@datagrok/sequence-translator 1.5.0 → 1.5.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (10) 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/package.json +1 -1
  7. package/src/package.ts +3 -0
  8. package/src/polytool/conversion/pt-misc.ts +13 -3
  9. package/src/polytool/conversion/pt-rules.ts +3 -1
  10. package/src/polytool/conversion/rule-manager.ts +31 -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 '${t}' must be installed for HelmHelper.`);return(await e[0].prepare().call()).getOutputParamValue()}o.JsInputBase,Error,r.input.helmAsync=async function(t,e){return(await i()).createHelmInput(t,e)}},890:(t,e,n)=>{"use strict";n.d(e,{pj:()=>p});var r,o,i,s,a,u,l,c=n(82);n(328);class f{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,r=f._createBuffer(n);if(e)for(let t=0;t<r.length;t++)r[t]=-1;this._data=r,this._length=n}else{if(!(t instanceof Uint32Array))throw new Error("Invalid constructor");this._data=t,this._length=e}}getRawData(){return this._data}assureGoez(t,e){if(t<0)throw new Error(`${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 Items"}(l||(l={}));new Uint32Array(65536);var h;async function p(){const t=c.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(h||(h={})),h.HAMMING,h.LEVENSHTEIN,h.NEEDLEMANN_WUNSCH,h.MONOMER_CHEMICAL_DISTANCE,i.Tanimoto,i.Dice,i.Asymmetric,i.BraunBlanquet,i.Cosine,i.Kulczynski,i.McConnaughey,i.RogotGoldberg,i.Russel,i.Sokal,i.Hamming,i.Euclidean,i.Tanimoto,i.Dice,i.Asymmetric,i.BraunBlanquet,i.Cosine,i.Kulczynski,i.McConnaughey,i.RogotGoldberg,i.Russel,i.Sokal,i.Hamming,i.Euclidean,i.Tanimoto,i.Dice,i.Cosine,i.Tanimoto,i.Asymmetric,i.Cosine,i.Sokal,h.HAMMING,h.LEVENSHTEIN,h.MONOMER_CHEMICAL_DISTANCE,h.NEEDLEMANN_WUNSCH,n(151),n(439)},151:(t,e,n)=>{"use strict";new 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A{constructor(t){this.th=t,this.formats=this.getFormats()}getFormatNames(){return this.formats.sort()}getCodesByFormat(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Codes cannot be obtained for HELM");return this.getFormatCodes(t)}getHelmToFormatDict(t){return this.validateFormat(t),function(t){const e={};return Object.values(t).forEach((t=>{Object.entries(t).forEach((([t,n])=>{const r=n.replace(/\)p/g,")").replace(/\]p/g,"]");void 0===e[r]?e[r]=[t]:e[r].push(t)}))})),Object.entries(e).forEach((([t,n])=>{const r=n.sort(w);e[t]=r[0]})),e}(this.th.jsonData.codesToHelmDict[t])}getFormatToHelmDict(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t];return Object.assign({},...Object.values(e))}getTargetFormatHelmCodes(t){this.validateFormat(t);const e=this.getHelmToFormatDict(t);return Object.keys(e).sort(w)}getTargetFormatHelmCodesRegExp(t){this.validateFormat(t);const e=this.getTargetFormatHelmCodes(t);return new RegExp(_(e)+"|.","g")}getFormatRegExp(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Helm RegExp can be built for non-HELM target formats");return this.getNonHelmFormatRegExp(t)}getPhosphateHelmCodesRegExp(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t],n=_(Array.from(new Set(Object.values(e[C.ti.LINKAGE]))).sort(w));return new RegExp(`${C.q7}.(${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: ${t}`)}isHelm(t){return t===d.NO.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(w)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(_(e)+"|\\([^()]*\\)|.","g")}}function _(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const E={LEFT:"RNA1{",RIGHT:"}$$$$"};class x{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new A(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===d.NO.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===d.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} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(_(Object.values(E)),"g");let r=t.replace(n,"");const o=this.formats.getHelmToFormatDict(e),i=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>i.includes(t)?o[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,C.iL).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),o=this.formats.getFormatRegExp(e),i=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(o,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${C.iL}.`),s=s.slice(0,-1),s[s.length-1]===C.q7&&(s=s.slice(0,-1)),s=s.replace(i,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${E.LEFT+s+E.RIGHT}`}}class T{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return d.NO.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const o=t[r];n[r]=e.getInvalidCodeIndex(o)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=g(this.libWrapper.getCodesByFormat(n));let o=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){o=e+1;break}r.some((e=>e===t.slice(o,o+e.length)))&&e.push(n)}return e}}var I=n(389);const P=$;var S=n.n(P);class L extends o.Package{get helmHelper(){if(!this._helmHelper)throw new Error("Package SequenceTranslator .helmHelper is not initialized");return this._helmHelper}get seqHelper(){return this._helmHelper.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 m(t,e).getInvalidCodeIndex(r));const o=n<0||""===t,i=I.span([]);S()(i).css("-webkit-text-fill-color","var(--grey-6)");const s=I.span([]);return S()(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 u(super.logger,t.debug)}startInit(t){this._initPromise=t}completeInit(t){this._helmHelper=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 '${t}' not found. Fallback to monomers sample path '${l}'.`),t=l),[this._jsonData,this._monomerLib]=await Promise.all([v(t),M(t)]),this._monomerLibWrapper=new b(this.monomerLib,this.jsonData)})()),this.initLibDataPromise}async getTranslationHelper(){return await r.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new m(t,this)}createFormatConverter(t,e){return new x(t,e,this)}createFormatDetector(t){return new T(t,this)}}async function M(t){const e=o.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const e=await(0,a.pj)();return await e.readLibrary(t,"monomer-lib.json")}finally{e.close()}}const O=["SS","AS"],N={SS:"Sense strand",AS:"Anti sense"},R=["3'","5'"];var D,H,B,F;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(D||(D={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(H||(H={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID",t.DATE="date"}(B||(B={})),function(t){t.CREATE="create",t.MODIFY="modify"}(F||(F={})),D.IS_ANTISENSE_STRAND_INCLUDED,D.NUCLEOTIDE_SEQUENCES,D.PHOSPHOROTHIOATE_LINKAGE_FLAGS,D.STRAND_TERMINUS_MODIFICATIONS,H.PATTERN_NAME,H.PATTERN_COMMENT,H.NUCLEOTIDES_WITH_NUMERIC_LABELS,Error,Error,n(802);const k=rxjs;var G;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))}}}(G||(G={}));var j=n(543),U=n.n(j),V=n(72),W=n.n(V),q=n(825),Y=n.n(q),K=n(659),z=n.n(K),J=n(56),Q=n.n(J),X=n(540),Z=n.n(X),tt=n(113),et=n.n(tt),nt=n(252),rt={};rt.styleTagTransform=et(),rt.setAttributes=Q(),rt.insert=z().bind(null,"head"),rt.domAPI=Y(),rt.insertStyleElement=Z(),W()(nt.A,rt),nt.A&&nt.A.locals&&nt.A.locals;class ot{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return I.divV([I.h1("PTO"),I.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=I.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),I.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=I.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),I.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class it{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=O.map((t=>this.constructControlsPanel(t)));return I.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return I.div([]);const e=this.constructHeader(),n=this.createControls(t);return I.block([I.h1(`${N[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return I.divH([I.div([I.divText("#")],{style:{width:"20px"}}),I.block75([I.divText("Modification")]),I.div([I.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return I.div(e.map(((t,e)=>I.divH([n[e],I.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const o=I.input.choice("",{value:n,items:e});return o.onInput.subscribe((()=>{const e=o.value;this.eventBus.setNucleotide(t,r,e)})),o}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=I.input.bool("",{value:e});r.onInput.subscribe((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.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=>I.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{S()(e[n]).empty(),S()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return I.label(r)}))}}class st{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof k.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class at{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new st}static open(t,e){at.isDialogOpen||(at.instance||(at.instance=new at(t,e)),at.instance.openDialog())}openDialog(){this.initialPatternConfig=U().cloneDeep(this.eventBus.getPatternConfig()),at.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=I.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=I.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{at.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new ot(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new it(this.eventBus,this.dataManager,this.subscriptions).create();S()(t).empty(),S()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}at.isDialogOpen=!1;class ut{constructor(t){this.eventBus=t,this.subscriptions=new st}static open(t){ut.isDialogOpen||(ut.instance||(ut.instance=new ut(t)),ut.instance.openDialog())}openDialog(){this.initialPatternConfig=U().cloneDeep(this.eventBus.getPatternConfig()),ut.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=I.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=I.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{ut.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new lt(this.eventBus).create();S()(t).empty(),S()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}ut.isDialogOpen=!1;class lt{constructor(t){this.eventBus=t}create(){const t=O.map((t=>this.constructControlsPanel(t)));return I.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return I.div([]);const e=this.createInputs(t);return I.block([I.h1(`${N[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...R].reverse():R).map((e=>this.createInputForTerminus(t,e)));return I.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=I.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];S()(e).css("resize","none")}}n(146);var ct=n(507),ft={};ft.styleTagTransform=et(),ft.setAttributes=Q(),ft.insert=z().bind(null,"head"),ft.domAPI=Y(),ft.insertStyleElement=Z(),W()(ct.A,ft),ct.A&&ct.A.locals&&ct.A.locals;var ht,pt=n(74),dt={};dt.styleTagTransform=et(),dt.setAttributes=Q(),dt.insert=z().bind(null,"head"),dt.domAPI=Y(),dt.insertStyleElement=Z(),W()(pt.A,dt),pt.A&&pt.A.locals&&pt.