!=(n=this.findNext(n,!0));)e+=t(n)?1:0;return e}andWithCountBits(t,e){if(0==this._length)return 0;let n=0;const r=this.lengthInInts;let o=0;for(;o<r-1;o++)for(let e=this._data[o]&t._data[o];0!=e;e>>>=8)n+=f._onBitCount[255&e];let i=this._data[o]&t._data[o];const s=31&this._length;for(0!=s&&(i&=~(4294967295<<s));0!=i;i>>>=8)n+=f._onBitCount[255&i];return e?n:this._length-n}clear(){this.setLength(0)}contains(t){return this.findNext(-1,t)>=0}get allTrue(){return this.countBits(!0)==this._length}get allFalse(){return this.countBits(!1)==this._length}get anyTrue(){return this.countBits(!0)>0}get anyFalse(){return this.countBits(!1)>0}findNext(t,e=!0){if(this.assureInRange(t,-1,this._length,"index"),t>=this._length-1)return-1;let n=31&(t=t<0?0:t+1);const r=this.lengthInInts;for(let o=Math.floor(t/32);o<r;o++){let r=e?this._data[o]:~this._data[o];if(0!=n)r&=4294967295<<n&4294967295,n=0;else if(!e&&-4294967296==r)continue;for(let e=0;0!=r;e+=8,r>>>=8){const n=f._firstOnBit[255&r];if(n>=0)return(t=n+32*o+e)>=this._length?-1:t}}return-1}findPrev(t,e=!0){if(0==t)return-1;this.assureInRange(t,-1,this._length,"index");let n=1+(t=t<0?this._length-1:t-1)&31;for(let r=Math.floor(t/32);r>=0;r--){let t=e?this._data[r]:~this._data[r];0!=n&&(t&=~(4294967295<<n),n=0);for(let e=24;0!=t;e-=8,t<<=8){const n=f._lastOnBit[t>>>24];if(n>=0)return n+32*r+e}}return-1}}f._onBitCount=Int8Array.from([0,1,1,2,1,2,2,3,1,2,2,3,2,3,3,4,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,4,5,5,6,5,6,6,7,5,6,6,7,6,7,7,8]),f._firstOnBit=Int8Array.from([-1,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,6,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,7,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,6,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0]),f._lastOnBit=Int8Array.from([-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7]),function(t){t.Levenshtein="Levenshtein",t.JaroWinkler="Jaro-Winkler",t.Manhattan="Manhattan",t.Onehot="One-Hot"}(r||(r={})),function(t){t.Euclidean="Euclidean"}(o||(o={})),function(t){t.Tanimoto="Tanimoto",t.Dice="Dice",t.Asymmetric="Asymmetric",t.BraunBlanquet="Braun-Blanquet",t.Cosine="Cosine",t.Kulczynski="Kulczynski",t.McConnaughey="Mc-Connaughey",t.RogotGoldberg="Rogot-Goldberg",t.Russel="Russel",t.Sokal="Sokal",t.Hamming="Hamming",t.Euclidean="Euclidean"}(i||(i={})),function(t){t.TanimotoIntArray="TanimotoIntArray"}(s||(s={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray",t.NumberArray="NumberArray"}(a||(a={})),function(t){t.Difference="Difference"}(u||(u={})),function(t){t.CommonItems="Common 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e=this.th.jsonData.codesToHelmDict[t],n=A(Array.from(new Set(Object.values(e[v.ti.LINKAGE]))).sort(b));return new RegExp(`${v.q7}.(${n})`,"g")}isValidFormat(t){return this.formats.includes(t)}getFormats(){return Object.keys(this.th.jsonData.codesToHelmDict)}validateFormat(t){if(!this.isValidFormat(t))throw new Error(`Invalid format: ${t}`)}isHelm(t){return t===h.NO.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(b)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(A(e)+"|\\([^()]*\\)|.","g")}}function A(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const _={LEFT:"RNA1{",RIGHT:"}$$$$"};class C{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new w(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===h.NO.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===h.NO.HELM)return this.formatToHelm(this.sequence,this.sourceFormat);if([this.sourceFormat,t].every((t=>e.includes(t)))){const e=this.formatToHelm(this.sequence,this.sourceFormat);return this.helmToFormat(e,t)}throw new Error(`ST: unsupported translation direction ${this.sourceFormat} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(A(Object.values(_)),"g");let r=t.replace(n,"");const o=this.formats.getHelmToFormatDict(e),i=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>i.includes(t)?o[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,v.iL).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),o=this.formats.getFormatRegExp(e),i=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(o,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${v.iL}.`),s=s.slice(0,-1),s[s.length-1]===v.q7&&(s=s.slice(0,-1)),s=s.replace(i,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${_.LEFT+s+_.RIGHT}`}}class E{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return h.NO.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const o=t[r];n[r]=e.getInvalidCodeIndex(o)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=p(this.libWrapper.getCodesByFormat(n));let o=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){o=e+1;break}r.some((e=>e===t.slice(o,o+e.length)))&&e.push(n)}return e}}var x=n(389);const T=$;var I=n.n(T);class P extends o.Package{get seqHelper(){if(!this._seqHelper)throw new Error("Package SequenceTranslator .seqHelper is not initialized");return this._seqHelper}get monomerLib(){if(!this._monomerLib)throw new Error("Monomer lib not loaded");return this._monomerLib}get jsonData(){if(!this._jsonData)throw new Error("Json data not loaded");return this._jsonData}get monomerLibWrapper(){if(!this._monomerLibWrapper)throw new Error("Monomer lib wrapper not loaded");return this._monomerLibWrapper}constructor(t={debug:!1}){super(),this.highlightInvalidSubsequence=t=>function(t,e){let n=0;const r=e.createFormatDetector(t).getFormat();null!==r&&(n=new d(t,e).getInvalidCodeIndex(r));const o=n<0||""===t,i=x.span([]);I()(i).css("-webkit-text-fill-color","var(--grey-6)");const s=x.span([]);return I()(s).css("-webkit-text-fill-color","red"),o?i.innerHTML=t:(i.innerHTML=t.slice(0,n),s.innerHTML=t.slice(n)),[i,s]}(t,this),super._logger=new s(super.logger,t.debug)}completeInit(t){this._seqHelper=t}async initLibData(){return this.initPromise||(this.initPromise=(async()=>{let t=(await this.getSettings()).MonomersPath;t&&await r.dapi.files.exists(t)||(this.logger.warning(`Monomers path '${t}' not found. Fallback to monomers sample path '${a}'.`),t=a),[this._jsonData,this._monomerLib]=await Promise.all([m(t),O(t)]),this._monomerLibWrapper=new y(this.monomerLib,this.jsonData)})()),this.initPromise}async getTranslationHelper(){return await r.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new d(t,this)}createFormatConverter(t,e){return new C(t,e,this)}createFormatDetector(t){return new E(t,this)}}async function O(t){const e=o.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const e=await(0,i.pj)();return await e.readLibrary(t,"monomer-lib.json")}finally{e.close()}}const S=["SS","AS"],N={SS:"Sense strand",AS:"Anti sense"},L=["3'","5'"];var M,D,B,R;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(M||(M={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(D||(D={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID",t.DATE="date"}(B||(B={})),function(t){t.CREATE="create",t.MODIFY="modify"}(R||(R={})),M.IS_ANTISENSE_STRAND_INCLUDED,M.NUCLEOTIDE_SEQUENCES,M.PHOSPHOROTHIOATE_LINKAGE_FLAGS,M.STRAND_TERMINUS_MODIFICATIONS,D.PATTERN_NAME,D.PATTERN_COMMENT,D.NUCLEOTIDES_WITH_NUMERIC_LABELS,Error,Error,n(802);const F=rxjs;var k;rxjs.operators,function(t){t.getTruncatedStrandData=function(t,e,n){return{nucleotides:t.slice(0,n),ptoFlags:e.slice(0,n+1)}},t.getExtendedStrandData=function(t,e,n,r){const o=n-t.length,i=t.concat(new Array(n-t.length).fill(r)),s=0===t.length?n+1:o;return{nucleotides:i,ptoFlags:e.concat(new Array(s).fill(!0))}}}(k||(k={}));var H=n(543),G=n.n(H),j=n(72),U=n.n(j),V=n(825),W=n.n(V),Y=n(659),q=n.n(Y),K=n(56),z=n.n(K),J=n(540),Q=n.n(J),Z=n(113),X=n.n(Z),tt=n(252),et={};et.styleTagTransform=X(),et.setAttributes=z(),et.insert=q().bind(null,"head"),et.domAPI=W(),et.insertStyleElement=Q(),U()(tt.A,et),tt.A&&tt.A.locals&&tt.A.locals;class nt{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return x.divV([x.h1("PTO"),x.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return S.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===S.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+S.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=x.input.bool("All PTO",{value:e});n.onInput.subscribe((()=>{const t=n.value;this.eventBus.setAllPTOLinkages(t)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((()=>{const t=this.eventBus.getPatternConfig().phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t);n.value=e}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),x.tooltip.bind(n.captionLabel,"Activate all phosphothioates"),n}addStyleToPtoInput(t){const e=t.captionLabel;e.classList.add("ui-label-right"),Object.assign(e.style,{textAlign:"left",maxWidth:"100px",minWidth:"40px",width:"auto"})}createFirstPtoInputs(){return S.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=x.input.bool(`First ${t} PTO`,{value:e});n.onInput.subscribe((()=>{const e=n.value;this.eventBus.setPhosphorothioateLinkageFlag(t,0,e)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const r=e[t][0];n.value=r}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),x.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class rt{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=S.map((t=>this.constructControlsPanel(t)));return x.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return x.div([]);const e=this.constructHeader(),n=this.createControls(t);return x.block([x.h1(`${N[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return x.divH([x.div([x.divText("#")],{style:{width:"20px"}}),x.block75([x.divText("Modification")]),x.div([x.