@datagrok/helm 2.1.34 → 2.2.1

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Files changed (30) hide show
  1. package/.eslintrc.json +1 -1
  2. package/CHANGELOG.md +30 -0
  3. package/dist/package-test.js +1 -1
  4. package/dist/package-test.js.map +1 -1
  5. package/dist/package.js +1 -1
  6. package/dist/package.js.map +1 -1
  7. package/package.json +12 -12
  8. package/src/cell-renderer.ts +21 -153
  9. package/src/constants.ts +0 -11
  10. package/src/helm-helper.ts +9 -10
  11. package/src/helm-monomer-placer.ts +21 -85
  12. package/src/helm-web-editor.ts +5 -2
  13. package/src/package-test.ts +6 -2
  14. package/src/package-utils.ts +150 -0
  15. package/src/package.ts +96 -100
  16. package/src/tests/get-monomer-tests.ts +210 -0
  17. package/src/tests/helm-service-tests.ts +97 -0
  18. package/src/tests/helm-tests.ts +1 -0
  19. package/src/tests/properties-widget-tests.ts +4 -2
  20. package/src/tests/renderers-tests.ts +97 -22
  21. package/src/types/dojo.ts +3 -0
  22. package/src/types/index.ts +0 -0
  23. package/src/utils/dummy-monomer.ts +184 -0
  24. package/src/utils/get-hovered.ts +104 -0
  25. package/src/utils/get-monomer.ts +111 -0
  26. package/src/utils/helm-grid-cell-renderer.ts +199 -0
  27. package/src/utils/helm-service.ts +130 -0
  28. package/src/utils/index.ts +7 -7
  29. package/webpack.config.js +7 -0
  30. /package/src/tests/{get-molfiles.ts → get-molfiles-tests.ts} +0 -0
package/dist/package-test.js CHANGED
@@ -1,2 +1,2 @@
1
- var helm_test;(()=>{var t={460:(t,e,n)=>{"use strict";n.d(e,{wW:()=>f});var s,i,r,o,a,l,h,c=n(888);n(200),n(852),n(923),n(688);class u{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,s=u._createBuffer(n);if(e)for(let t=0;t<s.length;t++)s[t]=-1;this._data=s,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,s){if(t<e||t>n)throw new Error(`Argument ${s} (${t}) out of range (${e}, ${n})`)}copy(t,e,n){for(let s=0;s<n;s++)e[s]=t[s]}copyFrom(t){if(this._length!=t._length)throw new Error(`Lengths differ (${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} != ${e._length})`);const n=new u(t._length);n._length=t._length,n._data=u._createBuffer(n._length),n._version=0;const s=t.lengthInInts;for(let i=0;i<s;i++)n._data[i]=t._data[i]&e._data[i];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new u(t.length);e._version=0;for(let n=0;n<e._length;n++)t[n]&&(e._data[Math.floor(n/32)]|=1<<(n%32&31));return e}static fromSeq(t,e){const n=new u(t);for(let s=0;s<t;++s)n.setBit(s,e(s));return n._version=0,n}static fromString(t){return u.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new u(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new u(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let s=0,i=0;for(;e-i>=4;)n._data[s++]=255&t[i]|(255&t[i+1])<<8|(255&t[i+2])<<16|(255&t[i+3])<<24,i+=4;return e-i==3&&(n._data[s]=(255&t[i+2])<<16),e-i==2&&(n._data[s]|=(255&t[i+1])<<8),e-i==1&&(n._data[s]|=255&t[i]),n._version=0,n}toString(){return`${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 u(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,s=this.lengthInInts;for(let t=0;t<s;t++)this._data[t]=n;this.incrementVersion(e)}setIndexes(t,e=!0,n=!0,s=!0){n&&this.setAll(!e,!1);for(const n of t)this.setFast(n,e);this.incrementVersion(s)}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,s=!0,i=!0){if(n&&i&&this.setAll(!e,!1),i)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(s)}getRange(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let s=t;s<e;++s)n.push(this.getBit(s));return u.fromValues(n)}getRangeAsList(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let s=t;s<e;++s)n.push(this.getBit(s));return n}setRange(t,e,n,s=!0){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length-1,"to");const i=Math.min(t,e),r=Math.max(t,e);if(n)for(let t=i;t<=r;t++)this.setTrue(t);else for(let t=i;t<=r;t++)this.setFalse(t);return this.incrementVersion(s),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 s=this._length;this.setLength(this._length+e);for(let n=s-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let s=t;s<t+e;s++)this.setBit(s,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 s=-1;-1!=(s=t.findNext(s,!e));)this.setFast(n++,this.getBit(s));this._length=n,this._version++}return this}getBit(t){return 0!=(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+=u._onBitCount[255&t];let n=this._data[e];const s=31&this._length;for(0!=s&&(n&=~(4294967295<<s));0!=n;n>>>=8)this._selectedCount+=u._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 s=this.lengthInInts;let i=0;for(;i<s-1;i++)for(let e=this._data[i]&t._data[i];0!=e;e>>>=8)n+=u._onBitCount[255&e];let r=this._data[i]&t._data[i];const o=31&this._length;for(0!=o&&(r&=~(4294967295<<o));0!=r;r>>>=8)n+=u._onBitCount[255&r];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 s=this.lengthInInts;for(let i=Math.floor(t/32);i<s;i++){let s=e?this._data[i]:~this._data[i];if(0!=n)s&=4294967295<<n&4294967295,n=0;else if(!e&&-4294967296==s)continue;for(let e=0;0!=s;e+=8,s>>>=8){const n=u._firstOnBit[255&s];if(n>=0)return(t=n+32*i+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 s=Math.floor(t/32);s>=0;s--){let t=e?this._data[s]:~this._data[s];0!=n&&(t&=~(4294967295<<n),n=0);for(let e=24;0!=t;e-=8,t<<=8){const n=u._lastOnBit[t>>>24];if(n>=0)return n+32*s+e}}return-1}}u._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]),u._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]),u._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"}(s||(s={})),function(t){t.Euclidean="Euclidean"}(i||(i={})),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"}(r||(r={})),function(t){t.TanimotoIntArray="TanimotoIntArray"}(o||(o={})),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 Items"}(h||(h={}));var g=n(384);async function f(){const t=c.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}r.Tanimoto,r.Dice,r.Asymmetric,r.BraunBlanquet,r.Cosine,r.Kulczynski,r.McConnaughey,r.RogotGoldberg,r.Russel,r.Sokal,r.Hamming,r.Euclidean,r.Tanimoto,r.Dice,r.Asymmetric,r.BraunBlanquet,r.Cosine,r.Kulczynski,r.McConnaughey,r.RogotGoldberg,r.Russel,r.Sokal,r.Hamming,r.Euclidean,r.Tanimoto,r.Dice,r.Cosine,r.Tanimoto,r.Asymmetric,r.Cosine,r.Sokal,g.Y.HAMMING,g.Y.LEVENSHTEIN,g.Y.MONOMER_CHEMICAL_DISTANCE,g.Y.NEEDLEMANN_WUNSCH},852:(t,e,n)=>{"use strict";n.d(e,{E1:()=>s,cT:()=>i});const s="p",i=new RegExp(`[rd]\\((\\w)\\)${s}?`,"g")},136:(t,e,n)=>{"use strict";n.d(e,{YF:()=>r,eQ:()=>o,qD:()=>s,y6:()=>l});var s,i=n(923);!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm"}(s||(s={}));const r=", ",o=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,a=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}},l=[new i._u("PT",a.fasta.peptide,.5),new i._u("DNA",a.fasta.dna,.55),new i._u("RNA",a.fasta.rna,.55)]},736:(t,e,n)=>{"use strict";n.d(e,{YF:()=>s.YF,g9:()=>i.g9,gX:()=>i.gX,oB:()=>i.oB,qD:()=>s.qD,y6:()=>s.y6});var s=n(136),i=n(502)},923:(t,e,n)=>{"use strict";n.d(e,{AD:()=>r,_u:()=>i,yK:()=>s});const s="";class i{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class r extends i{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}},502:(t,e,n)=>{"use strict";n.d(e,{Mx:()=>y,o5:()=>I,gX:()=>b,uw:()=>O,oB:()=>x,lh:()=>T,g9:()=>w});var s=n(888),i=n(848),r=n.n(i),o=n(923),a=n(136),l=n(688);class h extends Float32Array{}function c(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class u{static makePalette(t,e=!1,n=u){const s={};return t.forEach((t=>{const n=t[0],i=t[1];n.forEach(((t,n)=>{s[t]=this.colourPalette[i][e?0:n]}))})),new n(s)}constructor(t){this._palette=t}get(t){return this._palette[t]}}u.undefinedColor="rgb(100,100,100)",u.