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"}(ht||(ht={})),Error,Error,n(670);var gt=n(3);n(480),n(67);var mt=n(254),yt={};yt.styleTagTransform=et(),yt.setAttributes=Q(),yt.insert=z().bind(null,"head"),yt.domAPI=Y(),yt.insertStyleElement=Z(),W()(mt.A,yt),mt.A&&mt.A.locals&&mt.A.locals;var vt=n(70);n(124);var bt=n(312),Ct=n(991),wt=n.n(Ct);"object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,new Set;const At="object"==typeof process&&process?process:{};let _t=globalThis.AbortController,Et=globalThis.AbortSignal;if(void 0===_t){Et=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(t,e){this._onabort.push(e)}},_t=class{constructor(){e()}signal=new Et;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"!==At.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 At.emitWarning?At.emitWarning(n,r,o,i):console.error(`[${o}] ${r}: ${n}`))}}Symbol("type"),Symbol.iterator,Symbol.toStringTag,Map,n(151);var xt=n(599);function Tt(t,e){const n=t.tableColumn;if(!n)return;const r=function(t){return t.temp.MonomerHoverLinks??[]}(n);for(let n=r.length-1;n>=0;--n){const o=r[n],i=t.grid.col(o.targetCol.name);if(i&&!o.handler(t,e,i))break}}n(717),n(699),n(229),n(125);class It extends o.InputBase{constructor(t,e){super(I.input.column(t,e).dart,e?.onValueChanged),this.options=e}setColumnInputTable(t){I.input.setColumnInputTable(this,t,this.options?.filter)}}I.input.column2=function(t,e){return new It(t,e)},n(296),n(820),o.JsInputBase,o.JsInputBase;var Pt,St=n(269);!function(t){t.table="table",t.seqCol="seqCol",t.generateHelm="generateHelm",t.chiralityEngine="chiralityEngine",t.rules="rules"}(Pt||(Pt={}));var Lt=n(291);class Mt{onKeyDown(t,e){}onKeyPress(t,e){}onMouseEnter(t,e){}onMouseLeave(t,e){}onMouseDown(t,e){}onMouseUp(t,e){}onMouseMove(t,e){}onClick(t,e){}onDoubleClick(t,e){}}class Ot extends Mt{constructor(t,e,n){super(),this.gridCol=t,this.tableCol=e,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++Ot.viewerCounter,this.errors=[],this._onRendered=new k.Subject,this.tableCol&&this.tableCol.dataFrame&&this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.tableCol&&this.subs.push(r.events.onTableRemoved.subscribe((t=>{try{const e=t.args.dataFrame;this.tableCol?.dataFrame.id!==e.id||this.destroyed||this.destroy()}catch(t){this.logger.error(t)}}))),this.gridCol&&this.subs.push(r.events.onViewRemoving.subscribe((t=>{try{const e=t.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===e.id&&!this.destroyed&&this.destroy()}catch(t){this.logger.error(t)}})))}toLog(){return`${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,vt.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`)}}Ot.viewerCounter=-1;var Nt=n(192);const $t=Lt.zS;var Rt,Dt,Ht;!function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(Rt||(Rt={})),function(t){t.applyToBackground=".m.cellRenderer.applyToBackground"}(Dt||(Dt={})),function(t){t.MSA="MSA",t.classic="classic"}(Ht||(Ht={}));const Bt=new class{constructor(){this.color="rgb(100,100,100)",this.pivot=0,this.left=!1,this.transparencyRate=1,this.separator="",this.last=!1,this.drawStyle=Ht.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0}};function Ft(t,e,n,r,o,i,s){var a,u,l;const c=Object.assign(Object.assign({},Bt),s);s.logger?.debug("Bio: printLeftOrCentered(), start"),t.textAlign="start";let f=e.substring(0),h=c.last?"":c.separator;c.drawStyle===Ht.MSA&&(h="");let p=!0,d=!0,g="difference";if(null!=c.gridCell&&null!=c.gridCell.cell.column&&(p=c.gridCell.cell.column.temp["color-code"]??!0,d=c.gridCell.cell.column.temp["compare-with-current"]??!0,g=c.gridCell.cell.column.temp["highlight-difference"]??"difference"),c.referenceSequence){const t=c.referenceSequence[c.wordIdx];d&&c.referenceSequence.length>0&&"difference"===g&&(c.transparencyRate=f==t?.3:c.transparencyRate),d&&c.referenceSequence.length>0&&"equal"===g&&(c.transparencyRate=f!=t?.3:c.transparencyRate)}null!=c.maxLengthOfMonomer&&(f=$t(f,c.maxLengthOfMonomer));const m=f+h;(a=c.monomerTextSizeMap)[m]??(a[m]=t.measureText(m));let y=c.monomerTextSizeMap[m];(u=c.monomerTextSizeMap)[f]??(u[f]=t.measureText(f));let v=c.monomerTextSizeMap[f].width;const b=i/2-(y.fontBoundingBoxAscent+y.fontBoundingBoxDescent)/2+1;(l=c.monomerTextSizeMap)[h]??(l[h]=t.measureText(h));const C=c.monomerTextSizeMap[h].width;function w(e,o){const i=p?c.color:"rgb(0,0,0)";t.fillStyle=i,t.globalAlpha=c.transparencyRate,c.drawStyle===Ht.classic&&(t.fillText(f,n+e,r+b),t.fillStyle="#808080",t.fillText(h,n+o,r+b)),c.drawStyle===Ht.MSA&&t.fillText(f,n+e,r+b)}y=y.width,c.drawStyle===Ht.MSA&&(v=c.maxWord[c.wordIdx],y=c.maxWord[c.wordIdx]);const A=(c.maxWord[c.wordIdx]??0)-(c.maxWord[0]??0);if(c.left||y>o)return w(A,A+v),n+A+v+C;{const t=(o-y)/2;return w(t,t+v),n+A+t+v}}const kt="rgb(100,100,100)";class Gt extends Ot{constructor(t,e,n,r,i){super(t,e,n),this.monomerLengthLimit=r,this.propsProvider=i,this.colWidth=0,this._monomerLengthList=null,this.separatorWidth=5,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this.sysMonomerLib=null,this.padding=5,this.props=this.propsProvider(),this._processedRows=o.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),this.tableCol&&this.gridCol&&this.subs.push(this.tableCol.dataFrame.onCurrentRowChanged.subscribe((()=>{const t=this.tableCol.dataFrame;this.gridCol.grid,-1===t.currentRowIdx&&(this.tableCol.temp["reference-sequence"]=null,this.tableCol.temp["current-word"]=null,this.invalidateGrid())})))}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,bt.Q)(),this.invalidateGrid()})(),(async()=>{const t=await(0,a.pj)();this.sysMonomerLib=t.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}toLog(){return`MonomerPlacer<${this.viewerId}>`}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=o.BitSet.create(this.tableCol.length),this._monomerLengthList=null,this._monomerLengthMap={},this._monomerStructureMap={},super.reset(),this.invalidateGrid()}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}getCellMonomerLengths(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<e&&(this.colWidth=e,this.dirty=!0),this.dirty)try{this.reset()}catch(t){const[e,n]=(0,Nt.AP)(t);this.logger.error(e,void 0,n)}const r=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(t),o=new Array(r.length+1);o[0]=5;for(let t=1;t<o.length;t++)o[t]=o[t-1]+r[t-1];return[r,o]}getCellMonomerLengthsForSeq(t){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const e=this.seqHelper.getSeqHandler(this.tableCol),n=this.props.separatorWidth+1*this.props.monomerCharWidth,r=Math.ceil(this.colWidth/n),o=e.getSplitted(t),i=Math.min(r,o.length);let s=this._monomerLengthList[t];if(null===s||s.length<i){s=this._monomerLengthList[t]=new Array(o.length);let n=0;for(let t=0;t<i;++t){const r=o.getOriginal(t),i=this.props.monomerToShort(r,this.monomerLengthLimit),a=(e.isSeparator()?this.separatorWidth:this.props.separatorWidth)+i.length*this.props.monomerCharWidth;if(s[t]=a,n+=a,n>this.colWidth)break}}return s}getCellMonomerLengthsForSeqMsa(){var t;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(t=this._monomerLengthList)[0]??(t[0]=new Array(0));const e=this._monomerLengthList[0],{startIdx:n,endIdx:r}=(()=>{try{const t=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return t&&t.dart?{startIdx:Math.max(Math.floor((t?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((t?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(t){return{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}})(),o=this.props.separatorWidth+1*this.props.monomerCharWidth,i=Math.ceil(this.colWidth/o);for(let t=n;t<r;t++){if(this._processedRows.get(t)&&i<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t,i),r=Math.min(i,n.length);r>e.length&&e.push(...new Array(r-e.length).fill(o));let s=0;for(let t=0;t<r;++t){const r=n.getOriginal(t),o=this.props.monomerToShort(r,this.monomerLengthLimit),i=this.props.separatorWidth+o.length*this.props.monomerCharWidth;if(e[t]=Math.max(e[t]??0,i),s+=i,s>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,i)}return e}getPosition(t,e,n){const[r,o]=this.getCellMonomerLengths(t,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t).length?null:function(t,e){let n,r=100,o=0,i=t.length-1;for(;o<=i;){if(n=Math.floor((i+o)/2),t[n]<=e&&e<t[n+1])return n;if(e<t[n]?i=n-1:o=n+1,--r<=0)throw new Error(`Get position for pointer x = ${e} searching has not converged on ${JSON.stringify(t)}. `)}return null}(o,e)}setMonomerLengthLimit(t){this.monomerLengthLimit!=t&&(this.monomerLengthLimit=t,this.dirty=!0)}setSeparatorWidth(t){this.separatorWidth!=t&&(this.props.separatorWidth=t,this.dirty=!0)}render(t,e,n,r,o,i,s){if(!this.seqHelper)return;const a=this.gridCol,u=this.tableCol,l=window.devicePixelRatio,c=`${this.toLog()}.render()`;this.logger.debug(`${c}, start`);let f=this.monomerLengthLimit;if(Rt.maxMonomerLength in u.tags){const t=parseInt(u.getTag(Rt.maxMonomerLength));f=!isNaN(t)&&t?t:50}if(".mm.cellRenderer.maxMonomerLength"in u.temp){const t=u.temp[".mm.cellRenderer.maxMonomerLength"];f=!isNaN(t)&&t?t:50}t.save();try{const s=this.seqHelper.getSeqHandler(u);if("1"===u.temp[".mm.cellRenderer.settingsChanged"]||this.monomerLengthLimit!=f){let t=0;const e=8;t=u.temp[".mm.cellRenderer.gapLength"]??t,this.setMonomerLengthLimit(f),this.setSeparatorWidth(s.isMsa()?e:t),u.temp[".mm.cellRenderer.settingsChanged"]="0"}const[c,h]=this.getCellMonomerLengths(i.tableRowIndex,r),p=(c.length,i.cell.value,i.cell.rowIndex),d=(u.getTag(gt.gp.alphabet),50);r=function(t,e,n,r,o){return t?Math.max(Math.min(t.canvas.width/o-n,r)):Math.max(e.canvas.width/o-n,0)}(a?.grid,t,e,r,l),t.beginPath(),t.rect(e+this.padding,n+this.padding,r-this.padding-1,o-2*this.padding),t.clip(),t.font="12px monospace",t.textBaseline="top";const g=u.meta.units,m=u.getTag(gt.gp.aligned),y=u.getTag(gt.gp.separator)??"",v=this.props.separatorWidth+1*this.props.monomerCharWidth,b=Math.ceil(r/v),C=u.temp["reference-sequence"],w=this.tableCol.temp["current-word"];w&&-1===u?.dataFrame?.currentRowIdx&&(this.tableCol.temp["current-word"]=null);const A=(()=>{const t=s.getSplitter(b)(null!=C&&""!=C?C:w??"");return wt().count(0).take(t.length).map((e=>t.getOriginal(e))).toArray()})(),_=s.getSplitted(p);let E=Ht.classic;m&&m.includes("MSA")&&g==gt.Hi.SEPARATOR&&(E=Ht.MSA);const x=Math.min(_.length,b);for(let a=0;a<x;++a){const u=_.getOriginal(a),l=_.getCanonical(a);let c=kt;const p=this.getMonomerLib();if(p){const t=s.defaultBiotype;c=p.getMonomerTextColor(t,l)}t.fillStyle=kt;const g={color:c,pivot:0,left:!0,transparencyRate:1,separator:y,last:a===_.length-1,drawStyle:E,maxWord:h,wordIdx:a,gridCell:i,referenceSequence:A,maxLengthOfMonomer:f,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};if(Ft(t,u,e+this.padding,n,r,o,g),d>r)break}}catch(t){const[e,n]=(0,Nt.AP)(t);this.logger.error(e,void 0,n),this.errors.push(t)}finally{t.restore()}}onMouseMove(t,e){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==t.tableRowIndex)return;const r=t.bounds,o=e.offsetX-t.gridColumn.left+(t.gridColumn.left-r.x),i=this.getPosition(t.tableRowIndex,o,r.width);this.logger.debug(`${n}, start, argsX: ${o}, left: ${i}`);const s=this.seqHelper.getSeqHandler(this.tableCol),a=s.getSplitted(t.tableRowIndex);if(null!