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return x.div(e.map(((t,e)=>x.divH([n[e],x.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const o=x.input.choice("",{value:n,items:e});return o.onInput.subscribe((()=>{const e=o.value;this.eventBus.setNucleotide(t,r,e)})),o}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=x.input.bool("",{value:e});r.onInput.subscribe((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const o=e[t][n+1];r.value=o}));return this.subscriptions.add(o),r}))}computeDisplayedInputLabels(){const t=this.eventBus.getNucleotideSequences(),e=new Map;return S.forEach((n=>{let r=1;const o=t[n].map((t=>{if(function(t){return t.endsWith("(o)")}(t))return"";const e=String(r);return r++,e}));e.set(n,o)})),e}createLabelDivs(t){const e=this.createLabels(t).map((t=>x.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{I()(e[n]).empty(),I()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return x.label(r)}))}}class ot{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof F.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class it{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new ot}static open(t,e){it.isDialogOpen||(it.instance||(it.instance=new it(t,e)),it.instance.openDialog())}openDialog(){this.initialPatternConfig=G().cloneDeep(this.eventBus.getPatternConfig()),it.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=x.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=x.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{it.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new nt(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new rt(this.eventBus,this.dataManager,this.subscriptions).create();I()(t).empty(),I()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}it.isDialogOpen=!1;class st{constructor(t){this.eventBus=t,this.subscriptions=new ot}static open(t){st.isDialogOpen||(st.instance||(st.instance=new st(t)),st.instance.openDialog())}openDialog(){this.initialPatternConfig=G().cloneDeep(this.eventBus.getPatternConfig()),st.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=x.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=x.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{st.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new at(this.eventBus).create();I()(t).empty(),I()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}st.isDialogOpen=!1;class at{constructor(t){this.eventBus=t}create(){const t=S.map((t=>this.constructControlsPanel(t)));return x.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return x.div([]);const e=this.createInputs(t);return x.block([x.h1(`${N[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...L].reverse():L).map((e=>this.createInputForTerminus(t,e)));return x.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=x.input.textArea(e,{value:n});return this.applyStylingToInput(r),r.onInput.subscribe((()=>{const n=r.value;null!==n&&this.eventBus.updateTerminusModification(t,e,n)})),r}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];I()(e).css("resize","none")}}n(146);var ut=n(507),ct={};ct.styleTagTransform=X(),ct.setAttributes=z(),ct.insert=q().bind(null,"head"),ct.domAPI=W(),ct.insertStyleElement=Q(),U()(ut.A,ct),ut.A&&ut.A.locals&&ut.A.locals;var lt,ft=n(74),ht={};ht.styleTagTransform=X(),ht.setAttributes=z(),ht.insert=q().bind(null,"head"),ht.domAPI=W(),ht.insertStyleElement=Q(),U()(ft.A,ht),ft.A&&ft.A.locals&&ft.A.locals,function(t){t.TYPE="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t[t.MAX_ATOM_COUNT=999]="MAX_ATOM_COUNT",t.RGP_LINE_START="M RGP",t.ATOM_ALIAS_LINE_START="A ",t.END="M END"}(lt||(lt={})),Error,Error,n(670),n(3),n(480),n(67);var pt=n(254),dt={};dt.styleTagTransform=X(),dt.setAttributes=z(),dt.insert=q().bind(null,"head"),dt.domAPI=W(),dt.insertStyleElement=Q(),U()(pt.A,dt),pt.A&&pt.A.locals&&pt.A.locals;var gt=n(70);n(124),n(312),n(991),"object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,new Set;const mt="object"==typeof process&&process?process:{};let yt=globalThis.AbortController,vt=globalThis.AbortSignal;if(void 0===yt){vt=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(t,e){this._onabort.push(e)}},yt=class{constructor(){e()}signal=new vt;abort(t){if(!this.signal.aborted){this.signal.reason=t,this.signal.aborted=!0;for(const e of this.signal._onabort)e(t);this.signal.onabort?.(t)}}};let t="1"!==mt.env?.LRU_CACHE_IGNORE_AC_WARNING;const e=()=>{var n,r,o,i;t&&(t=!1,n="AbortController is not defined. If using lru-cache in node 14, load an AbortController polyfill from the `node-abort-controller` package. A minimal polyfill is provided for use by LRUCache.fetch(), but it should not be relied upon in other contexts (eg, passing it to other APIs that use AbortController/AbortSignal might have undesirable effects). You may disable this with LRU_CACHE_IGNORE_AC_WARNING=1 in the env.",r="NO_ABORT_CONTROLLER",o="ENOTSUP",i=e,"function"==typeof mt.emitWarning?mt.emitWarning(n,r,o,i):console.error(`[${o}] ${r}: ${n}`))}}Symbol("type"),Symbol.iterator,Symbol.toStringTag,Map,n(151),n(599),n(717),n(702),n(682);class bt extends o.InputBase{constructor(t,e){super(x.input.column(t,e).dart,e?.onValueChanged),this.options=e}setColumnInputTable(t){x.input.setColumnInputTable(this,t,this.options?.filter)}}var wt;x.input.column2=function(t,e){return new bt(t,e)},n(296),n(820),o.JsInputBase,o.JsInputBase,function(t){t.table="table",t.seqCol="seqCol",t.generateHelm="generateHelm",t.chiralityEngine="chiralityEngine",t.rules="rules"}(wt||(wt={}));class At{onKeyDown(t,e){}onKeyPress(t,e){}onMouseEnter(t,e){}onMouseLeave(t,e){}onMouseDown(t,e){}onMouseUp(t,e){}onMouseMove(t,e){}onClick(t,e){}onDoubleClick(t,e){}}class _t extends At{constructor(t,e,n){super(),this.gridCol=t,this.tableCol=e,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++_t.viewerCounter,this.errors=[],this._onRendered=new F.Subject,this.tableCol&&this.tableCol.dataFrame&&this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.tableCol&&this.subs.push(r.events.onTableRemoved.subscribe((t=>{try{const e=t.args.dataFrame;this.tableCol?.dataFrame.id!==e.id||this.destroyed||this.destroy()}catch(t){this.logger.error(t)}}))),this.gridCol&&this.subs.push(r.events.onViewRemoving.subscribe((t=>{try{const e=t.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===e.id&&!this.destroyed&&this.destroy()}catch(t){this.logger.error(t)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const t of this.subs)t.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(t){this.invalidateGrid()}async awaitRendered(t=1e4,e=`${t} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await(0,gt.PE)(this._onRendered,(()=>{}),(()=>{this.invalidate()}),t,`${n}, ${e}`),this.errors.length>0){const t=this.errors[0];throw this.errors=[],t}this.logger.debug(`${n}, end`)}}_t.viewerCounter=-1,n(192);var Ct,Et,xt,Tt=n(291);Tt.zS,function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(Ct||(Ct={})),function(t){t.applyToBackground=".m.cellRenderer.applyToBackground"}(Et||(Et={})),function(t){t.MSA="MSA",t.classic="classic"}(xt||(xt={})),new class{constructor(){this.color="rgb(100,100,100)",this.pivot=0,this.left=!1,this.transparencyRate=1,this.separator="",this.last=!1,this.drawStyle=xt.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0}},Tt.Mu;const It=new P({debug:!0})},682:(t,e,n)=>{"use strict";n.d(e,{by:()=>l,kl:()=>f,sW:()=>c});var r=n(328),o=(n(991),n(599)),i=(n(890),n(717),n(192)),s=n(124),a=n(296),u=n(544);class c{constructor(t,e,n){this.linkages=e,this.monomers=t,this.mol=n}static fromHelm(t){const e=t.split("$"),n=e[0].split("|"),r=e[1].split("|"),o=new Array(n.length),i=[];for(let t=0;t<n.length;t++){const e=n[t].indexOf("{"),r=n[t].indexOf("}");o[t]=n[t].slice(e+1,r).split(".")}for(let t=0;t<r.length;t++)if(""!==r[t]&&"V2.0"!==r[t]){const e=r[t].split(","),n=e[0].replace("PEPTIDE","")-1,o=e[1].replace("PEPTIDE","")-1,s=e[2].split("-"),a=s[0].split(":"),u=s[1].split(":");i.push({fChain:n,sChain:o,fMonomer:a[0],sMonomer:u[0],fR:a[1].replace("R",""),sR:u[1].replace("R","")})}return new c(o,i,null)}static fromNotation(t,e){const n=e.heterodimerCode,r=e.homodimerCode,o=[],i=[],s=null!==n?t.split(`(${e.heterodimerCode})`):"";null!==n&&s.length>1?(i.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),o.push(s[1].replaceAll("{","").replaceAll("}","")),o.push(s[2].replaceAll("{","").replaceAll("}",""))):o.push(t);for(let t=0;t<o.length;t++)if(null!==r&&o[t].includes(`(${r})`)){const e=o.length;i.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=o[t].replace(`(${r})`,""),s=n.indexOf("{"),a=n.slice(0,s),u=n.replace(a,"").replaceAll("{","").replaceAll("}","");o[t]=a+u,o.push(u)}for(let t=0;t<o.length;t++)if(null!==r&&o[t].includes(`(${r})`)){const e=o.length;i.