@datagrok/sequence-translator 1.8.0 → 1.9.1

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 (12) hide show
  1. package/CHANGELOG.md +4 -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 +3 -3
  7. package/src/apps/translator/view/ui.ts +1 -1
  8. package/src/package-test.ts +1 -1
  9. package/src/package.ts +7 -0
  10. package/src/polytool/pt-combine-dialog.ts +131 -0
  11. package/test-console-output-1.log +82 -104
  12. package/test-record-1.mp4 +0 -0
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={6717:(t,e,n)=>{"use strict";n.d(e,{j:()=>o});var r=n(6082);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()}},3599:(t,e,n)=>{"use strict";n.d(e,{o:()=>r.o});var r=n(6869)},9124:(t,e,n)=>{"use strict";n.d(e,{b2:()=>i});var r=n(7389),o=n(6082);async function i(){const t="Helm",e=o.Func.find({package:t,name:"getHelmHelper"});if(0===e.length)throw new Error(`Package '${t}' must be installed for HelmHelper.`);return(await e[0].prepare().call()).getOutputParamValue()}o.JsInputBase,Error,r.input.helmAsync=async function(t,e){return(await i()).createHelmInput(t,e)}},8438:(t,e,n)=>{"use strict";function r(t){return t.startsWith("[")&&t.endsWith("]")?t.slice(1,-1):t}n.d(e,{D:()=>r})},8123:(t,e,n)=>{"use strict";n.d(e,{u:()=>r});const r={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M RGP",V2K_A_LINE:"A ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:" 0 0 0 0 0 0 999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M V30 ",V3K_END:"M END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"}},2890:(t,e,n)=>{"use strict";n.d(e,{pj:()=>d});var r,o,i,s,a,l,u,c=n(6082);n(4328);class f{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,r=f._createBuffer(n);if(e)for(let t=0;t<r.length;t++)r[t]=-1;this._data=r,this._length=n}else{if(!(t instanceof Uint32Array))throw new Error("Invalid constructor");this._data=t,this._length=e}}getRawData(){return this._data}assureGoez(t,e){if(t<0)throw new Error(`${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"}(l||(l={})),function(t){t.CommonItems="Common 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E{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[A.ti.LINKAGE]))).sort(w));return new RegExp(`${A.q7}.(${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: ${t}`)}isHelm(t){return t===g.NO.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(w)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(_(e)+"|\\([^()]*\\)|.","g")}}function _(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const x={LEFT:"RNA1{",RIGHT:"}$$$$"};class T{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new E(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===g.NO.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===g.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} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(_(Object.values(x)),"g");let r=t.replace(n,"");const o=this.formats.getHelmToFormatDict(e),i=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>i.includes(t)?o[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,A.iL).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),o=this.formats.getFormatRegExp(e),i=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(o,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${A.iL}.`),s=s.slice(0,-1),s[s.length-1]===A.q7&&(s=s.slice(0,-1)),s=s.replace(i,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${x.LEFT+s+x.RIGHT}`}}class I{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return g.NO.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const o=t[r];n[r]=e.getInvalidCodeIndex(o)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=m(this.libWrapper.getCodesByFormat(n));let o=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){o=e+1;break}r.some((e=>e===t.slice(o,o+e.length)))&&e.push(n)}return e}}var N=n(7389);const S=$;var L=n.n(S);class P 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 y(t,e).getInvalidCodeIndex(r));const o=n<0||""===t,i=N.span([]);L()(i).css("-webkit-text-fill-color","var(--grey-6)");const s=N.span([]);return L()(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()=>{const t=await this.getSettings();let e=t instanceof Map?t.get("MonomersPath"):t.MonomersPath;e&&await r.dapi.files.exists(e)||(this.logger.warning(`Monomers path '${e}' not found. Fallback to monomers sample path '${c}'.`),e=c),[this._jsonData,this._monomerLib]=await Promise.all([b(e),O(e)]),this._monomerLibWrapper=new C(this.monomerLib,this.jsonData)})()),this.initLibDataPromise}async getTranslationHelper(){return await r.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new y(t,this)}createFormatConverter(t,e){return new T(t,e,this)}createFormatDetector(t){return new I(t,this)}}async function O(t){const e=o.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const e=await(0,l.pj)();return await e.readLibrary(t,"monomer-lib.json")}finally{e.close()}}const M=["SS","AS"],R={SS:"Sense strand",AS:"Anti sense"},D=["3'","5'"];var B,H,F,k;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(B||(B={})),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"}(k||(k={})),B.IS_ANTISENSE_STRAND_INCLUDED,B.NUCLEOTIDE_SEQUENCES,B.PHOSPHOROTHIOATE_LINKAGE_FLAGS,B.STRAND_TERMINUS_MODIFICATIONS,H.PATTERN_NAME,H.PATTERN_COMMENT,H.NUCLEOTIDES_WITH_NUMERIC_LABELS,Error,Error,n(4802);const G=rxjs;var U;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))}}}(U||(U={}));var j=n(2543),V=n.n(j),W=n(5072),Y=n.n(W),q=n(7825),K=n.n(q),z=n(7659),J=n.n(z),Q=n(5056),X=n.n(Q),Z=n(540),tt=n.n(Z),et=n(1113),nt=n.n(et),rt=n(9252),ot={};ot.styleTagTransform=nt(),ot.setAttributes=X(),ot.insert=J().bind(null,"head"),ot.domAPI=K(),ot.insertStyleElement=tt(),Y()(rt.A,ot),rt.A&&rt.A.locals&&rt.A.locals;class it{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return N.divV([N.h1("PTO"),N.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return M.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===M.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+M.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=N.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),N.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 M.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=N.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),N.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class st{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=M.map((t=>this.constructControlsPanel(t)));return N.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return N.div([]);const e=this.constructHeader(),n=this.createControls(t);return N.block([N.h1(`${R[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return N.divH([N.div([N.divText("#")],{style:{width:"20px"}}),N.block75([N.divText("Modification")]),N.div([N.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return N.div(e.map(((t,e)=>N.divH([n[e],N.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const o=N.input.choice("",{value:n,items:e});return o.onInput.subscribe((()=>{const e=o.value;this.eventBus.setNucleotide(t,r,e)})),o}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=N.input.bool("",{value:e});r.onInput.subscribe((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.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 M.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=>N.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{L()(e[n]).empty(),L()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return N.label(r)}))}}class at{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof G.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class lt{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new at}static open(t,e){lt.isDialogOpen||(lt.instance||(lt.instance=new lt(t,e)),lt.instance.openDialog())}openDialog(){this.initialPatternConfig=V().cloneDeep(this.eventBus.getPatternConfig()),lt.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=N.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=N.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{lt.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new it(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new st(this.eventBus,this.dataManager,this.subscriptions).create();L()(t).empty(),L()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}lt.isDialogOpen=!1;class ut{constructor(t){this.eventBus=t,this.subscriptions=new at}static open(t){ut.isDialogOpen||(ut.instance||(ut.instance=new ut(t)),ut.instance.openDialog())}openDialog(){this.initialPatternConfig=V().cloneDeep(this.eventBus.getPatternConfig()),ut.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=N.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=N.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{ut.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new ct(this.eventBus).create();L()(t).empty(),L()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}ut.isDialogOpen=!1;class ct{constructor(t){this.eventBus=t}create(){const t=M.map((t=>this.constructControlsPanel(t)));return N.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return N.div([]);const e=this.createInputs(t);return N.block([N.h1(`${R[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...D].reverse():D).map((e=>this.createInputForTerminus(t,e)));return N.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=N.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];L()(e).css("resize","none")}}n(9146);var ft=n(8507),ht={};ht.styleTagTransform=nt(),ht.setAttributes=X(),ht.insert=J().bind(null,"head"),ht.domAPI=K(),ht.insertStyleElement=tt(),Y()(ft.A,ht),ft.A&&ft.A.locals&&ft.A.locals;var dt,pt=n(2074),gt={};gt.styleTagTransform=nt(),gt.setAttributes=X(),gt.insert=J().bind(null,"head"),gt.domAPI=K(),gt.insertStyleElement=tt(),Y()(pt.A,gt),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"}(dt||(dt={})),Error,Error,n(5670);var mt=n(2003);n(3480),n(5067);var yt=n(5254),vt={};vt.styleTagTransform=nt(),vt.setAttributes=X(),vt.insert=J().bind(null,"head"),vt.domAPI=K(),vt.insertStyleElement=tt(),Y()(yt.A,vt),yt.A&&yt.A.locals&&yt.A.locals;var bt=n(8070);n(9124);var Ct=n(8312),At=n(1991),wt=n.n(At);"object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,new Set;const Et="object"==typeof process&&process?process:{};let _t=globalThis.AbortController,xt=globalThis.AbortSignal;if(void 0===_t){xt=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(t,e){this._onabort.push(e)}},_t=class{constructor(){e()}signal=new xt;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"!==Et.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 Et.emitWarning?Et.emitWarning(n,r,o,i):console.error(`[${o}] ${r}: ${n}`))}}Symbol("type"),Symbol.iterator,Symbol.toStringTag,n(6077),n(3561),n(9235);function Tt(t,e){try{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}}catch(t){console.error(t)}}n(6717),n(100),n(4229),n(5174),n(5412),n(6197);class It extends o.InputBase{constructor(t,e){super(N.input.column(t,e).dart,e?.onValueChanged),this.options=e}setColumnInputTable(t){N.input.setColumnInputTable(this,t,this.options?.filter)}}N.input.column2=function(t,e){return new It(t,e)},n(1296),n(3820),o.JsInputBase,o.JsInputBase;var Nt,St=n(6307);n(3151),function(t){t.table="table",t.seqCol="seqCol",t.generateHelm="generateHelm",t.chiralityEngine="chiralityEngine",t.rules="rules"}(Nt||(Nt={}));class Lt{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 Pt extends Lt{constructor(t,e,n){super(),this.gridCol=t,this.tableCol=e,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++Pt.viewerCounter,this.errors=[],this._onRendered=new G.Subject,this.tableCol&&this.tableCol.dataFrame&&(this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe((t=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(t){this.logger.error(t)}})))),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,bt.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`)}}Pt.viewerCounter=-1;var Ot=n(9192);const Mt=s.zS;var Rt,$t,Dt;!function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(Rt||(Rt={})),function(t){t.applyToBackground=".m.cellRenderer.applyToBackground"}($t||($t={})),function(t){t.MSA="MSA",t.classic="classic"}(Dt||(Dt={}));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=Dt.