==i&&i<a.length){const n=s.alphabet??gt.YI.UN,r={position:i,biotype:n===gt.YI.RNA||n===gt.YI.DNA?xt.o.NUCLEOTIDE:xt.o.AA,symbol:a.getCanonical(i)},o=[];let u=this._monomerStructureMap[r.symbol];{const t=this.getMonomerLib();u=this._monomerStructureMap[r.symbol]=t?t.getTooltip(r.biotype,r.symbol):I.divText("Monomer library is not available")}o.push(u),I.tooltip.show(I.divV(o),e.x+16,e.y+16),Tt(t,r)}else I.tooltip.hide(),Tt(t,null)}}class jt extends Gt{constructor(t,e,n,r){super(t,e,Wt.logger,n,(()=>({seqHandler:r.getSeqHandler(e),monomerCharWidth:7,separatorWidth:11,monomerToShort:gt.zS})))}onMouseMove(t,e){const n=t.bounds,r=e.offsetX-t.gridColumn.left+(t.gridColumn.left-n.x);this.getPosition(t.tableRowIndex,r,n.width),super.onMouseMove(t,e)}}class Ut{get defaultGapOriginal(){return""}constructor(t,e){this.separator=t,this.helmHelper=e,this.separatorSplitter=(0,gt.dh)(this.separator),this.splitter=this._splitter.bind(this)}setUnits(){}_splitter(t){const e=this.separatorSplitter(t);return new Vt(wt().count(0).take(e.length).map((t=>e.getOriginal(t))).toArray(),i.b9[i.Hi.SEPARATOR])}getHelm(t,e){return St.s.parseNotation(t,this.helmHelper).getNotationHelm()}createCellRendererBack(t,e){const n=new jt(t,e,4,this.helmHelper.seqHelper);return n.init().then((()=>{})),n}}class Vt extends Lt.Mu{getCanonical(t){if(this.isGap(t))return i._S;const e=this.getOriginal(t);let n=e;return e.startsWith("{")?n=e.slice(1):e.endsWith("}")?n=e.slice(0,-1):e.startsWith("(")?n=e.replace(/^\(.\d+\)/,""):e.endsWith(")")&&(n=e.replace(/\(\d+\)$/,"")),n}constructor(t,e){super(t,e)}}const Wt=new L({debug:!0});function qt(t,e){t.meta.units=i.Hi.CUSTOM,t.tags["polytool-data-role"]="template",t.temp[s.notationProvider]=new Ut(e,Wt.helmHelper)}},269:(t,e,n)=>{"use strict";n.d(e,{s:()=>s});var r=n(599),o=n(125),i=n(699);class s{constructor(t,e,n,r){this.helmHelper=r,this.linkages=e,this.monomers=t,this.mol=n}static parseHelm(t,e){const n=/(\w+\{.*\})\$(.*)\$(.*)\$(.*)\$/g.exec(t),i=[n[1],n[2],n[3],n[4]],a=i[0].split("|"),u=i[1].split("|"),l=new Array(a.length),c=[],f=e.createHelmWebEditor().editor.m;let h=0;const p=new JSDraw2.Point(0,0);for(let t=0;t<a.length;t++){const e=a[t].indexOf("{"),n=a[t].indexOf("}");l[t]=a[t].slice(e+1,n).split(".").map((t=>{return(e=t).startsWith("[")&&e.endsWith("]")?e.slice(1,-1):e;var e}));for(let e=0;e<l[t].length;e++){const n=l[t][e],o={type:r.o.AA,i:t,j:e,continuousId:h},i=new JSDraw2.Atom(p,n,o);if(f.addAtom(i),0!==e){const t=f.atoms[h-1],e=f.atoms[h],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,f.addBond(n)}h++,p.x+=JSDraw2.Editor.BONDLENGTH}p.y+=4*JSDraw2.Editor.BONDLENGTH}for(let t=0;t<u.length;t++)if(""!==u[t]&&"V2.0"!==u[t]){const e=u[t].split(","),n=parseInt(e[0].replace("PEPTIDE",""))-1,r=parseInt(e[1].replace("PEPTIDE",""))-1,i=e[2].split("-"),s=i[0].split(":"),a=i[1].split(":");c.push({fChain:n,sChain:r,fMonomer:(0,o.jX)(parseInt(s[0]),n,l),sMonomer:(0,o.jX)(parseInt(a[0]),r,l),fR:parseInt(s[1].replace("R","")),sR:parseInt(a[1].replace("R",""))})}for(let t=0;t<c.length;t++){const e=f.atoms[c[t].fMonomer-1],n=f.atoms[c[t].sMonomer-1],r=new JSDraw2.Bond(e,n);r.r1=c[t].fR,r.r2=c[t].sR,f.addBond(r)}return new s(l,c,f,e)}applyRules(t){const e=this.getNotation();return s.fromNotation(e,t,this.helmHelper)}static fromNotation(t,e,n){const o=e.heterodimerCode,i=e.homodimerCode,a=[],u=[],l=null!==o?t.split(`(${e.heterodimerCode})`):"";null!==o&&l.length>1?(u.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),a.push(l[1].replaceAll("{","").replaceAll("}","")),a.push(l[2].replaceAll("{","").replaceAll("}",""))):a.push(t);for(let t=0;t<a.length;t++)if(null!==i&&a[t].includes(`(${i})`)){const e=a.length;u.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=a[t].replace(`(${i})`,""),r=n.indexOf("{"),o=n.slice(0,r),s=n.replace(o,"").replaceAll("{","").replaceAll("}","");a[t]=o+s,a.push(s)}for(let t=0;t<a.length;t++)if(null!==i&&a[t].includes(`(${i})`)){const e=a.length;u.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=a[t].replace(`(${i})`,""),r=n.indexOf("{"),o=n.slice(0,r),s=n.replace(o,"").replaceAll("{","").replaceAll("}","");a[t]=o+s,a.push(s)}const c=new Array(a.length);for(let t=0;t<a.length;t++){const n=a[t].split("-"),r=this.getLinkedPositions(n,e.linkRules),[o,i,s,l,f]=this.getAllCycles(e.linkRules,n,r);new Array(o.length);for(let e=0;e<i.length;e++)u.push({fChain:t,sChain:t,fMonomer:i[e],sMonomer:s[e],fR:l[e],sR:f[e]});c[t]=o}const f=[],h=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),[o,i,s,a]=this.getAllReactants(e.reactionRules,c[t],n);if(i.length>=1){const n=new Array(s[0]-1),l=new Array(o.length-s[0]);for(let e=0;e<s[0]-1;e++){const i=n[e]=o[e],s={type:r.o.AA,i:t,j:e,continuousId:p},a=new JSDraw2.Atom(d,i,s);if(h.addAtom(a),e>0){const t=h.atoms[p-1],e=h.atoms[p],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,h.addBond(n)}p++}for(let e=s[0];e<o.length;e++){const n=l[e-s[0]]=o[e],i={type:r.o.AA,i:t,j:e,continuousId:p},a=new JSDraw2.Atom(d,n,i);if(h.addAtom(a),e>s[0]){const t=h.atoms[p-1],e=h.atoms[p],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,h.addBond(n)}p++}h.atoms[i[0]-1].elem=n[i[0]-1]=e.reactionRules[a[0]].name;for(let t=0;t<u.length;t++)u[t].fMonomer>s[0]&&(u[t].fMonomer-=s[0],u[t].fChain++),u[t].sMonomer>s[0]&&(u[t].sMonomer-=s[0],u[t].sChain++);u.push({fChain:0,sChain:0,fMonomer:i[0],sMonomer:s[0]-1,fR:3,sR:2}),u.push({fChain:0,sChain:1,fMonomer:i[0],sMonomer:1,fR:4,sR:1});const c=new Array(n.length);for(let t=0;t<n.length;t++)c[t]=`[${n[t]}]`;const g=new Array(l.length);for(let t=0;t<l.length;t++)g[t]=`[${l[t]}]`;f.push(n),f.push(l)}else{for(let e=0;e<c[t].length;e++){const n=c[t][e],o={type:r.o.AA,i:t,j:e,continuousId:p},i=new JSDraw2.Atom(d,n,o);if(h.addAtom(i),e>0){const t=h.atoms[p-1],e=h.atoms[p],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,h.addBond(n)}p++}f.push(c[t])}}for(const t of u){const e=h.atoms[t.fMonomer-1],n=h.atoms[t.sMonomer-1],r=new JSDraw2.Bond(e,n);r.r1=t.fR,r.r2=t.sR,h.addBond(r)}return new s(f,u,h,n)}static parseNotation(t,e){const n=[],o=[],i=e.createHelmWebEditor().editor.m,a=/(\(.\d+\))?\{[^\}]*\}/g,u=[];u.push(t.replaceAll(a,""));const l=t.matchAll(a);for(const t of l){const e=t[0];e&&u.push(e)}let c=0;for(let t=0;t<u.length;t++){const e=u[t].split("-"),r=new Array(e.length);let i=0;for(let n=0;n<e.length;n++){const s=e[n].replace("{","").replace("}","");""!==s?(r[n]=s,c++,i++):o.push({fChain:t,sChain:t+1,fMonomer:c,sMonomer:c+1,fR:1,sR:1})}n.push(r.slice(0,i))}c=0;const f=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 o=n[t][e],s={type:r.o.AA,i:t,j:e,continuousId:c},a=new JSDraw2.Atom(f,o,s);if(i.addAtom(a),0!==e){const t=i.atoms[c-1],e=i.atoms[c],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,i.addBond(n)}c++,f.x+=JSDraw2.Editor.BONDLENGTH}f.y+=4*JSDraw2.Editor.BONDLENGTH}for(let t=0;t<o.length;t++){const e=i.atoms[o[t].fMonomer-1],n=i.atoms[o[t].sMonomer-1],r=new JSDraw2.Bond(e,n);r.r1=o[t].fR,r.r2=o[t].sR,i.addBond(r)}return new s(n,o,i,e)}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+=`${(0,o.MH)(this.linkages[e].fMonomer-1,this.monomers)[0]+1}:R${this.linkages[e].fR}-`,t+=`${(0,o.MH)(this.linkages[e].sMonomer-1,this.monomers)[0]+1}:R${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=[];for(let r=0;r<e.length;r++){let o=!1,s=!1,a=!1,u=-1,l=-1;const c=`(${e[r].code})`,[f,h]=(0,i.Ln)(e[r]);if(f.length>0)for(let e=0;e<f.length;e++){for(let n=0;n<t.length;n++)if(t[n].includes(c)){if(o){if(a&&t[n]==h[e]+c){s=!0,l=n;break}if(a||t[n]!=f[e]+c)continue;s=!0,l=n;break}if(t[n]==f[e]+c)o=!0,a=!0,u=n;else{if(t[n]!=h[e]+c)continue;o=!0,a=!1,u=n}}o&&s&&(a?n.push([u,l,r]):n.push([l,u,r]))}else{for(let e=0;e<t.length;e++)if(t[e].includes(c)){if(o){if(a&&t[e]){s=!0,l=e;break}if(!a&&t[e]){s=!0,l=e;break}continue}o=!0,a=!0,u=e}if(!o||!s)continue;a?n.push([u,l,r]):n.push([l,u,r])}}return n}static getAllCycles(t,e,n){const r=[],o=[],i=[],s=[],a=n.length;for(let u=0;u<a;u++){if(-1==n[u][0])continue;const a=n[u][2],l=t[a].code;e[n[u][0]]=e[n[u][0]].replace(`(${l})`,""),e[n[u][1]]=e[n[u][1]].replace(`(${l})`,""),r.push(n[u][0]+1),o.push(n[u][1]+1),i.push(t[a].firstLinkingGroup),s.push(t[a].secondLinkingGroup)}return[e,r,o,i,s]}static getAllReactants(t,e,n){const r=[],o=[],i=[],s=n.length;for(let a=0;a<s;a++){if(-1==n[a][0])continue;const s=t[n[a][2]].code;e[n[a][0]]=e[n[a][0]].replace(`(${s})`,""),e[n[a][1]]=e[n[a][1]].replace(`(${s})`,""),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}}},229:(t,e,n)=>{"use strict";n.d(e,{b:()=>s});var r=n(192),o=n(269),i=n(511);function s(t,e,n){const s=new Array(t.length);for(let a=0;a<t.length;a++)try{if(null==t[a])s[a]="";else{const r=o.s.fromNotation(t[a],e,n);s[a]=r.getHelm()}}catch(t){const[e,n]=(0,r.AP)(t);i._package.logger.error(e,void 0,n),s[a]=""}return s}},125:(t,e,n)=>{"use strict";n.d(e,{AM:()=>y,MH:()=>f,Tl:()=>m,jX:()=>h});var r=n(328),o=n(991),i=n.n(o),s=n(890),a=n(717),u=n(699),l=n(296),c=n(192);function f(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 h(t,e,n){let r=0;for(let t=0;t<e;++t)r+=n[t].length;return r+t}function p(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),l=" 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r=n.reaction,o=n.name,[i,s]=(0,u.Ln)(n),a=new Array(i.length),c=new Array(i.length);for(let n=0;n<i.length;n++){const u=e.getMonomer("PEPTIDE",i[n]);if(!u)throw new l.bl("PEPTIDE",i[n]);const f=e.getMonomer("PEPTIDE",s[n]);if(!f)throw new l.bl("PEPTIDE",s[n]);const[h,m]=p(u,f),y={symbol:o,name:o,molfile:d(t,r,h,m,o),author:"",id:0,rgroups:g(u,f),smiles:"",polymerType:"PEPTIDE",monomerType:"Backbone",createDate:null};y.meta=Object.assign(y.meta??