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=o[t].replace(`(${r})`,""),s=n.indexOf("{"),a=n.slice(0,s),u=n.replace(a,"").replaceAll("{","").replaceAll("}","");o[t]=a+u,o.push(u)}const a=new Array(o.length);for(let t=0;t<o.length;t++){const n=o[t].split("-"),r=this.getLinkedPositions(n,e.linkRules),[s,u,c,l,f]=this.getAllCycles(e.linkRules,n,r);new Array(s.length);for(let e=0;e<u.length;e++)i.push({fChain:t,sChain:t,fMonomer:u[e],sMonomer:c[e],fR:l[e],sR:f[e]});a[t]=s}const u=[];for(let t=0;t<a.length;t++){const n=this.getLinkedPositions(a[t],e.reactionRules),[r,o,s,c]=this.getAllReactants(e.reactionRules,a[t],n);if(o.length>=1){const t=new Array(s[0]-1),n=new Array(r.length-s[0]);for(let e=0;e<s[0]-1;e++)t[e]=r[e];for(let t=s[0];t<r.length;t++)n[t-s[0]]=r[t];t[o[0]-1]=e.reactionRules[c[0]].name;for(let t=0;t<i.length;t++)i[t].fMonomer>s[0]&&(i[t].fMonomer-=s[0],i[t].fChain++),i[t].sMonomer>s[0]&&(i[t].sMonomer-=s[0],i[t].sChain++);i.push({fChain:0,sChain:0,fMonomer:o[0],sMonomer:s[0]-1,fR:3,sR:2}),i.push({fChain:0,sChain:1,fMonomer:o[0],sMonomer:1,fR:4,sR:1});const a=new Array(t.length);for(let e=0;e<t.length;e++)a[e]=`[${t[e]}]`;const l=new Array(n.length);for(let t=0;t<n.length;t++)l[t]=`[${n[t]}]`;u.push(t),u.push(n)}else u.push(a[t])}return new c(u,i,null)}static async parseNotation(t){const e=[],n=[],r=(await(0,s.b2)()).createHelmWebEditor().editor.m,i=/(\(.\d+\))?\{[^\}]*\}/g,a=[];a.push(t.replaceAll(i,""));const u=t.matchAll(i);for(const t of u){const e=t[0];e&&a.push(e)}let l=0;for(let t=0;t<a.length;t++){const r=a[t].split("-"),o=new Array(r.length);for(let e=0;e<r.length;e++){const i=r[e].replace("{","").replace("}","");""!==i?(o[e]=i,l++):n.push({fChain:t,sChain:t+1,fMonomer:l,sMonomer:l+1,fR:1,sR:1})}e.push(o)}l=0;const f=new JSDraw2.Point(0,0);for(let t=0;t<e.length;t++)for(let n=0;n<e[t].length;n++){if(e[t][n]){const i=e[t][n],s={type:o.o.AA,i:t,j:n},a=new JSDraw2.Atom(f,i,s);if(r.addAtom(a),0!==n){const t=r.atoms[l-1],e=r.atoms[l],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,r.addBond(n)}l++,f.x+=JSDraw2.Editor.BONDLENGTH}f.y+=4*JSDraw2.Editor.BONDLENGTH}for(let t=0;t<n.length;t++){const e=r.atoms[n[t].fMonomer-1],o=r.atoms[n[t].sMonomer-1],i=new JSDraw2.Bond(e,o);i.r1=n[t].fR,i.r2=n[t].sR,r.addBond(i)}return new c(e,n,r)}getHelmChanged(t,e){let n=0,r=0,o=0;t:for(let e=0;e<this.monomers.length;e++)for(let i=0;i<this.monomers[e].length;i++){if(n==t){r=e,o=i;break t}n++}const i=this.monomers[r][o];this.monomers[r][o]=`[${e}]`;const s=this.getHelm();return this.monomers[r][o]=i,s}getNotationHelm(){return this.getHelm()}getHelm(){let t="";for(let e=0;e<this.monomers.length;e++){e>0&&(t+="|"),t+=`PEPTIDE${e+1}{`;for(let n=0;n<this.monomers[e].length;n++){n>0&&(t+=".");const r=this.monomers[e][n];t+=r.length>1?`[${r}]`:r}t+="}"}t+="$";for(let e=0;e<this.linkages.length;e++)e>0&&(t+="|"),t+=`PEPTIDE${this.linkages[e].fChain+1},PEPTIDE${this.linkages[e].sChain+1},`,t+=`${this.linkages[e].fMonomer}:R${this.linkages[e].fR}-`,t+=`${this.linkages[e].sMonomer}:R${this.linkages[e].sR}`;return t+="$$$",t}getNotation(){const t=this.mol.atoms,e=this.mol.bonds,n=[],r=[];for(let t=0;t<e.length;t++)e[t].a1.bio.i!==e[t].a2.bio.i&&r.push(t);for(let e=0;e<t.length;e++){const r=t[e].bio?.i;r+1>n.length?n.push(1):n[r]++}const o=new Array(n.length);let i=0;for(let e=0;e<n.length;e++){const r=new Array(n[e]);for(let o=0;o<n[e];o++)r[o]=t[i].elem,i++;o[e]=r}let s="";for(let t=0;t<o.length;t++){let n="";for(let e=0;e<o[t].length;e++)n+=`${0==e?"":"-"}${o[t][e]}`;if(0!==t){const t=/(\(.\d+\))/,e=n.match(t);n=n.replace(e?.[0],""),n=`${e?e?.[0]:""}{${n}}`}else if(o.length>1){const t=0==e[r[0]].a1.bio.i&&0==e[r[0]].a1.bio.j,o=1==e[r[0]].a2.bio.i&&0==e[r[0]].a1.bio.j;t&&o&&(n+="-")}s+=n}return s}static getLinkedPositions(t,e){const n=new Array(e.length);for(let r=0;r<e.length;r++){let o=!1,i=!1,s=!1,a=-1,u=-1;const c=`(${e[r].code})`;for(let n=0;n<t.length;n++)if(t[n].includes(c)){if(o){if(s&&t[n]==e[r].secondMonomer+c){i=!0,u=n;break}if(s||t[n]!=e[r].firstMonomer+c)continue;i=!0,u=n;break}if(t[n]==e[r].firstMonomer+c)o=!0,s=!0,a=n;else{if(t[n]!=e[r].secondMonomer+c)continue;o=!0,s=!1,a=n}}n[r]=o&&i?s?[a,u,r]:[u,a,r]:[-1,-1,-1]}return n}static getAllCycles(t,e,n){const r=[],o=[],i=[],s=[],a=t.length;for(let u=0;u<a;u++){if(-1==n[u][0])continue;const a=e[n[u][0]],c=e[n[u][1]];e[n[u][0]]=e[n[u][0]].replace(a,t[u].firstSubstitution),e[n[u][1]]=e[n[u][1]].replace(c,t[u].secondSubstitution),r.push(n[u][0]+1),o.push(n[u][1]+1),i.push(t[u].firstLinkingGroup),s.push(t[u].secondLinkingGroup)}return[e,r,o,i,s]}static getAllReactants(t,e,n){const r=[],o=[],i=[],s=t.length;for(let a=0;a<s;a++){if(-1==n[a][0])continue;const 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Object.entries(o))(0,e.t6)(`${t}`,(async()=>{const t=(0,P.o)(n.src,"",n.params);(0,e.J6)(t,n.tgt.map((t=>[t.seq,t.name])))}))})),(0,e.L1)("PolyTool: Chain: parseNotation",(()=>{let t;(0,e.gM)((async()=>{t=await(0,T.b2)()}));const n={cyclized:{src:{seq:"R-F-C(1)-T-G-H-F-Y-P-C(1)-meI"},tgt:{helm:"PEPTIDE1{R.F.[C(1)].T.G.H.F.Y.P.[C(1)].[meI]}$$$$V2.0"}},dimerized1:{src:{seq:"(#2)Succ-{A(CHOL)-F-C(2)-T-G-H-Y-P-C(2)-NH2}"},tgt:{helm:"PEPTIDE1{[(#2)Succ]}|PEPTIDE2{[A(CHOL)].F.[C(2)].T.G.H.Y.P.[C(2)].[NH2]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$V2.0"}},dimerized2:{src:{seq:"($2)Succ-{R-F-C(1)-T-G-H-F-P-C(1)-NH2}($2){A(CHOL)-F-C(1)-T-G-H-F-P-C(1)-NH2}"},tgt:{helm:"PEPTIDE1{[($2)Succ]}|PEPTIDE2{R.F.[C(1)].T.G.H.F.P.[C(1)].[NH2]}|PEPTIDE3{[($2)A(CHOL)].F.[C(1)].T.G.H.F.P.[C(1)].[NH2]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$V2.0"}}};for(const[r,o]of Object.entries(n))(0,e.t6)(`${r}`,(async()=>{await(0,x.Q4)(["rules_example.json"]);const n=(await E.sW.parseNotation(o.src.seq)).mol,r=t.createHelmWebEditor();r.editor.setMol(n);const i=r.editor.getHelm();(0,e.E3)(i,o.tgt.helm)}),"reaction2"==r?{skipReason:"reverse reaction"}:void 0)}));var O=n(717);(0,e.L1)("toAtomicLevel",(()=>{let n,r,o;(0,e.gM)((async()=>{r=await(0,b.pj)(),n=await _(),o=await(0,O.j)(),await r.loadMonomerLibForTests()})),(0,e.Pl)((async()=>{await C(n),await r.loadMonomerLib(!0)})),(0,e.t6)("override",(async()=>{const n=r.getMonomerLib(),i=await S.files.readAsText("tests/polytool-reaction-lib.json"),s=JSON.parse(i).find((t=>"GGaz"===t.symbol));(0,e.E3)(null!=s,!0,"Monomer 'GGaz' not found.");const a={PEPTIDE:{GGaz:s}},u=n.override(a,"test"),c=await(0,d.Q)(),l=t.Column.fromList(t.COLUMN_TYPE.STRING,"helm",["PEPTIDE1{F.P.Y.[GGaz].H.A.A.G.G.A.C}|PEPTIDE2{A.A.A}$PEPTIDE1,PEPTIDE2,4:R4-1:R1|PEPTIDE1,PEPTIDE1,11:R2-4:R3$$$V2.0"]);l.semType=t.SEMTYPE.MACROMOLECULE,l.meta.units=g.Hi.HELM;const f=await c.helmToAtomicLevel(l,!1,!1,u);(0,e.E3)(null!=f.molCol,!0,"Result molCol is null");const h=f.molCol.get(0);(0,e.E3)(!!h,!0,"Molfile is empty");const p=o.get_mol(h);try{const t=p.get_inchi(),n=o.get_inchikey_for_inchi(t);(0,e.E3)(p.get_num_bonds(),103),(0,e.E3)(p.get_num_atoms(),98),(0,e.E3)(n,"XPQUTLNSNIMERR-WKBTUBAPSA-N")}finally{p.delete()}})),(0,e.t6)("getNewMonomer",(async()=>{const t=await(0,O.j)(),n=r.getMonomerLib(),o=(await(0,x.Q4)(["rules_example.json"])).reactionRules.find((t=>"GGaz"==t.name)),[i,s]=(0,E.kl)(t,n,o);(0,e.E3)(i,o.name);const a=t.get_mol(s.molfile);try{const n=a.get_inchi();t.get_inchikey_for_inchi(n),(0,e.E3)(a.get_num_bonds(),18),(0,e.E3)(a.get_num_atoms(),18)}finally{a.delete()}}))}));const S=new s;async function N(n,r,o){const i=await(0,e.N$)({category:n,test:r,testContext:o,verbose:!0});return t.DataFrame.fromObjects(i)}async function L(){await(0,e.Xb)(S,S.getModule("package-test.js"))}})(),sequencetranslator_test=r})();
2
+ var sequencetranslator_test;(()=>{var t={717:(t,e,n)=>{"use strict";n.d(e,{j:()=>o});var r=n(82);async function o(){const t=r.Func.find({package:"Chem",name:"getRdKitModule"});if(0===t.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await t[0].prepare().call()).getOutputParamValue()}},599:(t,e,n)=>{"use strict";n.d(e,{o:()=>r.o});var r=n(869)},124:(t,e,n)=>{"use strict";n.d(e,{b2:()=>i});var r=n(389),o=n(82);async function i(){const t="Helm",e=o.Func.find({package:t,name:"getHelmHelper"});if(0===e.length)throw new Error(`Package '${t}' must be installed for HelmHelper.`);return(await e[0].prepare().call()).getOutputParamValue()}o.JsInputBase,Error,r.input.helmAsync=async function(t,e){return(await i()).createHelmInput(t,e)}},890:(t,e,n)=>{"use strict";n.d(e,{pj:()=>p});var r,o,i,s,a,u,c,l=n(82);n(328);class f{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,r=f._createBuffer(n);if(e)for(let t=0;t<r.length;t++)r[t]=-1;this._data=r,this._length=n}else{if(!(t instanceof Uint32Array))throw new Error("Invalid constructor");this._data=t,this._length=e}}getRawData(){return this._data}assureGoez(t,e){if(t<0)throw new Error(`${e} should be greater than zero`)}assureInRange(t,e,n,r){if(t<e||t>n)throw new Error(`Argument ${r} (${t}) out of range (${e}, ${n})`)}copy(t,e,n){for(let r=0;r<n;r++)e[r]=t[r]}copyFrom(t){if(this._length!=t._length)throw new Error(`Lengths differ (${this._length} != ${t._length})`);this.copy(t._data,this._data,this.lengthInInts),this._version++}get length(){return this._length}get buffer(){return this._data}set buffer(t){this._data=t,this._version++}get version(){return this._version}set version(t){this._version=t}incrementVersion(t=!0){this._version++}get lengthInInts(){return Math.floor((this._length+31)/32)}get versionedName(){return this._version==this._versionedNameVersion?this._versionedName:""}set versionedName(t){this._versionedName=t,this._versionedNameVersion=this._version}get self(){return this}setLength(t){if(t<0)throw new Error("should be >= 0");if(t==this._length)return;const e=Math.floor((t+31)/32);if(e>this._data.length||e+this.SHRINK_THRESHOLD<this._data.length){const t=new Uint32Array(e);this.copy(this._data,t,e>this._data.length?this._data.length:e),this._data=t}t>this._length&&(this._length%32>0&&(this._data[this.lengthInInts-1]&=(1<<(this._length%32&31))-1),this._data.fill(0,this.lengthInInts,e)),this._length=t,this._version++}static fromAnd(t,e){if(t._length!