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0}};function Ht(t,e,n,r,o,i,s){var a,l,u;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===Dt.MSA&&(h="");let d=!0,p=!0,g="difference";if(null!=c.gridCell&&null!=c.gridCell.cell.column&&(d=c.gridCell.cell.column.temp["color-code"]??!0,p=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];p&&c.referenceSequence.length>0&&"difference"===g&&(c.transparencyRate=f==t?.3:c.transparencyRate),p&&c.referenceSequence.length>0&&"equal"===g&&(c.transparencyRate=f!=t?.3:c.transparencyRate)}null!=c.maxLengthOfMonomer&&(f=Mt(f,c.maxLengthOfMonomer));const m=f+h;(a=c.monomerTextSizeMap)[m]??(a[m]=t.measureText(m));let y=c.monomerTextSizeMap[m];(l=c.monomerTextSizeMap)[f]??(l[f]=t.measureText(f));let v=c.monomerTextSizeMap[f].width;const b=i/2-(y.fontBoundingBoxAscent+y.fontBoundingBoxDescent)/2+1;(u=c.monomerTextSizeMap)[h]??(u[h]=t.measureText(h));const C=c.monomerTextSizeMap[h].width;function A(e,o){const i=d?c.color:"rgb(0,0,0)";t.fillStyle=i,t.globalAlpha=c.transparencyRate,c.drawStyle===Dt.classic&&(t.fillText(f,n+e,r+b),t.fillStyle="#808080",t.fillText(h,n+o,r+b)),c.drawStyle===Dt.MSA&&t.fillText(f,n+e,r+b)}y=y.width,c.drawStyle===Dt.MSA&&(v=c.maxWord[c.wordIdx],y=c.maxWord[c.wordIdx]);const w=(c.maxWord[c.wordIdx]??0)-(c.maxWord[0]??0);if(c.left||y>o)return A(w,w+v),n+w+v+C;{const t=(o-y)/2;return A(t,t+v),n+w+t+v}}var Ft=n(3599);const kt="rgb(100,100,100)";class Gt extends Pt{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(t,e,n,r,i){super(t,e,n),this.monomerLengthLimit=r,this.propsProvider=i,this.colWidth=0,this._monomerLengthList=null,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,Ct.Q)(),this.invalidateGrid()})(),(async()=>{const t=await(0,l.pj)();this.sysMonomerLib=t.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(t){let e=12;return t&&t.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof t.temp[".mm.cellRenderer.fontSize"]&&!isNaN(t.temp[".mm.cellRenderer.fontSize"])&&(e=Math.max(t.temp[".mm.cellRenderer.fontSize"],1)),{font:`${e}px monospace`,fontWidth:.6*e}}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);return[r,this.getSummedMonomerLengths(r)]}getSummedMonomerLengths(t){const e=new Array(t.length+1);e[0]=5;for(let n=1;n<e.length;n++)e[n]=e[n-1]+t[n-1];let n=e[0];for(let t=1;t<e.length;t++)e[t]?n=e[t]:e[t]=n;return e}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.fontCharWidth,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.fontCharWidth;if(s[t]=a,n+=a,n>this.colWidth)break}}return s}getCellMonomerLengthsForSeqValue(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol),r=this.props.separatorWidth+1*this.props.fontCharWidth,o=Math.ceil(e/r),i=n.splitter(t),s=Math.min(o,i.length),a=new Array(s);let l=0;for(let t=0;t<s;++t){const r=i.getOriginal(t),o=this.props.monomerToShort(r,this.monomerLengthLimit),s=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+o.length*this.props.fontCharWidth;if(a[t]=s,l+=s,l>e)break}return a}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.fontCharWidth,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.fontCharWidth;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 ${JSON.stringify(t)}. `)}return null}(o,e)}setMonomerLengthLimit(t){this.monomerLengthLimit!=t&&(this.monomerLengthLimit=t,this.dirty=!0)}setSeparatorWidth(t){this.separatorWidth!=t&&(this.props.separatorWidth=t,this.dirty=!0)}render(t,e,n,r,o,i,s){const a=i.grid?.canvas===t.canvas;if(!this.seqHelper)return;const l=this.gridCol,u=this.tableCol,c=window.devicePixelRatio,f=`${this.toLog()}.render()`;this.logger.debug(`${f}, start`);let h=this.monomerLengthLimit;if(Rt.maxMonomerLength in u.tags){const t=parseInt(u.getTag(Rt.maxMonomerLength));h=!isNaN(t)&&t?t:50}if(".mm.cellRenderer.maxMonomerLength"in u.temp){const t=u.temp[".mm.cellRenderer.maxMonomerLength"];h=!isNaN(t)&&t?t:50}t.save();try{const s=this.seqHelper.getSeqHandler(u);if("1"===u.temp[".mm.cellRenderer.settingsChanged"]||this.monomerLengthLimit!=h){let t=0;const e=8;t=u.temp[".mm.cellRenderer.gapLength"]??t,this.setMonomerLengthLimit(h),this.setSeparatorWidth(s.isMsa()?e:t),u.temp[".mm.cellRenderer.settingsChanged"]="0"}let[f,d]=this.getCellMonomerLengths(i.tableRowIndex,r);f.length;const p=i.cell.value,g=i.cell.rowIndex,m=(u.getTag(mt.gp.alphabet),50);a&&(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)}(l?.grid,t,e,r,c)),t.beginPath(),t.rect(e+this.padding,n+this.padding,r-this.padding-1,o-2*this.padding),t.clip(),t.font=this.props?.font??"12px monospace",t.textBaseline="top";const y=u.meta.units,v=u.getTag(mt.gp.aligned),b=u.getTag(mt.gp.separator)??"",C=this.props.separatorWidth+1*this.props.fontCharWidth,A=Math.ceil(r/C),w=u.temp["reference-sequence"],E=this.tableCol.temp["current-word"];E&&-1===u?.dataFrame?.currentRowIdx&&(this.tableCol.temp["current-word"]=null);const _=(()=>{const t=s.getSplitter(A)(null!=w&&""!=w?w:E??"");return wt().count(0).take(t.length).map((e=>t.getOriginal(e))).toArray()})(),x=a?s.getSplitted(g):s.splitter(p);a||(d=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(p,r)));let T=Dt.classic;v&&v.includes("MSA")&&y==mt.Hi.SEPARATOR&&(T=Dt.MSA);const I=Math.min(x.length,A);for(let a=0;a<I;++a){const l=x.getOriginal(a),u=x.getCanonical(a);let c=kt;const f=this.getMonomerLib();if(f){const t=s.defaultBiotype;c=f.getMonomerTextColor(t,u)}t.fillStyle=kt;const p={color:c,pivot:0,left:!0,transparencyRate:1,separator:b,last:a===x.length-1,drawStyle:T,maxWord:d,wordIdx:a,gridCell:i,referenceSequence:_,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};if(Ht(t,l,e+this.padding,n,r,o,p),m>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??mt.YI.UN,r={position:i,biotype:n===mt.YI.RNA||n===mt.YI.DNA?Ft.o.NUCLEOTIDE:Ft.o.AA,symbol:a.getCanonical(i)},o=[];let l=this._monomerStructureMap[r.symbol];{const t=this.getMonomerLib();l=this._monomerStructureMap[r.symbol]=t?t.getTooltip(r.biotype,r.symbol):N.divText("Monomer library is not available")}o.push(l),N.tooltip.show(N.divV(o),e.x+16,e.y+16),Tt(t,r)}else N.tooltip.hide(),Tt(t,null)}}class Ut extends Gt{constructor(t,e,n,r){super(t,e,Wt.logger,n,(()=>{const t=r.getSeqHandler(e),{font:n,fontWidth:o}=Gt.getFontSettings(e);return{seqHandler:t,font:n,fontCharWidth:o,separatorWidth:11,monomerToShort:mt.zS}}))}onMouseMove(t,e){super.onMouseMove(t,e)}}class jt{get defaultGapOriginal(){return""}constructor(t,e){this.separator=t,this.helmHelper=e,this.separatorSplitter=(0,mt.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.fromSeparator(t,this.helmHelper).getHelm()}createCellRendererBack(t,e){const n=new Ut(t,e,4,this.helmHelper.seqHelper);return n.init().then((()=>{})),n}}class Vt extends s.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(/\(\d+\)$/,"")),n}constructor(t,e){super(t,e)}}const Wt=new P({debug:!0});function Yt(t,e){t.setTag("aligned","SEQ"),t.setTag("alphabet","UN"),t.setTag(".alphabetIsMultichar","true"),t.meta.units=i.Hi.CUSTOM,t.tags["polytool-data-role"]="template",t.temp[a.notationProvider]=new jt(e,Wt.helmHelper)}},5412:(t,e,n)=>{"use strict";n.d(e,{m:()=>l});var r=n(6082),o=n(4328),i=n(2890),s=n(6077),a=n(2003);async function l(t,e,n,l,u,c,f,h,d){const p=(await d.helmToAtomicLevel(t,l,u,f)).molCol,g=n.filter((t=>t)).length;if(c&&g>0){const t=new Array(g);let l=0;for(let r=0;r<n.length;r++)n[r]&&(t[l]=e[r],l++);const u=r.Column.fromStrings("helm",t);u.semType=r.SEMTYPE.MACROMOLECULE,u.meta.units=a.Hi.HELM,u.setTag(r.TAGS.CELL_RENDERER,"helm");const c=(await(0,i.pj)()).getMonomerLib();try{const t=await(0,s.C4)(r.DataFrame.create(0),u,c,d,h);l=0;for(let e=0;e<n.length;e++)n[e]&&(p.set(e,t.molCol.get(l)),l++)}catch(t){o.shell.warning("PolyTool was not able to linearize sequences")}}return function(t){for(let e=0;e<t.length;e++)t.set(e,t.get(e).replaceAll("undefined","H")),t.set(e,t.get(e).replaceAll("Oh","O")),t.set(e,t.get(e).replaceAll("0.000000 3","0.000000 0")),t.set(e,t.get(e).replaceAll("?","O")),t.set(e,t.get(e).replaceAll("0 3\n","0 0\n")),t.set(e,t.get(e).replaceAll("RGROUPS=(1 1)",""))}(p),p}},6307:(t,e,n)=>{"use strict";n.d(e,{s:()=>d});var r=n(2125),o=n(8438),i=n(100);function s(t,e){let n="";for(let t=0;t<e.length;t++){t>0&&(n+="|"),n+=`PEPTIDE${t+1}{`;for(let r=0;r<e[t].length;r++){r>0&&(n+=".");const o=e[t][r];n+=o.length>1?`[${o}]`:o}n+="}"}n+="$";for(let o=0;o<t.length;o++)o>0&&(n+="|"),n+=`PEPTIDE${t[o].fChain+1},PEPTIDE${t[o].sChain+1},`,n+=`${(0,r.M)(t[o].fMonomer-1,e)[0]+1}:R${t[o].fR}-`,n+=`${(0,r.M)(t[o].sMonomer-1,e)[0]+1}:R${t[o].sR}`;return n+="$$$V2.0",n}function a(t,e,n,r=0,o=[],i=[]){let[s,a,l,u,c]=[!1,!1,!1,-1,-1];for(let f=0;f<t.length;f++)if(t[f].includes(e)){if(s){if(l&&(n||t[f]==i[r]+e)){a=!0,c=f;break}if(l||!n&&t[f]!=o[r]+e)continue;a=!0,c=f;break}if(n)s=!0,l=!0,u=f;else if(t[f]==o[r]+e)s=!0,l=!0,u=f;else{if(t[f]!=i[r]+e)continue;s=!0,l=!!n,u=f}}return[s,a,l,u,c]}function l(t,e){const n=[];for(let r=0;r<e.length;r++){const o=`(${e[r].code})`,[s,l]=(0,i.Ln)(e[r]);if(s.length>0)for(let e=0;e<s.length;e++){const[i,u,c,f,h]=a(t,o,!1,e,s,l);i&&u&&(c?n.push({firstIdx:f,secondIdx:h,ruleIdx:r}):n.push({firstIdx:h,secondIdx:f,ruleIdx:r}))}else{const[e,i,s,l,u]=a(t,o,!0);if(!e||!i)continue;s?n.push({firstIdx:l,secondIdx:u,ruleIdx:r}):n.push({firstIdx:u,secondIdx:l,ruleIdx:r})}}return n}function u(t,e,n){const r=[],o=[],i=[],s=[],a=n.length;for(let l=0;l<a;l++){if(-1==n[l].firstIdx)continue;const a=n[l].ruleIdx,u=t[a].code;e[n[l].firstIdx]=e[n[l].firstIdx].replace(`(${u})`,""),e[n[l].secondIdx]=e[n[l].secondIdx].replace(`(${u})`,""),r.push(n[l].firstIdx+1),o.push(n[l].secondIdx+1),i.push(t[a].firstLinkingGroup),s.push(t[a].secondLinkingGroup)}return[r,o,i,s]}function c(t,e,n){const r=[],o=[],i=[],s=n.length;for(let a=0;a<s;a++){if(-1==n[a].firstIdx)continue;const s=n[a].firstIdx,l=n[a].secondIdx,u=n[a].ruleIdx,c=t[u].code;e[s]=e[s].replace(`(${c})`,"")+`_${t[u].name}`,e[l]=e[l].replace(`(${c})`,"")+`_${t[u].name}`,r.push(s+1),o.push(l+1),i.push(n[a].ruleIdx)}return[r,o,i]}var f=n(3599);function h(t,e,n){const r=n.createHelmWebEditor().editor.m;let o=0;const i=new JSDraw2.Point(0,0);for(let t=0;t<e.length;t++)for(let n=0;n<e[t].length;n++){if(e[t][n]){const s=e[t][n],a={type:f.o.AA,i:t,j:n,continuousId:o},l=new JSDraw2.Atom(i,s,a);if(r.addAtom(l),0!==n){const t=r.atoms[o-1],e=r.atoms[o],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,r.addBond(n)}o++,i.x+=JSDraw2.Editor.BONDLENGTH}i.y+=4*JSDraw2.Editor.BONDLENGTH}for(let e=0;e<t.length;e++){const n=r.atoms[t[e].fMonomer-1],o=r.atoms[t[e].sMonomer-1],i=new JSDraw2.Bond(n,o);i.r1=t[e].fR,i.r2=t[e].sR,r.addBond(i)}return r}class d{constructor(t,e,n){this.helmHelper=n,this.underRules=!1,this.posToPosUnderRules=[],this.linkages=e,this.monomers=t,this.mol=h(e,t,n)}static fromSeparator(t,e){const[n,r]=function(t){const e=[],n=[],r=/(\(.\d+\))?\{[^\}]*\}/g,o=[];o.push(t.replaceAll(r,""));const i=t.matchAll(r);for(const t of i){const e=t[0];e&&o.push(e)}let s=0;for(let t=0;t<o.length;t++){const r=o[t].split("-"),i=new Array(r.length);let a=0;for(let e=0;e<r.length;e++){const o=r[e].replace("{","").replace("}","");""!==o?(i[e]=o,s++,a++):n.push({fChain:t,sChain:t+1,fMonomer:s,sMonomer:s+1,fR:1,sR:1})}e.push(i.slice(0,a))}return[n,e]}(t);return new d(r,n,e)}static fromHelm(t,e){const[n,i]=function(t){const e=/(\w+\{.*\})\$(.*)\$(.*)\$(.*)\$/g.exec(t),n=[e[1],e[2],e[3],e[4]],i=n[0].split("|"),s=n[1].split("|"),a=new Array(i.length),l=[];for(let t=0;t<i.length;t++){const e=i[t].indexOf("{"),n=i[t].indexOf("}");a[t]=i[t].slice(e+1,n).split(".").map((t=>(0,o.D)(t)))}for(let t=0;t<s.length;t++)if(""!==s[t]&&"V2.0"!==s[t]){const e=s[t].split(","),n=parseInt(e[0].replace("PEPTIDE",""))-1,o=parseInt(e[1].replace("PEPTIDE",""))-1,i=e[2].split("-"),u=i[0].split(":"),c=i[1].split(":");l.push({fChain:n,sChain:o,fMonomer:(0,r.j)(parseInt(u[0]),n,a),sMonomer:(0,r.j)(parseInt(c[0]),o,a),fR:parseInt(u[1].replace("R","")),sR:parseInt(c[1].replace("R",""))})}return[l,a]}(t);return new d(i,n,e)}getNotation(){return function(t){const e=t.atoms,n=t.bonds,r=[],o=[];for(let t=0;t<n.length;t++)n[t].a1.bio.i!