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]};class g extends u{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,g)),this.lesk}static get GrokGroups(){return void 0===this.grokGroups&&(this.grokGroups=this.makePalette([[["C","U"],"yellow"],[["G","P"],"red"],[["A","V","I","L","M","F","Y","W"],"all_green"],[["R","H","K"],"light_blue"],[["D","E"],"dark_blue"],[["S","T","N","Q"],"orange"]],!1,g)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new g({D:"#E60A0A",E:"#E60A0A",C:"#E6E600",M:"#E6E600",K:"#145AFF",R:"#145AFF",S:"#FA9600",T:"#FA9600",F:"#3232AA",Y:"#3232AA",N:"#00DCDC",Q:"#00DCDC",G:"#EBEBEB",L:"#0F820F",V:"#0F820F",I:"#0F820F",A:"#C8C8C8",W:"#B45AB4",H:"#8282D2",P:"#DC9682",others:"#BEA06E"})),this.rasMol}get(t){const e=t in g.aaSynonyms?g.aaSynonyms[t]:t;return super.get(e)}}g.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class f{static getPalette(t="grok"){switch(t){case"grok":return g.GrokGroups;case"lesk":return g.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",s="";for(const i of t)"("==i?e++:")"==i?e--:e?n+=i:s+=i;return isNaN(parseInt(n))?[s,n]:[s,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[s,i]=this.getInnerOuter(t);if(s=s.length>6?`${s.slice(0,3)}...`:s,i=i.length>6?`${i.slice(0,3)}...`:i,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,i,1]:[this.undefinedColor,s,i,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,i,2]:[this.undefinedColor,s,i,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,i,3]:[this.undefinedColor,s,i,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,i,4]:[this.undefinedColor,s,i,4]}return[this.undefinedColor,s,i,0]}}f.SemType="Aminoacids",f.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",f.undefinedColor="rgb(100,100,100)",f.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},f.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},f.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},f.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class d{}d.SemType="Nucleotides",d.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",d.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class p{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class m{}class C extends m{static buildPalette(){return[].concat(...Object.values(u.colourPalette))}get(t){const e=p.hashCode(t)%C.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=s.Color.fromHtml(t),n=s.Color.g(e),i=s.Color.r(e),r=s.Color.b(e),o=Math.sqrt(Math.pow(0-i,2)+Math.pow(0-n,2)+Math.pow(0-r,2));return o>210?`rgb(${i/o*210},${n/o*210},${r/o*210})`:s.Color.toRgb(e)}(C.palette[e])}}C.palette=C.buildPalette();class y{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}constructor(t,e){this.mList=t,this.gapOriginalMonomer=e}}class A{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(t){return this.getOriginal(t)===l.oh[a.qD.FASTA]}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.isGap(t)?o.yK:this.seqS[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.seqS[t]}constructor(t){this.seqS=t}}const x=t=>{const e=r()(t.toString().matchAll(a.eQ)).map((t=>t[2]??t[1])).toArray();return new y(e,l.oh[a.qD.FASTA])},T=t=>t?new A(t):new y([],l.oh[a.qD.FASTA]);function b(t,e=void 0){return n=>{if(n){const s=n.replaceAll('"-"',"").replaceAll("'-'","").split(t,e);return new y(s,l.oh[a.qD.SEPARATOR])}return new y([],l.oh[a.qD.SEPARATOR])}}const E=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,_=/\[([^\[\]]+)]/g,w=t=>{E.lastIndex=0;const e=E.exec(t.toString()),n=e?e[2]:null,s=n?n.split("."):[];return new y(s.map((t=>{_.lastIndex=0;const e=_.exec(t);return e&&e.length>=2?e[1]:t})),l.oh[a.qD.HELM])},N=/([^\W_]+)/g;function O(t,e){if(t.length<=e)return t;const n=t.match(N),s=t.length>e||(n?.length??0)>1,i=n?.[0]??" ";return s?i.substring(0,e-1)+"…":i}function I(t,e,n="-"){const s=e.map((e=>{const s=function(t,e,n="-"){const s=new Set([...new Set(Object.keys(t)),...e]);s.delete(n);const i=[],r=[];for(const n of s)i.push(n in t?t[n]:0),r.push(e.has(n)?1:0);const o=new h(i),a=new h(r);return function(t,e){if(t.length!=e.length)throw new Error("The dimensionality of the vectors must match");let n=0;for(let s=0;s<t.length;s++)n+=t[s]*e[s];return n}(o,a)/(c(o)*c(a))}(t,e.alphabet,n);return new o.AD(e,t,s)}));let i;const r=Math.max(...s.map((t=>t.similarity>t.cutoff?t.similarity:-1)));return i=r>0?s.find((t=>t.similarity===r)).name:"UN",i}},688:(t,e,n)=>{"use strict";n.d(e,{YL:()=>d,oh:()=>f});var s=n(888),i=n(848),r=n.n(i),o=n(736),a=n(923),l=n(502),h=n(384),c=n(460),u=n(852);const g=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},f={[o.qD.FASTA]:"-",[o.qD.SEPARATOR]:"",[o.qD.HELM]:"*"};class d{constructor(t){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,t.type!==s.TYPE.STRING)throw new Error(`Unexpected column type '${t.type}', must be '${s.TYPE.STRING}'.`);this._column=t;const e=this._column.getTag(s.TAGS.UNITS);if(null==e)throw new Error("Units are not specified in column");if(this._units=e,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?f[o.qD.FASTA]:this.isHelm()?f[o.qD.HELM]:f[o.qD.SEPARATOR],!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())d.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag("separator");d.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(s.TAGS.UNITS)}'.`);d.setUnitsToHelmColumn(this)}if(!this.column.tags.has(".alphabetIsMultichar"))if(this.isHelm())this.column.setTag(".alphabetIsMultichar","true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '.alphabetIsMultichar' is mandatory.`);this.notationProvider=this.column.temp[g.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(t){if(t.column.semType!==s.SEMTYPE.MACROMOLECULE||t.column.getTag(s.TAGS.UNITS)!==o.qD.FASTA)throw new Error(`The column of notation '${o.qD.FASTA}' must be '${s.SEMTYPE.MACROMOLECULE}'.`);t.column.setTag(s.TAGS.UNITS,o.qD.FASTA),d.setTags(t)}static setUnitsToSeparatorColumn(t,e){if(t.column.semType!==s.SEMTYPE.MACROMOLECULE||t.column.getTag(s.TAGS.UNITS)!==o.qD.SEPARATOR)throw new Error(`The column of notation '${o.qD.SEPARATOR}' must be '${s.SEMTYPE.MACROMOLECULE}'.`);if(!e)throw new Error(`The column of notation '${o.qD.SEPARATOR}' must have the separator tag.`);t.column.setTag(s.TAGS.UNITS,o.qD.SEPARATOR),t.column.setTag("separator",e),d.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==s.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${o.qD.HELM}' must be '${s.SEMTYPE.MACROMOLECULE}'`);t.column.setTag(s.TAGS.UNITS,o.qD.HELM),d.setTags(t)}static setTags(t){const e=t.column.getTag(s.TAGS.UNITS),n=t.stats;if(Object.keys(n.freq).some((t=>t.length>1)),[o.qD.FASTA,o.qD.SEPARATOR].includes(e)){if(!t.column.getTag("alphabet")&&0===Object.keys(n.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag("aligned");null===e&&(e=n.sameLength?"SEQ.MSA":"SEQ",t.column.setTag("aligned",e));let s=t.column.getTag("alphabet");if(null===s&&(s=(0,l.o5)(n.freq,o.y6),t.column.setTag("alphabet",s)),"UN"===s){const e=Object.keys(n.freq).length,s=Object.keys(n.freq).some((t=>t.length>1));t.column.setTag(".alphabetSize",e.toString()),t.column.setTag(".alphabetIsMultichar",s?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const t=this.column.getTag("separator")??void 0;if(this.notation===o.qD.SEPARATOR&&void 0===t)throw new Error(`Separator is mandatory for column '${this.column.name}' of notation '${this.notation}'.`);return t}get aligned(){const t=this.column.getTag("aligned");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag("alphabet");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(".isHelmCompatible")}getAlphabetSize(){if(this.notation==o.qD.HELM||"UN"==this.alphabet){const t=this.column.getTag(".alphabetSize");let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case"PT":return 20;case"DNA":case"RNA":return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===o.qD.HELM||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}getSplitted(t){if(this.cached){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let e=this._splitted[t]?this._splitted[t].deref():void 0;if(!e){const n=this.column.get(t);e=this.splitter(n),this._splitted[t]=new WeakRef(e)}return e}{const e=this.column.get(t);return this.splitter(e)}}get stats(){if(null===this._stats){const t={};let e=!0,n=null;const s=this.column.length;for(let i=0;i<s;++i){const s=this.getSplitted(i);null==n?n=s.length:s.length!