=e._length)throw new Error(`Lengths differ (${t._length} != ${e._length})`);const n=new f(t._length);n._length=t._length,n._data=f._createBuffer(n._length),n._version=0;const r=t.lengthInInts;for(let o=0;o<r;o++)n._data[o]=t._data[o]&e._data[o];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new f(t.length);e._version=0;for(let n=0;n<e._length;n++)t[n]&&(e._data[Math.floor(n/32)]|=1<<(n%32&31));return e}static fromSeq(t,e){const n=new f(t);for(let r=0;r<t;++r)n.setBit(r,e(r));return n._version=0,n}static fromString(t){return f.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new f(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new f(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let r=0,o=0;for(;e-o>=4;)n._data[r++]=255&t[o]|(255&t[o+1])<<8|(255&t[o+2])<<16|(255&t[o+3])<<24,o+=4;return e-o==3&&(n._data[r]=(255&t[o+2])<<16),e-o==2&&(n._data[r]|=(255&t[o+1])<<8),e-o==1&&(n._data[r]|=255&t[o]),n._version=0,n}toString(){return`${this._length} bits, ${this.countBits(!0)} set`}equals(t){if(this==t)return!0;if(null==t)return!1;if(this._length!=t._length)return!1;if(0==this._length)return!0;for(let e=0;e<this._data.length-1;e++)if(this._data[e]!=t._data[e])return!1;for(let e=8*(this._data.length-1);e<this._length;e++)if(this.getBit(e)!=t.getBit(e))return!1;return!0}clone(){const t=new f(0,!1);return t._data=Uint32Array.from(this._data),t._length=this._length,t._version=this._version,t}init(t,e){this.setAll(!1,!1);for(let e=0;e<this._length;e++)t(e)&&(this._data[Math.floor(e/32)]|=1<<(e%32&31));return this.incrementVersion(e),this}invert(t=!0){for(let t=0;t<this._data.length;t++)this._data[t]^=-1;this.incrementVersion(t)}setAll(t,e=!1){const n=t?-1:0,r=this.lengthInInts;for(let t=0;t<r;t++)this._data[t]=n;this.incrementVersion(e)}setIndexes(t,e=!0,n=!0,r=!0){n&&this.setAll(!e,!1);for(const n of t)this.setFast(n,e);this.incrementVersion(r)}everyIndex(t,e=!0){for(const n of t)if(this.getBit(n)!=e)return!1;return!0}anyIndex(t,e=!0){for(const n of t)if(this.getBit(n)==e)return!0;return!1}setWhere(t,e=!0,n=!0,r=!0,o=!0){if(n&&o&&this.setAll(!e,!1),o)for(let n=0;n<this._length;n++)t(n)&&this.setFast(n,e);else for(let n=0;n<this._length;n++)this.setFast(n,t(n)?e:!e);this.incrementVersion(r)}getRange(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let r=t;r<e;++r)n.push(this.getBit(r));return f.fromValues(n)}getRangeAsList(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let r=t;r<e;++r)n.push(this.getBit(r));return n}setRange(t,e,n,r=!0){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length-1,"to");const o=Math.min(t,e),i=Math.max(t,e);if(n)for(let t=o;t<=i;t++)this.setTrue(t);else for(let t=o;t<=i;t++)this.setFalse(t);return this.incrementVersion(r),this}setRandom(t,e,n=!0){if(t<0||t>this._length)throw new Error("n must be >= 0 && <= Count");t>this._length/2&&this.setRandom(this._length-t,!e),this.setAll(!e);for(let n=0;n<t;){const t=Math.floor(Math.random()*this._length);this.getBit(t)!=e&&(this.setFast(t,e),n++)}this.incrementVersion(n)}and(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]&=t._data[e];return this.incrementVersion(e),this}andNot(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");const n=this.lengthInInts;for(let e=0;e<n;e++)this._data[e]&=~t._data[e];return this.incrementVersion(e),this}notAnd(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]=~this._data[e]&t._data[e];return this.incrementVersion(e),this}not(t=!0){for(let t=0,e=this.lengthInInts;t<e;t++)this._data[t]=~this._data[t];return this.incrementVersion(t),this}or(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]|=t._data[e];return this.incrementVersion(e),this}xor(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]^=t._data[e];return this.incrementVersion(e),this}insertAt(t,e,n=!1){if(this.assureInRange(t,0,this._length,"pos"),0==e)return;const r=this._length;this.setLength(this._length+e);for(let n=r-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let r=t;r<t+e;r++)this.setBit(r,n)}removeAt(t,e=1){if(e<0)throw new Error("n cannot be negative");if(this.assureInRange(t,0,this._length-e,"pos"),this.contains(!0))for(let n=t;n<this._length-e;n++)this.setBit(n,this.getBit(n+e));this.setLength(this._length-e)}removeByMask(t,e=!0){if(this._length!=t.length)throw new Error("length != mask.length");if(t==this)this.setLength(t.countBits(!e)),this.setAll(!e);else{let n=0;for(let r=-1;-1!=(r=t.findNext(r,!e));)this.setFast(n++,this.getBit(r));this._length=n,this._version++}return this}getBit(t){return!!(this._data[Math.floor(t/32)]&1<<(31&t))}setBit(t,e,n=!0){this.setFast(t,e),this._version++}setFast(t,e){e?this._data[Math.floor(t/32)]|=1<<(31&t):this._data[Math.floor(t/32)]&=~(1<<(31&t))}setTrue(t){this._data[Math.floor(t/32)]|=1<<(31&t)}setFalse(t){this._data[Math.floor(t/32)]&=~(1<<(31&t))}trueCount(){return this.countBits(!0)}falseCount(){return this.countBits(!1)}countBits(t){if(0==this._length)return 0;if(this._selectedCountVersion!=this._version){this._selectedCount=0;const t=this.lengthInInts;let e=0;for(;e<t-1;e++)for(let t=this._data[e];0!=t;t>>>=8)this._selectedCount+=f._onBitCount[255&t];let n=this._data[e];const r=31&this._length;for(0!=r&&(n&=~(4294967295<<r));0!=n;n>>>=8)this._selectedCount+=f._onBitCount[255&n];this._selectedCountVersion=this._version}return t?this._selectedCount:this._length-this._selectedCount}countWhere(t){let e=0;if(this.trueCount()==this._length)for(let n=0;n<this._length;n++)e+=t(n)?1:0;else for(let n=-1;-1!=(n=this.findNext(n,!0));)e+=t(n)?1:0;return e}andWithCountBits(t,e){if(0==this._length)return 0;let n=0;const r=this.lengthInInts;let o=0;for(;o<r-1;o++)for(let e=this._data[o]&t._data[o];0!=e;e>>>=8)n+=f._onBitCount[255&e];let i=this._data[o]&t._data[o];const s=31&this._length;for(0!=s&&(i&=~(4294967295<<s));0!=i;i>>>=8)n+=f._onBitCount[255&i];return e?n:this._length-n}clear(){this.setLength(0)}contains(t){return this.findNext(-1,t)>=0}get allTrue(){return this.countBits(!0)==this._length}get allFalse(){return this.countBits(!1)==this._length}get anyTrue(){return this.countBits(!0)>0}get anyFalse(){return this.countBits(!1)>0}findNext(t,e=!0){if(this.assureInRange(t,-1,this._length,"index"),t>=this._length-1)return-1;let n=31&(t=t<0?0:t+1);const r=this.lengthInInts;for(let o=Math.floor(t/32);o<r;o++){let r=e?this._data[o]:~this._data[o];if(0!=n)r&=4294967295<<n&4294967295,n=0;else if(!e&&-4294967296==r)continue;for(let e=0;0!=r;e+=8,r>>>=8){const n=f._firstOnBit[255&r];if(n>=0)return(t=n+32*o+e)>=this._length?-1:t}}return-1}findPrev(t,e=!0){if(0==t)return-1;this.assureInRange(t,-1,this._length,"index");let n=1+(t=t<0?this._length-1:t-1)&31;for(let r=Math.floor(t/32);r>=0;r--){let t=e?this._data[r]:~this._data[r];0!=n&&(t&=~(4294967295<<n),n=0);for(let e=24;0!=t;e-=8,t<<=8){const n=f._lastOnBit[t>>>24];if(n>=0)return n+32*r+e}}return-1}}f._onBitCount=Int8Array.from([0,1,1,2,1,2,2,3,1,2,2,3,2,3,3,4,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,4,5,5,6,5,6,6,7,5,6,6,7,6,7,7,8]),f._firstOnBit=Int8Array.from([-1,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,6,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,7,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,6,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0]),f._lastOnBit=Int8Array.from([-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7]),function(t){t.Levenshtein="Levenshtein",t.JaroWinkler="Jaro-Winkler",t.Manhattan="Manhattan",t.Onehot="One-Hot"}(r||(r={})),function(t){t.Euclidean="Euclidean"}(o||(o={})),function(t){t.Tanimoto="Tanimoto",t.Dice="Dice",t.Asymmetric="Asymmetric",t.BraunBlanquet="Braun-Blanquet",t.Cosine="Cosine",t.Kulczynski="Kulczynski",t.McConnaughey="Mc-Connaughey",t.RogotGoldberg="Rogot-Goldberg",t.Russel="Russel",t.Sokal="Sokal",t.Hamming="Hamming",t.Euclidean="Euclidean"}(i||(i={})),function(t){t.TanimotoIntArray="TanimotoIntArray"}(s||(s={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray",t.NumberArray="NumberArray"}(a||(a={})),function(t){t.Difference="Difference"}(u||(u={})),function(t){t.CommonItems="Common 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this.getNonHelmFormatRegExp(t)}getPhosphateHelmCodesRegExp(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t],n=w(Array.from(new Set(Object.values(e[v.ti.LINKAGE]))).sort(b));return new RegExp(`${v.q7}.(${n})`,"g")}isValidFormat(t){return this.formats.includes(t)}getFormats(){return Object.keys(this.th.jsonData.codesToHelmDict)}validateFormat(t){if(!this.isValidFormat(t))throw new Error(`Invalid format: ${t}`)}isHelm(t){return t===h.NO.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(b)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(w(e)+"|\\([^()]*\\)|.","g")}}function w(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const A={LEFT:"RNA1{",RIGHT:"}$$$$"};class E{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new C(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===h.NO.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===h.NO.HELM)return this.formatToHelm(this.sequence,this.sourceFormat);if([this.sourceFormat,t].every((t=>e.includes(t)))){const e=this.formatToHelm(this.sequence,this.sourceFormat);return this.helmToFormat(e,t)}throw new Error(`ST: unsupported translation direction ${this.sourceFormat} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(w(Object.values(A)),"g");let r=t.replace(n,"");const o=this.formats.getHelmToFormatDict(e),i=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>i.includes(t)?o[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,v.iL).