{},{colors:{default:{line:"#2083D5",text:"#2083D5",background:"#F2F2F5"}}}),a[n]=o,c[n]=y}return[a,c]}async function y(t){const e=(await(0,s.pj)()).getMonomerLib(),n=await(0,a.j)(),r={};for(let o=0;o<t.reactionRules.length;o++){const[i,s]=m(n,e,t.reactionRules[o]);for(let t=0;t<i.length;t++)r[i[t]]=s[t]}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(""))}},699:(t,e,n)=>{"use strict";n.d(e,{Ln:()=>p,Q4:()=>h});var r=n(82);n(328),n(389),n(991),n(511),n(124),n(229),n(439);const o="System:AppData/SequenceTranslator/polytool-rules/",i="code",s="firstMonomers",a="secondMonomers",u="name",l="firstLinkingGroup",c="secondLinkingGroup";class f{constructor(t,e,n,r){this.homodimerCode=t,this.heterodimerCode=e,this.linkRules=n,this.reactionRules=r}set homodimer(t){this.homodimerCode=t}set heterodimer(t){this.heterodimerCode=t}addLinkRules(t){for(let e=0;e<t.length;e++)this.linkRules.push(t[e])}addSynthesisRules(t){for(let e=0;e<t.length;e++)this.reactionRules.push(t[e])}getLinkRulesDf(){const t=this.linkRules.length,e=r.Column.int(i,t),n=r.Column.string(s,t),o=r.Column.string(a,t),u=r.Column.int(l,t),f=r.Column.int(c,t);for(let r=0;r<t;r++)e.set(r,this.linkRules[r].code),n.set(r,this.linkRules[r].firstMonomers.toString()),o.set(r,this.linkRules[r].secondMonomers.toString()),u.set(r,this.linkRules[r].firstLinkingGroup),f.set(r,this.linkRules[r].secondLinkingGroup);return r.DataFrame.fromColumns([e,n,o,u,f])}getSynthesisRulesDf(){const t=this.reactionRules.length,e=r.Column.int(i,t),n=r.Column.string(s,t),o=r.Column.string(a,t),l=r.Column.string(u,t),c=r.Column.string("firstReactant",t),f=r.Column.string("secondReactant",t),h=r.Column.string("product",t);for(let r=0;r<t;r++){e.set(r,this.reactionRules[r].code),n.set(r,this.reactionRules[r].firstMonomers.toString()),o.set(r,this.reactionRules[r].secondMonomers.toString()),l.set(r,this.reactionRules[r].name);const t=this.reactionRules[r].reaction.split(">>"),i=t[0].split(".");c.set(r,i[0]),f.set(r,i[1]),h.set(r,t[1])}return c.semType=r.SEMTYPE.MOLECULE,f.semType=r.SEMTYPE.MOLECULE,h.semType=r.SEMTYPE.MOLECULE,r.DataFrame.fromColumns([l,c,f,h,e,n,o])}setLinkRules(t){const e=t.rowCount,n=new Array(e),r=t.columns.byName(i),o=t.columns.byName(s),u=t.columns.byName(a),f=t.columns.byName(l),h=t.columns.byName(c);for(let t=0;t<e;t++){const e={code:r.get(t),firstMonomers:o.get(t).split(","),secondMonomers:u.get(t).split(","),firstLinkingGroup:f.get(t),secondLinkingGroup:h.get(t)};n[t]=e}this.linkRules=n}setSynthesisRules(t){const e=t.rowCount,n=new Array(e),r=t.columns.byName(i),o=t.columns.byName(s),l=t.columns.byName(a),c=t.columns.byName(u),f=t.columns.byName("firstReactant"),h=t.columns.byName("secondReactant"),p=t.columns.byName("product");for(let t=0;t<e;t++){const e=`${f.get(t)}.${h.get(t)}>>${p.get(t)}`,i={code:r.get(t),firstMonomers:o.get(t).split(","),secondMonomers:l.get(t).split(","),reaction:e,name:c.get(t)};n[t]=i}this.reactionRules=n}}async function h(t){const e=new r.FileSource(o),n=new f(null,null,[],[]);for(let r=0;r<t.length;r++){const i=await e.readAsText(t[r].replace(o,"")),s=JSON.parse(i);n.homodimer=s.homodimerCode,n.heterodimer=s.heterodimerCode,n.addLinkRules(s.linkRules),n.addSynthesisRules(s.reactionRules)}return n}function p(t){const e=t.firstMonomers.length*t.secondMonomers.length,n=new Array(e),r=new Array(e);let o=0;for(let e=0;e<t.firstMonomers.length;e++)for(let i=0;i<t.secondMonomers.length;i++)n[o]=t.firstMonomers[e],r[o]=t.secondMonomers[i],o++;return[n,r]}},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],l=o[i*s+n]=t.clone(),c=l.atoms[a].elem;l.atoms[a].elem=u;const f=c?.length>1?`[${c}]`:c,h=u?.length>1?`[${u}]`:u;l.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 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o={single1:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,placeholders:[{position:4,monomers:["K","P","F4COO"]},{position:6,monomers:["Y","T"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5P"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5[F4COO]"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7T"}]},"single-with-original":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,placeholders:[{position:4,monomers:["K","P","F4COO"]},{position:6,monomers:["Y","T"]}],keepOriginal:!0},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:""},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5P"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5[F4COO]"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7T"}]},matrix1:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Matrix,placeholders:[{position:1,monomers:["D","L"]},{position:4,monomers:["K","P","F4COO"]},{position:6,monomers:["Y","T"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].D.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5K-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5K-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5P-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5P-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5[F4COO]-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5[F4COO]-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5K-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5K-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5P-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5P-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5[F4COO]-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5[F4COO]-[Tic]7T"}]}};for(const[t,n]of Object.entries(o))(0,e.t6)(`${t}`,(async()=>{const t=(0,L.o)(n.src,"",n.params);(0,e.J6)(t,n.tgt.map((t=>[t.seq,t.name])))}))})),(0,e.L1)("PolyTool: Enumerate",(()=>{let t,n,r;(0,e.gM)((async()=>{t=await(0,x.b2)(),n=await(0,b.pj)(),r=await A(),await n.loadMonomerLibForTests()})),(0,e.Pl)((async()=>{await _(r),await n.loadMonomerLib(!0)}));const o={breadth1:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"}]},"breadth1-with-original":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]}],keepOriginal:!0},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:""},{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"}]},breadth2:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K","Y"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"},{seq:"PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5Y"}]},"breadth-double":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]},{start:2,end:4,monomers:["Y"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-K3Y"},{seq:"PEPTIDE1{[Ac(1)].F.K.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.K.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-P5Y"},{seq:"PEPTIDE1{[Ac(1)].F.Y.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-K4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-P5Y"},{seq:"PEPTIDE1{[Ac(1)].F.Y.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-K5Y"}]}};for(const[t,n]of Object.entries(o))(0,e.t6)(`${t}`,(async()=>{const t=(0,L.o)(n.src,"",n.params);(0,e.J6)(t,n.tgt.map((t=>[t.seq,t.name])))}))}));var M=n(269);(0,e.L1)("PolyTool: Chain: parseNotation",(()=>{let t;(0,e.gM)((async()=>{t=await(0,x.b2)()}));const n={cyclized:{src:{seq:"R-F-C(1)-T-G-H-F-Y-P-C(1)-meI"},tgt:{helm:"PEPTIDE1{R.F.[C(1)].T.G.H.F.Y.P.[C(1)].[meI]}$$$$V2.0"}},dimerized1:{src:{seq:"(#3)Succ-{A(CHOL)-F-C(1)-T-G-H-Y-P-C(1)-NH2}"},tgt:{helm:"PEPTIDE1{[(#3)Succ]}|PEPTIDE2{[A(CHOL)].F.[C(1)].T.G.H.Y.P.[C(1)].[NH2]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$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,P.Q4)(["rules_example.json"]);const n=await M.s.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,I.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,I.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$$$V2.0",mmHelm:"PEPTIDE1{[(#3)Succ].[{A(CHOL)].F.C.T.G.H.Y.P.C.[NH2}]}$PEPTIDE1,PEPTIDE1,4:R3-10:R3$$$V2.0"},tgt:{templateChain:{monomerCount:[1,10],linkageCount:1},mmChain:{monomerCount:[11],linkageCount:1}}},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$$$V2.0",mmHelm:"PEPTIDE1{[($3)Succ].[{R].F.C.T.G.H.F.P.C.[NH2}($3){A(CHOL)].F.[C(1)].Y.H.G.D.N.[C(1)].[meI}]}$PEPTIDE1,PEPTIDE1,4:R3-10:R3$$$V2.0"},tgt:{templateChain:{monomerCount:[1,10,10],linkageCount:1},mmChain:{monomerCount:[20],linkageCount:1}}}};for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`fromNotation-${r}`,(async()=>{const n=await(0,P.Q4)(["rules_example.json"]),r=M.s.fromNotation(o.templateSeq,n,t);r.check(!0),(0,e.J6)(r.monomers.map((t=>t.length)),i.mmChain.monomerCount),(0,e.E3)(r.linkages.length,i.mmChain.linkageCount),(0,e.E3)(r.getHelm(),o.mmHelm)}),"reaction2"==r?{skipReason:"reverse reaction"}:void 0);for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`parseNotation-${r}`,(async()=>{await(0,P.Q4)(["rules_example.json"]);const n=M.s.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-${r}`,(async()=>{await(0,P.Q4)(["rules_example.json"]);const n=M.s.parseHelm(o.templateHelm,t);n.check(!0),(0,e.J6)(n.monomers.map((t=>t.length)),i.templateChain.monomerCount),(0,e.E3)(n.linkages.length,i.templateChain.linkageCount),(0,e.E3)(n.getHelm(),o.templateHelm),(0,e.E3)(n.getNotation(),o.templateSeq)}));for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`applyRules-${r}`,(async()=>{const n=await(0,P.Q4)(["rules_example.json"]),r=M.s.parseNotation(o.templateSeq,t),s=await r.applyRules(n);s.check(!0),(0,e.J6)(s.monomers.map((t=>t.length)),i.mmChain.monomerCount),(0,e.E3)(s.linkages.length,i.mmChain.linkageCount),(0,e.E3)(s.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,E.j)(),await r.loadMonomerLibForTests()})),(0,e.Pl)((async()=>{await _(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"),l=await(0,d.Q)(),c=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"]);c.semType=t.SEMTYPE.MACROMOLECULE,c.meta.units=g.Hi.HELM;const f=await l.helmToAtomicLevel(c,!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,E.j)(),n=r.getMonomerLib(),o=(await(0,P.Q4)(["rules_example.json"])).reactionRules.find((t=>"GGaz"==t.name)),[i,s]=(0,I.Tl)(t,n,o);(0,e.E3)(i[0],o.name);const a=t.get_mol(s[0].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 $(){await(0,e.Xb)(O,O.getModule("package-test.js"))}})(),sequencetranslator_test=r})();
2
+ var sequencetranslator_test;(()=>{var t={717:(t,e,n)=>{"use strict";n.d(e,{j:()=>o});var r=n(82);async function o(){const t=r.Func.find({package:"Chem",name:"getRdKitModule"});if(0===t.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await t[0].prepare().call()).getOutputParamValue()}},599:(t,e,n)=>{"use strict";n.d(e,{o:()=>r.o});var r=n(869)},124:(t,e,n)=>{"use strict";n.d(e,{b2:()=>i});var r=n(389),o=n(82);async function i(){const t="Helm",e=o.Func.find({package:t,name:"getHelmHelper"});if(0===e.length)throw new Error(`Package '${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,l,c=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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RegExp(E(e)+"|.","g")}getFormatRegExp(t){if(this.validateFormat(t),this.isHelm(t))throw new Error("Helm RegExp can be built for non-HELM target formats");return this.getNonHelmFormatRegExp(t)}getPhosphateHelmCodesRegExp(t){this.validateFormat(t);const e=this.th.jsonData.codesToHelmDict[t],n=E(Array.from(new Set(Object.values(e[C.ti.LINKAGE]))).sort(w));return new RegExp(`${C.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: ${t}`)}isHelm(t){return t===d.NO.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(w)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(E(e)+"|\\([^()]*\\)|.","g")}}function E(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const _={LEFT:"RNA1{",RIGHT:"}$$$$"};class x{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new A(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===d.NO.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===d.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} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(E(Object.values(_)),"g");let r=t.replace(n,"");const o=this.formats.getHelmToFormatDict(e),i=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>i.includes(t)?o[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,C.iL).