==n&&(e=!1);for(const e of s.canonicals)e in t||(t[e]=0),t[e]+=1}this._stats={freq:t,sameLength:e}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...r().count(0).take(this.column.length).map((t=>this.getSplitted(t).length)))),this._maxLength}get posList(){if(null===this._posList){const t=this.column.getTag(".positionNames");this._posList=t?t.split(o.YF).map((t=>t.trim())):r().count(1).take(this.maxLength).map((t=>t.toString())).toArray()}return this._posList}isFasta(){return this.notation===o.qD.FASTA}isSeparator(){return this.notation===o.qD.SEPARATOR}isHelm(){return this.notation===o.qD.HELM}isRna(){return"RNA"===this.alphabet}isDna(){return"DNA"===this.alphabet}isPeptide(){return"PT"===this.alphabet}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(t){return!t||t===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(o.qD.FASTA))return o.qD.FASTA;if(this.units.toLowerCase().startsWith(o.qD.SEPARATOR))return o.qD.SEPARATOR;if(this.units.toLowerCase().startsWith(o.qD.HELM))return o.qD.HELM;throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`)}getHelmWrappers(){return[this.isDna()||this.isRna()||this.isHelmCompatible()?"RNA1{":"PEPTIDE1{",this.isDna()?"d(":this.isRna()?"r(":"",this.isDna()||this.isRna()?")p":"","}$$$$"]}getNewColumn(t,e,n,i){const r=this.column,a=t.toLowerCase()+"("+r.name+")",l=n??r.dataFrame.columns.getUnusedName(a),h=s.Column.fromList("string",l,i??new Array(this.column.length).fill(""));if(h.semType=s.SEMTYPE.MACROMOLECULE,h.setTag(s.TAGS.UNITS,t),t===o.qD.SEPARATOR){if(!e)throw new Error(`Notation '${o.qD.SEPARATOR}' requires separator value.`);h.setTag("separator",e)}h.setTag(s.TAGS.CELL_RENDERER,"sequence");const c=r.getTag("aligned");c&&h.setTag("aligned",c);let u=r.getTag("alphabet");u||this.notation!==o.qD.HELM||t===o.qD.HELM||(u="UN"),null!=u&&h.setTag("alphabet",u);let g=r.getTag(".alphabetSize");null!=u&&g&&h.setTag(".alphabetSize",g);const f=r.getTag(".alphabetIsMultichar");return null!=u&&void 0!==f&&h.setTag(".alphabetIsMultichar",f),t==o.qD.HELM&&(g=this.getAlphabetSize().toString(),h.setTag(".alphabetSize",g)),h}getNewColumnFromList(t,e){return this.getNewColumn(this.notation,this.separator,t,e)}static getNewColumn(t){const e=d.forColumn(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),[o.qD.FASTA,o.qD.SEPARATOR,o.qD.HELM].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,e,n){if(!d.unitsStringIsValid(n))throw new Error("Invalid format of 'units' parameter");const i=s.Column.fromList("string",e,new Array(t).fill(""));return i.semType=s.SEMTYPE.MACROMOLECULE,i.setTag(s.TAGS.UNITS,n),i}getSplitter(t){let e=null;if(e=this.notationProvider?this.notationProvider.splitter:null,e)return e;if(this.units.toLowerCase().startsWith(o.qD.FASTA))return null===this.column.getTag("alphabet")||this.getAlphabetIsMultichar()?o.oB:l.lh;if(this.units.toLowerCase().startsWith(o.qD.SEPARATOR))return(0,o.gX)(this.separator,t);if(this.units.toLowerCase().startsWith(o.qD.HELM))return o.g9;throw new Error(`Unexpected units ${this.units} .`)}split(t){return this.splitter(t)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");return this.isMsa()?h.Y.HAMMING:(this.alphabet,h.Y.LEVENSHTEIN)}getDistanceFunction(){return h.S[this.getDistanceFunctionName()]()}async 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this._joiner||(this._joiner=this.getJoiner()),this._joiner}getJoiner(t){const e=t?t.notation:this.notation,n=t?t.separator:this.separator;let s;const i=this;switch(e){case o.qD.FASTA:s=function(t){return i.joinToFasta(t,i.isHelm())};break;case o.qD.SEPARATOR:if(!n)throw new Error(`Separator is mandatory for notation '${e}'.`);s=function(t){return p(t,n,i.isHelm())};break;case o.qD.HELM:{const t="DNA"===i.alphabet||"RNA"===i.alphabet,e=i.getHelmWrappers();s=function(n){return m(n,e,t)};break}default:throw new Error(`Unexpected notation '${e}'.`)}return s}getConverter(t,e=void 0){if(t===o.qD.SEPARATOR&&!e)throw new Error(`Target separator is not specified for target units '${o.qD.SEPARATOR}'.`);const n=this;if(t===o.qD.FASTA)return function(t){return n.convertToFasta(t)};if(t===o.qD.HELM)return function(t){return n.convertToHelm(t)};if(t===o.qD.SEPARATOR)return function(t){return n.convertToSeparator(t,e)};throw new Error}static forColumn(t){let e=t.temp[g.seqHandler];return 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pairsOfBondedAtoms(){var t;return null!==(t=this._pairsOfBondedAtoms)&&void 0!==t||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var t;return null!==(t=this._bondTypes)&&void 0!==t||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:t,bondCount:e}=this.parseAtomAndBondCounts();this._atomCount=t,this._bondCount=e}getNextColumnIdx(t){for(;!this.isWhitespace(t);)++t;for(;this.isWhitespace(t);)++t;return t}shiftIdxToSpecifiedColumn(t,e){let n=t;const s=this.isWhitespace(n)?e:e-1;for(let t=0;t<s;t++)n=this.getNextColumnIdx(n);return n}parseAtomTypes(){const t=this.atomCount,e=new Array(t);let n=this.getAtomBlockIdx();for(let s=0;s<t;s++)n=this.shiftIdxToAtomType(n),e[s]=this.parseAtomType(n),n=this.getNextLineIdx(n);return e}parseAtomCoordinates(){const t=new Float32Array(this.atomCount),e=new Float32Array(this.atomCount),n=new Float32Array(this.atomCount);let s=this.getAtomBlockIdx();for(let i=0;i<this.atomCount;i++){s=this.shiftIdxToXColumn(s);for(const r of[t,e,n])r[i]=this.parseFloatValue(s),s=this.getNextColumnIdx(s);s=this.getNextLineIdx(s)}return{x:t,y:e,z:n}}parseBondedAtomPairs(){const t=new Array(this.bondCount);let e=this.getBondBlockIdx();for(let n=0;n<this.bondCount;n++){e=this.shiftIdxToBondedAtomsPair(e);const s=new Uint16Array(2);s[0]=this.parseIntValue(e),e=this.getNextColumnIdx(e),s[1]=this.parseIntValue(e),t[n]=s,e=this.getNextLineIdx(e)}return t}parseBondTypes(){const t=this.bondCount,e=new Uint16Array(t);let n=this.getBondBlockIdx();for(let s=0;s<t;s++)n=this.shiftIdxToBondType(n),e[s]=this.parseIntValue(n),n=this.getNextLineIdx(n);return e}isWhitespace(t){const e=this.fileContent[t];return" "===e||"\t"===e}getNextLineIdx(t){return"\n"!==this.fileContent[t]?this.fileContent.indexOf("\n",t)+1:t+1}parseFloatValue(t){return this.parseNumericValue(parseFloat,t)}parseIntValue(t){return this.parseNumericValue(parseInt,t)}parseNumericValue(t,e){let n=e+1;for(;!this.isWhitespace(n);)++n;return t(this.fileContent.substring(e,n))}}class j extends K{constructor(t){super(t),this.init(t)}init(t){super.init(t)}parseAtomType(t){let e=t,n=e;return this.isQuote(e)?(n=this.getNextIdenticalChar(e),e++):n=this.fileContent.indexOf(" ",n),this.fileContent.substring(e,n)}isQuote(t){const e=this.fileContent[t].charCodeAt(0);return 39===e||34===e}getNextIdenticalChar(t){const e=this.fileContent[t];return e?this.fileContent.indexOf(e,t+1):-1}isQuery(){return this.isQueryOrFragment(((t,e)=>{return 39===t||34===t||76===t&&!((n=this.fileContent.charCodeAt(e+1))>64&&n<91||n>96&&n<123);var n}))}isFragment(){return this.isQueryOrFragment((t=>82===t||42===t))}isQueryOrFragment(t){const e=this.atomCount;let n=this.getAtomBlockIdx();for(let s=0;s<e;s++){if(n=this.shiftIdxToAtomType(n),t(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}class z extends j{constructor(t){super(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map,e=this.fileContent.split("\n");e.filter((t=>t.startsWith(q.RGP_LINE_START))).forEach((e=>{const n=this.getAtomIdxToRgpIdxList(e);for(const[e,s]of n){if(t.has(e))throw new Error(`R group ${e} is already in the map`);t.set(e,s)}}));const n=e.map(((t,e)=>{if(t.startsWith(q.ATOM_ALIAS_LINE_START))return e})).filter((t=>void 0!