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),o=this.formats.getFormatRegExp(e),i=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(o,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${v.iL}.`),s=s.slice(0,-1),s[s.length-1]===v.q7&&(s=s.slice(0,-1)),s=s.replace(i,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${A.LEFT+s+A.RIGHT}`}}class _{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return h.NO.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const o=t[r];n[r]=e.getInvalidCodeIndex(o)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=p(this.libWrapper.getCodesByFormat(n));let o=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){o=e+1;break}r.some((e=>e===t.slice(o,o+e.length)))&&e.push(n)}return e}}var x=n(389);const T=$;var I=n.n(T);class P extends o.Package{get seqHelper(){if(!this._seqHelper)throw new Error("Package SequenceTranslator .seqHelper is not initialized");return this._seqHelper}get monomerLib(){if(!this._monomerLib)throw new Error("Monomer lib not loaded");return this._monomerLib}get jsonData(){if(!this._jsonData)throw new Error("Json data not loaded");return this._jsonData}get monomerLibWrapper(){if(!this._monomerLibWrapper)throw new Error("Monomer lib wrapper not loaded");return this._monomerLibWrapper}get initPromise(){return this._initPromise}constructor(t={debug:!1}){super(),this.highlightInvalidSubsequence=t=>function(t,e){let n=0;const r=e.createFormatDetector(t).getFormat();null!==r&&(n=new d(t,e).getInvalidCodeIndex(r));const o=n<0||""===t,i=x.span([]);I()(i).css("-webkit-text-fill-color","var(--grey-6)");const s=x.span([]);return I()(s).css("-webkit-text-fill-color","red"),o?i.innerHTML=t:(i.innerHTML=t.slice(0,n),s.innerHTML=t.slice(n)),[i,s]}(t,this),super._logger=new s(super.logger,t.debug)}startInit(t){this._initPromise=t}completeInit(t){this._seqHelper=t}async initLibData(){return this.initLibDataPromise||(this.initLibDataPromise=(async()=>{let t=(await this.getSettings()).MonomersPath;t&&await r.dapi.files.exists(t)||(this.logger.warning(`Monomers path '${t}' not found. Fallback to monomers sample path '${a}'.`),t=a),[this._jsonData,this._monomerLib]=await Promise.all([m(t),S(t)]),this._monomerLibWrapper=new y(this.monomerLib,this.jsonData)})()),this.initLibDataPromise}async getTranslationHelper(){return await r.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new d(t,this)}createFormatConverter(t,e){return new E(t,e,this)}createFormatDetector(t){return new _(t,this)}}async function S(t){const e=o.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const e=await(0,i.pj)();return await e.readLibrary(t,"monomer-lib.json")}finally{e.close()}}const O=["SS","AS"],N={SS:"Sense strand",AS:"Anti sense"},L=["3'","5'"];var M,D,R,B;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(M||(M={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(D||(D={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID",t.DATE="date"}(R||(R={})),function(t){t.CREATE="create",t.MODIFY="modify"}(B||(B={})),M.IS_ANTISENSE_STRAND_INCLUDED,M.NUCLEOTIDE_SEQUENCES,M.PHOSPHOROTHIOATE_LINKAGE_FLAGS,M.STRAND_TERMINUS_MODIFICATIONS,D.PATTERN_NAME,D.PATTERN_COMMENT,D.NUCLEOTIDES_WITH_NUMERIC_LABELS,Error,Error,n(802);const F=rxjs;var H;rxjs.operators,function(t){t.getTruncatedStrandData=function(t,e,n){return{nucleotides:t.slice(0,n),ptoFlags:e.slice(0,n+1)}},t.getExtendedStrandData=function(t,e,n,r){const o=n-t.length,i=t.concat(new Array(n-t.length).fill(r)),s=0===t.length?n+1:o;return{nucleotides:i,ptoFlags:e.concat(new Array(s).fill(!0))}}}(H||(H={}));var k=n(543),G=n.n(k),j=n(72),U=n.n(j),V=n(825),W=n.n(V),Y=n(659),q=n.n(Y),K=n(56),z=n.n(K),J=n(540),Q=n.n(J),X=n(113),Z=n.n(X),tt=n(252),et={};et.styleTagTransform=Z(),et.setAttributes=z(),et.insert=q().bind(null,"head"),et.domAPI=W(),et.insertStyleElement=Q(),U()(tt.A,et),tt.A&&tt.A.locals&&tt.A.locals;class nt{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return x.divV([x.h1("PTO"),x.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return O.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===O.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+O.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=x.input.bool("All PTO",{value:e});n.onInput.subscribe((()=>{const t=n.value;this.eventBus.setAllPTOLinkages(t)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((()=>{const t=this.eventBus.getPatternConfig().phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t);n.value=e}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),x.tooltip.bind(n.captionLabel,"Activate all phosphothioates"),n}addStyleToPtoInput(t){const e=t.captionLabel;e.classList.add("ui-label-right"),Object.assign(e.style,{textAlign:"left",maxWidth:"100px",minWidth:"40px",width:"auto"})}createFirstPtoInputs(){return O.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=x.input.bool(`First ${t} PTO`,{value:e});n.onInput.subscribe((()=>{const e=n.value;this.eventBus.setPhosphorothioateLinkageFlag(t,0,e)}));const r=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const r=e[t][0];n.value=r}));return this.subscriptions.add(r),this.addStyleToPtoInput(n),x.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class rt{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=O.map((t=>this.constructControlsPanel(t)));return x.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return x.div([]);const e=this.constructHeader(),n=this.createControls(t);return x.block([x.h1(`${N[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return x.divH([x.div([x.divText("#")],{style:{width:"20px"}}),x.block75([x.divText("Modification")]),x.div([x.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return x.div(e.map(((t,e)=>x.divH([n[e],x.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const o=x.input.choice("",{value:n,items:e});return o.onInput.subscribe((()=>{const e=o.value;this.eventBus.setNucleotide(t,r,e)})),o}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=x.input.bool("",{value:e});r.onInput.subscribe((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.subscribe((e=>{const o=e[t][n+1];r.value=o}));return this.subscriptions.add(o),r}))}computeDisplayedInputLabels(){const t=this.eventBus.getNucleotideSequences(),e=new Map;return O.forEach((n=>{let r=1;const o=t[n].map((t=>{if(function(t){return t.endsWith("(o)")}(t))return"";const e=String(r);return r++,e}));e.set(n,o)})),e}createLabelDivs(t){const e=this.createLabels(t).map((t=>x.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{I()(e[n]).empty(),I()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return x.label(r)}))}}class ot{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof F.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class it{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new ot}static open(t,e){it.isDialogOpen||(it.instance||(it.instance=new it(t,e)),it.instance.openDialog())}openDialog(){this.initialPatternConfig=G().cloneDeep(this.eventBus.getPatternConfig()),it.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=x.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=x.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{it.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new nt(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new rt(this.eventBus,this.dataManager,this.subscriptions).create();I()(t).empty(),I()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}it.isDialogOpen=!1;class st{constructor(t){this.eventBus=t,this.subscriptions=new ot}static open(t){st.isDialogOpen||(st.instance||(st.instance=new st(t)),st.instance.openDialog())}openDialog(){this.initialPatternConfig=G().cloneDeep(this.eventBus.getPatternConfig()),st.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=x.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=x.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{st.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new at(this.eventBus).create();I()(t).empty(),I()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}st.isDialogOpen=!1;class at{constructor(t){this.eventBus=t}create(){const t=O.map((t=>this.constructControlsPanel(t)));return x.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return x.div([]);const e=this.createInputs(t);return x.block([x.h1(`${N[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...L].reverse():L).map((e=>this.createInputForTerminus(t,e)));return x.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=x.input.textArea(e,{value:n});return this.applyStylingToInput(r),r.onInput.subscribe((()=>{const n=r.value;null!