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),o=this.formats.getFormatRegExp(e),i=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(o,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${C.iL}.`),s=s.slice(0,-1),s[s.length-1]===C.q7&&(s=s.slice(0,-1)),s=s.replace(i,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${_.LEFT+s+_.RIGHT}`}}class T{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return d.NO.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const o=t[r];n[r]=e.getInvalidCodeIndex(o)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=g(this.libWrapper.getCodesByFormat(n));let o=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){o=e+1;break}r.some((e=>e===t.slice(o,o+e.length)))&&e.push(n)}return e}}var I=n(389);const P=$;var S=n.n(P);class L extends o.Package{get helmHelper(){if(!this._helmHelper)throw new Error("Package SequenceTranslator .helmHelper is not initialized");return this._helmHelper}get seqHelper(){return this._helmHelper.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 m(t,e).getInvalidCodeIndex(r));const o=n<0||""===t,i=I.span([]);S()(i).css("-webkit-text-fill-color","var(--grey-6)");const s=I.span([]);return S()(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 u(super.logger,t.debug)}startInit(t){this._initPromise=t}completeInit(t){this._helmHelper=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 '${t}' not found. Fallback to monomers sample path '${l}'.`),t=l),[this._jsonData,this._monomerLib]=await Promise.all([v(t),M(t)]),this._monomerLibWrapper=new b(this.monomerLib,this.jsonData)})()),this.initLibDataPromise}async getTranslationHelper(){return await r.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new m(t,this)}createFormatConverter(t,e){return new x(t,e,this)}createFormatDetector(t){return new T(t,this)}}async function M(t){const e=o.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const e=await(0,a.pj)();return await e.readLibrary(t,"monomer-lib.json")}finally{e.close()}}const N=["SS","AS"],O={SS:"Sense strand",AS:"Anti sense"},R=["3'","5'"];var D,H,F,B;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(D||(D={})),function(t){t.PATTERN_NAME="patternName",t.PATTERN_COMMENT="patternComment",t.NUCLEOTIDES_WITH_NUMERIC_LABELS="nucleotidesWithNumericLabels"}(H||(H={})),function(t){t.PATTERN_CONFIG="patternConfig",t.AUTHOR_ID="authorID",t.DATE="date"}(F||(F={})),function(t){t.CREATE="create",t.MODIFY="modify"}(B||(B={})),D.IS_ANTISENSE_STRAND_INCLUDED,D.NUCLEOTIDE_SEQUENCES,D.PHOSPHOROTHIOATE_LINKAGE_FLAGS,D.STRAND_TERMINUS_MODIFICATIONS,H.PATTERN_NAME,H.PATTERN_COMMENT,H.NUCLEOTIDES_WITH_NUMERIC_LABELS,Error,Error,n(802);const k=rxjs;var G;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))}}}(G||(G={}));var j=n(543),U=n.n(j),V=n(72),W=n.n(V),q=n(825),Y=n.n(q),K=n(659),z=n.n(K),J=n(56),Q=n.n(J),X=n(540),Z=n.n(X),tt=n(113),et=n.n(tt),nt=n(252),rt={};rt.styleTagTransform=et(),rt.setAttributes=Q(),rt.insert=z().bind(null,"head"),rt.domAPI=Y(),rt.insertStyleElement=Z(),W()(nt.A,rt),nt.A&&nt.A.locals&&nt.A.locals;class ot{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return I.divV([I.h1("PTO"),I.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return N.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===N.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+N.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=I.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),I.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 N.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=I.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),I.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class it{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=N.map((t=>this.constructControlsPanel(t)));return I.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return I.div([]);const e=this.constructHeader(),n=this.createControls(t);return I.block([I.h1(`${O[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return I.divH([I.div([I.divText("#")],{style:{width:"20px"}}),I.block75([I.divText("Modification")]),I.div([I.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return I.div(e.map(((t,e)=>I.divH([n[e],I.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const o=I.input.choice("",{value:n,items:e});return o.onInput.subscribe((()=>{const e=o.value;this.eventBus.setNucleotide(t,r,e)})),o}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=I.input.bool("",{value:e});r.onInput.subscribe((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.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 N.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=>I.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{S()(e[n]).empty(),S()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return I.label(r)}))}}class st{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof k.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class at{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new st}static open(t,e){at.isDialogOpen||(at.instance||(at.instance=new at(t,e)),at.instance.openDialog())}openDialog(){this.initialPatternConfig=U().cloneDeep(this.eventBus.getPatternConfig()),at.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=I.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=I.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{at.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new ot(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new it(this.eventBus,this.dataManager,this.subscriptions).create();S()(t).empty(),S()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}at.isDialogOpen=!1;class ut{constructor(t){this.eventBus=t,this.subscriptions=new st}static open(t){ut.isDialogOpen||(ut.instance||(ut.instance=new ut(t)),ut.instance.openDialog())}openDialog(){this.initialPatternConfig=U().cloneDeep(this.eventBus.getPatternConfig()),ut.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=I.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=I.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{ut.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new lt(this.eventBus).create();S()(t).empty(),S()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}ut.isDialogOpen=!1;class lt{constructor(t){this.eventBus=t}create(){const t=N.map((t=>this.constructControlsPanel(t)));return I.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return I.div([]);const e=this.createInputs(t);return I.block([I.h1(`${O[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...R].reverse():R).map((e=>this.createInputForTerminus(t,e)));return I.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=I.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];S()(e).css("resize","none")}}n(146);var ct=n(507),ft={};ft.styleTagTransform=et(),ft.setAttributes=Q(),ft.insert=z().bind(null,"head"),ft.domAPI=Y(),ft.insertStyleElement=Z(),W()(ct.A,ft),ct.A&&ct.A.locals&&ct.A.locals;var ht,pt=n(74),dt={};dt.styleTagTransform=et(),dt.setAttributes=Q(),dt.insert=z().bind(null,"head"),dt.domAPI=Y(),dt.insertStyleElement=Z(),W()(pt.A,dt),pt.A&&pt.A.locals&&pt.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"}(ht||(ht={})),Error,Error,n(670);var gt=n(3);n(480),n(67);var mt=n(254),yt={};yt.styleTagTransform=et(),yt.setAttributes=Q(),yt.insert=z().bind(null,"head"),yt.domAPI=Y(),yt.insertStyleElement=Z(),W()(mt.A,yt),mt.A&&mt.A.locals&&mt.A.locals;var vt=n(70);n(124);var bt=n(312),Ct=n(991),wt=n.n(Ct);"object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,new Set;const At="object"==typeof process&&process?process:{};let Et=globalThis.AbortController,_t=globalThis.AbortSignal;if(void 0===Et){_t=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(t,e){this._onabort.push(e)}},Et=class{constructor(){e()}signal=new _t;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"!==At.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 At.emitWarning?At.emitWarning(n,r,o,i):console.error(`[${o}] ${r}: ${n}`))}}Symbol("type"),Symbol.iterator,Symbol.toStringTag,Map,n(151);var xt=n(599);function Tt(t,e){const n=t.tableColumn;if(!n)return;const r=function(t){return t.temp.MonomerHoverLinks??[]}(n);for(let n=r.length-1;n>=0;--n){const o=r[n],i=t.grid.col(o.targetCol.name);if(i&&!o.handler(t,e,i))break}}n(717),n(699),n(229),n(125);class It extends o.InputBase{constructor(t,e){super(I.input.column(t,e).dart,e?.onValueChanged),this.options=e}setColumnInputTable(t){I.input.setColumnInputTable(this,t,this.options?.filter)}}I.input.column2=function(t,e){return new It(t,e)},n(296),n(820),o.JsInputBase,o.JsInputBase;var Pt,St=n(269);!function(t){t.table="table",t.seqCol="seqCol",t.generateHelm="generateHelm",t.chiralityEngine="chiralityEngine",t.rules="rules"}(Pt||(Pt={}));var Lt=n(291);class Mt{onKeyDown(t,e){}onKeyPress(t,e){}onMouseEnter(t,e){}onMouseLeave(t,e){}onMouseDown(t,e){}onMouseUp(t,e){}onMouseMove(t,e){}onClick(t,e){}onDoubleClick(t,e){}}class Nt extends Mt{constructor(t,e,n){super(),this.gridCol=t,this.tableCol=e,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++Nt.viewerCounter,this.errors=[],this._onRendered=new k.Subject,this.tableCol&&this.tableCol.dataFrame&&this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.tableCol&&this.subs.push(r.events.onTableRemoved.subscribe((t=>{try{const e=t.args.dataFrame;this.tableCol?.dataFrame.id!==e.id||this.destroyed||this.destroy()}catch(t){this.logger.error(t)}}))),this.gridCol&&this.subs.push(r.events.onViewRemoving.subscribe((t=>{try{const e=t.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===e.id&&!this.destroyed&&this.destroy()}catch(t){this.logger.error(t)}})))}toLog(){return`${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,vt.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`)}}Nt.viewerCounter=-1;var Ot=n(192);const $t=Lt.zS;var Rt,Dt,Ht;!function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(Rt||(Rt={})),function(t){t.applyToBackground=".m.cellRenderer.applyToBackground"}(Dt||(Dt={})),function(t){t.MSA="MSA",t.classic="classic"}(Ht||(Ht={}));const Ft=new class{constructor(){this.color="rgb(100,100,100)",this.pivot=0,this.left=!1,this.transparencyRate=1,this.separator="",this.last=!1,this.drawStyle=Ht.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0}};function Bt(t,e,n,r,o,i,s){var a,u,l;const c=Object.assign(Object.assign({},Ft),s);s.logger?.debug("Bio: printLeftOrCentered(), start"),t.textAlign="start";let f=e.substring(0),h=c.last?"":c.separator;c.drawStyle===Ht.MSA&&(h="");let p=!0,d=!0,g="difference";if(null!=c.gridCell&&null!=c.gridCell.cell.column&&(p=c.gridCell.cell.column.temp["color-code"]??!0,d=c.gridCell.cell.column.temp["compare-with-current"]??!0,g=c.gridCell.cell.column.temp["highlight-difference"]??"difference"),c.referenceSequence){const t=c.referenceSequence[c.wordIdx];d&&c.referenceSequence.length>0&&"difference"===g&&(c.transparencyRate=f==t?.3:c.transparencyRate),d&&c.referenceSequence.length>0&&"equal"===g&&(c.transparencyRate=f!