==t)),s=n.map((t=>e[t])),i=n.map((t=>e[t+1]));s.forEach(((e,n)=>{const s=parseInt(e.split(/\s+/)[1])-1,r=parseInt(i[n].substring(1));if(t.has(r))throw new Error(`R group ${r} is already in the map`);t.set(r,s)}));const r=this.getRGroupAtomicIndices().filter((e=>!Array.from(t.values()).includes(e)));if(0!==r.length)throw new Error(`Unaccounted R group indices: ${r}`);return t}getAtomIdxToRgpIdxList(t){const e=t.split(/\s+/).filter((t=>t)).slice(3).map((t=>parseInt(t))),n=new Array(e.length/2);for(let t=0;t<e.length;t+=2)n[t/2]=[e[t+1],e[t]-1];return n}getRGroupAtomicIndices(){return this.atomTypes.map(((t,e)=>{if(t.includes("R#"))return e})).filter((t=>void 0!==t))}static isValidMolfile(t){return-1!==t.indexOf(q.TYPE)&&-1!==t.indexOf(q.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,q.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<q.NUM_OF_HEADER_LINES;++e)t=this.getNextLineIdx(t);return t}getAtomBlockIdx(){let t=this.getCountsLineIdx();return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){return this.getNextColumnIdx(t)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,q.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,q.BOND_TYPE_COL)}getBondBlockIdx(){let t=this.getAtomBlockIdx();for(let e=0;e<this.atomCount;e++)t=this.getNextLineIdx(t);return t}parseAtomAndBondCounts(){let t=this.getCountsLineIdx(),e=t+q.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=q.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class Q extends j{constructor(t){super(t),this.init(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map;return this.getAtomLines().forEach(((e,n)=>{const s=e.match(/RGROUPS=\(([\d\s]+)\)/);if(s){const e=s[1].split(/\s+/).map((t=>parseInt(t)));if(e.length>2)throw new Error(`R group data ${e} has more than 2 elements`);const i=e[1];if(t.has(i))throw new Error(`R group ${i} is already in the map`);t.set(i,n)}})),t}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M V30 BEGIN BOND"))}static isValidMolfile(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M V30 COUNTS ")+14,e=this.fileContent.indexOf(" ",t+1);const n=parseInt(this.fileContent.substring(t,e));return t=e+1,e=this.fileContent.indexOf(" ",t+1),{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class J{constructor(){}static getInstance(t){if(J.isMolfileV2K(t))return new z(t);if(J.isMolfileV3K(t))return new Q(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return z.isValidMolfile(t)}static isMolfileV3K(t){return Q.isValidMolfile(t)}}async function X(t,e=5e3){await P(100),await function(t,e,n,s=0,i="timeout"){return r(this,void 0,void 0,(function*(){return new Promise(((r,o)=>{const a=t.subscribe((t=>{try{e(t),r("OK")}catch(t){o(t)}a.unsubscribe(),clearTimeout(l)})),l=setTimeout((()=>{a.unsubscribe(),o(i)}),s);n()}))}))}(t.onAfterDrawContent,(()=>{}),(()=>{t.invalidate()}),e)}O("getMolfiles",(()=>{let n,s;I((async()=>{n=await(0,H.wW)(),s=await B(),await V(),await n.loadLibraries(!0)})),S((async()=>{await U(s),await n.loadLibraries(!0)})),b("linear1",(async()=>{const n=t.DataFrame.fromCsv("Helm, atoms, bonds\nPEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV}$$$$,11,10\nPEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV}$$$$,11,10\nPEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$$,9,8"),s=n.getCol("Helm"),i=e.shell.addTableView(n);rt.logger.debug("Helm/getMolfiles/linear1, grid awaiting 1"),await X(i.grid,5e3),rt.logger.debug("Helm/getMolfiles/linear1, grid awaited 1");const r=await e.functions.call("Helm:getMolfiles",{col:s});E(r.length,s.length);const o=r.toList().map((t=>J.getInstance(t)));N(o.map((t=>t.atomCount)),n.getCol("atoms").toList()),N(o.map((t=>t.bondCount)),n.getCol("bonds").toList()),rt.logger.debug("Helm/getMolfiles/linear1, grid awaiting 2"),await X(i.grid,5e3),rt.logger.debug("Helm/getMolfiles/linear1, grid awaited 2")}))}));var Z=n(688),tt=n(980);const et={Helm:{seq:"PEPTIDE1{I.H.A.C.T.[Thr_PO3H2].[Aca].[D-Tyr_Et]}|PEPTIDE2{E.A.[meG]}$PEPTIDE1,PEPTIDE2,4:R3-1:R1$$$V2.0",units:Y.qD.HELM,res:{formula:"C58H94N13O21SP","molecular weight":1372.48,"extinction coefficient":1.55}},separator:{seq:"I/H/A/C/T/Thr_PO3H2/Aca/D-Tyr_Et",units:Y.qD.SEPARATOR,separator:"/",alphabet:"UN",res:{formula:"C47H77N10O15SP","molecular weight":1085.21,"extinction coefficient":1.55}},separator2:{seq:"meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Aze/dV/E/N////Phe_4Me",units:Y.qD.SEPARATOR,separator:"/",alphabet:"UN",res:{formula:"C91H146N19O25P","molecular weight":1937.21,"extinction coefficient":1.49}},"separator-gaps":{seq:"I/H/A//T/Thr_PO3H2/Aca/D-Tyr_Et",units:Y.qD.SEPARATOR,separator:"/",alphabet:"UN",res:{formula:"C44H72N9O14P","molecular weight":982.07,"extinction coefficient":1.49}},"fasta-PT":{seq:"IHACTTAY",units:Y.qD.FASTA,alphabet:"PT",res:{formula:"C38H58N10O12S","molecular weight":878.99,"extinction coefficient":1.55}},"fasta-DNA":{seq:"ACGTATTCC",units:Y.qD.FASTA,alphabet:"DNA",res:{formula:"C87H113N30O56P9","molecular weight":2753.76,"extinction coefficient":91.74}}};function nt(e,n,s,i,r){const o=t.Column.fromList(t.COLUMN_TYPE.STRING,"seq",[e]);o.semType=t.SEMTYPE.MACROMOLECULE,o.setTag(t.TAGS.UNITS,n),s&&o.setTag("separator",s),i&&o.setTag("alphabet",i);const a=Z.YL.forColumn(o);w((0,tt.C)(e,a),r)}O("properties-widget",(()=>{let t,e=null;I((async()=>{t=await(0,H.wW)(),e=B(),await V(),await t.loadLibraries(!0)})),S((async()=>{await U(e),await t.loadLibraries(!0)}));for(const[t,e]of Object.entries(et))b(t,(async()=>{nt(e.seq,e.units,e.separator,e.alphabet,e.res)}))}));var st=n(52);async function it(t,e){N((0,st.w)(t),e)}O("getAllParts",(()=>{const t={peptideSimpleSingleChar:{seq:"PEPTIDE1{L.V.A}$$$$",tgt:["PEPTIDE1{","L",".","V",".","A","}$$$$"]},peptideSimpleMultiChar:{seq:"PEPTIDE1{[Ac].V.A}$$$$",tgt:["PEPTIDE1{[","Ac","].","V",".","A","}$$$$"]}};for(const[e,n]of Object.entries(t))b(`${e}`,(async()=>{await it(n.seq,n.tgt)}))}));const rt=new t.Package;async function ot(n,s,o){const a=await function(n){var s,o,a,y,A,b,_;return r(this,void 0,void 0,(function*(){const w=null===(o=null===(s=e.functions.getCurrentCall())||void 0===s?void 0:s.func)||void 0===o?void 0:o.package;yield function(n,s){var o;return r(this,void 0,void 0,(function*(){const s=n.id;if(C[s])return;const a=g;if(void 0!==a[f]||void 0!==a[d]||Object.keys(a).find((t=>t.startsWith(f)||t.startsWith(m))))return void(C[s]=!0);if("DevTools"===n.name){const e=t.Func.find({tags:["dartTest"]});for(const t of e){const e=t.name.split(/\s*\|\s*/g),n=null!==(o=e.pop())&&void 0!==o?o:t.name,s=e.length?m+": "+e.join(": "):m;void 0===a[s]&&(a[s]={tests:[],clear:!0}),a[s].tests.push(new T(s,n,(()=>r(this,void 0,void 0,(function*(){return yield t.apply()}))),{isAggregated:t.outputs.length>0,timeout:3e5}))}}const l=[],h=[],c=[],u=yield e.dapi.functions.filter(`package.id = "${s}"`).list(),y=new RegExp(/skip:\s*([^,\s]+)|wait:\s*(\d+)|cat:\s*([^,\s]+)|timeout:\s*(\d+)/g);for(const t of u){const n=t.options.test,s=t.options.demoPath;if(n&&Array.isArray(n)&&n.length)for(let s=0;s<n.length;s++){const i=n[s].matchAll(y),o={};Array.from(i).forEach((t=>{t[0].startsWith("skip")?o.skip=t[1]:t[0].startsWith("wait")?o.wait=parseInt(t[2]):t[0].startsWith("cat")?o.cat=t[3]:t[0].startsWith("timeout")&&(o.timeout=parseInt(t[4]))}));const h=new T(f,1===n.length?t.name:`${t.name} ${s+1}`,(()=>r(this,void 0,void 0,(function*(){const i=yield e.functions.eval(L(n[s],t));if(o.wait&&(yield P(o.wait)),"boolean"==typeof i&&!i)throw`Failed: ${n[s]}, expected true, got ${i}`}))),{skipReason:o.skip,timeout:o.timeout});if(o.cat){const t=f+": "+o.cat;h.category=t,void 0===a[t]&&(a[t]={tests:[],clear:!0}),a[t].tests.push(h)}else l.push(h)}if(s){const n=t.options.demoWait?parseInt(t.options.demoWait):void 0,s=new T(d,t.friendlyName,(()=>r(this,void 0,void 0,(function*(){if(e.shell.lastError="",yield t.apply(),yield P(n||2e3),e.shell.lastError)throw new Error(e.shell.lastError)}))),{skipReason:t.options.demoSkip});h.push(s)}if(t.hasTag("semTypeDetector")){const e=new T(p,t.friendlyName,(()=>r(this,void 0,void 0,(function*(){const e=[];for(const n of i.clone().columns){const s=yield t.apply([n]);e.push(s||n.semType)}E(e.filter((t=>t)).length,1)}))),{skipReason:t.options.skipTest});c.push(e)}}C[s]=!0,l.length&&(a[f]={tests:l,clear:!0}),h.length&&(a[d]={tests:h,clear:!0}),c.length&&(a[p]={tests:c,clear:!1})}))}(w);const N=[];console.log("Running tests"),null!