==n&&this.eventBus.updateTerminusModification(t,e,n)})),r}applyStylingToInput(t){const e=t.root.getElementsByTagName("textarea")[0];I()(e).css("resize","none")}}n(146);var ut=n(507),ct={};ct.styleTagTransform=Z(),ct.setAttributes=z(),ct.insert=q().bind(null,"head"),ct.domAPI=W(),ct.insertStyleElement=Q(),U()(ut.A,ct),ut.A&&ut.A.locals&&ut.A.locals;var lt,ft=n(74),ht={};ht.styleTagTransform=Z(),ht.setAttributes=z(),ht.insert=q().bind(null,"head"),ht.domAPI=W(),ht.insertStyleElement=Q(),U()(ft.A,ht),ft.A&&ft.A.locals&&ft.A.locals,function(t){t.TYPE="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t[t.MAX_ATOM_COUNT=999]="MAX_ATOM_COUNT",t.RGP_LINE_START="M RGP",t.ATOM_ALIAS_LINE_START="A ",t.END="M END"}(lt||(lt={})),Error,Error,n(670),n(3),n(480),n(67);var pt=n(254),dt={};dt.styleTagTransform=Z(),dt.setAttributes=z(),dt.insert=q().bind(null,"head"),dt.domAPI=W(),dt.insertStyleElement=Q(),U()(pt.A,dt),pt.A&&pt.A.locals&&pt.A.locals;var gt=n(70);n(124),n(312),n(991),"object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,new Set;const mt="object"==typeof process&&process?process:{};let yt=globalThis.AbortController,vt=globalThis.AbortSignal;if(void 0===yt){vt=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(t,e){this._onabort.push(e)}},yt=class{constructor(){e()}signal=new vt;abort(t){if(!this.signal.aborted){this.signal.reason=t,this.signal.aborted=!0;for(const e of this.signal._onabort)e(t);this.signal.onabort?.(t)}}};let t="1"!==mt.env?.LRU_CACHE_IGNORE_AC_WARNING;const e=()=>{var n,r,o,i;t&&(t=!1,n="AbortController is not defined. If using lru-cache in node 14, load an AbortController polyfill from the `node-abort-controller` package. A minimal polyfill is provided for use by LRUCache.fetch(), but it should not be relied upon in other contexts (eg, passing it to other APIs that use AbortController/AbortSignal might have undesirable effects). You may disable this with LRU_CACHE_IGNORE_AC_WARNING=1 in the env.",r="NO_ABORT_CONTROLLER",o="ENOTSUP",i=e,"function"==typeof mt.emitWarning?mt.emitWarning(n,r,o,i):console.error(`[${o}] ${r}: ${n}`))}}Symbol("type"),Symbol.iterator,Symbol.toStringTag,Map,n(151),n(599),n(717),n(702),n(948);class bt extends o.InputBase{constructor(t,e){super(x.input.column(t,e).dart,e?.onValueChanged),this.options=e}setColumnInputTable(t){x.input.setColumnInputTable(this,t,this.options?.filter)}}var Ct;x.input.column2=function(t,e){return new bt(t,e)},n(296),n(820),o.JsInputBase,o.JsInputBase,function(t){t.table="table",t.seqCol="seqCol",t.generateHelm="generateHelm",t.chiralityEngine="chiralityEngine",t.rules="rules"}(Ct||(Ct={}));class wt{onKeyDown(t,e){}onKeyPress(t,e){}onMouseEnter(t,e){}onMouseLeave(t,e){}onMouseDown(t,e){}onMouseUp(t,e){}onMouseMove(t,e){}onClick(t,e){}onDoubleClick(t,e){}}class At extends wt{constructor(t,e,n){super(),this.gridCol=t,this.tableCol=e,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++At.viewerCounter,this.errors=[],this._onRendered=new F.Subject,this.tableCol&&this.tableCol.dataFrame&&this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.tableCol&&this.subs.push(r.events.onTableRemoved.subscribe((t=>{try{const e=t.args.dataFrame;this.tableCol?.dataFrame.id!==e.id||this.destroyed||this.destroy()}catch(t){this.logger.error(t)}}))),this.gridCol&&this.subs.push(r.events.onViewRemoving.subscribe((t=>{try{const e=t.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===e.id&&!this.destroyed&&this.destroy()}catch(t){this.logger.error(t)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const t of this.subs)t.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(t){this.invalidateGrid()}async awaitRendered(t=1e4,e=`${t} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await(0,gt.PE)(this._onRendered,(()=>{}),(()=>{this.invalidate()}),t,`${n}, ${e}`),this.errors.length>0){const t=this.errors[0];throw this.errors=[],t}this.logger.debug(`${n}, end`)}}At.viewerCounter=-1,n(192);var Et,_t,xt,Tt=n(291);Tt.zS,function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(Et||(Et={})),function(t){t.applyToBackground=".m.cellRenderer.applyToBackground"}(_t||(_t={})),function(t){t.MSA="MSA",t.classic="classic"}(xt||(xt={})),new class{constructor(){this.color="rgb(100,100,100)",this.pivot=0,this.left=!1,this.transparencyRate=1,this.separator="",this.last=!1,this.drawStyle=xt.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0}},Tt.Mu;const It=new P({debug:!0})},948:(t,e,n)=>{"use strict";n.d(e,{sW:()=>h,by:()=>p,MH:()=>m,kl:()=>d,jX:()=>y,AM:()=>g});var r=n(328),o=n(991),i=n.n(o),s=n(599),a=n(890),u=n(717),c=n(192),l=n(296),f=n(544);class h{constructor(t,e,n){this.linkages=e,this.monomers=t,this.mol=n}static parseHelm(t,e){const n=/(\w+\{.*\})\$(.*)\$(.*)\$(.*)\$/g.exec(t),r=[n[1],n[2],n[3],n[4]],o=r[0].split("|"),i=r[1].split("|"),a=new Array(o.length),u=[],c=e.createHelmWebEditor().editor.m;let l=0;const f=new JSDraw2.Point(0,0);for(let t=0;t<o.length;t++){const e=o[t].indexOf("{"),n=o[t].indexOf("}");a[t]=o[t].slice(e+1,n).split(".").map((t=>{return(e=t).startsWith("[")&&e.endsWith("]")?e.slice(1,-1):e;var e}));for(let e=0;e<a[t].length;e++){const n=a[t][e],r={type:s.o.AA,i:t,j:e,continuousId:l},o=new JSDraw2.Atom(f,n,r);if(c.addAtom(o),0!==e){const t=c.atoms[l-1],e=c.atoms[l],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,c.addBond(n)}l++,f.x+=JSDraw2.Editor.BONDLENGTH}f.y+=4*JSDraw2.Editor.BONDLENGTH}for(let t=0;t<i.length;t++)if(""!==i[t]&&"V2.0"!==i[t]){const e=i[t].split(","),n=parseInt(e[0].replace("PEPTIDE",""))-1,r=parseInt(e[1].replace("PEPTIDE",""))-1,o=e[2].split("-"),s=o[0].split(":"),c=o[1].split(":");u.push({fChain:n,sChain:r,fMonomer:y(parseInt(s[0]),n,a),sMonomer:y(parseInt(c[0]),r,a),fR:parseInt(s[1].replace("R","")),sR:parseInt(c[1].replace("R",""))})}for(let t=0;t<u.length;t++){const e=c.atoms[u[t].fMonomer-1],n=c.atoms[u[t].sMonomer-1],r=new JSDraw2.Bond(e,n);r.r1=u[t].fR,r.r2=u[t].sR,c.addBond(r)}return new h(a,u,c)}applyRules(t){throw this.monomers.map((t=>[...t])),this.linkages,this.mol.clone(),new Error("not implemented")}static fromNotation(t,e,n){const r=e.heterodimerCode,o=e.homodimerCode,i=[],a=[],u=null!==r?t.split(`(${e.heterodimerCode})`):"";null!==r&&u.length>1?(a.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),i.push(u[1].replaceAll("{","").replaceAll("}","")),i.push(u[2].replaceAll("{","").replaceAll("}",""))):i.push(t);for(let t=0;t<i.length;t++)if(null!==o&&i[t].includes(`(${o})`)){const e=i.length;a.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=i[t].replace(`(${o})`,""),r=n.indexOf("{"),s=n.slice(0,r),u=n.replace(s,"").replaceAll("{","").replaceAll("}","");i[t]=s+u,i.push(u)}for(let t=0;t<i.length;t++)if(null!==o&&i[t].includes(`(${o})`)){const e=i.length;a.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=i[t].replace(`(${o})`,""),r=n.indexOf("{"),s=n.slice(0,r),u=n.replace(s,"").replaceAll("{","").replaceAll("}","");i[t]=s+u,i.push(u)}const c=new Array(i.length);for(let t=0;t<i.length;t++){const n=i[t].split("-"),r=this.getLinkedPositions(n,e.linkRules),[o,s,u,l,f]=this.getAllCycles(e.linkRules,n,r);new Array(o.length);for(let e=0;e<s.length;e++)a.push({fChain:t,sChain:t,fMonomer:s[e],sMonomer:u[e],fR:l[e],sR:f[e]});c[t]=o}const l=[],f=n.createHelmWebEditor().editor.m;let p=0;const d=new JSDraw2.Point(0,0);for(let t=0;t<c.length;t++){const n=this.getLinkedPositions(c[t],e.reactionRules),[r,o,i,u]=this.getAllReactants(e.reactionRules,c[t],n);if(o.length>=1){const n=new Array(i[0]-1),c=new Array(r.length-i[0]);for(let e=0;e<i[0]-1;e++){const o=n[e]=r[e],i={type:s.o.AA,i:t,j:e,continuousId:p},a=new JSDraw2.Atom(d,o,i);if(f.addAtom(a),e>0){const t=f.atoms[p-1],e=f.atoms[p],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,f.addBond(n)}p++}for(let e=i[0];e<r.length;e++){const n=c[e-i[0]]=r[e],o={type:s.o.AA,i:t,j:e,continuousId:p},a=new JSDraw2.Atom(d,n,o);if(f.addAtom(a),e>i[0]){const t=f.atoms[p-1],e=f.atoms[p],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,f.addBond(n)}p++}f.atoms[o[0]-1].elem=n[o[0]-1]=e.reactionRules[u[0]].name;for(let t=0;t<a.length;t++)a[t].fMonomer>i[0]&&(a[t].fMonomer-=i[0],a[t].fChain++),a[t].sMonomer>i[0]&&(a[t].sMonomer-=i[0],a[t].sChain++);a.push({fChain:0,sChain:0,fMonomer:o[0],sMonomer:i[0]-1,fR:3,sR:2}),a.push({fChain:0,sChain:1,fMonomer:o[0],sMonomer:1,fR:4,sR:1});const h=new Array(n.length);for(let t=0;t<n.length;t++)h[t]=`[${n[t]}]`;const g=new Array(c.length);for(let t=0;t<c.length;t++)g[t]=`[${c[t]}]`;l.push(n),l.push(c)}else{for(let e=0;e<c[t].length;e++){const n=c[t][e],r={type:s.o.AA,i:t,j:e,continuousId:p},o=new JSDraw2.Atom(d,n,r);if(f.addAtom(o),e>0){const t=f.atoms[p-1],e=f.atoms[p],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,f.addBond(n)}p++}l.push(c[t])}}for(const t of a){const e=f.atoms[t.fMonomer-1],n=f.atoms[t.sMonomer-1],r=new JSDraw2.Bond(e,n);r.r1=t.fR,r.r2=t.sR,f.addBond(r)}return new h(l,a,f)}static parseNotation(t,e){const n=[],r=[],o=e.createHelmWebEditor().editor.m,i=/(\(.\d+\))?\{[^\}]*\}/g,a=[];a.push(t.replaceAll(i,""));const u=t.matchAll(i);for(const t of u){const e=t[0];e&&a.push(e)}let c=0;for(let t=0;t<a.length;t++){const e=a[t].split("-"),o=new Array(e.length);let i=0;for(let n=0;n<e.length;n++){const s=e[n].replace("{","").replace("}","");""!==s?(o[n]=s,c++,i++):r.push({fChain:t,sChain:t+1,fMonomer:c,sMonomer:c+1,fR:1,sR:1})}n.push(o.slice(0,i))}c=0;const l=new JSDraw2.Point(0,0);for(let t=0;t<n.length;t++)for(let e=0;e<n[t].length;e++){if(n[t][e]){const r=n[t][e],i={type:s.o.AA,i:t,j:e,continuousId:c},a=new JSDraw2.Atom(l,r,i);if(o.addAtom(a),0!==e){const t=o.atoms[c-1],e=o.atoms[c],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,o.addBond(n)}c++,l.x+=JSDraw2.Editor.BONDLENGTH}l.y+=4*JSDraw2.Editor.BONDLENGTH}for(let t=0;t<r.length;t++){const e=o.atoms[r[t].fMonomer-1],n=o.atoms[r[t].sMonomer-1],i=new JSDraw2.Bond(e,n);i.r1=r[t].fR,i.r2=r[t].sR,o.addBond(i)}return new h(n,r,o)}getHelmChanged(t,e){let n=0,r=0,o=0;t:for(let e=0;e<this.monomers.length;e++)for(let i=0;i<this.monomers[e].length;i++){if(n==t){r=e,o=i;break t}n++}const i=this.monomers[r][o];this.monomers[r][o]=`[${e}]`;const s=this.getHelm();return this.monomers[r][o]=i,s}getNotationHelm(){return this.getHelm()}getHelm(){let t="";for(let e=0;e<this.monomers.length;e++){e>0&&(t+="|"),t+=`PEPTIDE${e+1}{`;for(let n=0;n<this.monomers[e].length;n++){n>0&&(t+=".");const r=this.monomers[e][n];t+=r.length>1?