==n[t].a2.bio.i&&o.push(t);for(let t=0;t<e.length;t++){const n=e[t].bio?.i;n+1>r.length?r.push(1):r[n]++}const i=new Array(r.length);let s=0;for(let t=0;t<r.length;t++){const n=new Array(r[t]);for(let o=0;o<r[t];o++)n[o]=e[s].elem,s++;i[t]=n}let a="";for(let t=0;t<i.length;t++){let e="";for(let n=0;n<i[t].length;n++)e+=`${0==n?"":"-"}${i[t][n]}`;if(0!==t){const t=/(\(.\d+\))/,n=e.match(t);e=e.replace(n?.[0],""),e=`${n?n?.[0]:""}{${e}}`}else if(i.length>1){const t=0==n[o[0]].a1.bio.i&&0==n[o[0]].a1.bio.j,r=1==n[o[0]].a2.bio.i&&0==n[o[0]].a1.bio.j;t&&r&&(e+="-")}a+=e}return a}(this.mol)}getHelm(){return this.underRules?s(this.linkagesUnderRules,this.monomersUnderRules):s(this.linkages,this.monomers)}applyRules(t){const e=this.getNotation(),[n,r,o]=function(t,e){const n=[],r=[],o=[],i=e.heterodimerCode,s=e.homodimerCode,a=null!==i?t.split(`(${e.heterodimerCode})`):"";null!==i&&a.length>1?(o.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),n.push(a[1].replaceAll("{","").replaceAll("}","")),n.push(a[2].replaceAll("{","").replaceAll("}","")),r.push(!1),r.push(!1)):(n.push(t),r.push(!1));for(let t=0;t<n.length;t++)if(null!==s&&n[t].includes(`(${s})`)){const e=n.length;o.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const i=n[t].replace(`(${s})`,""),a=i.indexOf("{"),l=i.slice(0,a),u=i.replace(l,"").replaceAll("{","").replaceAll("}","");n[t]=l+u,n.push(u),r.push(!0)}return[o,n,r]}(e,t),i=new Array(r.length);let s=0;for(let t=0;t<r.length;t++)if(i[t]=r[t].split("-"),o[t]){const e=this.posToPosUnderRules.length-i[t].length;for(let n=0;n<i[t].length;n++)this.posToPosUnderRules[e+n].push(s),s++}else for(let e=0;e<i[t].length;e++)this.posToPosUnderRules.push([s]),s++;!function(t,e,n){for(let r=0;r<t.length;r++){const o=t[r],i=l(o,n.linkRules),[s,a,c,f]=u(n.linkRules,o,i);for(let t=0;t<s.length;t++)e.push({fChain:r,sChain:r,fMonomer:s[t],sMonomer:a[t],fR:c[t],sR:f[t]});t[r]=o}}(i,n,t),function(t,e,n){for(let r=0;r<t.length;r++){const o=l(t[r],n.reactionRules),[i,s,a]=c(n.reactionRules,t[r],o);i.length>=1&&(e.push({fChain:r,sChain:t.length,fMonomer:i[0],sMonomer:1,fR:3,sR:1}),e.push({fChain:r,sChain:t.length,fMonomer:s[0],sMonomer:1,fR:3,sR:2}),t.push([n.reactionRules[a[0]].name]))}}(i,n,t),this.underRules=!0,this.linkagesUnderRules=n,this.monomersUnderRules=i,this.molUnderRules=h(n,i,this.helmHelper)}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}}},4229:(t,e,n)=>{"use strict";n.d(e,{b:()=>s});var r=n(9192),o=n(6307),i=n(8742);function s(t,e,n){const s=new Array(t.length),a=new Array(t.length),l=new Array(t.length);for(let u=0;u<t.length;u++)try{if(null==t[u])s[u]="";else{const r=o.s.fromSeparator(t[u],n);r.applyRules(e),a[u]=!(r.monomersUnderRules.length>1||r.linkagesUnderRules.length>0),s[u]=r.getHelm(),l[u]=r.posToPosUnderRules}}catch(t){const[e,n]=(0,r.AP)(t);i._package.logger.error(e,void 0,n),s[u]=""}return[s,a,l]}},2125:(t,e,n)=>{"use strict";function r(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 o(t,e,n){let r=0;for(let t=0;t<e;++t)r+=n[t].length;return r+t}n.d(e,{M:()=>r,j:()=>o})},100:(t,e,n)=>{"use strict";n.d(e,{Ln:()=>V,Q4:()=>j});var r=n(6082),o=n(7389),i=n(4328);n(1991);var s=n(8742),a=n(9124),l=n(4229),u=n(439);const c="Links",f="Reactions";class h{constructor(t,e){this.v=null,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=o.input.string("Homo dimer",{value:n,onValueChanged:()=>{},nullable:!1}),this.heteroDimerInput=o.input.string("Hetero dimer",{value:r,onValueChanged:()=>{},nullable:!1})}async getAndAddView(){if(this.v)try{const t=Array.from(i.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");i.shell.v=t}catch(t){this.v=null}return this.v||(this.v=r.View.create(),this.v.name=`Manage Polytool Rules - ${this.fileName}`,this.v.append(await this.getForm()),this.v=i.shell.addView(this.v),i.shell.v=this.v),this.v}static async getInstance(t){if(!this.instances[t]){const e=await j([t]);this.instances[t]=new h(e,t)}return this.instances[t]}save(){this.rules.homodimerCode=this.homoDimerInput.value,this.rules.heterodimerCode=this.heteroDimerInput.value,this.rules.setLinkRules(this.linkRuleDataFrame),this.rules.setSynthesisRules(this.synthRuleDataFrame);const t={homodimerCode:this.rules.homodimerCode,heterodimerCode:this.rules.heterodimerCode,linkRules:this.rules.linkRules,reactionRules:this.rules.reactionRules},e=JSON.stringify(t,void 0,2);s._package.files.writeAsText(`polytool-rules/${this.fileName}`,e),i.shell.info(`Polytool rules at ${this.fileName} was updated`)}createGridDiv(t,e,n){const r=o.h1(t,"polytool-grid-header");o.tooltip.bind(r,n),r.style.marginTop="10px",r.style.marginRight="10px",e.root.style.height="100%";const i=o.splitV([o.box(r,{style:{maxHeight:"60px"}}),e.root]);return i.style.height="100%",i}async getLinkExamplesGrid(){const t=[];for(let e=0;e<this.rules.linkRules.length;e++){const n=this.rules.linkRules[e].code,[r,o]=V(this.rules.linkRules[e]);for(let e=0;e<r.length;e++){const i=`${r[e]}(${n})-A-A-A-A-${o[e]}(${n})`;t.push(i)}}const e=await(0,a.b2)(),[n,o,i]=(0,l.b)(t,this.rules,e),c=r.Column.fromStrings("Monomers",t),f=r.Column.fromStrings("Helm",n);return(0,s.applyNotationProviderForCyclized)(c,"-"),c.semType=r.SEMTYPE.MACROMOLECULE,f.semType=r.SEMTYPE.MACROMOLECULE,f.meta.units=u.Hi.HELM,f.setTag(r.TAGS.CELL_RENDERER,"helm"),r.DataFrame.fromColumns([c,f]).plot.grid()}async getReactionExamplesGrid(){const t=[];for(let e=0;e<this.rules.reactionRules.length;e++){const n=this.rules.reactionRules[e].code,[r,o]=V(this.rules.reactionRules[e]);for(let e=0;e<r.length;e++){const i=`${r[e]}(${n})-A-A-A-A-${o[e]}(${n})`;t.push(i)}}const e=await(0,a.b2)(),[n,o,i]=(0,l.b)(t,this.rules,e),c=r.Column.fromStrings("Monomers",t),f=r.Column.fromStrings("Helm",n);return c.semType=r.SEMTYPE.MACROMOLECULE,(0,s.applyNotationProviderForCyclized)(c,"-"),f.semType=r.SEMTYPE.MACROMOLECULE,f.meta.units=u.Hi.HELM,f.setTag(r.TAGS.CELL_RENDERER,"helm"),r.DataFrame.fromColumns([c,f]).plot.grid()}async getForm(){r.TabControl;const t=this.createGridDiv("Rules",this.linkRuleDataFrame.plot.grid({showAddNewRowIcon:!0}),"specification for monomers to link and linking positions"),e=this.createGridDiv("Examples",await this.getLinkExamplesGrid(),"specification for monomers to link and linking positions");t.style.width="50%",e.style.width="50%";const n=o.h1("Monomers","polytool-grid-header");o.tooltip.bind(n,"Click different cobination to see how monomers will link"),this.linkCards=await this.rules.getLinkCards();const i=o.splitV([o.box(n,{style:{maxHeight:"30px"}}),this.linkCards[0].root]);this.linkCards[0].render(),await this.linkCards[0].reset(),this.linkRuleDataFrame.currentRowIdx=0,this.linkRuleDataFrame.onCurrentRowChanged.subscribe((async()=>{const t=this.linkRuleDataFrame.currentRowIdx;-1!==t&&(o.empty(i),i.append(o.splitV([o.box(n,{style:{maxHeight:"30px"}}),this.linkCards[t].root]))),this.linkCards[t].render(),await this.linkCards[t].reset()}));const s=o.splitH([t,i],null,!0),a=this.createGridDiv("Rules",this.synthRuleDataFrame.plot.grid({showAddNewRowIcon:!0})),l=this.createGridDiv("Examples",await this.getReactionExamplesGrid());a.style.width="50%",l.style.width="50%";const u=o.divH([a,l]),h=o.divV([this.homoDimerInput,this.heteroDimerInput]),d=o.tabControl({Links:s,Reactions:u,Dimers:h},!1);o.tooltip.bind(d.getPane(c).header,"Specify rules to link monomers based on HELM notation"),o.tooltip.bind(d.getPane(f).header,"Specify rules to perform reactions within monomers"),o.tooltip.bind(d.getPane("Dimers").header,"Specify symbols for homodimeric and heterodimeric codes"),d.root.style.height="100%",d.root.style.width="100%",d.root.classList.add("rules-manager-form-tab-control"),d.header.style.marginBottom="10px";const p=o.divV([d.root]),g=[o.bigButton("Save",(()=>{this.save()})),o.button("Add rule",(()=>{const t=d.currentPane.name;t==c?this.linkRuleDataFrame.rows.addNew():t==f&&this.synthRuleDataFrame.rows.addNew()}))];return this.v.setRibbonPanels([g]),p.style.height="100%",p.style.alignItems="center",d.root}}h.instances={};var d=n(5072),p=n.n(d),g=n(7825),m=n.n(g),y=n(7659),v=n.n(y),b=n(5056),C=n.n(b),A=n(540),w=n.n(A),E=n(1113),_=n.n(E),x=n(890),T={};T.styleTagTransform=_(),T.setAttributes=C(),T.insert=v().bind(null,"head"),T.domAPI=m(),T.insertStyleElement=w(),p()(x.A,T),x.A&&x.A.locals&&x.A.locals;var I=n(2003),N=n(6717),S=n(8312),L=n(5174),P=n(5412);class O{get selected(){return this._selected}set selected(t){this._selected=t,this.root.style.border=t?"2px solid var(--green-2)":"2px solid var(--grey-2)"}constructor(t){this.monomer=t,this.root=o.divV([],{classes:"monomer-card-rule-root"}),this._selected=!1}render(){if(this.monomer){o.empty(this.root);const t=this.monomer.smiles&&i.chem.checkSmiles(this.monomer.smiles)?i.chem.drawMolecule(this.monomer.smiles,150,120):i.chem.drawMolecule(this.monomer.molfile??"",150,120);this.root.appendChild(t);const e=o.divH([o.divText("Monomer Name: "),o.divText(this.monomer.name)],{classes:"monomer-card-info-rules"});if(this.root.appendChild(e),o.tooltip.bind(e,this.monomer.name),this.monomer.lib?.source){const t=o.divH([o.divText("Source: "),o.divText(this.monomer.lib.source)],{classes:"monomer-card-info-rules"});this.root.appendChild(t),o.tooltip.bind(t,this.monomer.lib.source)}const n=o.divH([o.divText("Polymer Type: "),o.divText(this.monomer.polymerType)],{classes:"monomer-card-info-rules"});this.root.appendChild(n),o.tooltip.bind(n,this.monomer.polymerType),o.tooltip.bind(this.root,"Select Monomer")}}}class M{constructor(t,e,n,r,i){if(this.firstMonomers=t,this.secondMonomers=e,this.code=r,this.rules=i,this.root=o.divH([],{style:{alignItems:"center",width:"100%",overflow:"hidden",visibility:"visible"},classes:"monomer-cards"}),t.length>0){this.actionable=!0;const r=o.divH([],{style:{overflowX:"auto",width:"100%"}}),i=o.divH([],{style:{overflowX:"auto",width:"100%"}});this.resulting=o.divH([],{style:{overflowX:"auto",width:"100%",minHeight:"150px"}});const s=o.divV([r,i,this.resulting]);this.cardsFirst=t.map((t=>new O(n.getMonomer("PEPTIDE",t)))),this.cardsSecond=e.map((t=>new O(n.getMonomer("PEPTIDE",t)))),this.cardsFirst.forEach((t=>{t.root.onclick=()=>{this.cardsFirst.forEach((t=>t.selected=!1)),t.selected=!0,this.firstCard=t,this.reset()},r.appendChild(t.root)})),this.cardsSecond.forEach((t=>{t.root.onclick=()=>{this.cardsSecond.forEach((t=>t.selected=!1)),t.selected=!0,this.secondCard=t,this.reset()},i.appendChild(t.root)})),this.cardsFirst[0].selected=!0,this.cardsSecond[0].selected=!0,this.firstCard=this.cardsFirst[0],this.secondCard=this.cardsSecond[0],this.root.appendChild(s)}else{const t=o.divV(["Rule is active for all monomers, no examples to show"]);this.root.appendChild(t),this.actionable=!1}}async reset(){if(this.actionable){const t=[`${this.firstCard.monomer?.symbol}(${this.code})-A-A-A-A-${this.secondCard.monomer?.symbol}(${this.code})`],e=await(0,a.b2)(),[n,s,u]=(0,l.b)(t,this.rules,e),c=r.Column.fromType(r.COLUMN_TYPE.STRING,"helm",n.length).init((t=>n[t]));c.semType=r.SEMTYPE.MACROMOLECULE,c.meta.units=I.Hi.HELM,c.setTag(r.TAGS.CELL_RENDERER,"helm");const f=await(0,N.j)(),h=await(0,S.Q)(),d=await(0,L.A)(this.rules),p=c.temp;c.temp=p;const g=(await(0,P.m)(c,n,s,!0,!1,!1,d,f,h)).get(0),m=g&&i.chem.checkSmiles(g)?i.chem.drawMolecule(g,150,120):i.chem.drawMolecule(g??"",150,120);o.empty(this.resulting),this.resulting.append(o.divH([m],{style:{overflowX:"auto",width:"100%",minHeight:"150px"}}))}}render(){this.actionable&&(this.cardsFirst.forEach((t=>t.render())),this.cardsSecond.forEach((t=>t.render())))}}var R=n(2890);const $="System:AppData/SequenceTranslator/polytool-rules/",D="code",B="firstMonomers",H="secondMonomers",F="name",k="firstLinkingGroup",G="secondLinkingGroup";class U{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(D,t);e.setTag("friendlyName","Code");const n=r.Column.string(B,t);n.setTag("friendlyName","First monomers"),n.semType=r.SEMTYPE.MACROMOLECULE,(0,s.applyNotationProviderForCyclized)(n,",");const o=r.Column.string(H,t);o.setTag("friendlyName","Second monomers"),o.semType=r.SEMTYPE.MACROMOLECULE,(0,s.applyNotationProviderForCyclized)(o,",");const i=r.Column.int(k,t);i.setTag("friendlyName","First group");const a=r.Column.int(G,t);a.setTag("friendlyName","Second group");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),a.set(r,this.linkRules[r].secondLinkingGroup);return r.DataFrame.fromColumns([e,n,o,i,a])}async getLinkCards(){const t=this.linkRules.length,e=new Array(t),n=(await(0,R.pj)()).getMonomerLib();for(let r=0;r<t;r++)e[r]=new M(this.linkRules[r].firstMonomers,this.linkRules[r].secondMonomers,n,this.linkRules[r].code,this);return e}getSynthesisRulesDf(){const t=this.reactionRules.length,e=r.Column.int(D,t);e.setTag("friendlyName","Code");const n=r.Column.string(B,t);n.setTag("friendlyName","First monomers");const o=r.Column.string(H,t);o.setTag("friendlyName","Second monomers");const i=r.Column.string(F,t);i.setTag("friendlyName","Name");const s=r.Column.string("firstReactant",t);s.setTag("friendlyName","First reactant");const a=r.Column.string("secondReactant",t);a.setTag("friendlyName","Second 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Array(e),r=t.columns.byName(D),o=t.columns.byName(B),i=t.columns.byName(H),s=t.columns.byName(F),a=t.columns.byName("firstReactant"),l=t.columns.byName("secondReactant"),u=t.columns.byName("product");for(let t=0;t<e;t++){const e=`${a.get(t)}.