=n||(n={}),null!==(a=(_=n).testContext)&&void 0!==a||(_.testContext=new x),e.shell.lastError="";const O=[],I=function(){const t=[];return console.log=(...e)=>{t.push(...e),l(...e)},console.info=(...e)=>{t.push(...e),h(...e)},console.warn=(...e)=>{t.push(...e),c(...e)},console.error=(...e)=>{t.push(...e),u(...e)},t}();try{for(const[s,i]of Object.entries(g)){if((null==n?void 0:n.category)&&!s.toLowerCase().startsWith(null==n?void 0:n.category.toLowerCase())||(null===(y=n.exclude)||void 0===y?void 0:y.some((t=>s.startsWith(t)))))continue;l(`Started ${s} category`),O.push(s);const r=null===(A=i.tests)||void 0===A?void 0:A.every((t=>{var e;return null===(e=t.options)||void 0===e?void 0:e.skipReason}));try{i.before&&!r&&(yield i.before())}catch(t){i.beforeStatus=M(t)}const o=null!==(b=i.tests)&&void 0!==b?b:[],a=[];if(i.clear)for(let s=0;s<o.length;s++)a.push(yield v(o[s],null==n?void 0:n.test,I,i.timeout,w.name,n.verbose)),e.shell.closeAll(),t.Balloon.closeAll();else for(let t=0;t<o.length;t++)a.push(yield v(o[t],null==n?void 0:n.test,I,i.timeout,w.name,n.verbose));const h=a.filter((t=>"skipped"!=t.result));try{i.after&&!r&&(yield i.after())}catch(t){i.afterStatus=M(t)}i.afterStatus&&h.push({category:s,name:"after",result:i.afterStatus,success:!1,ms:0,skipped:!1}),i.beforeStatus&&h.push({category:s,name:"before",result:i.beforeStatus,success:!1,ms:0,skipped:!1}),N.push(...h)}}finally{console.log=l,console.info=h,console.warn=c,console.error=u}if(n.testContext.catchUnhandled&&(yield P(1e3),e.shell.lastError.length>0&&N.push({category:"Unhandled exceptions",name:"exceptions",result:e.shell.lastError,success:!1,ms:0,skipped:!1})),!n.test&&N.length){const s=N.filter((t=>t.success)).length,i=N.filter((t=>t.skipped)).length,r=N.filter((t=>!t.success)),o=w.name;for(const t of O){const n=N.filter((e=>e.category===t)),s=n.filter((t=>!t.success)).length,i={success:0===s,passed:n.filter((t=>t.success)).length,skipped:n.filter((t=>t.skipped)).length,failed:s,type:"package",packageName:o,category:t};e.log.usage(`${o}: ${t}`,i,`category-package ${o}: ${t}`)}if(!n.category){const t={success:0===r.length,passed:s,skipped:i,failed:r.length,type:"package",packageName:o};e.log.usage(o,t,`package-package ${o}`)}if(n.testContext.report){const e=new t.Logger,n="Package @package tested: @successful successful, @skipped skipped, @failed failed tests",o={successful:s,skipped:i,failed:r.length,package:w};for(const t of r)Object.assign(o,{[`${t.category} | ${t.name}`]:t.result});e.log(n,o,"package-tested")}}return N}))}({category:n,test:s,testContext:o});return t.DataFrame.fromObjects(a)}})(),helm_test=s})();
1
+ var helm_test;(()=>{var t={460:(t,e,n)=>{"use strict";n.d(e,{wW:()=>d});var r,s,i,o,l,a,u,h=n(888);n(200);class c{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,r=c._createBuffer(n);if(e)for(let t=0;t<r.length;t++)r[t]=-1;this._data=r,this._length=n}else{if(!(t instanceof Uint32Array))throw new Error("Invalid constructor");this._data=t,this._length=e}}getRawData(){return this._data}assureGoez(t,e){if(t<0)throw new Error(`${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} != ${e._length})`);const n=new c(t._length);n._length=t._length,n._data=c._createBuffer(n._length),n._version=0;const r=t.lengthInInts;for(let s=0;s<r;s++)n._data[s]=t._data[s]&e._data[s];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new c(t.length);e._version=0;for(let n=0;n<e._length;n++)t[n]&&(e._data[Math.floor(n/32)]|=1<<(n%32&31));return e}static fromSeq(t,e){const n=new c(t);for(let r=0;r<t;++r)n.setBit(r,e(r));return n._version=0,n}static fromString(t){return c.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new c(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new c(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let r=0,s=0;for(;e-s>=4;)n._data[r++]=255&t[s]|(255&t[s+1])<<8|(255&t[s+2])<<16|(255&t[s+3])<<24,s+=4;return e-s==3&&(n._data[r]=(255&t[s+2])<<16),e-s==2&&(n._data[r]|=(255&t[s+1])<<8),e-s==1&&(n._data[r]|=255&t[s]),n._version=0,n}toString(){return`${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 c(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,s=!0){if(n&&s&&this.setAll(!e,!1),s)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 c.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 s=Math.min(t,e),i=Math.max(t,e);if(n)for(let t=s;t<=i;t++)this.setTrue(t);else for(let t=s;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 0!=(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+=c._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+=c._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 s=0;for(;s<r-1;s++)for(let e=this._data[s]&t._data[s];0!=e;e>>>=8)n+=c._onBitCount[255&e];let i=this._data[s]&t._data[s];const o=31&this._length;for(0!=o&&(i&=~(4294967295<<o));0!=i;i>>>=8)n+=c._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 s=Math.floor(t/32);s<r;s++){let r=e?this._data[s]:~this._data[s];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=c._firstOnBit[255&r];if(n>=0)return(t=n+32*s+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=c._lastOnBit[t>>>24];if(n>=0)return n+32*r+e}}return-1}}c._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]),c._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]),c._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"}(s||(s={})),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"}(o||(o={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray",t.NumberArray="NumberArray"}(l||(l={})),function(t){t.Difference="Difference"}(a||(a={})),function(t){t.CommonItems="Common Items"}(u||(u={}));var g=n(384);async function d(){const t=h.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}i.Tanimoto,i.Dice,i.Asymmetric,i.BraunBlanquet,i.Cosine,i.Kulczynski,i.McConnaughey,i.RogotGoldberg,i.Russel,i.Sokal,i.Hamming,i.Euclidean,i.Tanimoto,i.Dice,i.Asymmetric,i.BraunBlanquet,i.Cosine,i.Kulczynski,i.McConnaughey,i.RogotGoldberg,i.Russel,i.Sokal,i.Hamming,i.Euclidean,i.Tanimoto,i.Dice,i.Cosine,i.Tanimoto,i.Asymmetric,i.Cosine,i.Sokal,g.Y.HAMMING,g.Y.LEVENSHTEIN,g.Y.MONOMER_CHEMICAL_DISTANCE,g.Y.NEEDLEMANN_WUNSCH,n(852),n(923),n(688)},516:(t,e,n)=>{"use strict";function r(t){let e;switch(t){case"HELM_BASE":case"HELM_SUGAR":case"HELM_LINKER":case"HELM_NUCLETIDE":case"nucleotide":e="RNA";break;case"HELM_AA":e="PEPTIDE";break;case"HELM_CHEM":e="CHEM";break;case"HELM_BLOB":e="BLOB";break;default:e="PEPTIDE",console.warn(`Unexpected HelmType '${t}'`)}return e}n.d(e,{y:()=>r})},248:(t,e,n)=>{"use strict";n.d(e,{I5:()=>h,_m:()=>l,y4:()=>u});var r=n(888),s=n(304),i=n(872),o=n(544);class l{constructor(t,e,n){this.backColor=t,this.width=e,this.height=n}}class a{constructor(t,e,n,r){this.name=t,this.props=e,this.onAfterRender=n,this.isPriority=r}}class u{constructor(t,e=3,n=0,r=3,s=1e3){this.logger=t,this.retryLimit=e,this._errorCount=n,this.errorLimit=r,this.taskTimout=s,this.consumerCounter=0,this._busy=!1,this._sweeperHandle=null,this.viewerId=++u.viewerCounter,this._queue=[],this._queueDict={},this._sweepToggle(!1)}toLog(){return`${this.constructor.name}<${this.viewerId}>`}get errorCount(){return this._errorCount}render(t,e,n,r=0){const s=`${this.toLog()}.render()`;if(this.logger.debug(`${s}, start key: ${n?.toString()}`),void 0!