=t?.3:c.transparencyRate)}null!=c.maxLengthOfMonomer&&(f=$t(f,c.maxLengthOfMonomer));const m=f+h;(a=c.monomerTextSizeMap)[m]??(a[m]=t.measureText(m));let y=c.monomerTextSizeMap[m];(u=c.monomerTextSizeMap)[f]??(u[f]=t.measureText(f));let v=c.monomerTextSizeMap[f].width;const b=i/2-(y.fontBoundingBoxAscent+y.fontBoundingBoxDescent)/2+1;(l=c.monomerTextSizeMap)[h]??(l[h]=t.measureText(h));const C=c.monomerTextSizeMap[h].width;function w(e,o){const i=p?c.color:"rgb(0,0,0)";t.fillStyle=i,t.globalAlpha=c.transparencyRate,c.drawStyle===Ht.classic&&(t.fillText(f,n+e,r+b),t.fillStyle="#808080",t.fillText(h,n+o,r+b)),c.drawStyle===Ht.MSA&&t.fillText(f,n+e,r+b)}y=y.width,c.drawStyle===Ht.MSA&&(v=c.maxWord[c.wordIdx],y=c.maxWord[c.wordIdx]);const A=(c.maxWord[c.wordIdx]??0)-(c.maxWord[0]??0);if(c.left||y>o)return w(A,A+v),n+A+v+C;{const t=(o-y)/2;return w(t,t+v),n+A+t+v}}const kt="rgb(100,100,100)";class Gt extends Nt{constructor(t,e,n,r,i){super(t,e,n),this.monomerLengthLimit=r,this.propsProvider=i,this.colWidth=0,this._monomerLengthList=null,this.separatorWidth=5,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this.sysMonomerLib=null,this.padding=5,this.props=this.propsProvider(),this._processedRows=o.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),this.tableCol&&this.gridCol&&this.subs.push(this.tableCol.dataFrame.onCurrentRowChanged.subscribe((()=>{const t=this.tableCol.dataFrame;this.gridCol.grid,-1===t.currentRowIdx&&(this.tableCol.temp["reference-sequence"]=null,this.tableCol.temp["current-word"]=null,this.invalidateGrid())})))}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,bt.Q)(),this.invalidateGrid()})(),(async()=>{const t=await(0,a.pj)();this.sysMonomerLib=t.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}toLog(){return`MonomerPlacer<${this.viewerId}>`}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=o.BitSet.create(this.tableCol.length),this._monomerLengthList=null,this._monomerLengthMap={},this._monomerStructureMap={},super.reset(),this.invalidateGrid()}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}getCellMonomerLengths(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<e&&(this.colWidth=e,this.dirty=!0),this.dirty)try{this.reset()}catch(t){const[e,n]=(0,Ot.AP)(t);this.logger.error(e,void 0,n)}const r=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(t),o=new Array(r.length+1);o[0]=5;for(let t=1;t<o.length;t++)o[t]=o[t-1]+r[t-1];return[r,o]}getCellMonomerLengthsForSeq(t){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const e=this.seqHelper.getSeqHandler(this.tableCol),n=this.props.separatorWidth+1*this.props.monomerCharWidth,r=Math.ceil(this.colWidth/n),o=e.getSplitted(t),i=Math.min(r,o.length);let s=this._monomerLengthList[t];if(null===s||s.length<i){s=this._monomerLengthList[t]=new Array(o.length);let n=0;for(let t=0;t<i;++t){const r=o.getOriginal(t),i=this.props.monomerToShort(r,this.monomerLengthLimit),a=(e.isSeparator()?this.separatorWidth:this.props.separatorWidth)+i.length*this.props.monomerCharWidth;if(s[t]=a,n+=a,n>this.colWidth)break}}return s}getCellMonomerLengthsForSeqMsa(){var t;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(t=this._monomerLengthList)[0]??(t[0]=new Array(0));const e=this._monomerLengthList[0],{startIdx:n,endIdx:r}=(()=>{try{const t=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return t&&t.dart?{startIdx:Math.max(Math.floor((t?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((t?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(t){return{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}})(),o=this.props.separatorWidth+1*this.props.monomerCharWidth,i=Math.ceil(this.colWidth/o);for(let t=n;t<r;t++){if(this._processedRows.get(t)&&i<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t,i),r=Math.min(i,n.length);r>e.length&&e.push(...new Array(r-e.length).fill(o));let s=0;for(let t=0;t<r;++t){const r=n.getOriginal(t),o=this.props.monomerToShort(r,this.monomerLengthLimit),i=this.props.separatorWidth+o.length*this.props.monomerCharWidth;if(e[t]=Math.max(e[t]??0,i),s+=i,s>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,i)}return e}getPosition(t,e,n){const[r,o]=this.getCellMonomerLengths(t,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(t).length?null:function(t,e){let n,r=100,o=0,i=t.length-1;for(;o<=i;){if(n=Math.floor((i+o)/2),t[n]<=e&&e<t[n+1])return n;if(e<t[n]?i=n-1:o=n+1,--r<=0)throw new Error(`Get position for pointer x = ${e} searching has not converged on ${JSON.stringify(t)}. `)}return null}(o,e)}setMonomerLengthLimit(t){this.monomerLengthLimit!=t&&(this.monomerLengthLimit=t,this.dirty=!0)}setSeparatorWidth(t){this.separatorWidth!=t&&(this.props.separatorWidth=t,this.dirty=!0)}render(t,e,n,r,o,i,s){if(!this.seqHelper)return;const a=this.gridCol,u=this.tableCol,l=window.devicePixelRatio,c=`${this.toLog()}.render()`;this.logger.debug(`${c}, start`);let f=this.monomerLengthLimit;if(Rt.maxMonomerLength in u.tags){const t=parseInt(u.getTag(Rt.maxMonomerLength));f=!isNaN(t)&&t?t:50}if(".mm.cellRenderer.maxMonomerLength"in u.temp){const t=u.temp[".mm.cellRenderer.maxMonomerLength"];f=!isNaN(t)&&t?t:50}t.save();try{const s=this.seqHelper.getSeqHandler(u);if("1"===u.temp[".mm.cellRenderer.settingsChanged"]||this.monomerLengthLimit!=f){let t=0;const e=8;t=u.temp[".mm.cellRenderer.gapLength"]??t,this.setMonomerLengthLimit(f),this.setSeparatorWidth(s.isMsa()?e:t),u.temp[".mm.cellRenderer.settingsChanged"]="0"}const[c,h]=this.getCellMonomerLengths(i.tableRowIndex,r),p=(c.length,i.cell.value,i.cell.rowIndex),d=(u.getTag(gt.gp.alphabet),50);r=function(t,e,n,r,o){return t?Math.max(Math.min(t.canvas.width/o-n,r)):Math.max(e.canvas.width/o-n,0)}(a?.grid,t,e,r,l),t.beginPath(),t.rect(e+this.padding,n+this.padding,r-this.padding-1,o-2*this.padding),t.clip(),t.font="12px monospace",t.textBaseline="top";const g=u.meta.units,m=u.getTag(gt.gp.aligned),y=u.getTag(gt.gp.separator)??"",v=this.props.separatorWidth+1*this.props.monomerCharWidth,b=Math.ceil(r/v),C=u.temp["reference-sequence"],w=this.tableCol.temp["current-word"];w&&-1===u?.dataFrame?.currentRowIdx&&(this.tableCol.temp["current-word"]=null);const A=(()=>{const t=s.getSplitter(b)(null!=C&&""!=C?C:w??"");return wt().count(0).take(t.length).map((e=>t.getOriginal(e))).toArray()})(),E=s.getSplitted(p);let _=Ht.classic;m&&m.includes("MSA")&&g==gt.Hi.SEPARATOR&&(_=Ht.MSA);const x=Math.min(E.length,b);for(let a=0;a<x;++a){const u=E.getOriginal(a),l=E.getCanonical(a);let c=kt;const p=this.getMonomerLib();if(p){const t=s.defaultBiotype;c=p.getMonomerTextColor(t,l)}t.fillStyle=kt;const g={color:c,pivot:0,left:!0,transparencyRate:1,separator:y,last:a===E.length-1,drawStyle:_,maxWord:h,wordIdx:a,gridCell:i,referenceSequence:A,maxLengthOfMonomer:f,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};if(Bt(t,u,e+this.padding,n,r,o,g),d>r)break}}catch(t){const[e,n]=(0,Ot.AP)(t);this.logger.error(e,void 0,n),this.errors.push(t)}finally{t.restore()}}onMouseMove(t,e){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==t.tableRowIndex)return;const r=t.bounds,o=e.offsetX-t.gridColumn.left+(t.gridColumn.left-r.x),i=this.getPosition(t.tableRowIndex,o,r.width);this.logger.debug(`${n}, start, argsX: ${o}, left: ${i}`);const s=this.seqHelper.getSeqHandler(this.tableCol),a=s.getSplitted(t.tableRowIndex);if(null!==i&&i<a.length){const n=s.alphabet??gt.YI.UN,r={position:i,biotype:n===gt.YI.RNA||n===gt.YI.DNA?xt.o.NUCLEOTIDE:xt.o.AA,symbol:a.getCanonical(i)},o=[];let u=this._monomerStructureMap[r.symbol];{const t=this.getMonomerLib();u=this._monomerStructureMap[r.symbol]=t?t.getTooltip(r.biotype,r.symbol):I.divText("Monomer library is not available")}o.push(u),I.tooltip.show(I.divV(o),e.x+16,e.y+16),Tt(t,r)}else I.tooltip.hide(),Tt(t,null)}}class jt extends Gt{constructor(t,e,n,r){super(t,e,Wt.logger,n,(()=>({seqHandler:r.getSeqHandler(e),monomerCharWidth:7,separatorWidth:11,monomerToShort:gt.zS})))}onMouseMove(t,e){const n=t.bounds,r=e.offsetX-t.gridColumn.left+(t.gridColumn.left-n.x);this.getPosition(t.tableRowIndex,r,n.width),super.onMouseMove(t,e)}}class Ut{get defaultGapOriginal(){return""}constructor(t,e){this.separator=t,this.helmHelper=e,this.separatorSplitter=(0,gt.dh)(this.separator),this.splitter=this._splitter.bind(this)}setUnits(){}_splitter(t){const e=this.separatorSplitter(t);return new Vt(wt().count(0).take(e.length).map((t=>e.getOriginal(t))).toArray(),i.b9[i.Hi.SEPARATOR])}getHelm(t,e){return St.s.parseNotation(t,this.helmHelper).getNotationHelm()}createCellRendererBack(t,e){const n=new jt(t,e,4,this.helmHelper.seqHelper);return n.init().then((()=>{})),n}}class Vt extends Lt.Mu{getCanonical(t){if(this.isGap(t))return i._S;const e=this.getOriginal(t);let n=e;return e.startsWith("{")?n=e.slice(1):e.endsWith("}")?n=e.slice(0,-1):e.startsWith("(")?n=e.replace(/^\(.\d+\)/,""):e.endsWith(")")&&(n=e.replace(/\(\d+\)$/,"")),n}constructor(t,e){super(t,e)}}const Wt=new L({debug:!0});function qt(t,e){t.setTag("aligned","SEQ"),t.setTag("alphabet","UN"),t.setTag(".alphabetIsMultichar","true"),t.meta.units=i.Hi.CUSTOM,t.tags["polytool-data-role"]="template",t.temp[s.notationProvider]=new Ut(e,Wt.helmHelper)}},269:(t,e,n)=>{"use strict";n.d(e,{s:()=>s});var r=n(599),o=n(125),i=n(699);class s{constructor(t,e,n,r){this.helmHelper=r,this.linkages=e,this.monomers=t,this.mol=n}static parseHelm(t,e){const n=/(\w+\{.*\})\$(.*)\$(.*)\$(.*)\$/g.exec(t),i=[n[1],n[2],n[3],n[4]],a=i[0].split("|"),u=i[1].split("|"),l=new Array(a.length),c=[],f=e.createHelmWebEditor().editor.m;let h=0;const p=new JSDraw2.Point(0,0);for(let t=0;t<a.length;t++){const e=a[t].indexOf("{"),n=a[t].indexOf("}");l[t]=a[t].slice(e+1,n).split(".").map((t=>{return(e=t).startsWith("[")&&e.endsWith("]")?e.slice(1,-1):e;var e}));for(let e=0;e<l[t].length;e++){const n=l[t][e],o={type:r.o.AA,i:t,j:e,continuousId:h},i=new JSDraw2.Atom(p,n,o);if(f.addAtom(i),0!==e){const t=f.atoms[h-1],e=f.atoms[h],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,f.addBond(n)}h++,p.x+=JSDraw2.Editor.BONDLENGTH}p.y+=4*JSDraw2.Editor.BONDLENGTH}for(let t=0;t<u.length;t++)if(""!==u[t]&&"V2.0"!==u[t]){const e=u[t].split(","),n=parseInt(e[0].replace("PEPTIDE",""))-1,r=parseInt(e[1].replace("PEPTIDE",""))-1,i=e[2].split("-"),s=i[0].split(":"),a=i[1].split(":");c.push({fChain:n,sChain:r,fMonomer:(0,o.jX)(parseInt(s[0]),n,l),sMonomer:(0,o.jX)(parseInt(a[0]),r,l),fR:parseInt(s[1].replace("R","")),sR:parseInt(a[1].replace("R",""))})}for(let t=0;t<c.length;t++){const e=f.atoms[c[t].fMonomer-1],n=f.atoms[c[t].sMonomer-1],r=new JSDraw2.Bond(e,n);r.r1=c[t].fR,r.r2=c[t].sR,f.addBond(r)}return new s(l,c,f,e)}applyRules(t){const e=this.getNotation();return s.fromNotation(e,t,this.helmHelper)}static fromNotation(t,e,n){const o=e.heterodimerCode,i=e.homodimerCode,a=[],u=[],l=null!