${l.get(t)}>>${u.get(t)}`,c=o.get(t).split(","),f=i.get(t).split(","),h={code:r.get(t),firstMonomers:""!==c[0]?c:[],secondMonomers:""!==f[0]?f:[],reaction:e,name:s.get(t)};n[t]=h}this.reactionRules=n}}async function j(t){const e=new r.FileSource($),n=new U(null,null,[],[]);for(let r=0;r<t.length;r++){const o=await e.readAsText(t[r].replace($,"")),i=JSON.parse(o);n.homodimer=i.homodimerCode,n.heterodimer=i.heterodimerCode,n.addLinkRules(i.linkRules),n.addSynthesisRules(i.reactionRules)}return n}function V(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 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Object.entries(r))(0,e.t6)(`innerIdx-${t}`,(async()=>{const[t,r]=(0,O.M)(i,s);(0,e.E3)(t,n),(0,e.E3)(r,o)}));for(const[t,{inIdx:n,spIdx:o,outIdx:i,monomers:s}]of Object.entries(r))(0,e.t6)(`outerIdx-${t}`,(async()=>{const t=(0,O.j)(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:0}}},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-${r}`,(async()=>{const n=await(0,N.Q4)(["rules_example.json"]),r=P.s.fromSeparator(o.templateSeq,t);r.applyRules(n),r.check(!0),(0,e.J6)(r.monomers.map((t=>t.length)),i.mmChain.monomerCount),(0,e.E3)(r.linkages.length,i.mmChain.linkageCount),(0,e.E3)(r.getHelm(),o.mmHelm)}),{skipReason:"3157"});for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`parseNotation-${r}`,(async()=>{await(0,N.Q4)(["rules_example.json"]);const n=P.s.fromSeparator(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-${r}`,(async()=>{await(0,N.Q4)(["rules_example.json"]);const n=P.s.fromHelm(o.templateHelm,t);n.check(!0),(0,e.J6)(n.monomers.map((t=>t.length)),i.templateChain.monomerCount),(0,e.E3)(n.linkages.length,i.templateChain.linkageCount),(0,e.E3)(n.getHelm(),o.templateHelm),(0,e.E3)(n.getNotation(),o.templateSeq)}));for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`applyRules-${r}`,(async()=>{const n=await(0,N.Q4)(["rules_example.json"]),r=P.s.fromSeparator(o.templateSeq,t);r.applyRules(n),r.check(!0),(0,e.J6)(r.monomers.map((t=>t.length)),i.mmChain.monomerCount),(0,e.E3)(r.linkages.length,i.mmChain.linkageCount),(0,e.E3)(r.getHelm(),o.mmHelm)}),{skipReason:"applyRules is not implemented"})})),(0,e.L1)("toAtomicLevel",(()=>{let n,r,o;(0,e.gM)((async()=>{r=await(0,b.pj)(),n=await w(),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 M.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}},l=n.override(a,"test"),u=await(0,p.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 u.helmToAtomicLevel(c,!1,!1,l);(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 d=o.get_mol(h);try{const t=d.get_inchi(),n=o.get_inchikey_for_inchi(t);(0,e.E3)(d.get_num_bonds(),103),(0,e.E3)(d.get_num_atoms(),98),(0,e.E3)(n,"XPQUTLNSNIMERR-WKBTUBAPSA-N")}finally{d.delete()}})),(0,e.t6)("getNewMonomer",(async()=>{const t=await(0,_.j)(),n=r.getMonomerLib(),o=(await(0,N.Q4)(["rules_example.json"])).reactionRules.find((t=>"GGaz"==t.name)),[i,s]=(0,I.T)(t,n,o);(0,e.E3)(i[0],"azG_GGaz");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(),7),(0,e.E3)(a.get_num_atoms(),8)}finally{a.delete()}}))}));const M=new s;async function R(n,r,o){const i=await(0,e.N$)({category:n,test:r,testContext:o,verbose:!0});return t.DataFrame.fromObjects(i)}async function $(){await(0,e.Xb)(M,M.getModule("package-test.js"))}})(),sequencetranslator_test=r})();
2
+ var sequencetranslator_test;(()=>{var t={6717:(t,e,n)=>{"use strict";n.d(e,{j:()=>o});var r=n(6082);async function o(){const t=r.Func.find({package:"Chem",name:"getRdKitModule"});if(0===t.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await t[0].prepare().call()).getOutputParamValue()}},3599:(t,e,n)=>{"use strict";n.d(e,{o:()=>r.o});var r=n(6869)},9124:(t,e,n)=>{"use strict";n.d(e,{b2:()=>i});var r=n(7389),o=n(6082);async function i(){const t="Helm",e=o.Func.find({package:t,name:"getHelmHelper"});if(0===e.length)throw new Error(`Package '${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)}},8438:(t,e,n)=>{"use strict";function r(t){return t.startsWith("[")&&t.endsWith("]")?t.slice(1,-1):t}n.d(e,{D:()=>r})},8123:(t,e,n)=>{"use strict";n.d(e,{u:()=>r});const r={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M RGP",V2K_A_LINE:"A ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:" 0 0 0 0 0 0 999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M V30 ",V3K_END:"M END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"}},2890:(t,e,n)=>{"use strict";n.d(e,{pj:()=>d});var r,o,i,s,a,l,u,c=n(6082);n(4328);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 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r=0;r<n;r++)c=t.indexOf("V30",c)+4,c=t.indexOf(" ",c)+1,c=t.indexOf(" ",c)+1,f=t.indexOf(" ",c)+1,f=t.indexOf(" ",f),c=(t=t.slice(0,c)+e.x[r]+" "+e.y[r]+t.slice(f)).indexOf("\n",c)+1;return t}function i(t){let e=(t=t.replaceAll("\r","")).indexOf("COUNTS")+7,n=t.indexOf(" ",e);const r=parseInt(t.substring(e,n));return e=n+1,n=t.indexOf(" ",e),{natom:r,nbond:parseInt(t.substring(e,n))}}function s(t){const e=i(t);let n=t.indexOf("M V30 BEGIN ATOM");n=t.indexOf("\n",n);let r=n;const o=Array(e.natom),s=Array(e.natom),a=Array(e.natom),l=Array(e.natom);for(let i=0;i<e.natom;i++)n=t.indexOf("V30",n)+4,r=t.indexOf(" ",n),o[i]=parseInt(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),s[i]=t.substring(n,r),n=r+1,r=t.indexOf(" ",n),a[i]=parseFloat(t.substring(n,r)),n=r+1,r=t.indexOf(" ",n),l[i]=parseFloat(t.substring(n,r)),n=t.indexOf("\n",n)+1;return{atomIndex:o,atomType:s,x:a,y:l}}n.d(e,{cx:()=>s,vS:()=>r})},9537:(t,e,n)=>{"use strict";n.d(e,{iL:()=>i,q7:()=>o,ti:()=>r});const r={NUCLEOSIDE:"nucleoside",LINKAGE:"phosphateBackbone"},o="p",i="<?>"},3480:(t,e,n)=>{"use strict";n.d(e,{C6:()=>l,Hs:()=>a,OT:()=>u,bD:()=>s});var r=n(6686),o=n(5067),i=n(9537);function s(t,e,n,o){const i=Object.keys(o.jsonData.codesToHelmDict).concat([r.NO.HELM]);if(!t||-1!==e&&n!==r.NO.HELM)return{};if(!i.includes(n))throw new Error(`${n} format is not supported by SequenceTranslator`);const s=i.filter((t=>t!=n)).sort(((t,e)=>t.localeCompare(e))),l=o.createFormatConverter(t,n),u=Object.fromEntries(s.map((t=>{let e;try{e=l.convertTo(t)}catch{e=null}return[t,e]})).filter((([t,e])=>e))),c=a(n===r.NO.HELM?t:u[r.NO.HELM],o.monomerLibWrapper);return c&&(u.Nucleotides=c),u}function a(t,e){const n=new RegExp("\\([^()]*\\)","g"),o=t.match(n);return o?o.map((t=>{const n=t.replace(/[\[\]()]/g,"");return r.AL.includes(n)?n:e.getNaturalAnalogBySymbol(n)})).map((t=>t||i.iL)).join(""):null}function l(t,e,n,i){const s=i.createFormatConverter(t,e);return n===o.qP?a(s.convertTo(r.NO.HELM),i.monomerLibWrapper):s.convertTo(n)}function u(t){return Object.keys(t.jsonData.codesToHelmDict).concat([r.NO.HELM,o.qP]).sort()}},5067:(t,e,n)=>{"use strict";n.d(e,{U_:()=>o,n_:()=>r,qP:()=>i});const r="Copied",o="Copy sequence",i="Nucleotides"},1950:(t,e,n)=>{"use strict";n.d(e,{_package:()=>Wt,applyNotationProviderForCyclized:()=>Yt});var r=n(4328),o=n(6082),i=n(439),s=n(7291);const a=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}};o.SemanticValue;var l=n(2890);class u{constructor(t,e,n=""){this.target=t,this.debugEnabled=e,this.prefix=n}error(t,e,n){return this.target.error(this.prefix+t,e,n)}warning(t,e){return this.target.warning(this.prefix+t,e)}info(t,e){return this.target.info(this.prefix+t,e)}debug(t,e){if(this.debugEnabled)return this.target.debug(this.prefix+t,e)}}const c="System:AppData/SequenceTranslator/monomers-sample",f="pattern-app-data.json",h="formats-to-helm.json",d="codes-to-symbols.json",p="linkers.json";var g=n(6686);function m(t){return t.sort(((t,e)=>e.length-t.length))}class y{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper}getInvalidCodeIndex(t){if(t===g.NO.HELM)return this.sequence.length;const e=["r","d"],n=m(this.libWrapper.getCodesByFormat(t));let r=0;for(;r<this.sequence.length;){const t=n.find((t=>t===this.sequence.substring(r,r+t.length)));if(!t)break;if(r>1&&g.AL.includes(this.sequence[r])&&e.includes(this.sequence[r-2]))break;if(e.includes(this.sequence[r+1])&&g.AL.includes(this.sequence[r])){r++;break}r+=t.length}return r===this.sequence.length&&(r=-1),r}isValidSequence(t){return-1===this.getInvalidCodeIndex(t)}}class v{constructor(t,e,n,r){this.patternAppData=t,this.codesToHelmDict=e,this.codesToSymbolsDict=n,this.monomersWithPhosphate=r}}async function b(t){const e=await Promise.all([f,h,d,p].map((e=>async function(t,e){const n=t.endsWith("/")?`${t}${e}`:`${t}/${e}`;try{const t=await r.dapi.files.readAsText(n);return JSON.parse(t)}catch(t){console.error(`Error loading json from '${n}':`,t)}}(t,e))));return new v(e[0],e[1],e[2],e[3])}class C{constructor(t,e){if(this.lib=t,this.jsonData=e,null===this.lib)throw new Error("SequenceTranslator: monomer library is null");this.allMonomers=this.getAllMonomers()}formatMonomerForViewer(t){const e={};return e.name=t.symbol,e.symbol=t.symbol,e.molfile=t.molfile,this.getAllFormats().forEach((n=>{if(n===g.NO.HELM)return;const r=this.jsonData.codesToSymbolsDict[n],o=Object.keys(r).filter((e=>r[e]===t.symbol));e[n]=o.join(", ")})),e}getAllMonomers(){const t=this.lib.getPolymerTypes();let e=[];for(const n of t){const t=this.lib.getMonomerSymbolsByType(n).map((t=>this.lib.getMonomer(n,t))).filter((t=>null!==t));e=e.concat(t)}return e}getMonomer(t){const e=this.lib.getMonomer("RNA",t);if(void 0===e)throw new Error(`SequenceTranslator: no monomer with symbol ${t}`);return e}getMolfileBySymbol(t){return this.getMonomer(t).molfile}getNaturalAnalogBySymbol(t){const e=this.getMonomer(t).naturalAnalog;if(!e)throw new Error(`ST: no natural analog for ${t}`);return e}isModification(t){return!!this.getMolfileBySymbol(t).includes("MODIFICATION")}getCodeToSymbolMap(t){return new Map(Object.entries(this.jsonData.codesToSymbolsDict[t]))}getCodesByFormat(t){return Object.keys(this.jsonData.codesToSymbolsDict[t])}getAllFormats(){return Object.keys(this.jsonData.codesToSymbolsDict)}getTableForViewer(){const t=this.allMonomers.map((t=>this.formatMonomerForViewer(t)));return o.DataFrame.fromObjects(t)}getCodesToWeightsMap(){const t=new Map;return Object.entries(this.jsonData.codesToSymbolsDict).forEach((([e,n])=>{Object.entries(n).forEach((([e,n])=>{const r=this.getMonomer(n),o=r.meta?.molecularWeight;t.set(e,o)}))})),t}}var A=n(9537);const w=(t,e)=>e.length-t.length;class E{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[A.ti.LINKAGE]))).sort(w));return new RegExp(`${A.q7}.