==n){if(n in this._queueDict){const t=this._queue.findIndex((t=>t.key===n));this._queue.splice(t,1)}this.logger.debug(`${s}, _queueDict[ key: ${n?.toString()} ] = <task>`),this._queueDict[n]=e}return this.logger.debug(`${s}, _queue.push(), key: ${n?.toString()}`),null===t&&(t=++this.consumerCounter),this._queue.push({consumerId:t,key:n,task:e,tryCount:r,dt:window.performance.now()}),this._busy||(this._sweepToggle(this._busy=!0),this.logger.debug(`${s}, window.requestAnimationFrame() -> this._processQueue() `),window.requestAnimationFrame((()=>{this._processQueue()}))),t}isBusy(t){return this._queue.some((e=>e.consumerId===t))}getTask(){if(0==this._queue.length)return;let t;const e=this._queue[0];if(e.task.isPriority&&!e.task.isPriority()){let n=null;for(let t=0;t<this._queue.length;++t){const r=this._queue[t];if(r.consumerId===e.consumerId&&r.task.isPriority){if(r.task.isPriority()){n=t;break}{const e=this._queue.splice(t);this._queue.push(...e)}}}null!==n&&(t=this._queue.splice(n,1)[0])}return t||(t=this._queue.shift()),t}_processQueue(){const t=`${this.toLog()}._processQueue()`;if(0===this._queue.length)return;this.logger.debug(`${t}, queue: ${JSON.stringify(this._queue.map((t=>t.key)))}`);let e=null;const n=n=>{const r=`${t}.finallyProcessQueue( <- ${n} )`;e&&e.unsubscribe(),this._queue.length>0?(this.logger.debug(`${r}, window.requestAnimationFrame() -> this._processQueue() `),window.requestAnimationFrame((()=>{this._processQueue()}))):(this.logger.debug(`${r}, this._busy = false`),this._sweepToggle(this._busy=!1))},r=this.getTask();if(!r)return this.logger.error(`${t}, queueItem = undefined `),void n("no queue item");const{consumerId:s,key:o,task:l,tryCount:a,dt:u}=r;if(void 0!==o&&(this.logger.debug(`${t}, key: ${o.toString()}`),delete this._queueDict[o]),a>this.retryLimit)return this.logger.warning(`${t}, skip task, key: ${o?.toString()}, tryCount: ${a}`),void n("try count limit");let h,c=!1;const g=window.setTimeout((()=>{c||(this.logger.warning(`${t}.timeoutHandle(), not handled, key: ${o?.toString()}.\n The .requestRender() overridden method must call renderHandler callback from args.`),this._errorCount+=1,this.render(s,l,o,a+1),n("timeout"))}),1e3);this.requestRender(o,l,(e=>{this.logger.debug(`${t}.renderHandler(), key: ${o?.toString()}`),this.onRendered(o,l,h,e)&&(c=!0,window.clearTimeout(g),n("render"))})).then((n=>{const r=`${t}, requestRender().then()`;e=n[0],h=n[1];const s=n[2];void 0===h&&console.warn(`${r}, this.requestRender.then() emptyCanvasHash undefined`),s()})).catch((e=>{const r=`${t}, requestRender().catch()`,[u,h]=(0,i.g$)(e);this.logger.error(u,void 0,h),window.clearTimeout(g),this._errorCount+=1,this.render(s,l,o,a+1),n(`${r}`)}))}_sweepQueue(){const t=`${this.toLog()}._sweepQueue()`,e=window.performance.now();let n=0;for(let r=this._queue.length-1;r>=0;r--){const{key:s,task:i,dt:o}=this._queue[r];e-o>this.taskTimout&&(this.logger.warning(`${t}, remove task key = ${s?.toString()}`),this._queue.splice(r),delete this._queueDict[s],++n)}this._sweepToggle(this._busy=this._queue.length>0),!this._busy&&n&&this.logger.warning(`${t}, ${n} task(s) had been swept`)}_sweepToggle(t){const e=`${this.toLog()}._sweepToggle( busy = ${t} )`;return t&&null!==this._sweeperHandle&&(this.logger.debug(`${e}, disable queue sweeper`),window.clearInterval(this._sweeperHandle),this._sweeperHandle=null),t||null!==this._sweeperHandle||(this.logger.debug(`${e}, enable queue sweeper`),this._sweeperHandle=window.setInterval((()=>{this._sweepQueue()}),500)),t}}u.viewerCounter=-1;class h extends o.W{constructor(t,e,n,r=!0){super(t,e,n),this.cacheEnabled=r,this.taskQueueMap=new Map,this.imageCache=new 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u=a.getContext("2d");u||(u=s.canvas(a.width,a.height).getContext("2d"),u.drawImage(a,0,0));const h=u.getImageData(0,0,a.width,a.height);this.renderOnGrid(t,new r.Rect(e,n,i,o),l,h),this.imageCache.set(g,h)}finally{t.restore(),this.taskQueueMap.delete(g),0===this.taskQueueMap.size&&this._onRendered.next()}}),this.gridCol?()=>{const t=l.grid;return t.vertScroll.min-1<=l.gridRow&&l.gridRow<=t.vertScroll.max}:void 0);this.taskQueueMap.set(g,h),this.consumerId=c.render(this.consumerId,h,g)}else this.logger.debug(`PdbRenderer.render(), from imageCache[${g}]`),this.renderOnGrid(t,m,l,d);this.consumerId&&c.isBusy(this.consumerId)||this._onRendered.next()}catch(t){const e=t instanceof Error?t.message:t.toString();this.logger.error(`BsV:PdbGridCellRenderer.render() no rethrown error: ${e}`,void 0,t instanceof Error?t.stack:void 0)}finally{t.restore()}}renderCellImageData(t,e,n,r){const i=window.devicePixelRatio,o=s.canvas(r.width,r.height);o.getContext("2d").putImageData(r,0,0);const l=(e.width-1)*i,a=(e.height-1)*i,u=s.canvas(l,a),h=Math.min(l/r.width,a/r.height),c=(l-r.width*h)/2,g=(a-r.height*h)/2,d=u.getContext("2d");d.transform(h,0,0,h,c,g),d.drawImage(o,0,0);const m=d.getImageData(0,0,l,a);return this.renderOnGrid(t,e,n,m),!0}renderOnGrid(t,e,n,s){const i=`renderOnGridCell( gRow = ${n.gridRow} )`,o=`${this.toLog()}.${i}`,l=window.devicePixelRatio;this.logger.debug(`${o}, start`),t.save();try{if(t.resetTransform(),this.gridCol){const t=this.gridCol.grid,r=Math.floor(t.vertScroll.min);e.y=((n.gridRow-r)*t.props.rowHeight+t.colHeaderHeight)*l;let s=0;for(let e=0;e<this.gridCol.idx;e++){const n=t.columns.byIndex(e);s+=n.visible?n.width:0}e.x=(s-t.horzScroll.min)*l}const i=new r.Rect(e.x+l,e.y+l,(e.width-1)*l,(e.height-1)*l);t.beginPath(),t.rect(i.x,i.y,i.width,i.height),t.clip(),t.putImageData(s,e.x+l,e.y+l)}finally{t.restore()}}}},544:(t,e,n)=>{"use strict";n.d(e,{M:()=>o,W:()=>l});var r=n(200),s=n(468),i=n(272);function o(t){let 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r=n(136),s=n(502)},923:(t,e,n)=>{"use strict";n.d(e,{AD:()=>i,_u:()=>s,yK:()=>r});const r="";class s{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class i extends s{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}},502:(t,e,n)=>{"use strict";n.d(e,{Mx:()=>y,o5:()=>O,gX:()=>E,oB:()=>A,lh:()=>x,g9:()=>T});var r=n(888),s=n(848),i=n.n(s),o=n(923),l=n(136),a=n(688);class u extends Float32Array{}function h(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class c{static makePalette(t,e=!1,n=c){const r={};return t.forEach((t=>{const n=t[0],s=t[1];n.forEach(((t,n)=>{r[t]=this.colourPalette[s][e?0:n]}))})),new n(r)}constructor(t){this._palette=t}get(t){return this._palette[t]}}c.undefinedColor="rgb(100,100,100)",c.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]};class g extends c{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,g)),this.lesk}static get GrokGroups(){return void 0===this.grokGroups&&(this.grokGroups=this.makePalette([[["C","U"],"yellow"],[["G","P"],"red"],[["A","V","I","L","M","F","Y","W"],"all_green"],[["R","H","K"],"light_blue"],[["D","E"],"dark_blue"],[["S","T","N","Q"],"orange"]],!1,g)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new g({D:"#E60A0A",E:"#E60A0A",C:"#E6E600",M:"#E6E600",K:"#145AFF",R:"#145AFF",S:"#FA9600",T:"#FA9600",F:"#3232AA",Y:"#3232AA",N:"#00DCDC",Q:"#00DCDC",G:"#EBEBEB",L:"#0F820F",V:"#0F820F",I:"#0F820F",A:"#C8C8C8",W:"#B45AB4",H:"#8282D2",P:"#DC9682",others:"#BEA06E"})),this.rasMol}get(t){const e=t in g.aaSynonyms?g.aaSynonyms[t]:t;return super.get(e)}}g.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class d{static getPalette(t="grok"){switch(t){case"grok":return g.GrokGroups;case"lesk":return g.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",r="";for(const s of t)"("==s?e++:")"==s?e--:e?n+=s:r+=s;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[r,s]=this.getInnerOuter(t);if(r=r.length>6?