`[${r}]`:r}t+="}"}t+="$";for(let e=0;e<this.linkages.length;e++)e>0&&(t+="|"),t+=`PEPTIDE${this.linkages[e].fChain+1},PEPTIDE${this.linkages[e].sChain+1},`,t+=`${m(this.linkages[e].fMonomer-1,this.monomers)[0]+1}:R${this.linkages[e].fR}-`,t+=`${m(this.linkages[e].sMonomer-1,this.monomers)[0]+1}:R${this.linkages[e].sR}`;return t+="$$$V2.0",t}getNotation(){const t=this.mol.atoms,e=this.mol.bonds,n=[],r=[];for(let t=0;t<e.length;t++)e[t].a1.bio.i!==e[t].a2.bio.i&&r.push(t);for(let e=0;e<t.length;e++){const r=t[e].bio?.i;r+1>n.length?n.push(1):n[r]++}const o=new Array(n.length);let i=0;for(let e=0;e<n.length;e++){const r=new Array(n[e]);for(let o=0;o<n[e];o++)r[o]=t[i].elem,i++;o[e]=r}let s="";for(let t=0;t<o.length;t++){let n="";for(let e=0;e<o[t].length;e++)n+=`${0==e?"":"-"}${o[t][e]}`;if(0!==t){const t=/(\(.\d+\))/,e=n.match(t);n=n.replace(e?.[0],""),n=`${e?e?.[0]:""}{${n}}`}else if(o.length>1){const t=0==e[r[0]].a1.bio.i&&0==e[r[0]].a1.bio.j,o=1==e[r[0]].a2.bio.i&&0==e[r[0]].a1.bio.j;t&&o&&(n+="-")}s+=n}return s}static getLinkedPositions(t,e){const n=new Array(e.length);for(let r=0;r<e.length;r++){let o=!1,i=!1,s=!1,a=-1,u=-1;const c=`(${e[r].code})`;for(let n=0;n<t.length;n++)if(t[n].includes(c)){if(o){if(s&&t[n]==e[r].secondMonomer+c){i=!0,u=n;break}if(s||t[n]!=e[r].firstMonomer+c)continue;i=!0,u=n;break}if(t[n]==e[r].firstMonomer+c)o=!0,s=!0,a=n;else{if(t[n]!=e[r].secondMonomer+c)continue;o=!0,s=!1,a=n}}n[r]=o&&i?s?[a,u,r]:[u,a,r]:[-1,-1,-1]}return n}static getAllCycles(t,e,n){const r=[],o=[],i=[],s=[],a=t.length;for(let u=0;u<a;u++){if(-1==n[u][0])continue;const a=e[n[u][0]],c=e[n[u][1]];e[n[u][0]]=e[n[u][0]].replace(a,t[u].firstSubstitution),e[n[u][1]]=e[n[u][1]].replace(c,t[u].secondSubstitution),r.push(n[u][0]+1),o.push(n[u][1]+1),i.push(t[u].firstLinkingGroup),s.push(t[u].secondLinkingGroup)}return[e,r,o,i,s]}static getAllReactants(t,e,n){const r=[],o=[],i=[],s=t.length;for(let a=0;a<s;a++){if(-1==n[a][0])continue;const s=e[n[a][0]],u=e[n[a][1]];e[n[a][0]]=e[n[a][0]].replace(s,t[a].firstMonomer),e[n[a][1]]=e[n[a][1]].replace(u,t[a].secondMonomer),r.push(n[a][0]+1),o.push(n[a][1]+1),i.push(n[a][2])}return[e,r,o,i]}check(t=!1){const e=[],n=this.monomers.map((t=>t.length)).reduce(((t,e)=>t+e),0);this.mol.atoms.length!==n&&e.push(`The mol atoms count ${this.mol.atoms.length} does not match the total number ${n} of chains' monomers.`);const r=this.monomers.map((t=>t.length-1)).reduce(((t,e)=>t+e),0)+this.linkages.length;this.mol.bonds.length!==r&&e.push(`The mol bonds count ${this.mol.bonds.length} does not match the total number ${r} in- and inter-chain linkages.`);let o=0;for(let t=0;t<this.monomers.length;++t){const n=this.monomers[t];for(let t=0;t<n.length;++t)try{const r=n[t],i=this.mol.atoms[o];i.bio.continuousId!==o&&e.push(`Atom #${o} has incorrect .bio.continuousId: ${i.bio.continuousId}.`),i.elem!==r&&e.push(`Atom #${o} elem: '${i.elem}' does not match chain monomer: '${r}'.`)}finally{o++}}if(t&&e.length>0)throw new Error(`Chain errors:\n${e.map((t=>` ${t}`)).join("\n")}`);return e}}function p(t,e,n){const r=new Array(t.length);for(let o=0;o<t.length;o++)try{if(null==t[o])r[o]="";else{const i=h.fromNotation(t[o],e,n);r[o]=i.getHelm()}}catch(t){const[e,n]=(0,c.AP)(t);f._package.logger.error(e,void 0,n),r[o]=""}return r}function d(t,e,n){const o=n.reaction,i=n.name,s=e.getMonomer("PEPTIDE",n.firstMonomer);if(!s)throw new l.bl("PEPTIDE",n.firstMonomer);const a=e.getMonomer("PEPTIDE",n.secondMonomer);if(!a)throw new l.bl("PEPTIDE",n.secondMonomer);const[u,f]=function(t,e){const n=t.molfile;let r=e.molfile;const o=t.rgroups.length,i=r.indexOf("M RGP");if(-1!==i){const t=r.substring(i+6,i+9),e=Number(t);for(let t=0;t<e;t++){const e=i+9+4+8*t,n=i+9+8+8*t,s=r.substring(e,n),a=Number(s)+o,u=Math.floor(Math.log10(a)+1),c=" ".repeat(4-u)+String(a);r=r.substring(0,e)+c+r.substring(n,r.length)}}return[n,r]}(s,a),h=function(t,e,n,o,i){let s=null,a=null,u=null,f=null,h=null,p=null,d="";try{if(s=t.get_rxn(e),!s)throw new l.J5(e);a=new t.MolList,u=t.get_mol(n),f=t.get_mol(o),a.append(u),a.append(f),h=s.run_reactants(a,1),p=h.get(0).next(),d=p?.get_molblock()}catch(t){const[e,n]=(0,c.AP)(t);throw r.shell.error(`Can not assemble monomer '${i}': ${e}.`),t}finally{s?.delete(),a?.delete(),u?.delete(),f?.delete(),h?.delete(),p?.delete()}return d}(t,o,u,f,i),p=function(t,e){const n=new Array(t?.rgroups.length+e?.rgroups.length),r=t?.rgroups.length,o=e?.rgroups.length;for(let e=0;e<r;e++)n[e]=t?.rgroups[e];for(let t=0;t<o;t++){const o=e?.rgroups[t].label.replace("R",""),i=Number(o)+r,s={capGroupSMILES:e?.rgroups[t].capGroupSMILES.replace(o,String(i)),alternateId:e?.rgroups[t].alternateId.replace(o,String(i)),capGroupName:e?.rgroups[t].capGroupName,label:e?.rgroups[t].label.replace(o,String(i))};n[t+r]=s}return n}(s,a),d={symbol:i,name:i,molfile:h,author:"",id:0,rgroups:p,smiles:"",polymerType:"PEPTIDE",monomerType:"Backbone",createDate:null};return d.meta=Object.assign(d.meta??{},{colors:{default:{line:"#2083D5",text:"#2083D5",background:"#F2F2F5"}}}),[i,d]}async function g(t){const e=(await(0,a.pj)()).getMonomerLib(),n=await(0,u.j)(),r={};for(let o=0;o<t.reactionRules.length;o++){const[i,s]=d(n,e,t.reactionRules[o]);r[i]=s}const o={PEPTIDE:r};return e.override(o,"ST-PT-reactions."+i().repeat(1).map((()=>Math.floor(36*Math.random()).toString(36))).take(4).toArray().join(""))}function m(t,e){let n,r=t;for(n=0;n<e.length&&r>=e[n].length;++n)r-=e[n].length;return[r,n]}function y(t,e,n){let r=0;for(let t=0;t<e;++t)r+=n[t].length;return r+t}},820:(t,e,n)=>{"use strict";n.d(e,{o:()=>i});var r=n(296);function o(t,e,n,r){const o=new Array(r.length*(n-e+1));for(let i=0;i<r.length;++i){const s=n-e+1;for(let n=0;n<s;++n){const a=e+n,u=r[i],c=o[i*s+n]=t.clone(),l=c.atoms[a].elem;c.atoms[a].elem=u;const f=l?.length>1?`[${l}]`:l,h=u?.length>1?`[${u}]`:u;c.name=`${t.name}-${f}${a+1}${h}`}}return o}function i(t,e,n){const i=new JSDraw2.MolHandler,s=new org.helm.webeditor.Plugin(i);org.helm.webeditor.IO.parseHelm(s,t,new JSDraw2.Point(0,0),void 0);const a=i.m;a.name=e;let u=[];if(n.placeholders)switch(n.type){case r.aK.Single:u=function(t,e){return e.map((e=>o(t,e.position,e.position,e.monomers))).reduce(((t,e)=>t.concat(e)),[])}(i.m,n.placeholders);break;case r.aK.Matrix:u=function(t,e){let n=[t];for(const t of e){const e=n.map((e=>o(e,t.position,t.position,t.monomers)));n=e.reduce(((t,e)=>t.concat(e)),[])}return n}(i.m,n.placeholders)}let c=[];n.breadthPlaceholders&&(c=function(t,e){if(0==e.length)return[];let n=[t];for(const t of e){const e=n.map((e=>o(e,t.start,t.end,t.monomers)));n=e.reduce(((t,e)=>t.concat(e)),[])}return n}(i.m,n.breadthPlaceholders)),u=u.concat(c),n.keepOriginal&&(u=[a,...u]);const l=u.map((t=>[org.helm.webeditor.IO.getHelm(t),t.name]));return l}},702:(t,e,n)=>{"use strict";n.d(e,{Q4:()=>l});var r=n(82),o=n(328);n(389),n(991);const 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o={single1:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:P.aK.Single,placeholders:[{position:4,monomers:["K","P","F4COO"]},{position:6,monomers:["Y","T"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5P"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5[F4COO]"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7T"}]},"single-with-original":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:P.aK.Single,placeholders:[{position:4,monomers:["K","P","F4COO"]},{position:6,monomers:["Y","T"]}],keepOriginal:!0},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:""},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5P"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5[F4COO]"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7T"}]},matrix1:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:P.aK.Matrix,placeholders:[{position:1,monomers:["D","L"]},{position:4,monomers:["K","P","F4COO"]},{position:6,monomers:["Y","T"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].D.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5K-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5K-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5P-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5P-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5[F4COO]-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5[F4COO]-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5K-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5K-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5P-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5P-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5[F4COO]-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5[F4COO]-[Tic]7T"}]}};for(const[t,n]of Object.entries(o))(0,e.t6)(`${t}`,(async()=>{const t=(0,S.o)(n.src,"",n.params);(0,e.J6)(t,n.tgt.map((t=>[t.seq,t.name])))}))})),(0,e.L1)("PolyTool: Enumerate",(()=>{let t,n,r;(0,e.gM)((async()=>{t=await(0,x.b2)(),n=await(0,b.pj)(),r=await A(),await n.loadMonomerLibForTests()})),(0,e.Pl)((async()=>{await E(r),await n.loadMonomerLib(!0)}));const o={breadth1:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:P.