(${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: ${t}`)}isHelm(t){return t===g.NO.HELM}getFormatCodes(t){const e=this.getFormatToHelmDict(t);return Object.keys(e).sort(w)}getNonHelmFormatRegExp(t){const e=this.getCodesByFormat(t);return new RegExp(_(e)+"|\\([^()]*\\)|.","g")}}function _(t){return t.map((t=>t.replace(/[.*+?^${}()|[\]\\]/g,"\\$&"))).map((t=>t.includes("(")||t.includes(")")?t:`(?<!\\([^()]*)${t}(?![^()]*\\))`)).join("|")}const x={LEFT:"RNA1{",RIGHT:"}$$$$"};class T{constructor(t,e,n){this.sequence=t,this.sourceFormat=e,this.th=n,this.formats=new E(this.th)}convertTo(t){const e=this.formats.getFormatNames();if(this.sourceFormat===g.NO.HELM&&e.includes(t))return this.helmToFormat(this.sequence,t);if(e.includes(this.sourceFormat)&&t===g.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} -> ${t}`)}helmToFormat(t,e){const n=new RegExp(_(Object.values(x)),"g");let r=t.replace(n,"");const o=this.formats.getHelmToFormatDict(e),i=this.formats.getTargetFormatHelmCodes(e),s=this.formats.getTargetFormatHelmCodesRegExp(e);return r=r.replace(s,(t=>i.includes(t)?o[t]:"p"===t||"."===t?t:"?")).replace(/\?+/g,A.iL).replace(/p\.|\./g,""),r=r.replace(/<empty>/g,""),r=r.replace(/\/\//g,"/"),r}formatToHelm(t,e){const n=this.formats.getFormatToHelmDict(e),r=this.formats.getCodesByFormat(e),o=this.formats.getFormatRegExp(e),i=this.formats.getPhosphateHelmCodesRegExp(e);let s=t?t.replace(o,(t=>r.includes(t)?n[t]+".":"?")):"";return s=s.replace(/\?+/g,`${A.iL}.`),s=s.slice(0,-1),s[s.length-1]===A.q7&&(s=s.slice(0,-1)),s=s.replace(i,((t,e)=>e)),s=s.replace(/<empty>/g,""),`${x.LEFT+s+x.RIGHT}`}}class I{constructor(t,e){this.sequence=t,this.th=e,this.libWrapper=this.th.monomerLibWrapper,this.formats=Object.keys(this.th.jsonData.codesToHelmDict)}getFormat(){if(this.sequence.startsWith("RNA"))return g.NO.HELM;const t=this.getListOfPossibleSynthesizersByFirstMatchedCode();if(0===t.length)return null;const e=this.th.createSequenceValidator(this.sequence),n=Array(t.length).fill(0);for(let r=0;r<t.length;++r){const o=t[r];n[r]=e.getInvalidCodeIndex(o)}const r=n.some((t=>-1===t))?-1:Math.max(...n);return t[n.indexOf(r)]}getListOfPossibleSynthesizersByFirstMatchedCode(){const t=this.sequence,e=[];for(const n of this.formats){const r=m(this.libWrapper.getCodesByFormat(n));let o=0;for(let e=0;e<t.length;e++)if(")"===t[e]&&e!==t.length-1){o=e+1;break}r.some((e=>e===t.slice(o,o+e.length)))&&e.push(n)}return e}}var N=n(7389);const S=$;var L=n.n(S);class P 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 y(t,e).getInvalidCodeIndex(r));const o=n<0||""===t,i=N.span([]);L()(i).css("-webkit-text-fill-color","var(--grey-6)");const s=N.span([]);return L()(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()=>{const t=await this.getSettings();let e=t instanceof Map?t.get("MonomersPath"):t.MonomersPath;e&&await r.dapi.files.exists(e)||(this.logger.warning(`Monomers path '${e}' not found. Fallback to monomers sample path '${c}'.`),e=c),[this._jsonData,this._monomerLib]=await Promise.all([b(e),O(e)]),this._monomerLibWrapper=new C(this.monomerLib,this.jsonData)})()),this.initLibDataPromise}async getTranslationHelper(){return await r.functions.call(`${this.name}:getTranslationHelper`)}createSequenceValidator(t){return new y(t,this)}createFormatConverter(t,e){return new T(t,e,this)}createFormatDetector(t){return new I(t,this)}}async function O(t){const e=o.TaskBarProgressIndicator.create("Initializing Oligo Toolkit monomer library ...");try{const e=await(0,l.pj)();return await e.readLibrary(t,"monomer-lib.json")}finally{e.close()}}const M=["SS","AS"],R={SS:"Sense strand",AS:"Anti sense"},D=["3'","5'"];var B,H,F,k;!function(t){t.IS_ANTISENSE_STRAND_INCLUDED="isAntisenseStrandIncluded",t.NUCLEOTIDE_SEQUENCES="nucleotideSequences",t.PHOSPHOROTHIOATE_LINKAGE_FLAGS="phosphorothioateLinkageFlags",t.STRAND_TERMINUS_MODIFICATIONS="strandTerminusModifications"}(B||(B={})),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"}(k||(k={})),B.IS_ANTISENSE_STRAND_INCLUDED,B.NUCLEOTIDE_SEQUENCES,B.PHOSPHOROTHIOATE_LINKAGE_FLAGS,B.STRAND_TERMINUS_MODIFICATIONS,H.PATTERN_NAME,H.PATTERN_COMMENT,H.NUCLEOTIDES_WITH_NUMERIC_LABELS,Error,Error,n(4802);const G=rxjs;var U;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))}}}(U||(U={}));var j=n(2543),V=n.n(j),W=n(5072),Y=n.n(W),q=n(7825),K=n.n(q),z=n(7659),J=n.n(z),Q=n(5056),X=n.n(Q),Z=n(540),tt=n.n(Z),et=n(1113),nt=n.n(et),rt=n(9252),ot={};ot.styleTagTransform=nt(),ot.setAttributes=X(),ot.insert=J().bind(null,"head"),ot.domAPI=K(),ot.insertStyleElement=tt(),Y()(rt.A,ot),rt.A&&rt.A.locals&&rt.A.locals;class it{constructor(t,e,n){this.eventBus=t,this.initialPatternConfig=e,this.subscriptions=n}create(){return N.divV([N.h1("PTO"),N.divH([this.createAllPtoActivationInput().root,...this.createFirstPtoInputs().map((t=>t.root))],{style:{gap:"12px"}})])}areAllPtoLinkagesSet(t){return M.map((e=>t[e].filter((t=>t)).length)).reduce(((t,e)=>t+e),0)===M.map((t=>this.initialPatternConfig.nucleotideSequences[t].length)).reduce(((t,e)=>t+e),0)+M.filter((e=>t[e].length)).length}createAllPtoActivationInput(){const t=this.initialPatternConfig.phosphorothioateLinkageFlags,e=this.areAllPtoLinkagesSet(t),n=N.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),N.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 M.map((t=>{if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return;const e=this.isFirstPtoActive(t),n=N.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),N.tooltip.bind(n.captionLabel,`Activate first phosphothioate in ${t}`),n})).filter((t=>void 0!==t))}isFirstPtoActive(t){return this.initialPatternConfig.phosphorothioateLinkageFlags[t][0]}}class st{constructor(t,e,n){this.eventBus=t,this.dataManager=e,this.subscriptions=n;const r=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.displayedInputLabels=this.computeDisplayedInputLabels()}));this.subscriptions.add(r)}create(){const t=M.map((t=>this.constructControlsPanel(t)));return N.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return N.div([]);const e=this.constructHeader(),n=this.createControls(t);return N.block([N.h1(`${R[t]}`),e,n],{style:{paddingTop:"12px"}})}constructHeader(){return N.divH([N.div([N.divText("#")],{style:{width:"20px"}}),N.block75([N.divText("Modification")]),N.div([N.divText("PTO")])])}createControls(t){const e=this.createNucleobaseInputs(t),n=this.createLabelDivs(t),r=this.createPTOFlagInputs(t);return N.div(e.map(((t,e)=>N.divH([n[e],N.block75([t.root]),r[e].root],{style:{alignItems:"center"}}))))}createNucleobaseInputs(t){const e=this.dataManager.fetchAvailableNucleotideBases().sort(((t,e)=>t.toLowerCase().localeCompare(e.toLowerCase())));return this.eventBus.getNucleotideSequences()[t].map(((n,r)=>{const o=N.input.choice("",{value:n,items:e});return o.onInput.subscribe((()=>{const e=o.value;this.eventBus.setNucleotide(t,r,e)})),o}))}createPTOFlagInputs(t){return this.eventBus.getPhosphorothioateLinkageFlags()[t].slice(1).map(((e,n)=>{const r=N.input.bool("",{value:e});r.onInput.subscribe((()=>{const e=r.value;this.eventBus.setPhosphorothioateLinkageFlag(t,n+1,e)}));const o=this.eventBus.phosphorothioateLingeFlagsChanged$.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 M.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=>N.div([t],{style:{width:"20px"}}))),n=this.eventBus.nucleotideSequencesChanged$.subscribe((()=>{this.createLabels(t).forEach(((t,n)=>{L()(e[n]).empty(),L()(e[n]).append(t)}))}));return this.subscriptions.add(n),e}createLabels(t){return this.eventBus.getNucleotideSequences()[t].map(((e,n)=>{const r=this.displayedInputLabels.get(t)[n];return N.label(r)}))}}class at{constructor(){this.rxjsSubscriptions=[],this.dgSubscriptions=[]}add(t){t instanceof G.Subscription?this.rxjsSubscriptions.push(t):this.dgSubscriptions.push(t)}unsubscribeAll(){for(const t of[this.rxjsSubscriptions,this.dgSubscriptions])t.forEach((t=>t.unsubscribe())),t.length=0}}class lt{constructor(t,e){this.eventBus=t,this.dataManager=e,this.subscriptions=new at}static open(t,e){lt.isDialogOpen||(lt.instance||(lt.instance=new lt(t,e)),lt.instance.openDialog())}openDialog(){this.initialPatternConfig=V().cloneDeep(this.eventBus.getPatternConfig()),lt.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=N.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=N.dialog("Edit strands").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{lt.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new it(this.eventBus,this.initialPatternConfig,this.subscriptions).create(),n=new st(this.eventBus,this.dataManager,this.subscriptions).create();L()(t).empty(),L()(t).append(e,n)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}lt.isDialogOpen=!1;class ut{constructor(t){this.eventBus=t,this.subscriptions=new at}static open(t){ut.isDialogOpen||(ut.instance||(ut.instance=new ut(t)),ut.instance.openDialog())}openDialog(){this.initialPatternConfig=V().cloneDeep(this.eventBus.getPatternConfig()),ut.isDialogOpen=!0,this.createDialog().show()}createDialog(){const t=N.divV([]);this.subscriptions.add(this.eventBus.strandsUpdated$.subscribe((()=>this.onStrandsUpdated(t))));const e=N.dialog("Edit terminal modifications").add(t).onOK((()=>{})).onCancel((()=>this.resetToInitialState()));return this.subscriptions.add(e.onClose.subscribe((()=>{ut.isDialogOpen=!1,this.subscriptions.unsubscribeAll()}))),e}onStrandsUpdated(t){const e=new ct(this.eventBus).create();L()(t).empty(),L()(t).append(e)}resetToInitialState(){this.eventBus.setPatternConfig(this.initialPatternConfig)}}ut.isDialogOpen=!1;class ct{constructor(t){this.eventBus=t}create(){const t=M.map((t=>this.constructControlsPanel(t)));return N.divH(t,{style:{gap:"24px"}})}constructControlsPanel(t){if(!this.eventBus.isAntisenseStrandActive()&&"AS"===t)return N.div([]);const e=this.createInputs(t);return N.block([N.h1(`${R[t]}`),e],{style:{paddingTop:"12px"}})}createInputs(t){const e=("SS"===t?[...D].reverse():D).map((e=>this.createInputForTerminus(t,e)));return N.form(e)}createInputForTerminus(t,e){const n=this.eventBus.getTerminalModifications()[t][e],r=N.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];L()(e).css("resize","none")}}n(9146);var ft=n(8507),ht={};ht.styleTagTransform=nt(),ht.setAttributes=X(),ht.insert=J().bind(null,"head"),ht.domAPI=K(),ht.insertStyleElement=tt(),Y()(ft.A,ht),ft.A&&ft.A.locals&&ft.A.locals;var dt,pt=n(2074),gt={};gt.styleTagTransform=nt(),gt.setAttributes=X(),gt.insert=J().bind(null,"head"),gt.domAPI=K(),gt.insertStyleElement=tt(),Y()(pt.A,gt),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"}(dt||(dt={})),Error,Error,n(5670);var mt=n(2003);n(3480),n(5067);var yt=n(5254),vt={};vt.styleTagTransform=nt(),vt.setAttributes=X(),vt.insert=J().bind(null,"head"),vt.domAPI=K(),vt.insertStyleElement=tt(),Y()(yt.A,vt),yt.A&&yt.A.locals&&yt.A.locals;var bt=n(8070);n(9124);var Ct=n(8312),At=n(1991),wt=n.n(At);"object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,new Set;const Et="object"==typeof process&&process?process:{};let _t=globalThis.AbortController,xt=globalThis.AbortSignal;if(void 0===_t){xt=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(t,e){this._onabort.push(e)}},_t=class{constructor(){e()}signal=new xt;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"!==Et.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 Et.emitWarning?Et.emitWarning(n,r,o,i):console.error(`[${o}] ${r}: ${n}`))}}Symbol("type"),Symbol.iterator,Symbol.toStringTag,n(6077),n(3561),n(9235);function Tt(t,e){try{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}}catch(t){console.error(t)}}n(6717),n(100),n(4229),n(5174),n(5412),n(6197);class It extends o.InputBase{constructor(t,e){super(N.input.column(t,e).dart,e?.onValueChanged),this.options=e}setColumnInputTable(t){N.input.setColumnInputTable(this,t,this.options?.filter)}}N.input.column2=function(t,e){return new It(t,e)},n(1296),n(3820),o.JsInputBase,o.JsInputBase;var Nt,St=n(6307);n(3151),function(t){t.table="table",t.seqCol="seqCol",t.generateHelm="generateHelm",t.chiralityEngine="chiralityEngine",t.rules="rules"}(Nt||(Nt={}));class Lt{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 Pt extends Lt{constructor(t,e,n){super(),this.gridCol=t,this.tableCol=e,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++Pt.viewerCounter,this.errors=[],this._onRendered=new G.Subject,this.tableCol&&this.tableCol.dataFrame&&(this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe((t=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(t){this.logger.error(t)}})))),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,bt.