`${r.slice(0,3)}...`:r,s=s.length>6?`${s.slice(0,3)}...`:s,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,s,1]:[this.undefinedColor,r,s,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,s,2]:[this.undefinedColor,r,s,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,s,3]:[this.undefinedColor,r,s,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,s,4]:[this.undefinedColor,r,s,4]}return[this.undefinedColor,r,s,0]}}d.SemType="Aminoacids",d.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",d.undefinedColor="rgb(100,100,100)",d.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},d.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},d.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},d.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class m{}m.SemType="Nucleotides",m.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",m.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class p{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class f{}class C extends f{static buildPalette(){return[].concat(...Object.values(c.colourPalette))}get(t){const e=p.hashCode(t)%C.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=r.Color.fromHtml(t),n=r.Color.g(e),s=r.Color.r(e),i=r.Color.b(e),o=Math.sqrt(Math.pow(0-s,2)+Math.pow(0-n,2)+Math.pow(0-i,2));return o>210?`rgb(${s/o*210},${n/o*210},${i/o*210})`:r.Color.toRgb(e)}(C.palette[e])}}C.palette=C.buildPalette();class y{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.mList[t]}constructor(t,e){this.mList=t,this.gapOriginalMonomer=e}}class b{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(t){return this.getOriginal(t)===a.oh[l.qD.FASTA]}getCanonical(t){if(this.length<=t)throw new Error("Index out of bounds");return this.isGap(t)?o.yK:this.seqS[t]}getOriginal(t){if(this.length<=t)throw new Error("Index out of bounds");return this.seqS[t]}constructor(t){this.seqS=t}}const A=t=>{const e=i()(t.toString().matchAll(l.eQ)).map((t=>t[2]??t[1])).toArray();return new y(e,a.oh[l.qD.FASTA])},x=t=>t?new b(t):new y([],a.oh[l.qD.FASTA]);function E(t,e=void 0){return n=>{if(n){let r;const s=new RegExp(String.raw`"-"|'-'|[^${t}]+`,"g");if(void 0!==e){s.lastIndex=0,r=new Array(e);let t=null,i=0;for(;null!==(t=s.exec(n))&&i<e;)r[i++]=t[0].replace('"-"',"").replace("'-'","");r.splice(i)}else r=n.replaceAll('"-"',"").replaceAll("'-'","").split(t,e);return new y(r,a.oh[l.qD.SEPARATOR])}return new y([],a.oh[l.qD.SEPARATOR])}}const _=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,w=/\[([^\[\]]+)]/g,T=t=>{_.lastIndex=0;const e=_.exec(t.toString()),n=e?e[2]:null,r=n?n.split("."):[];return new y(r.map((t=>{w.lastIndex=0;const e=w.exec(t);return e&&e.length>=2?e[1]:t})),a.oh[l.qD.HELM])};function O(t,e,n="-"){const r=e.map((e=>{const r=function(t,e,n="-"){const r=new Set([...new Set(Object.keys(t)),...e]);r.delete(n);const s=[],i=[];for(const n of r)s.push(n in t?t[n]:0),i.push(e.has(n)?1:0);const o=new u(s),l=new u(i);return function(t,e){if(t.length!=e.length)throw new Error("The dimensionality of the vectors must match");let n=0;for(let r=0;r<t.length;r++)n+=t[r]*e[r];return n}(o,l)/(h(o)*h(l))}(t,e.alphabet,n);return new o.AD(e,t,r)}));let s;const i=Math.max(...r.map((t=>t.similarity>t.cutoff?t.similarity:-1)));return s=i>0?r.find((t=>t.similarity===i)).name:"UN",s}},688:(t,e,n)=>{"use strict";n.d(e,{YL:()=>m,oh:()=>d});var r=n(888),s=n(848),i=n.n(s),o=n(736),l=n(923),a=n(502),u=n(384),h=n(460),c=n(852);const g=new class{constructor(){this.seqHandler="seq-handler",this.notationProvider="seq-handler.notation-provider"}},d={[o.qD.FASTA]:"-",[o.qD.SEPARATOR]:"",[o.qD.HELM]:"*"};class m{constructor(t){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,t.type!==r.TYPE.STRING)throw new Error(`Unexpected column type '${t.type}', must be '${r.TYPE.STRING}'.`);this._column=t;const e=this._column.getTag(r.TAGS.UNITS);if(null==e)throw new Error("Units are not specified in column");if(this._units=e,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?d[o.qD.FASTA]:this.isHelm()?d[o.qD.HELM]:d[o.qD.SEPARATOR],!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())m.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag("separator");m.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(r.TAGS.UNITS)}'.`);m.setUnitsToHelmColumn(this)}if(!this.column.tags.has(".alphabetIsMultichar"))if(this.isHelm())this.column.setTag(".alphabetIsMultichar","true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '.alphabetIsMultichar' is mandatory.`);this.notationProvider=this.column.temp[g.notationProvider]??null,this.columnVersion=this.column.version}static setUnitsToFastaColumn(t){if(t.column.semType!==r.SEMTYPE.MACROMOLECULE||t.column.getTag(r.TAGS.UNITS)!==o.qD.FASTA)throw new Error(`The column of notation '${o.qD.FASTA}' must be '${r.SEMTYPE.MACROMOLECULE}'.`);t.column.setTag(r.TAGS.UNITS,o.qD.FASTA),m.setTags(t)}static setUnitsToSeparatorColumn(t,e){if(t.column.semType!==r.SEMTYPE.MACROMOLECULE||t.column.getTag(r.TAGS.UNITS)!==o.qD.SEPARATOR)throw new Error(`The column of notation '${o.qD.SEPARATOR}' must be '${r.SEMTYPE.MACROMOLECULE}'.`);if(!e)throw new Error(`The column of notation '${o.qD.SEPARATOR}' must have the separator tag.`);t.column.setTag(r.TAGS.UNITS,o.qD.SEPARATOR),t.column.setTag("separator",e),m.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==r.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${o.qD.HELM}' must be '${r.SEMTYPE.MACROMOLECULE}'`);t.column.setTag(r.TAGS.UNITS,o.qD.HELM),m.setTags(t)}static setTags(t){const e=t.column.getTag(r.TAGS.UNITS),n=t.stats;if(Object.keys(n.freq).some((t=>t.length>1)),[o.qD.FASTA,o.qD.SEPARATOR].includes(e)){if(!t.column.getTag("alphabet")&&0===Object.keys(n.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag("aligned");null===e&&(e=n.sameLength?"SEQ.MSA":"SEQ",t.column.setTag("aligned",e));let r=t.column.getTag("alphabet");if(null===r&&(r=(0,a.o5)(n.freq,o.y6),t.column.setTag("alphabet",r)),"UN"===r){const e=Object.keys(n.freq).length,r=Object.keys(n.freq).some((t=>t.length>1));t.column.setTag(".alphabetSize",e.toString()),t.column.setTag(".alphabetIsMultichar",r?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const t=this.column.getTag("separator")??void 0;if(this.notation===o.qD.SEPARATOR&&void 0===t)throw new Error(`Separator is mandatory for column '${this.column.name}' of notation '${this.notation}'.`);return t}get aligned(){const t=this.column.getTag("aligned");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag("alphabet");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(".isHelmCompatible")}getAlphabetSize(){if(this.notation==o.qD.HELM||"UN"==this.alphabet){const t=this.column.getTag(".alphabetSize");let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case"PT":return 20;case"DNA":case"RNA":return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===o.qD.HELM||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}getSplitted(t,e){if(this.cached&&void 0===e){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let e=this._splitted[t]?this._splitted[t].deref():void 0;if(!e){const n=this.column.get(t);e=this.splitter(n),this._splitted[t]=new WeakRef(e)}return e}{const n=this.column.get(t);return this.getSplitter(e)(n)}}get stats(){if(null===this._stats){const t={};let e=!0,n=null;const r=this.column.length;for(let s=0;s<r;++s){const r=this.getSplitted(s);null==n?n=r.length:r.length!