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"}]},"breadth1-with-original":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:P.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]}],keepOriginal:!0},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:""},{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"}]},breadth2:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:P.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K","Y"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"},{seq:"PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5Y"}]},"breadth-double":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:P.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]},{start:2,end:4,monomers:["Y"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-K3Y"},{seq:"PEPTIDE1{[Ac(1)].F.K.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.K.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-P5Y"},{seq:"PEPTIDE1{[Ac(1)].F.Y.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-K4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-P5Y"},{seq:"PEPTIDE1{[Ac(1)].F.Y.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-K5Y"}]}};for(const[t,n]of Object.entries(o))(0,e.t6)(`${t}`,(async()=>{const t=(0,S.o)(n.src,"",n.params);(0,e.J6)(t,n.tgt.map((t=>[t.seq,t.name])))}))})),(0,e.L1)("PolyTool: Chain: parseNotation",(()=>{let t;(0,e.gM)((async()=>{t=await(0,x.b2)()}));const n={cyclized:{src:{seq:"R-F-C(1)-T-G-H-F-Y-P-C(1)-meI"},tgt:{helm:"PEPTIDE1{R.F.[C(1)].T.G.H.F.Y.P.[C(1)].[meI]}$$$$V2.0"}},dimerized1:{src:{seq:"(#3)Succ-{A(CHOL)-F-C(1)-T-G-H-Y-P-C(1)-NH2}"},tgt:{helm:"PEPTIDE1{[(#3)Succ]}|PEPTIDE2{[A(CHOL)].F.[C(1)].T.G.H.Y.P.[C(1)].[NH2]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$V2.0"}},dimerized2:{src:{seq:"($3)Succ-{R-F-C(1)-T-G-H-F-P-C(1)-NH2}($2){A(CHOL)-F-C(1)-T-G-H-F-P-C(1)-NH2}"},tgt:{helm:"PEPTIDE1{[($3)Succ]}|PEPTIDE2{R.F.[C(1)].T.G.H.F.P.[C(1)].[NH2]}|PEPTIDE3{[($2)A(CHOL)].F.[C(1)].T.G.H.F.P.[C(1)].[NH2]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$V2.0"}}};for(const[r,o]of Object.entries(n))(0,e.t6)(`${r}`,(async()=>{await(0,I.Q4)(["rules_example.json"]);const n=await T.sW.parseNotation(o.src.seq,t),r=n.mol,i=t.createHelmWebEditor();i.editor.setMol(r);const s=i.editor.getHelm(),a=n.getNotationHelm();(0,e.E3)(s,o.tgt.helm),(0,e.E3)(a,o.tgt.helm)}),"reaction2"==r?{skipReason:"reverse reaction"}:void 0);const r={"0-in-4-4-3":{inIdx:0,spIdx:0,outIdx:0,monomers:[["0","1","2","3"],["4","5","6","7"],["8","9","10"]]},"3-in-4-4-3":{inIdx:3,spIdx:0,outIdx:3,monomers:[["0","1","2","3"],["4","5","6","7"],["8","9","10"]]},"4-in-4-4-3":{inIdx:0,spIdx:1,outIdx:4,monomers:[["0","1","2","3"],["4","5","6","7"],["8","9","10"]]},"7-in-4-4-3":{inIdx:3,spIdx:1,outIdx:7,monomers:[["0","1","2","3"],["4","5","6","7"],["8","9","10"]]},"8-in-4-4-3":{inIdx:0,spIdx:2,outIdx:8,monomers:[["0","1","2","3"],["4","5","6","7"],["8","9","10"]]},"0-in-1-1-6-3":{inIdx:0,spIdx:0,outIdx:0,monomers:[["0"],["1"],["2","3","4","5","6","7"],["8","9","10"]]},"1-in-1-1-6-3":{inIdx:0,spIdx:1,outIdx:1,monomers:[["0"],["1"],["2","3","4","5","6","7"],["8","9","10"]]},"2-in-1-1-6-3":{inIdx:0,spIdx:2,outIdx:2,monomers:[["0"],["1"],["2","3","4","5","6","7"],["8","9","10"]]},"3-in-1-1-6-3":{inIdx:1,spIdx:2,outIdx:3,monomers:[["0"],["1"],["2","3","4","5","6","7"],["8","9","10"]]},"7-in-1-1-6-3":{inIdx:5,spIdx:2,outIdx:7,monomers:[["0"],["1"],["2","3","4","5","6","7"],["8","9","10"]]},"8-in-1-1-6-3":{inIdx:0,spIdx:3,outIdx:8,monomers:[["0"],["1"],["2","3","4","5","6","7"],["8","9","10"]]}};for(const[t,{inIdx:n,spIdx:o,outIdx:i,monomers:s}]of Object.entries(r))(0,e.t6)(`innerIdx-${t}`,(async()=>{const[t,r]=(0,T.MH)(i,s);(0,e.E3)(t,n),(0,e.E3)(r,o)}));for(const[t,{inIdx:n,spIdx:o,outIdx:i,monomers:s}]of Object.entries(r))(0,e.t6)(`outerIdx-${t}`,(async()=>{const t=(0,T.jX)(n,o,s);(0,e.E3)(t,i)}))})),(0,e.L1)("PolyTool: Chain",(()=>{let t;(0,e.gM)((async()=>{t=await(0,x.b2)()}));const n={cyclized:{data:{templateSeq:"R-F-C(1)-T-G-H-F-Y-P-C(1)-meI",templateHelm:"PEPTIDE1{R.F.[C(1)].T.G.H.F.Y.P.[C(1)].[meI]}$$$$V2.0",mmHelm:"PEPTIDE1{R.F.C.T.G.H.F.Y.P.C.[meI]}$PEPTIDE1,PEPTIDE1,3:R3-10:R3$$$V2.0"},tgt:{templateChain:{monomerCount:[11],linkageCount:0},mmChain:{monomerCount:[11],linkageCount:1}}},reaction1:{data:{templateSeq:"R-F-azG(4)-T-G-H-F-Y-P-aG(4)-meI",templateHelm:"PEPTIDE1{R.F.[azG(4)].T.G.H.F.Y.P.[aG(4)].[meI]}$$$$V2.0",mmHelm:"PEPTIDE1{R.F.[GGaz].T.G.H.F.Y.P}|PEPTIDE2{[meI]}$PEPTIDE1,PEPTIDE1,3:R3-9:R2|PEPTIDE1,PEPTIDE2,3:R4-1:R1$$$V2.0"},tgt:{templateChain:{monomerCount:[11],linkageCount:0},mmChain:{monomerCount:[9,1],linkageCount:2}}},reaction2:{data:{templateSeq:"R-F-aG(4)-T-G-H-F-Y-P-azG(4)-meI",templateHelm:"PEPTIDE1{R.F.[aG(4)].T.G.H.F.Y.P.[azG(4)].[meI]}$$$$V2.0",mmHelm:"PEPTIDE1{R.F}|PEPTIDE2{T.G.H.F.Y.P.[GGaz].[meI]}$PEPTIDE1,PEPTIDE2,2:R2-7:R3|PEPTIDE2,PEPTIDE2,1:R1-7:R4,$$$V2.0"},tgt:{templateChain:{monomerCount:[11],linkageCount:0},mmChain:{monomerCount:[2,8],linkageCount:2}}},dimerized1:{data:{templateSeq:"(#3)Succ-{A(CHOL)-F-C(1)-T-G-H-Y-P-C(1)-NH2}",templateHelm:"PEPTIDE1{[(#3)Succ]}|PEPTIDE2{[A(CHOL)].F.[C(1)].T.G.H.Y.P.[C(1)].[NH2]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$V2.0",mmHelm:"PEPTIDE1{[Succ].[A(CHOL)].F.C.T.G.H.Y.P.C.[NH2]}|PEPTIDE2{[A(CHOL)].F.C.T.G.H.Y.P.C.[NH2]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1|PEPTIDE1,PEPTIDE1,4:R3-10:R3|PEPTIDE2,PEPTIDE2,3:R3-9:R3$$$V2.0"},tgt:{templateChain:{monomerCount:[1,10],linkageCount:1},mmChain:{monomerCount:[11,10],linkageCount:3}}},dimerized2:{data:{templateSeq:"($3)Succ-{R-F-C(1)-T-G-H-F-P-C(1)-NH2}($3){A(CHOL)-F-C(1)-Y-H-G-D-N-C(1)-meI}",templateHelm:"PEPTIDE1{[($3)Succ]}|PEPTIDE2{R.F.[C(1)].T.G.H.F.P.[C(1)].[NH2]}|PEPTIDE3{[($3)A(CHOL)].F.[C(1)].Y.H.G.D.N.[C(1)].[meI]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$V2.0",mmHelm:"PEPTIDE1{[Succ].R.F.C.T.G.H.F.P.C.[NH2]}|PEPTIDE2{[A(CHOL)].F.C.Y.H.G.D.N.C.[meI]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1|PEPTIDE1,PEPTIDE1,4:R3-10:R3|PEPTIDE2,PEPTIDE2,3:R3-9:R3$$$V2.0"},tgt:{templateChain:{monomerCount:[1,10,10],linkageCount:1},mmChain:{monomerCount:[11,10],linkageCount:3}}}};for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`fromNotation-${r}`,(async()=>{const n=await(0,I.Q4)(["rules_example.json"]),r=T.sW.fromNotation(o.templateSeq,n,t);r.check(!0),(0,e.J6)(r.monomers.map((t=>t.length)),i.mmChain.monomerCount),(0,e.E3)(r.linkages.length,i.mmChain.linkageCount),(0,e.E3)(r.getHelm(),o.mmHelm)}),"reaction2"==r?{skipReason:"reverse reaction"}:void 0);for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`parseNotation-${r}`,(async()=>{await(0,I.Q4)(["rules_example.json"]);const n=T.sW.parseNotation(o.templateSeq,t);n.check(!0),(0,e.J6)(n.monomers.map((t=>t.length)),i.templateChain.monomerCount),(0,e.E3)(n.linkages.length,i.templateChain.linkageCount),(0,e.E3)(n.getHelm(),o.templateHelm),(0,e.E3)(n.getNotation(),o.templateSeq)}));for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`parseHelm-${r}`,(async()=>{await(0,I.Q4)(["rules_example.json"]);const n=T.sW.parseHelm(o.templateHelm,t);n.check(!0),(0,e.J6)(n.monomers.map((t=>t.length)),i.templateChain.monomerCount),(0,e.E3)(n.linkages.length,i.templateChain.linkageCount),(0,e.E3)(n.getHelm(),o.templateHelm),(0,e.E3)(n.getNotation(),o.templateSeq)}));for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`applyRules-${r}`,(async()=>{const n=await(0,I.Q4)(["rules_example.json"]),r=T.sW.parseNotation(o.templateSeq,t).applyRules(n);r.check(!0),(0,e.J6)(r.monomers.map((t=>t.length)),i.mmChain.monomerCount),(0,e.E3)(r.linkages.length,i.mmChain.linkageCount),(0,e.E3)(r.getHelm(),o.mmHelm)}),{skipReason:"applyRules is not implemented"})})),(0,e.L1)("toAtomicLevel",(()=>{let n,r,o;(0,e.gM)((async()=>{r=await(0,b.pj)(),n=await A(),o=await(0,_.j)(),await r.loadMonomerLibForTests()})),(0,e.Pl)((async()=>{await E(n),await r.loadMonomerLib(!0)})),(0,e.t6)("override",(async()=>{const n=r.getMonomerLib(),i=await O.files.readAsText("tests/polytool-reaction-lib.json"),s=JSON.parse(i).find((t=>"GGaz"===t.symbol));(0,e.E3)(null!=s,!0,"Monomer 'GGaz' not found.");const a={PEPTIDE:{GGaz:s}},u=n.override(a,"test"),c=await(0,d.Q)(),l=t.Column.fromList(t.COLUMN_TYPE.STRING,"helm",["PEPTIDE1{F.P.Y.[GGaz].H.A.A.G.G.A.C}|PEPTIDE2{A.A.A}$PEPTIDE1,PEPTIDE2,4:R4-1:R1|PEPTIDE1,PEPTIDE1,11:R2-4:R3$$$V2.0"]);l.semType=t.SEMTYPE.MACROMOLECULE,l.meta.units=g.Hi.HELM;const f=await c.helmToAtomicLevel(l,!1,!1,u);(0,e.E3)(null!=f.molCol,!0,"Result molCol is null");const h=f.molCol.get(0);(0,e.E3)(!!h,!0,"Molfile is empty");const p=o.get_mol(h);try{const t=p.get_inchi(),n=o.get_inchikey_for_inchi(t);(0,e.E3)(p.get_num_bonds(),103),(0,e.E3)(p.get_num_atoms(),98),(0,e.E3)(n,"XPQUTLNSNIMERR-WKBTUBAPSA-N")}finally{p.delete()}})),(0,e.t6)("getNewMonomer",(async()=>{const t=await(0,_.j)(),n=r.getMonomerLib(),o=(await(0,I.Q4)(["rules_example.json"])).reactionRules.find((t=>"GGaz"==t.name)),[i,s]=(0,T.kl)(t,n,o);(0,e.E3)(i,o.name);const a=t.get_mol(s.molfile);try{const n=a.get_inchi();t.get_inchikey_for_inchi(n),(0,e.E3)(a.get_num_bonds(),18),(0,e.E3)(a.get_num_atoms(),18)}finally{a.delete()}}))}));const O=new s;async function N(n,r,o){const i=await(0,e.N$)({category:n,test:r,testContext:o,verbose:!0});return t.DataFrame.fromObjects(i)}async function L(){await(0,e.Xb)(O,O.getModule("package-test.js"))}})(),sequencetranslator_test=r})();
3
3
  //# sourceMappingURL=package-test.js.map