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`)}}Pt.viewerCounter=-1;var Ot=n(9192);const Mt=s.zS;var Rt,$t,Dt;!function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(Rt||(Rt={})),function(t){t.applyToBackground=".m.cellRenderer.applyToBackground"}($t||($t={})),function(t){t.MSA="MSA",t.classic="classic"}(Dt||(Dt={}));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=Dt.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0}};function Ht(t,e,n,r,o,i,s){var a,l,u;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===Dt.MSA&&(h="");let d=!0,p=!0,g="difference";if(null!=c.gridCell&&null!=c.gridCell.cell.column&&(d=c.gridCell.cell.column.temp["color-code"]??!0,p=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];p&&c.referenceSequence.length>0&&"difference"===g&&(c.transparencyRate=f==t?.3:c.transparencyRate),p&&c.referenceSequence.length>0&&"equal"===g&&(c.transparencyRate=f!=t?.3:c.transparencyRate)}null!=c.maxLengthOfMonomer&&(f=Mt(f,c.maxLengthOfMonomer));const m=f+h;(a=c.monomerTextSizeMap)[m]??(a[m]=t.measureText(m));let y=c.monomerTextSizeMap[m];(l=c.monomerTextSizeMap)[f]??(l[f]=t.measureText(f));let v=c.monomerTextSizeMap[f].width;const b=i/2-(y.fontBoundingBoxAscent+y.fontBoundingBoxDescent)/2+1;(u=c.monomerTextSizeMap)[h]??(u[h]=t.measureText(h));const C=c.monomerTextSizeMap[h].width;function A(e,o){const i=d?c.color:"rgb(0,0,0)";t.fillStyle=i,t.globalAlpha=c.transparencyRate,c.drawStyle===Dt.classic&&(t.fillText(f,n+e,r+b),t.fillStyle="#808080",t.fillText(h,n+o,r+b)),c.drawStyle===Dt.MSA&&t.fillText(f,n+e,r+b)}y=y.width,c.drawStyle===Dt.MSA&&(v=c.maxWord[c.wordIdx],y=c.maxWord[c.wordIdx]);const w=(c.maxWord[c.wordIdx]??0)-(c.maxWord[0]??0);if(c.left||y>o)return A(w,w+v),n+w+v+C;{const t=(o-y)/2;return A(t,t+v),n+w+t+v}}var Ft=n(3599);const kt="rgb(100,100,100)";class Gt extends Pt{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(t,e,n,r,i){super(t,e,n),this.monomerLengthLimit=r,this.propsProvider=i,this.colWidth=0,this._monomerLengthList=null,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,Ct.Q)(),this.invalidateGrid()})(),(async()=>{const t=await(0,l.pj)();this.sysMonomerLib=t.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(t){let e=12;return t&&t.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof t.temp[".mm.cellRenderer.fontSize"]&&!isNaN(t.temp[".mm.cellRenderer.fontSize"])&&(e=Math.max(t.temp[".mm.cellRenderer.fontSize"],1)),{font:`${e}px monospace`,fontWidth:.6*e}}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);return[r,this.getSummedMonomerLengths(r)]}getSummedMonomerLengths(t){const e=new Array(t.length+1);e[0]=5;for(let n=1;n<e.length;n++)e[n]=e[n-1]+t[n-1];let n=e[0];for(let t=1;t<e.length;t++)e[t]?n=e[t]:e[t]=n;return e}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.fontCharWidth,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.fontCharWidth;if(s[t]=a,n+=a,n>this.colWidth)break}}return s}getCellMonomerLengthsForSeqValue(t,e){const n=this.seqHelper.getSeqHandler(this.tableCol),r=this.props.separatorWidth+1*this.props.fontCharWidth,o=Math.ceil(e/r),i=n.splitter(t),s=Math.min(o,i.length),a=new Array(s);let l=0;for(let t=0;t<s;++t){const r=i.getOriginal(t),o=this.props.monomerToShort(r,this.monomerLengthLimit),s=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+o.length*this.props.fontCharWidth;if(a[t]=s,l+=s,l>e)break}return a}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.fontCharWidth,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.fontCharWidth;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 ${JSON.stringify(t)}. `)}return null}(o,e)}setMonomerLengthLimit(t){this.monomerLengthLimit!=t&&(this.monomerLengthLimit=t,this.dirty=!0)}setSeparatorWidth(t){this.separatorWidth!=t&&(this.props.separatorWidth=t,this.dirty=!0)}render(t,e,n,r,o,i,s){const a=i.grid?.canvas===t.canvas;if(!this.seqHelper)return;const l=this.gridCol,u=this.tableCol,c=window.devicePixelRatio,f=`${this.toLog()}.render()`;this.logger.debug(`${f}, start`);let h=this.monomerLengthLimit;if(Rt.maxMonomerLength in u.tags){const t=parseInt(u.getTag(Rt.maxMonomerLength));h=!isNaN(t)&&t?t:50}if(".mm.cellRenderer.maxMonomerLength"in u.temp){const t=u.temp[".mm.cellRenderer.maxMonomerLength"];h=!isNaN(t)&&t?t:50}t.save();try{const s=this.seqHelper.getSeqHandler(u);if("1"===u.temp[".mm.cellRenderer.settingsChanged"]||this.monomerLengthLimit!=h){let t=0;const e=8;t=u.temp[".mm.cellRenderer.gapLength"]??t,this.setMonomerLengthLimit(h),this.setSeparatorWidth(s.isMsa()?e:t),u.temp[".mm.cellRenderer.settingsChanged"]="0"}let[f,d]=this.getCellMonomerLengths(i.tableRowIndex,r);f.length;const p=i.cell.value,g=i.cell.rowIndex,m=(u.getTag(mt.gp.alphabet),50);a&&(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)}(l?.grid,t,e,r,c)),t.beginPath(),t.rect(e+this.padding,n+this.padding,r-this.padding-1,o-2*this.padding),t.clip(),t.font=this.props?.font??"12px monospace",t.textBaseline="top";const y=u.meta.units,v=u.getTag(mt.gp.aligned),b=u.getTag(mt.gp.separator)??"",C=this.props.separatorWidth+1*this.props.fontCharWidth,A=Math.ceil(r/C),w=u.temp["reference-sequence"],E=this.tableCol.temp["current-word"];E&&-1===u?.dataFrame?.currentRowIdx&&(this.tableCol.temp["current-word"]=null);const _=(()=>{const t=s.getSplitter(A)(null!=w&&""!=w?w:E??"");return wt().count(0).take(t.length).map((e=>t.getOriginal(e))).toArray()})(),x=a?s.getSplitted(g):s.splitter(p);a||(d=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(p,r)));let T=Dt.classic;v&&v.includes("MSA")&&y==mt.Hi.SEPARATOR&&(T=Dt.MSA);const I=Math.min(x.length,A);for(let a=0;a<I;++a){const l=x.getOriginal(a),u=x.getCanonical(a);let c=kt;const f=this.getMonomerLib();if(f){const t=s.defaultBiotype;c=f.getMonomerTextColor(t,u)}t.fillStyle=kt;const p={color:c,pivot:0,left:!0,transparencyRate:1,separator:b,last:a===x.length-1,drawStyle:T,maxWord:d,wordIdx:a,gridCell:i,referenceSequence:_,maxLengthOfMonomer:h,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};if(Ht(t,l,e+this.padding,n,r,o,p),m>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??mt.YI.UN,r={position:i,biotype:n===mt.YI.RNA||n===mt.YI.DNA?Ft.o.NUCLEOTIDE:Ft.o.AA,symbol:a.getCanonical(i)},o=[];let l=this._monomerStructureMap[r.symbol];{const t=this.getMonomerLib();l=this._monomerStructureMap[r.symbol]=t?t.getTooltip(r.biotype,r.symbol):N.divText("Monomer library is not available")}o.push(l),N.tooltip.show(N.divV(o),e.x+16,e.y+16),Tt(t,r)}else N.tooltip.hide(),Tt(t,null)}}class Ut extends Gt{constructor(t,e,n,r){super(t,e,Wt.logger,n,(()=>{const t=r.getSeqHandler(e),{font:n,fontWidth:o}=Gt.getFontSettings(e);return{seqHandler:t,font:n,fontCharWidth:o,separatorWidth:11,monomerToShort:mt.zS}}))}onMouseMove(t,e){super.onMouseMove(t,e)}}class jt{get defaultGapOriginal(){return""}constructor(t,e){this.separator=t,this.helmHelper=e,this.separatorSplitter=(0,mt.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.fromSeparator(t,this.helmHelper).getHelm()}createCellRendererBack(t,e){const n=new Ut(t,e,4,this.helmHelper.seqHelper);return n.init().then((()=>{})),n}}class Vt extends s.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(/\(\d+\)$/,"")),n}constructor(t,e){super(t,e)}}const Wt=new P({debug:!0});function Yt(t,e){t.setTag("aligned","SEQ"),t.setTag("alphabet","UN"),t.setTag(".alphabetIsMultichar","true"),t.meta.units=i.Hi.CUSTOM,t.tags["polytool-data-role"]="template",t.temp[a.notationProvider]=new jt(e,Wt.helmHelper)}},5412:(t,e,n)=>{"use strict";n.d(e,{m:()=>l});var r=n(6082),o=n(4328),i=n(2890),s=n(6077),a=n(2003);async function l(t,e,n,l,u,c,f,h,d){const p=(await d.helmToAtomicLevel(t,l,u,f)).molCol,g=n.filter((t=>t)).length;if(c&&g>0){const t=new Array(g);let l=0;for(let r=0;r<n.length;r++)n[r]&&(t[l]=e[r],l++);const u=r.Column.fromStrings("helm",t);u.semType=r.SEMTYPE.MACROMOLECULE,u.meta.units=a.Hi.HELM,u.setTag(r.TAGS.CELL_RENDERER,"helm");const c=(await(0,i.pj)()).getMonomerLib();try{const t=await(0,s.C4)(r.DataFrame.create(0),u,c,d,h);l=0;for(let e=0;e<n.length;e++)n[e]&&(p.set(e,t.molCol.get(l)),l++)}catch(t){o.shell.warning("PolyTool was not able to linearize sequences")}}return function(t){for(let e=0;e<t.length;e++)t.set(e,t.get(e).replaceAll("undefined","H")),t.set(e,t.get(e).replaceAll("Oh","O")),t.set(e,t.get(e).replaceAll("0.000000 3","0.000000 0")),t.set(e,t.get(e).replaceAll("?","O")),t.set(e,t.get(e).replaceAll("0 3\n","0 0\n")),t.set(e,t.get(e).replaceAll("RGROUPS=(1 1)",""))}(p),p}},6307:(t,e,n)=>{"use strict";n.d(e,{s:()=>d});var r=n(2125),o=n(8438),i=n(100);function s(t,e){let n="";for(let t=0;t<e.length;t++){t>0&&(n+="|"),n+=`PEPTIDE${t+1}{`;for(let r=0;r<e[t].length;r++){r>0&&(n+=".");const o=e[t][r];n+=o.length>1?`[${o}]`:o}n+="}"}n+="$";for(let o=0;o<t.length;o++)o>0&&(n+="|"),n+=`PEPTIDE${t[o].fChain+1},PEPTIDE${t[o].sChain+1},`,n+=`${(0,r.M)(t[o].fMonomer-1,e)[0]+1}:R${t[o].fR}-`,n+=`${(0,r.M)(t[o].sMonomer-1,e)[0]+1}:R${t[o].sR}`;return n+="$$$V2.0",n}function a(t,e,n,r=0,o=[],i=[]){let[s,a,l,u,c]=[!1,!1,!1,-1,-1];for(let f=0;f<t.length;f++)if(t[f].includes(e)){if(s){if(l&&(n||t[f]==i[r]+e)){a=!0,c=f;break}if(l||!n&&t[f]!=o[r]+e)continue;a=!0,c=f;break}if(n)s=!0,l=!0,u=f;else if(t[f]==o[r]+e)s=!0,l=!0,u=f;else{if(t[f]!=i[r]+e)continue;s=!0,l=!!n,u=f}}return[s,a,l,u,c]}function l(t,e){const n=[];for(let r=0;r<e.length;r++){const o=`(${e[r].code})`,[s,l]=(0,i.Ln)(e[r]);if(s.length>0)for(let e=0;e<s.length;e++){const[i,u,c,f,h]=a(t,o,!1,e,s,l);i&&u&&(c?n.push({firstIdx:f,secondIdx:h,ruleIdx:r}):n.push({firstIdx:h,secondIdx:f,ruleIdx:r}))}else{const[e,i,s,l,u]=a(t,o,!0);if(!e||!i)continue;s?n.push({firstIdx:l,secondIdx:u,ruleIdx:r}):n.push({firstIdx:u,secondIdx:l,ruleIdx:r})}}return n}function u(t,e,n){const r=[],o=[],i=[],s=[],a=n.length;for(let l=0;l<a;l++){if(-1==n[l].firstIdx)continue;const a=n[l].ruleIdx,u=t[a].code;e[n[l].firstIdx]=e[n[l].firstIdx].replace(`(${u})`,""),e[n[l].secondIdx]=e[n[l].secondIdx].replace(`(${u})`,""),r.push(n[l].firstIdx+1),o.push(n[l].secondIdx+1),i.push(t[a].firstLinkingGroup),s.push(t[a].secondLinkingGroup)}return[r,o,i,s]}function c(t,e,n){const r=[],o=[],i=[],s=n.length;for(let a=0;a<s;a++){if(-1==n[a].firstIdx)continue;const s=n[a].firstIdx,l=n[a].secondIdx,u=n[a].ruleIdx,c=t[u].code;e[s]=e[s].replace(`(${c})`,"")+`_${t[u].name}`,e[l]=e[l].replace(`(${c})`,"")+`_${t[u].name}`,r.push(s+1),o.push(l+1),i.push(n[a].ruleIdx)}return[r,o,i]}var f=n(3599);function h(t,e,n){const r=n.createHelmWebEditor().editor.m;let o=0;const i=new JSDraw2.Point(0,0);for(let t=0;t<e.length;t++)for(let n=0;n<e[t].length;n++){if(e[t][n]){const s=e[t][n],a={type:f.o.AA,i:t,j:n,continuousId:o},l=new JSDraw2.Atom(i,s,a);if(r.addAtom(l),0!==n){const t=r.atoms[o-1],e=r.atoms[o],n=new JSDraw2.Bond(t,e);n.r1=2,n.r2=1,r.addBond(n)}o++,i.x+=JSDraw2.Editor.BONDLENGTH}i.y+=4*JSDraw2.Editor.BONDLENGTH}for(let e=0;e<t.length;e++){const n=r.atoms[t[e].fMonomer-1],o=r.atoms[t[e].sMonomer-1],i=new JSDraw2.Bond(n,o);i.r1=t[e].fR,i.r2=t[e].sR,r.addBond(i)}return r}class d{constructor(t,e,n){this.helmHelper=n,this.underRules=!1,this.posToPosUnderRules=[],this.linkages=e,this.monomers=t,this.mol=h(e,t,n)}static fromSeparator(t,e){const[n,r]=function(t){const e=[],n=[],r=/(\(.\d+\))?\{[^\}]*\}/g,o=[];o.push(t.replaceAll(r,""));const i=t.matchAll(r);for(const t of i){const e=t[0];e&&o.push(e)}let s=0;for(let t=0;t<o.length;t++){const r=o[t].split("-"),i=new Array(r.length);let a=0;for(let e=0;e<r.length;e++){const o=r[e].replace("{","").replace("}","");""!==o?