==o?t.split(`(${e.heterodimerCode})`):"";null!==o&&l.length>1?(u.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),a.push(l[1].replaceAll("{","").replaceAll("}","")),a.push(l[2].replaceAll("{","").replaceAll("}",""))):a.push(t);for(let t=0;t<a.length;t++)if(null!==i&&a[t].includes(`(${i})`)){const e=a.length;u.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=a[t].replace(`(${i})`,""),r=n.indexOf("{"),o=n.slice(0,r),s=n.replace(o,"").replaceAll("{","").replaceAll("}","");a[t]=o+s,a.push(s)}for(let t=0;t<a.length;t++)if(null!==i&&a[t].includes(`(${i})`)){const e=a.length;u.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const n=a[t].replace(`(${i})`,""),r=n.indexOf("{"),o=n.slice(0,r),s=n.replace(o,"").replaceAll("{","").replaceAll("}","");a[t]=o+s,a.push(s)}const c=new Array(a.length);for(let t=0;t<a.length;t++){const n=a[t].split("-"),r=this.getLinkedPositions(n,e.linkRules),[o,i,s,l,f]=this.getAllCycles(e.linkRules,n,r);new Array(o.length);for(let e=0;e<i.length;e++)u.push({fChain:t,sChain:t,fMonomer:i[e],sMonomer:s[e],fR:l[e],sR:f[e]});c[t]=o}const f=[],h=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),[o,i,s,a]=this.getAllReactants(e.reactionRules,c[t],n);if(i.length>=1){const n=new Array(s[0]-1),l=new Array(o.length-s[0]);for(let e=0;e<s[0]-1;e++){const i=n[e]=o[e],s={type:r.o.AA,i:t,j:e,continuousId:p},a=new JSDraw2.Atom(d,i,s);if(h.addAtom(a),e>0){const t=h.atoms[p-1],e=h.atoms[p],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,h.addBond(n)}p++}for(let e=s[0];e<o.length;e++){const n=l[e-s[0]]=o[e],i={type:r.o.AA,i:t,j:e,continuousId:p},a=new JSDraw2.Atom(d,n,i);if(h.addAtom(a),e>s[0]){const t=h.atoms[p-1],e=h.atoms[p],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,h.addBond(n)}p++}h.atoms[i[0]-1].elem=n[i[0]-1]=e.reactionRules[a[0]].name;for(let t=0;t<u.length;t++)u[t].fMonomer>s[0]&&(u[t].fMonomer-=s[0],u[t].fChain++),u[t].sMonomer>s[0]&&(u[t].sMonomer-=s[0],u[t].sChain++);u.push({fChain:0,sChain:0,fMonomer:i[0],sMonomer:s[0]-1,fR:3,sR:2}),u.push({fChain:0,sChain:1,fMonomer:i[0],sMonomer:1,fR:4,sR:1});const c=new Array(n.length);for(let t=0;t<n.length;t++)c[t]=`[${n[t]}]`;const g=new Array(l.length);for(let t=0;t<l.length;t++)g[t]=`[${l[t]}]`;f.push(n),f.push(l)}else{for(let e=0;e<c[t].length;e++){const n=c[t][e],o={type:r.o.AA,i:t,j:e,continuousId:p},i=new JSDraw2.Atom(d,n,o);if(h.addAtom(i),e>0){const t=h.atoms[p-1],e=h.atoms[p],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,h.addBond(n)}p++}f.push(c[t])}}for(const t of u){const e=h.atoms[t.fMonomer-1],n=h.atoms[t.sMonomer-1],r=new JSDraw2.Bond(e,n);r.r1=t.fR,r.r2=t.sR,h.addBond(r)}return new s(f,u,h,n)}static parseNotation(t,e){const n=[],o=[],i=e.createHelmWebEditor().editor.m,a=/(\(.\d+\))?\{[^\}]*\}/g,u=[];u.push(t.replaceAll(a,""));const l=t.matchAll(a);for(const t of l){const e=t[0];e&&u.push(e)}let c=0;for(let t=0;t<u.length;t++){const e=u[t].split("-"),r=new Array(e.length);let i=0;for(let n=0;n<e.length;n++){const s=e[n].replace("{","").replace("}","");""!==s?(r[n]=s,c++,i++):o.push({fChain:t,sChain:t+1,fMonomer:c,sMonomer:c+1,fR:1,sR:1})}n.push(r.slice(0,i))}c=0;const f=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 o=n[t][e],s={type:r.o.AA,i:t,j:e,continuousId:c},a=new JSDraw2.Atom(f,o,s);if(i.addAtom(a),0!==e){const t=i.atoms[c-1],e=i.atoms[c],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,i.addBond(n)}c++,f.x+=JSDraw2.Editor.BONDLENGTH}f.y+=4*JSDraw2.Editor.BONDLENGTH}for(let t=0;t<o.length;t++){const e=i.atoms[o[t].fMonomer-1],n=i.atoms[o[t].sMonomer-1],r=new JSDraw2.Bond(e,n);r.r1=o[t].fR,r.r2=o[t].sR,i.addBond(r)}return new s(n,o,i,e)}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+=`${(0,o.MH)(this.linkages[e].fMonomer-1,this.monomers)[0]+1}:R${this.linkages[e].fR}-`,t+=`${(0,o.MH)(this.linkages[e].sMonomer-1,this.monomers)[0]+1}:R${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=[];for(let r=0;r<e.length;r++){let o=!1,s=!1,a=!1,u=-1,l=-1;const c=`(${e[r].code})`,[f,h]=(0,i.Ln)(e[r]);if(f.length>0)for(let e=0;e<f.length;e++){for(let n=0;n<t.length;n++)if(t[n].includes(c)){if(o){if(a&&t[n]==h[e]+c){s=!0,l=n;break}if(a||t[n]!=f[e]+c)continue;s=!0,l=n;break}if(t[n]==f[e]+c)o=!0,a=!0,u=n;else{if(t[n]!=h[e]+c)continue;o=!0,a=!1,u=n}}o&&s&&(a?n.push([u,l,r]):n.push([l,u,r]))}else{for(let e=0;e<t.length;e++)if(t[e].includes(c)){if(o){if(a&&t[e]){s=!0,l=e;break}if(!a&&t[e]){s=!0,l=e;break}continue}o=!0,a=!0,u=e}if(!o||!s)continue;a?n.push([u,l,r]):n.push([l,u,r])}}return n}static getAllCycles(t,e,n){const r=[],o=[],i=[],s=[],a=n.length;for(let u=0;u<a;u++){if(-1==n[u][0])continue;const a=n[u][2],l=t[a].code;e[n[u][0]]=e[n[u][0]].replace(`(${l})`,""),e[n[u][1]]=e[n[u][1]].replace(`(${l})`,""),r.push(n[u][0]+1),o.push(n[u][1]+1),i.push(t[a].firstLinkingGroup),s.push(t[a].secondLinkingGroup)}return[e,r,o,i,s]}static getAllReactants(t,e,n){const r=[],o=[],i=[],s=n.length;for(let a=0;a<s;a++){if(-1==n[a][0])continue;const s=t[n[a][2]].code;e[n[a][0]]=e[n[a][0]].replace(`(${s})`,""),e[n[a][1]]=e[n[a][1]].replace(`(${s})`,""),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=>` ${t}`)).join("\n")}`);return e}}},229:(t,e,n)=>{"use strict";n.d(e,{b:()=>s});var r=n(192),o=n(269),i=n(511);function s(t,e,n){const s=new Array(t.length);for(let a=0;a<t.length;a++)try{if(null==t[a])s[a]="";else{const r=o.s.fromNotation(t[a],e,n);s[a]=r.getHelm()}}catch(t){const[e,n]=(0,r.AP)(t);i._package.logger.error(e,void 0,n),s[a]=""}return s}},125:(t,e,n)=>{"use strict";n.d(e,{AM:()=>y,MH:()=>f,Tl:()=>m,jX:()=>h});var r=n(328),o=n(991),i=n.n(o),s=n(890),a=n(717),u=n(699),l=n(296),c=n(192);function f(t,e){let n,r=t;for(n=0;n<e.length&&r>=e[n].length;++n)r-=e[n].length;return[r,n]}function h(t,e,n){let r=0;for(let t=0;t<e;++t)r+=n[t].length;return r+t}function p(t,e){const n=t.molfile;let r=e.molfile;const o=t.rgroups.length,i=r.indexOf("M RGP");if(-1!==i){const t=r.substring(i+6,i+9),e=Number(t);for(let t=0;t<e;t++){const e=i+9+4+8*t,n=i+9+8+8*t,s=r.substring(e,n),a=Number(s)+o,u=Math.floor(Math.log10(a)+1),l=" ".repeat(4-u)+String(a);r=r.substring(0,e)+l+r.substring(n,r.length)}}return[n,r]}function d(t,e,n,o,i){let s=null,a=null,u=null,f=null,h=null,p=null,d="";try{if(s=t.get_rxn(e),!s)throw new l.J5(e);a=new t.MolList,u=t.get_mol(n),f=t.get_mol(o),a.append(u),a.append(f),h=s.run_reactants(a,1),p=h.get(0).next(),d=p?.get_molblock()}catch(t){const[e,n]=(0,c.AP)(t);throw r.shell.error(`Can not assemble monomer '${i}': ${e}.`),t}finally{s?.delete(),a?.delete(),u?.delete(),f?.delete(),h?.delete(),p?.delete()}return d}function g(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}function m(t,e,n){const r=n.reaction,o=n.name,[i,s]=(0,u.Ln)(n),a=new Array(i.length),c=new Array(i.length);for(let n=0;n<i.length;n++){const u=e.getMonomer("PEPTIDE",i[n]);if(!u)throw new l.bl("PEPTIDE",i[n]);const f=e.getMonomer("PEPTIDE",s[n]);if(!f)throw new l.bl("PEPTIDE",s[n]);const[h,m]=p(u,f),y={symbol:o,name:o,molfile:d(t,r,h,m,o),author:"",id:0,rgroups:g(u,f),smiles:"",polymerType:"PEPTIDE",monomerType:"Backbone",createDate:null};y.meta=Object.assign(y.meta??{},{colors:{default:{line:"#2083D5",text:"#2083D5",background:"#F2F2F5"}}}),a[n]=o,c[n]=y}return[a,c]}async function y(t){const e=(await(0,s.pj)()).getMonomerLib(),n=await(0,a.j)(),r={};let o=[],u=[];for(let i=0;i<t.reactionRules.length;i++)try{[o,u]=m(n,e,t.reactionRules[i])}catch(t){o=[],u=[],console.error(t)}finally{for(let t=0;t<o.length;t++)r[o[t]]=u[t]}const l={PEPTIDE:r};return e.override(l,"ST-PT-reactions."+i().repeat(1).map((()=>Math.floor(36*Math.random()).toString(36))).take(4).toArray().join(""))}},699:(t,e,n)=>{"use strict";n.d(e,{Ln:()=>b,Q4:()=>v});var r=n(82),o=n(328);n(389),n(991);var i=n(511),s=n(124),a=n(229),u=n(439);class l{constructor(t,e){this.v=null,this.currentTab="",this.rules=t,this.linkRuleDataFrame=this.rules.getLinkRulesDf(),this.synthRuleDataFrame=this.rules.getSynthesisRulesDf(),this.fileName=e;const n=this.rules.homodimerCode?this.rules.homodimerCode:"",r=this.rules.heterodimerCode?this.rules.heterodimerCode:"";this.homoDimerInput=ui.input.string("Homo dimer",{value:n,onValueChanged:()=>{},nullable:!1}),this.heteroDimerInput=ui.input.string("Hetero dimer",{value:r,onValueChanged:()=>{},nullable:!1})}async getAndAddView(){if(this.v)try{const t=Array.from(o.shell.views).find((t=>t.name===this.v.name));if(!t)throw this.v.detach(),this.v.close(),new Error("View is closed, making it null in catch statement");o.shell.v=t}catch(t){this.v=null}return this.v||(this.v=r.View.create(),this.v.name=`Manage Polytool Rules - ${this.fileName}`,this.v.append(await this.getForm()),this.v=o.shell.addView(this.v),o.shell.v=this.v),this.v}static async getInstance(t){if(!this.instances[t]){const e=await v([t]);this.instances[t]=new l(e,t)}return this.instances[t]}save(){this.rules.homodimerCode=this.homoDimerInput.value,this.rules.heterodimerCode=this.heteroDimerInput.value,this.rules.setLinkRules(this.linkRuleDataFrame),this.rules.setSynthesisRules(this.synthRuleDataFrame);const t={homodimerCode:this.rules.homodimerCode,heterodimerCode:this.rules.heterodimerCode,linkRules:this.rules.linkRules,reactionRules:this.rules.reactionRules},e=JSON.stringify(t,void 0,2);i._package.files.writeAsText(`polytool-rules/${this.fileName}`,e),o.shell.info(`Polytool rules at ${this.fileName} was updated`)}createGridDiv(t,e){const n=ui.h1(t,"polytool-grid-header");return e.root.prepend(n),e.root.style.height="100%",e.root}async getLinkExamplesGrid(){const t=[];for(let e=0;e<this.rules.linkRules.length;e++){const n=this.rules.linkRules[e].code,[r,o]=b(this.rules.linkRules[e]);for(let e=0;e<r.length;e++){const i=`${r[e]}(${n})-A-A-A-A-${o[e]}(${n})-A`;t.push(i)}}const e=await(0,s.b2)(),n=(0,a.b)(t,this.rules,e),o=r.Column.fromStrings("monomers",t),l=r.Column.fromStrings("helm",n);return(0,i.applyNotationProviderForCyclized)(o,"-"),o.semType=r.SEMTYPE.MACROMOLECULE,l.semType=r.SEMTYPE.MACROMOLECULE,l.meta.units=u.Hi.HELM,l.setTag(r.TAGS.CELL_RENDERER,"helm"),r.DataFrame.fromColumns([o,l]).plot.grid()}async getReactionExamplesGrid(){const t=[];for(let e=0;e<this.rules.reactionRules.length;e++){const n=this.rules.reactionRules[e].code,[r,o]=b(this.rules.reactionRules[e]);for(let e=0;e<r.length;e++){const i=`${r[e]}(${n})-A-A-A-A-${o[e]}(${n})`;t.push(i)}}const e=await(0,s.b2)(),n=(0,a.b)(t,this.rules,e),o=r.Column.fromStrings("monomers",t),l=r.Column.fromStrings("helm",n);return o.semType=r.SEMTYPE.MACROMOLECULE,(0,i.applyNotationProviderForCyclized)(o,"-"),l.semType=r.SEMTYPE.MACROMOLECULE,l.meta.units=u.Hi.HELM,l.setTag(r.TAGS.CELL_RENDERER,"helm"),r.DataFrame.fromColumns([o,l]).plot.grid()}async getForm(){r.TabControl;const t=ui.divV([this.homoDimerInput,this.heteroDimerInput]),e=await this.getLinkExamplesGrid(),n=await this.getReactionExamplesGrid(),o=ui.tabControl({Links:e,Reactions:n,Dimers:t},!1);o.root.style.height="90%",o.root.style.width="100%",o.root.classList.add("rules-manager-form-tab-control"),o.header.style.marginBottom="10px";const i=this.createGridDiv("Link rules",this.linkRuleDataFrame.plot.grid({showAddNewRowIcon:!0})),s=this.createGridDiv("Reaction rules",this.synthRuleDataFrame.plot.grid({showAddNewRowIcon:!0}));i.style.width="100%",s.style.width="100%";const a=[i,s,ui.div()];a[0].style.removeProperty("display"),a[1].style.display="none",a[2].style.display="none",o.onTabChanged.subscribe((()=>{this.currentTab=o.currentPane.name;const t=o.panes.findIndex((t=>t.name==this.currentTab));for(let e=0;e<a.length;e++)e==t?a[e].style.removeProperty("display"):a[e].style.display="none"}));const u=ui.bigButton("Save changes",(()=>{this.save()})),l=ui.divV([o.root,u]);l.style.height="100%",l.style.alignItems="center";const c=ui.splitH([l,ui.divV(a,{style:{width:"100%"}})],{style:{width:"100%"}},!0);return c.style.height="100%",c}}l.instances={};const c="System:AppData/SequenceTranslator/polytool-rules/",f="code",h="firstMonomers",p="secondMonomers",d="name",g="firstLinkingGroup",m="secondLinkingGroup";class y{constructor(t,e,n,r){this.homodimerCode=t,this.heterodimerCode=e,this.linkRules=n,this.reactionRules=r}set homodimer(t){this.homodimerCode=t}set heterodimer(t){this.heterodimerCode=t}addLinkRules(t){for(let e=0;e<t.length;e++)this.linkRules.push(t[e])}addSynthesisRules(t){for(let e=0;e<t.length;e++)this.reactionRules.push(t[e])}getLinkRulesDf(){const t=this.linkRules.length,e=r.Column.int(f,t),n=r.Column.string(h,t),o=r.Column.string(p,t),i=r.Column.int(g,t),s=r.Column.int(m,t);for(let r=0;r<t;r++)e.set(r,this.linkRules[r].code),n.set(r,this.linkRules[r].firstMonomers.toString()),o.set(r,this.linkRules[r].secondMonomers.toString()),i.set(r,this.linkRules[r].firstLinkingGroup),s.set(r,this.linkRules[r].secondLinkingGroup);return r.DataFrame.fromColumns([e,n,o,i,s])}getSynthesisRulesDf(){const t=this.reactionRules.length,e=r.Column.int(f,t),n=r.Column.string(h,t),o=r.Column.string(p,t),i=r.Column.string(d,t),s=r.Column.string("firstReactant",t),a=r.Column.string("secondReactant",t),u=r.Column.string("product",t);for(let r=0;r<t;r++){e.set(r,this.reactionRules[r].code),n.set(r,this.reactionRules[r].firstMonomers.toString()),o.set(r,this.reactionRules[r].secondMonomers.toString()),i.set(r,this.reactionRules[r].name);const t=this.reactionRules[r].reaction.split(">>"),l=t[0].split(".");s.set(r,l[0]),a.set(r,l[1]),u.set(r,t[1])}return s.semType=r.SEMTYPE.MOLECULE,a.semType=r.SEMTYPE.MOLECULE,u.semType=r.SEMTYPE.MOLECULE,r.DataFrame.fromColumns([i,s,a,u,e,n,o])}setLinkRules(t){const e=t.rowCount,n=new Array(e),r=t.columns.byName(f),o=t.columns.byName(h),i=t.columns.byName(p),s=t.columns.byName(g),a=t.columns.byName(m);for(let t=0;t<e;t++){const e={code:r.get(t),firstMonomers:o.get(t).split(","),secondMonomers:i.get(t).split(","),firstLinkingGroup:s.get(t),secondLinkingGroup:a.get(t)};n[t]=e}this.linkRules=n}setSynthesisRules(t){const e=t.rowCount,n=new Array(e),r=t.columns.byName(f),o=t.columns.byName(h),i=t.columns.byName(p),s=t.columns.byName(d),a=t.columns.byName("firstReactant"),u=t.columns.byName("secondReactant"),l=t.columns.byName("product");for(let t=0;t<e;t++){const e=`${a.get(t)}.${u.get(t)}>>${l.get(t)}`,c={code:r.get(t),firstMonomers:o.get(t).split(","),secondMonomers:i.get(t).split(","),reaction:e,name:s.get(t)};n[t]=c}this.reactionRules=n}}async function v(t){const e=new r.FileSource(c),n=new y(null,null,[],[]);for(let r=0;r<t.length;r++){const o=await e.readAsText(t[r].replace(c,"")),i=JSON.parse(o);n.homodimer=i.homodimerCode,n.heterodimer=i.heterodimerCode,n.addLinkRules(i.linkRules),n.addSynthesisRules(i.reactionRules)}return n}function b(t){const e=t.firstMonomers.length*t.secondMonomers.length,n=new Array(e),r=new Array(e);let o=0;for(let e=0;e<t.firstMonomers.length;e++)for(let i=0;i<t.secondMonomers.length;i++)n[o]=t.firstMonomers[e],r[o]=t.secondMonomers[i],o++;return[n,r]}},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],l=o[i*s+n]=t.clone(),c=l.atoms[a].elem;l.atoms[a].elem=u;const f=c?.length>1?`[${c}]`:c,h=u?.length>1?`[${u}]`:u;l.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 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o={single1:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,placeholders:[{position:4,monomers:["K","P","F4COO"]},{position:6,monomers:["Y","T"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5P"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5[F4COO]"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7T"}]},"single-with-original":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,placeholders:[{position:4,monomers:["K","P","F4COO"]},{position:6,monomers:["Y","T"]}],keepOriginal:!0},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:""},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5P"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5[F4COO]"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-[Tic]7T"}]},matrix1:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Matrix,placeholders:[{position:1,monomers:["D","L"]},{position:4,monomers:["K","P","F4COO"]},{position:6,monomers:["Y","T"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].D.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5K-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5K-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5P-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5P-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5[F4COO]-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2D-P5[F4COO]-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5K-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5K-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5P-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5P-[Tic]7T"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5[F4COO]-[Tic]7Y"},{seq:"PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0",name:"-F2L-P5[F4COO]-[Tic]7T"}]}};for(const[t,n]of Object.entries(o))(0,e.t6)(`${t}`,(async()=>{const t=(0,L.o)(n.src,"",n.params);(0,e.J6)(t,n.tgt.map((t=>[t.seq,t.name])))}))})),(0,e.L1)("PolyTool: Enumerate",(()=>{let t,n,r;(0,e.gM)((async()=>{t=await(0,x.b2)(),n=await(0,b.pj)(),r=await A(),await n.loadMonomerLibForTests()})),(0,e.Pl)((async()=>{await E(r),await n.loadMonomerLib(!0)}));const o={breadth1:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"}]},"breadth1-with-original":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]}],keepOriginal:!0},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:""},{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"}]},breadth2:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K","Y"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"},{seq:"PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5Y"}]},"breadth-double":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]},{start:2,end:4,monomers:["Y"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-K3Y"},{seq:"PEPTIDE1{[Ac(1)].F.K.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.K.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-P5Y"},{seq:"PEPTIDE1{[Ac(1)].F.Y.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-K4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-P5Y"},{seq:"PEPTIDE1{[Ac(1)].F.Y.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-K5Y"}]}};for(const[t,n]of Object.entries(o))(0,e.t6)(`${t}`,(async()=>{const t=(0,L.o)(n.src,"",n.params);(0,e.J6)(t,n.tgt.map((t=>[t.seq,t.name])))}))}));var M=n(269);(0,e.L1)("PolyTool: Chain: parseNotation",(()=>{let t;(0,e.gM)((async()=>{t=await(0,x.b2)()}));const n={cyclized:{src:{seq:"R-F-C(1)-T-G-H-F-Y-P-C(1)-meI"},tgt:{helm:"PEPTIDE1{R.F.[C(1)].T.G.H.F.Y.P.[C(1)].[meI]}$$$$V2.0"}},dimerized1:{src:{seq:"(#3)Succ-{A(CHOL)-F-C(1)-T-G-H-Y-P-C(1)-NH2}"},tgt:{helm:"PEPTIDE1{[(#3)Succ]}|PEPTIDE2{[A(CHOL)].F.[C(1)].T.G.H.Y.P.[C(1)].[NH2]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$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,P.Q4)(["rules_example.json"]);const n=await M.s.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,I.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,I.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$$$V2.0",mmHelm:"PEPTIDE1{[(#3)Succ].[{A(CHOL)].F.C.T.G.H.Y.P.C.[NH2}]}$PEPTIDE1,PEPTIDE1,4:R3-10:R3$$$V2.0"},tgt:{templateChain:{monomerCount:[1,10],linkageCount:1},mmChain:{monomerCount:[11],linkageCount:1}}},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$$$V2.0",mmHelm:"PEPTIDE1{[($3)Succ].[{R].F.C.T.G.H.F.P.C.[NH2}($3){A(CHOL)].F.[C(1)].Y.H.G.D.N.[C(1)].[meI}]}$PEPTIDE1,PEPTIDE1,4:R3-10:R3$$$V2.0"},tgt:{templateChain:{monomerCount:[1,10,10],linkageCount:1},mmChain:{monomerCount:[20],linkageCount:1}}}};for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`fromNotation-${r}`,(async()=>{const n=await(0,P.Q4)(["rules_example.json"]),r=M.s.fromNotation(o.templateSeq,n,t);r.check(!0),(0,e.J6)(r.monomers.map((t=>t.length)),i.mmChain.monomerCount),(0,e.E3)(r.linkages.length,i.mmChain.linkageCount),(0,e.E3)(r.getHelm(),o.mmHelm)}),"reaction2"==r?{skipReason:"reverse reaction"}:void 0);for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`parseNotation-${r}`,(async()=>{await(0,P.Q4)(["rules_example.json"]);const n=M.s.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-${r}`,(async()=>{await(0,P.Q4)(["rules_example.json"]);const n=M.s.parseHelm(o.templateHelm,t);n.check(!0),(0,e.J6)(n.monomers.map((t=>t.length)),i.templateChain.monomerCount),(0,e.E3)(n.linkages.length,i.templateChain.linkageCount),(0,e.E3)(n.getHelm(),o.templateHelm),(0,e.E3)(n.getNotation(),o.templateSeq)}));for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`applyRules-${r}`,(async()=>{const n=await(0,P.Q4)(["rules_example.json"]),r=M.s.parseNotation(o.templateSeq,t),s=await r.applyRules(n);s.check(!0),(0,e.J6)(s.monomers.map((t=>t.length)),i.mmChain.monomerCount),(0,e.E3)(s.linkages.length,i.mmChain.linkageCount),(0,e.E3)(s.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 N.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"),l=await(0,d.Q)(),c=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"]);c.semType=t.SEMTYPE.MACROMOLECULE,c.meta.units=g.Hi.HELM;const f=await l.helmToAtomicLevel(c,!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,P.Q4)(["rules_example.json"])).reactionRules.find((t=>"GGaz"==t.name)),[i,s]=(0,I.Tl)(t,n,o);(0,e.E3)(i[0],o.name);const a=t.get_mol(s[0].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 N=new s;async function O(n,r,o){const i=await(0,e.N$)({category:n,test:r,testContext:o,verbose:!0});return t.DataFrame.fromObjects(i)}async function $(){await(0,e.Xb)(N,N.getModule("package-test.js"))}})(),sequencetranslator_test=r})();
3
3
  //# sourceMappingURL=package-test.js.map