(i[e]=o,s++,a++):n.push({fChain:t,sChain:t+1,fMonomer:s,sMonomer:s+1,fR:1,sR:1})}e.push(i.slice(0,a))}return[n,e]}(t);return new d(r,n,e)}static fromHelm(t,e){const[n,i]=function(t){const e=/(\w+\{.*\})\$(.*)\$(.*)\$(.*)\$/g.exec(t),n=[e[1],e[2],e[3],e[4]],i=n[0].split("|"),s=n[1].split("|"),a=new Array(i.length),l=[];for(let t=0;t<i.length;t++){const e=i[t].indexOf("{"),n=i[t].indexOf("}");a[t]=i[t].slice(e+1,n).split(".").map((t=>(0,o.D)(t)))}for(let t=0;t<s.length;t++)if(""!==s[t]&&"V2.0"!==s[t]){const e=s[t].split(","),n=parseInt(e[0].replace("PEPTIDE",""))-1,o=parseInt(e[1].replace("PEPTIDE",""))-1,i=e[2].split("-"),u=i[0].split(":"),c=i[1].split(":");l.push({fChain:n,sChain:o,fMonomer:(0,r.j)(parseInt(u[0]),n,a),sMonomer:(0,r.j)(parseInt(c[0]),o,a),fR:parseInt(u[1].replace("R","")),sR:parseInt(c[1].replace("R",""))})}return[l,a]}(t);return new d(i,n,e)}getNotation(){return function(t){const e=t.atoms,n=t.bonds,r=[],o=[];for(let t=0;t<n.length;t++)n[t].a1.bio.i!==n[t].a2.bio.i&&o.push(t);for(let t=0;t<e.length;t++){const n=e[t].bio?.i;n+1>r.length?r.push(1):r[n]++}const i=new Array(r.length);let s=0;for(let t=0;t<r.length;t++){const n=new Array(r[t]);for(let o=0;o<r[t];o++)n[o]=e[s].elem,s++;i[t]=n}let a="";for(let t=0;t<i.length;t++){let e="";for(let n=0;n<i[t].length;n++)e+=`${0==n?"":"-"}${i[t][n]}`;if(0!==t){const t=/(\(.\d+\))/,n=e.match(t);e=e.replace(n?.[0],""),e=`${n?n?.[0]:""}{${e}}`}else if(i.length>1){const t=0==n[o[0]].a1.bio.i&&0==n[o[0]].a1.bio.j,r=1==n[o[0]].a2.bio.i&&0==n[o[0]].a1.bio.j;t&&r&&(e+="-")}a+=e}return a}(this.mol)}getHelm(){return this.underRules?s(this.linkagesUnderRules,this.monomersUnderRules):s(this.linkages,this.monomers)}applyRules(t){const e=this.getNotation(),[n,r,o]=function(t,e){const n=[],r=[],o=[],i=e.heterodimerCode,s=e.homodimerCode,a=null!==i?t.split(`(${e.heterodimerCode})`):"";null!==i&&a.length>1?(o.push({fChain:0,sChain:1,fMonomer:1,sMonomer:1,fR:1,sR:1}),n.push(a[1].replaceAll("{","").replaceAll("}","")),n.push(a[2].replaceAll("{","").replaceAll("}","")),r.push(!1),r.push(!1)):(n.push(t),r.push(!1));for(let t=0;t<n.length;t++)if(null!==s&&n[t].includes(`(${s})`)){const e=n.length;o.push({fChain:t,sChain:e,fMonomer:1,sMonomer:1,fR:1,sR:1});const i=n[t].replace(`(${s})`,""),a=i.indexOf("{"),l=i.slice(0,a),u=i.replace(l,"").replaceAll("{","").replaceAll("}","");n[t]=l+u,n.push(u),r.push(!0)}return[o,n,r]}(e,t),i=new Array(r.length);let s=0;for(let t=0;t<r.length;t++)if(i[t]=r[t].split("-"),o[t]){const e=this.posToPosUnderRules.length-i[t].length;for(let n=0;n<i[t].length;n++)this.posToPosUnderRules[e+n].push(s),s++}else for(let e=0;e<i[t].length;e++)this.posToPosUnderRules.push([s]),s++;!function(t,e,n){for(let r=0;r<t.length;r++){const o=t[r],i=l(o,n.linkRules),[s,a,c,f]=u(n.linkRules,o,i);for(let t=0;t<s.length;t++)e.push({fChain:r,sChain:r,fMonomer:s[t],sMonomer:a[t],fR:c[t],sR:f[t]});t[r]=o}}(i,n,t),function(t,e,n){for(let r=0;r<t.length;r++){const o=l(t[r],n.reactionRules),[i,s,a]=c(n.reactionRules,t[r],o);i.length>=1&&(e.push({fChain:r,sChain:t.length,fMonomer:i[0],sMonomer:1,fR:3,sR:1}),e.push({fChain:r,sChain:t.length,fMonomer:s[0],sMonomer:1,fR:3,sR:2}),t.push([n.reactionRules[a[0]].name]))}}(i,n,t),this.underRules=!0,this.linkagesUnderRules=n,this.monomersUnderRules=i,this.molUnderRules=h(n,i,this.helmHelper)}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}}},4229:(t,e,n)=>{"use strict";n.d(e,{b:()=>s});var r=n(9192),o=n(6307),i=n(1950);function s(t,e,n){const s=new Array(t.length),a=new Array(t.length),l=new Array(t.length);for(let u=0;u<t.length;u++)try{if(null==t[u])s[u]="";else{const r=o.s.fromSeparator(t[u],n);r.applyRules(e),a[u]=!(r.monomersUnderRules.length>1||r.linkagesUnderRules.length>0),s[u]=r.getHelm(),l[u]=r.posToPosUnderRules}}catch(t){const[e,n]=(0,r.AP)(t);i._package.logger.error(e,void 0,n),s[u]=""}return[s,a,l]}},2125:(t,e,n)=>{"use strict";function r(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 o(t,e,n){let r=0;for(let t=0;t<e;++t)r+=n[t].length;return r+t}n.d(e,{M:()=>r,j:()=>o})},100:(t,e,n)=>{"use strict";n.d(e,{Ln:()=>V,Q4:()=>j});var r=n(6082),o=n(7389),i=n(4328);n(1991);var s=n(1950),a=n(9124),l=n(4229),u=n(439);const c="Links",f="Reactions";class h{constructor(t,e){this.v=null,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=o.input.string("Homo dimer",{value:n,onValueChanged:()=>{},nullable:!1}),this.heteroDimerInput=o.input.string("Hetero dimer",{value:r,onValueChanged:()=>{},nullable:!1})}async getAndAddView(){if(this.v)try{const t=Array.from(i.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");i.shell.v=t}catch(t){this.v=null}return this.v||(this.v=r.View.create(),this.v.name=`Manage Polytool Rules - ${this.fileName}`,this.v.append(await this.getForm()),this.v=i.shell.addView(this.v),i.shell.v=this.v),this.v}static async getInstance(t){if(!this.instances[t]){const e=await j([t]);this.instances[t]=new h(e,t)}return this.instances[t]}save(){this.rules.homodimerCode=this.homoDimerInput.value,this.rules.heterodimerCode=this.heteroDimerInput.value,this.rules.setLinkRules(this.linkRuleDataFrame),this.rules.setSynthesisRules(this.synthRuleDataFrame);const t={homodimerCode:this.rules.homodimerCode,heterodimerCode:this.rules.heterodimerCode,linkRules:this.rules.linkRules,reactionRules:this.rules.reactionRules},e=JSON.stringify(t,void 0,2);s._package.files.writeAsText(`polytool-rules/${this.fileName}`,e),i.shell.info(`Polytool rules at ${this.fileName} was updated`)}createGridDiv(t,e,n){const r=o.h1(t,"polytool-grid-header");o.tooltip.bind(r,n),r.style.marginTop="10px",r.style.marginRight="10px",e.root.style.height="100%";const i=o.splitV([o.box(r,{style:{maxHeight:"60px"}}),e.root]);return i.style.height="100%",i}async getLinkExamplesGrid(){const t=[];for(let e=0;e<this.rules.linkRules.length;e++){const n=this.rules.linkRules[e].code,[r,o]=V(this.rules.linkRules[e]);for(let e=0;e<r.length;e++){const i=`${r[e]}(${n})-A-A-A-A-${o[e]}(${n})`;t.push(i)}}const e=await(0,a.b2)(),[n,o,i]=(0,l.b)(t,this.rules,e),c=r.Column.fromStrings("Monomers",t),f=r.Column.fromStrings("Helm",n);return(0,s.applyNotationProviderForCyclized)(c,"-"),c.semType=r.SEMTYPE.MACROMOLECULE,f.semType=r.SEMTYPE.MACROMOLECULE,f.meta.units=u.Hi.HELM,f.setTag(r.TAGS.CELL_RENDERER,"helm"),r.DataFrame.fromColumns([c,f]).plot.grid()}async getReactionExamplesGrid(){const t=[];for(let e=0;e<this.rules.reactionRules.length;e++){const n=this.rules.reactionRules[e].code,[r,o]=V(this.rules.reactionRules[e]);for(let e=0;e<r.length;e++){const i=`${r[e]}(${n})-A-A-A-A-${o[e]}(${n})`;t.push(i)}}const e=await(0,a.b2)(),[n,o,i]=(0,l.b)(t,this.rules,e),c=r.Column.fromStrings("Monomers",t),f=r.Column.fromStrings("Helm",n);return c.semType=r.SEMTYPE.MACROMOLECULE,(0,s.applyNotationProviderForCyclized)(c,"-"),f.semType=r.SEMTYPE.MACROMOLECULE,f.meta.units=u.Hi.HELM,f.setTag(r.TAGS.CELL_RENDERER,"helm"),r.DataFrame.fromColumns([c,f]).plot.grid()}async getForm(){r.TabControl;const t=this.createGridDiv("Rules",this.linkRuleDataFrame.plot.grid({showAddNewRowIcon:!0}),"specification for monomers to link and linking positions"),e=this.createGridDiv("Examples",await this.getLinkExamplesGrid(),"specification for monomers to link and linking positions");t.style.width="50%",e.style.width="50%";const n=o.h1("Monomers","polytool-grid-header");o.tooltip.bind(n,"Click different cobination to see how monomers will link"),this.linkCards=await this.rules.getLinkCards();const i=o.splitV([o.box(n,{style:{maxHeight:"30px"}}),this.linkCards[0].root]);this.linkCards[0].render(),await this.linkCards[0].reset(),this.linkRuleDataFrame.currentRowIdx=0,this.linkRuleDataFrame.onCurrentRowChanged.subscribe((async()=>{const t=this.linkRuleDataFrame.currentRowIdx;-1!==t&&(o.empty(i),i.append(o.splitV([o.box(n,{style:{maxHeight:"30px"}}),this.linkCards[t].root]))),this.linkCards[t].render(),await this.linkCards[t].reset()}));const s=o.splitH([t,i],null,!0),a=this.createGridDiv("Rules",this.synthRuleDataFrame.plot.grid({showAddNewRowIcon:!0})),l=this.createGridDiv("Examples",await this.getReactionExamplesGrid());a.style.width="50%",l.style.width="50%";const u=o.divH([a,l]),h=o.divV([this.homoDimerInput,this.heteroDimerInput]),d=o.tabControl({Links:s,Reactions:u,Dimers:h},!1);o.tooltip.bind(d.getPane(c).header,"Specify rules to link monomers based on HELM notation"),o.tooltip.bind(d.getPane(f).header,"Specify rules to perform reactions within monomers"),o.tooltip.bind(d.getPane("Dimers").header,"Specify symbols for homodimeric and heterodimeric codes"),d.root.style.height="100%",d.root.style.width="100%",d.root.classList.add("rules-manager-form-tab-control"),d.header.style.marginBottom="10px";const p=o.divV([d.root]),g=[o.bigButton("Save",(()=>{this.save()})),o.button("Add rule",(()=>{const t=d.currentPane.name;t==c?this.linkRuleDataFrame.rows.addNew():t==f&&this.synthRuleDataFrame.rows.addNew()}))];return this.v.setRibbonPanels([g]),p.style.height="100%",p.style.alignItems="center",d.root}}h.instances={};var d=n(5072),p=n.n(d),g=n(7825),m=n.n(g),y=n(7659),v=n.n(y),b=n(5056),C=n.n(b),A=n(540),w=n.n(A),E=n(1113),_=n.n(E),x=n(890),T={};T.styleTagTransform=_(),T.setAttributes=C(),T.insert=v().bind(null,"head"),T.domAPI=m(),T.insertStyleElement=w(),p()(x.A,T),x.A&&x.A.locals&&x.A.locals;var I=n(2003),N=n(6717),S=n(8312),L=n(5174),P=n(5412);class O{get selected(){return this._selected}set selected(t){this._selected=t,this.root.style.border=t?"2px solid var(--green-2)":"2px solid var(--grey-2)"}constructor(t){this.monomer=t,this.root=o.divV([],{classes:"monomer-card-rule-root"}),this._selected=!1}render(){if(this.monomer){o.empty(this.root);const t=this.monomer.smiles&&i.chem.checkSmiles(this.monomer.smiles)?i.chem.drawMolecule(this.monomer.smiles,150,120):i.chem.drawMolecule(this.monomer.molfile??"",150,120);this.root.appendChild(t);const e=o.divH([o.divText("Monomer Name: "),o.divText(this.monomer.name)],{classes:"monomer-card-info-rules"});if(this.root.appendChild(e),o.tooltip.bind(e,this.monomer.name),this.monomer.lib?.source){const t=o.divH([o.divText("Source: "),o.divText(this.monomer.lib.source)],{classes:"monomer-card-info-rules"});this.root.appendChild(t),o.tooltip.bind(t,this.monomer.lib.source)}const n=o.divH([o.divText("Polymer Type: "),o.divText(this.monomer.polymerType)],{classes:"monomer-card-info-rules"});this.root.appendChild(n),o.tooltip.bind(n,this.monomer.polymerType),o.tooltip.bind(this.root,"Select Monomer")}}}class M{constructor(t,e,n,r,i){if(this.firstMonomers=t,this.secondMonomers=e,this.code=r,this.rules=i,this.root=o.divH([],{style:{alignItems:"center",width:"100%",overflow:"hidden",visibility:"visible"},classes:"monomer-cards"}),t.length>0){this.actionable=!0;const r=o.divH([],{style:{overflowX:"auto",width:"100%"}}),i=o.divH([],{style:{overflowX:"auto",width:"100%"}});this.resulting=o.divH([],{style:{overflowX:"auto",width:"100%",minHeight:"150px"}});const s=o.divV([r,i,this.resulting]);this.cardsFirst=t.map((t=>new O(n.getMonomer("PEPTIDE",t)))),this.cardsSecond=e.map((t=>new O(n.getMonomer("PEPTIDE",t)))),this.cardsFirst.forEach((t=>{t.root.onclick=()=>{this.cardsFirst.forEach((t=>t.selected=!1)),t.selected=!0,this.firstCard=t,this.reset()},r.appendChild(t.root)})),this.cardsSecond.forEach((t=>{t.root.onclick=()=>{this.cardsSecond.forEach((t=>t.selected=!1)),t.selected=!0,this.secondCard=t,this.reset()},i.appendChild(t.root)})),this.cardsFirst[0].selected=!0,this.cardsSecond[0].selected=!0,this.firstCard=this.cardsFirst[0],this.secondCard=this.cardsSecond[0],this.root.appendChild(s)}else{const t=o.divV(["Rule is active for all monomers, no examples to show"]);this.root.appendChild(t),this.actionable=!1}}async reset(){if(this.actionable){const t=[`${this.firstCard.monomer?.symbol}(${this.code})-A-A-A-A-${this.secondCard.monomer?.symbol}(${this.code})`],e=await(0,a.b2)(),[n,s,u]=(0,l.b)(t,this.rules,e),c=r.Column.fromType(r.COLUMN_TYPE.STRING,"helm",n.length).init((t=>n[t]));c.semType=r.SEMTYPE.MACROMOLECULE,c.meta.units=I.Hi.HELM,c.setTag(r.TAGS.CELL_RENDERER,"helm");const f=await(0,N.j)(),h=await(0,S.Q)(),d=await(0,L.A)(this.rules),p=c.temp;c.temp=p;const g=(await(0,P.m)(c,n,s,!0,!1,!1,d,f,h)).get(0),m=g&&i.chem.checkSmiles(g)?i.chem.drawMolecule(g,150,120):i.chem.drawMolecule(g??"",150,120);o.empty(this.resulting),this.resulting.append(o.divH([m],{style:{overflowX:"auto",width:"100%",minHeight:"150px"}}))}}render(){this.actionable&&(this.cardsFirst.forEach((t=>t.render())),this.cardsSecond.forEach((t=>t.render())))}}var R=n(2890);const $="System:AppData/SequenceTranslator/polytool-rules/",D="code",B="firstMonomers",H="secondMonomers",F="name",k="firstLinkingGroup",G="secondLinkingGroup";class U{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(D,t);e.setTag("friendlyName","Code");const n=r.Column.string(B,t);n.setTag("friendlyName","First monomers"),n.semType=r.SEMTYPE.MACROMOLECULE,(0,s.applyNotationProviderForCyclized)(n,",");const o=r.Column.string(H,t);o.setTag("friendlyName","Second monomers"),o.semType=r.SEMTYPE.MACROMOLECULE,(0,s.applyNotationProviderForCyclized)(o,",");const i=r.Column.int(k,t);i.setTag("friendlyName","First group");const a=r.Column.int(G,t);a.setTag("friendlyName","Second group");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),a.set(r,this.linkRules[r].secondLinkingGroup);return r.DataFrame.fromColumns([e,n,o,i,a])}async getLinkCards(){const t=this.linkRules.length,e=new Array(t),n=(await(0,R.pj)()).getMonomerLib();for(let r=0;r<t;r++)e[r]=new M(this.linkRules[r].firstMonomers,this.linkRules[r].secondMonomers,n,this.linkRules[r].code,this);return e}getSynthesisRulesDf(){const t=this.reactionRules.length,e=r.Column.int(D,t);e.setTag("friendlyName","Code");const n=r.Column.string(B,t);n.setTag("friendlyName","First monomers");const o=r.Column.string(H,t);o.setTag("friendlyName","Second monomers");const i=r.Column.string(F,t);i.setTag("friendlyName","Name");const s=r.Column.string("firstReactant",t);s.setTag("friendlyName","First reactant");const a=r.Column.string("secondReactant",t);a.setTag("friendlyName","Second reactant");const l=r.Column.string("product",t);l.setTag("friendlyName","Product");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(">>"),u=t[0].split(".");s.set(r,u[0]),a.set(r,u[1]),l.set(r,t[1])}return s.semType=r.SEMTYPE.MOLECULE,a.semType=r.SEMTYPE.MOLECULE,l.semType=r.SEMTYPE.MOLECULE,r.DataFrame.fromColumns([i,s,a,l,e,n,o])}setLinkRules(t){const e=t.rowCount,n=new Array(e),r=t.columns.byName(D),o=t.columns.byName(B),i=t.columns.byName(H),s=t.columns.byName(k),a=t.columns.byName(G);for(let t=0;t<e;t++){const e=o.get(t).split(","),l=i.get(t).split(","),u={code:r.get(t),firstMonomers:""!==e[0]?e:[],secondMonomers:""!==l[0]?l:[],firstLinkingGroup:s.get(t),secondLinkingGroup:a.get(t)};n[t]=u}this.linkRules=n}setSynthesisRules(t){const e=t.rowCount,n=new Array(e),r=t.columns.byName(D),o=t.columns.byName(B),i=t.columns.byName(H),s=t.columns.byName(F),a=t.columns.byName("firstReactant"),l=t.columns.byName("secondReactant"),u=t.columns.byName("product");for(let t=0;t<e;t++){const e=`${a.get(t)}.${l.get(t)}>>${u.get(t)}`,c=o.get(t).split(","),f=i.get(t).split(","),h={code:r.get(t),firstMonomers:""!==c[0]?c:[],secondMonomers:""!==f[0]?f:[],reaction:e,name:s.get(t)};n[t]=h}this.reactionRules=n}}async function j(t){const e=new r.FileSource($),n=new U(null,null,[],[]);for(let r=0;r<t.length;r++){const o=await e.readAsText(t[r].replace($,"")),i=JSON.parse(o);n.homodimer=i.homodimerCode,n.heterodimer=i.heterodimerCode,n.addLinkRules(i.linkRules),n.addSynthesisRules(i.reactionRules)}return n}function V(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]}},5174:(t,e,n)=>{"use strict";n.d(e,{A:()=>c,T:()=>f});var r=n(6717),o=n(1296),i=n(9192),s=n(4328),a=n(1991),l=n.n(a),u=n(2890);async function c(t){const e=(await(0,u.pj)()).getMonomerLib(),n=await(0,r.j)(),o={};let i=[],a=[];for(let r=0;r<t.reactionRules.length;r++)try{[i,a]=f(n,e,t.reactionRules[r])}catch(t){i=[],a=[],console.error(t),s.shell.warning(t)}finally{for(let t=0;t<i.length;t++)o[i[t]]=a[t]}const c={PEPTIDE:o};return e.override(c,"ST-PT-reactions."+l().repeat(1).map((()=>Math.floor(36*Math.random()).toString(36))).take(4).toArray().join(""))}function f(t,e,n){const r=n.reaction,a=n.name,l=n.firstMonomers.length+n.secondMonomers.length+1,u=n.reaction.split(">>"),c=u[0].split("."),f=new Array(l),g=new Array(l),m=new Array(l),y=d(t,r),v=`${c[0]}>>[C:1]C`,b=`${c[1]}>>[C:2]C`,C=d(t,v),A=d(t,b);let w=0;for(let r=0;r<n.firstMonomers.length;r++){const i=e.getMonomer("PEPTIDE",n.firstMonomers[r]);if(!i)throw new o.bl("PEPTIDE",n.firstMonomers[r]);const s=h(t,i.molfile,C,i.name);m[w]=s,f[w]=`${i.symbol}_${a}`,w++}for(let r=0;r<n.secondMonomers.length;r++){const i=e.getMonomer("PEPTIDE",n.secondMonomers[r]);if(!i)throw new o.bl("PEPTIDE",n.secondMonomers[r]);const s=h(t,i.molfile,A,i.name);m[w]=s,f[w]=`${i.symbol}_${a}`,w++}let E=null,_="";try{E=t.get_mol(u[1]),_=E?.get_molblock()}catch(t){const[e,n]=(0,i.AP)(t);throw s.shell.error(`Can not assemble monomer '${a}': ${e}.`),t}finally{E?.delete()}m[w]=_,f[w]=a;for(let t=0;t<l-1;t++)m[t]=m[t].replace(" 0.0000 0.0000 0.0000 C "," 0.0000 0.0000 0.0000 R# ").replace("M RGP 2","M RGP 3 2 3");m[l-1]=function(t){const e=t.replace("M RAD","M RGP").split("\n"),n=4+Number(e[3].substring(0,3))+Number(e[3].substring(3,6)),r=Number(e[n].substring(9,13)),o=Number(e[n].substring(17,21));e[n]=e[n].substring(0,13)+" 1"+e[n].substring(17,21)+" 2",e[3+r]=e[3+r].substring(0,30)+" R# 0 0 0 0 0 0 0 0 0 0 0 0",e[3+o]=e[3+o].substring(0,30)+" R# 0 0 0 0 0 0 0 0 0 0 0 0";let i="";for(let t=0;t<e.length;t++)i+=e[t]+"\n";return i}(m[l-1]);for(let t=0;t<l;t++){const e=t==l-1,n={symbol:f[t],name:f[t],molfile:m[t],author:"",id:0,rgroups:p(e),smiles:"",polymerType:"PEPTIDE",monomerType:"Backbone",createDate:null};n.meta=Object.assign(n.meta??{},{colors:{default:{line:"#2083D5",text:"#2083D5",background:"#F2F2F5"}}}),f[t]=f[t],g[t]=n}return y.delete(),C.delete(),A.delete(),[f,g]}function h(t,e,n,r){let o=null,a=null,l=null,u=null,c="";try{o=new t.MolList,a=t.get_mol(e),o.append(a),l=n.run_reactants(o,1),u=l.get(0).next(),c=u?.get_molblock()}catch(t){const[e,n]=(0,i.AP)(t);throw s.shell.error(`Can not assemble monomer '${r}': ${e}.`),t}finally{o?.delete(),a?.delete(),l?.delete(),u?.delete()}return c}function d(t,e){let n=null;try{if(n=t.get_rxn(e),!n)throw new o.J5(e)}catch(t){n?.delete();const[r,o]=(0,i.AP)(t);throw s.shell.error(`Can not assemble monomer '${e}': ${r}.`),t}return n}function p(t){if(t){const t=new Array(2),e={capGroupSMILES:"[*:1][H]",alternateId:"R1-H",capGroupName:"H",label:"R1"},n={capGroupSMILES:"[*:2][H]",alternateId:"R2-H",capGroupName:"H",label:"R2"};return t[0]=e,t[1]=n,t}return[{capGroupSMILES:"[*:3][H]",alternateId:"R3-H",capGroupName:"H",label:"R3"}]}},3820:(t,e,n)=>{"use strict";n.d(e,{o:()=>i});var r=n(1296);function o(t,e,n,r){const o=new Array(r.length*(n-e+1));for(let i=0;i<r.length;++i){const s=n-e+1;for(let n=0;n<s;++n){const a=e+n,l=r[i],u=o[i*s+n]=t.clone(),c=u.atoms[a].elem;u.atoms[a].elem=l;const f=c?.length>1?`[${c}]`:c,h=l?.length>1?`[${l}]`:l;u.name=`${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 l=[];if(n.placeholders)switch(n.type){case r.aK.Single:l=function(t,e){return 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o={breadth1:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"}]},"breadth1-with-original":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]}],keepOriginal:!0},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:""},{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"}]},breadth2:{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K","Y"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K"},{seq:"PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5Y"}]},"breadth-double":{src:"PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",params:{type:S.aK.Single,breadthPlaceholders:[{start:2,end:4,monomers:["K"]},{start:2,end:4,monomers:["Y"]}]},tgt:[{seq:"PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-K3Y"},{seq:"PEPTIDE1{[Ac(1)].F.K.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.K.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-W3K-P5Y"},{seq:"PEPTIDE1{[Ac(1)].F.Y.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-K4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.K.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-G4K-P5Y"},{seq:"PEPTIDE1{[Ac(1)].F.Y.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-W3Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.Y.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-G4Y"},{seq:"PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0",name:"-P5K-K5Y"}]}};for(const[t,n]of Object.entries(o))(0,e.t6)(`${t}`,(async()=>{const t=(0,L.o)(n.src,"",n.params);(0,e.J6)(t,n.tgt.map((t=>[t.seq,t.name])))}))}));var P=n(6307),O=n(2125);(0,e.L1)("PolyTool: Chain: parseNotation",(()=>{let t;(0,e.gM)((async()=>{t=await(0,x.b2)()}));const n={cyclized:{src:{seq:"R-F-C(1)-T-G-H-F-Y-P-C(1)-meI"},tgt:{helm:"PEPTIDE1{R.F.[C(1)].T.G.H.F.Y.P.[C(1)].[meI]}$$$$V2.0"}},dimerized1:{src:{seq:"(#3)Succ-{A(CHOL)-F-C(1)-T-G-H-Y-P-C(1)-NH2}"},tgt:{helm:"PEPTIDE1{[(#3)Succ]}|PEPTIDE2{[A(CHOL)].F.[C(1)].T.G.H.Y.P.[C(1)].[NH2]}$PEPTIDE1,PEPTIDE2,1:R1-1:R1$$$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,N.Q4)(["rules_example.json"]);const n=await P.s.fromSeparator(o.src.seq,t),r=n.mol,i=t.createHelmWebEditor();i.editor.setMol(r);const s=i.editor.getHelm(),a=n.getHelm();(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,O.M)(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,O.j)(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:0}}},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-${r}`,(async()=>{const n=await(0,N.Q4)(["rules_example.json"]),r=P.s.fromSeparator(o.templateSeq,t);r.applyRules(n),r.check(!0),(0,e.J6)(r.monomers.map((t=>t.length)),i.mmChain.monomerCount),(0,e.E3)(r.linkages.length,i.mmChain.linkageCount),(0,e.E3)(r.getHelm(),o.mmHelm)}),{skipReason:"3157"});for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`parseNotation-${r}`,(async()=>{await(0,N.Q4)(["rules_example.json"]);const n=P.s.fromSeparator(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-${r}`,(async()=>{await(0,N.Q4)(["rules_example.json"]);const n=P.s.fromHelm(o.templateHelm,t);n.check(!0),(0,e.J6)(n.monomers.map((t=>t.length)),i.templateChain.monomerCount),(0,e.E3)(n.linkages.length,i.templateChain.linkageCount),(0,e.E3)(n.getHelm(),o.templateHelm),(0,e.E3)(n.getNotation(),o.templateSeq)}));for(const[r,{data:o,tgt:i}]of Object.entries(n))(0,e.t6)(`applyRules-${r}`,(async()=>{const n=await(0,N.Q4)(["rules_example.json"]),r=P.s.fromSeparator(o.templateSeq,t);r.applyRules(n),r.check(!0),(0,e.J6)(r.monomers.map((t=>t.length)),i.mmChain.monomerCount),(0,e.E3)(r.linkages.length,i.mmChain.linkageCount),(0,e.E3)(r.getHelm(),o.mmHelm)}),{skipReason:"applyRules is not implemented"})})),(0,e.L1)("toAtomicLevel",(()=>{let n,r,o;(0,e.gM)((async()=>{r=await(0,b.pj)(),n=await w(),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 M.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}},l=n.override(a,"test"),u=await(0,p.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 u.helmToAtomicLevel(c,!1,!1,l);(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 d=o.get_mol(h);try{const t=d.get_inchi(),n=o.get_inchikey_for_inchi(t);(0,e.E3)(d.get_num_bonds(),103),(0,e.E3)(d.get_num_atoms(),98),(0,e.E3)(n,"XPQUTLNSNIMERR-WKBTUBAPSA-N")}finally{d.delete()}})),(0,e.t6)("getNewMonomer",(async()=>{const t=await(0,_.j)(),n=r.getMonomerLib(),o=(await(0,N.Q4)(["rules_example.json"])).reactionRules.find((t=>"GGaz"==t.name)),[i,s]=(0,I.T)(t,n,o);(0,e.E3)(i[0],"azG_GGaz");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(),7),(0,e.E3)(a.get_num_atoms(),8)}finally{a.delete()}}))}));const M=new s;async function R(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)(M,M.getModule("package-test.js"))}})(),sequencetranslator_test=r})();
3
3
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