==n&&(e=!1);for(const e of r.canonicals)e in t||(t[e]=0),t[e]+=1}this._stats={freq:t,sameLength:e}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...i().count(0).take(this.column.length).map((t=>this.getSplitted(t).length)))),this._maxLength}get posList(){if(null===this._posList){const t=this.column.getTag(".positionNames");this._posList=t?t.split(o.YF).map((t=>t.trim())):i().count(1).take(this.maxLength).map((t=>t.toString())).toArray()}return this._posList}isFasta(){return this.notation===o.qD.FASTA}isSeparator(){return this.notation===o.qD.SEPARATOR}isHelm(){return this.notation===o.qD.HELM}isRna(){return"RNA"===this.alphabet}isDna(){return"DNA"===this.alphabet}isPeptide(){return"PT"===this.alphabet}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(t){return!t||t===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(o.qD.FASTA))return o.qD.FASTA;if(this.units.toLowerCase().startsWith(o.qD.SEPARATOR))return o.qD.SEPARATOR;if(this.units.toLowerCase().startsWith(o.qD.HELM))return o.qD.HELM;throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`)}getHelmWrappers(){return[this.isDna()||this.isRna()||this.isHelmCompatible()?"RNA1{":"PEPTIDE1{",this.isDna()?"d(":this.isRna()?"r(":"",this.isDna()||this.isRna()?")p":"","}$$$$"]}getNewColumn(t,e,n,s){const i=this.column,l=t.toLowerCase()+"("+i.name+")",a=n??i.dataFrame.columns.getUnusedName(l),u=r.Column.fromList("string",a,s??new Array(this.column.length).fill(""));if(u.semType=r.SEMTYPE.MACROMOLECULE,u.setTag(r.TAGS.UNITS,t),t===o.qD.SEPARATOR){if(!e)throw new Error(`Notation '${o.qD.SEPARATOR}' requires separator value.`);u.setTag("separator",e)}u.setTag(r.TAGS.CELL_RENDERER,"sequence");const h=i.getTag("aligned");h&&u.setTag("aligned",h);let c=i.getTag("alphabet");c||this.notation!==o.qD.HELM||t===o.qD.HELM||(c="UN"),null!=c&&u.setTag("alphabet",c);let g=i.getTag(".alphabetSize");null!=c&&g&&u.setTag(".alphabetSize",g);const d=i.getTag(".alphabetIsMultichar");return null!=c&&void 0!==d&&u.setTag(".alphabetIsMultichar",d),t==o.qD.HELM&&(g=this.getAlphabetSize().toString(),u.setTag(".alphabetSize",g)),u}getNewColumnFromList(t,e){return this.getNewColumn(this.notation,this.separator,t,e)}static getNewColumn(t){const e=m.forColumn(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),[o.qD.FASTA,o.qD.SEPARATOR,o.qD.HELM].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,e,n){if(!m.unitsStringIsValid(n))throw new Error("Invalid format of 'units' parameter");const s=r.Column.fromList("string",e,new Array(t).fill(""));return s.semType=r.SEMTYPE.MACROMOLECULE,s.setTag(r.TAGS.UNITS,n),s}getSplitter(t){let e=null;if(e=this.notationProvider?this.notationProvider.splitter:null,e)return e;if(this.units.toLowerCase().startsWith(o.qD.FASTA))return null===this.column.getTag("alphabet")||this.getAlphabetIsMultichar()?o.oB:a.lh;if(this.units.toLowerCase().startsWith(o.qD.SEPARATOR))return(0,o.gX)(this.separator,t);if(this.units.toLowerCase().startsWith(o.qD.HELM))return o.g9;throw new Error(`Unexpected units ${this.units} .`)}split(t){return this.splitter(t)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");return this.isMsa()?u.Y.HAMMING:(this.alphabet,u.Y.LEVENSHTEIN)}getDistanceFunction(){return u.S[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const t=(await(0,h.wW)()).getBioLib().getMonomerSymbolsByType("PEPTIDE"),e=new Set(t),n=((0,o.gX)(this.separator),new Set),r=this.column.length,s=this.column.getRawData();for(let t=0;t<r;++t){const r=s[t];if(!(r in n)){n.add(r);const s=this.getSplitted(t);for(const t of s.canonicals)if(!e.has(t))return this.column.setTag(".isHelmCompatible","false"),!1}}return this.column.setTag(".isHelmCompatible","true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(t){return t===o.qD.FASTA}toSeparator(t){return t===o.qD.SEPARATOR}toHelm(t){return t===o.qD.HELM}convertHelmToFastaSeparator(t,e,n,r){r||(r=this.toFasta(e)?d[o.qD.FASTA]:d[o.qD.SEPARATOR]),n||(n=this.toFasta(e)?"":this.separator);const s=t.startsWith("RNA"),i=this.splitter(t),l=[];for(let t=0;t<i.length;++t){let n=i.getOriginal(t);if(s&&(n=n.replace(c.cT,"")),n===d[o.qD.HELM])l.push(r);else if(this.toFasta(e)&&n.length>1){const t="["+n+"]";l.push(t)}else l.push(n)}return l.join(n)}convert(t,e){const n=this.getJoiner({notation:t,separator:e}),r=this.getNewColumn(t,e);return r.init((t=>{const e=this.getSplitted(t);return n(e)})),r}getRegion(t,e,n){const r=this.getNewColumn(this.notation,this.separator);r.name=n;const s=t??0,i=e??this.maxLength-1,l=this.getJoiner(),u=i-s+1,h=d[this.notation];r.init((t=>{const e=this.getSplitted(t),n=new Array(u);for(let t=0;t<u;++t){const r=s+t;n[t]=r<e.length?e.getOriginal(r):h}return l(new a.Mx(n,h))}));const c=t=>{const e=t.split(",").map((t=>t.trim())),n=new Array(u);for(let t=0;t<u;++t){const r=s+t;n[t]=r<e.length?e[r]:"?"}return n.join(o.YF)},g=this.column.getTag(".positionNames");g&&r.setTag(".positionNames",c(g));const m=this.column.getTag(".positionLabels");return m&&r.setTag(".positionLabels",c(m)),r}get joiner(){return this._joiner||(this._joiner=this.getJoiner()),this._joiner}getJoiner(t){const e=t?t.notation:this.notation,n=t?t.separator:this.separator;let r;const s=this;switch(e){case o.qD.FASTA:r=function(t){return s.joinToFasta(t,s.isHelm())};break;case o.qD.SEPARATOR:if(!n)throw new Error(`Separator is mandatory for notation '${e}'.`);r=function(t){return p(t,n,s.isHelm())};break;case o.qD.HELM:{const t="DNA"===s.alphabet||"RNA"===s.alphabet,e=s.getHelmWrappers();r=function(n){return f(n,e,t)};break}default:throw new Error(`Unexpected notation '${e}'.`)}return r}getConverter(t,e=void 0){if(t===o.qD.SEPARATOR&&!e)throw new Error(`Target separator is not specified for target units '${o.qD.SEPARATOR}'.`);const n=this;if(t===o.qD.FASTA)return function(t){return n.convertToFasta(t)};if(t===o.qD.HELM)return function(t){return n.convertToHelm(t)};if(t===o.qD.SEPARATOR)return function(t){return n.convertToSeparator(t,e)};throw new Error}static forColumn(t){let e=t.temp[g.seqHandler];return e&&e.columnVersion===t.version||(e=t.temp[g.seqHandler]=new m(t)),e}joinToFasta(t,e){const n=new Array(t.length);for(let r=0;r<t.length;++r){const s=t.getOriginal(r);let i=t.getOriginal(r);e&&(i=i.replace(c.cT,"$1")),s===l.yK?i=d[o.qD.FASTA]:s===c.E1?i="":i.length>1&&(i="["+i+"]"),n[r]=i}return n.join("")}convertToFasta(t){const e=this.splitter,n=this.isHelm()?this.splitterAsHelmNucl(t):e(t);return this.joinToFasta(n,this.isHelm())}convertToSeparator(t,e){return p(this.isHelm()?this.splitterAsHelmNucl(t):this.splitter(t),e,this.isHelm())}convertToHelm(t){const e=this.getHelmWrappers(),n=t.startsWith("DNA")||t.startsWith("RNA");return f(this.splitter(t),e,n)}splitterAsHelmNucl(t){const e=this.splitter(t),n=new Array(e.length),r=t.startsWith("DNA"),s=t.startsWith("RNA");for(let t=0;t<e.length;++t){let i=e.getOriginal(t);(r||s)&&(i=i.replace(c.cT,"$1"),i=i===c.E1?null:i),n[t]=i||null}return new a.Mx(n.filter((t=>!!t)),d[o.qD.HELM])}}function p(t,e,n){const r=new Array(t.length);for(let e=0;e<t.length;++e){const s=t.getCanonical(e);let i=t.getOriginal(e);n&&(i=i.replace(c.cT,"$1")),s===l.yK?i=d[o.qD.SEPARATOR]:s===c.E1&&(i=""),r[e]=i}return r.join(e)}function f(t,e,n){const[r,s,i,a]=e,u=new Array(t.length);for(let e=0;e<t.length;++e){const r=t.getCanonical(e);let a=t.getOriginal(e);r===l.yK?a=d[o.qD.HELM]:(n&&(a=a.replace(c.cT,"$1")),a=1===a.length?`${s}${a}${i}`:`${s}[${a}]${i}`),u[e]=a}return`${r}${u.join(".")}${a}`}},824:(t,e,n)=>{"use strict";n.d(e,{Cu:()=>o,cF:()=>l,st:()=>i});var r=n(888),s=n(248);class i extends s._m{constructor(t,e,n,r){super(e,n,r),this.helm=t}}class o extends s.y4{}async function l(){const t=r.Func.find({package:"Helm",name:"getHelmService"});if(0===t.length)throw new Error('Package "Helm" must be installed for Helm services.');return(await t[0].prepare().call()).getOutputParamValue()}},384:(t,e,n)=>{"use strict";function r(t={}){const e=function(){if(!t||!t.scoringMatrix||!t.alphabetIndexes)return(t,e)=>t===e?0:1;if(t.scoringMatrix.length!==Object.keys(t.alphabetIndexes).length)throw new Error("Scoring matrix and alphabet indexes should have the same length");const e=t.alphabetIndexes,n=t.scoringMatrix,r=Math.min(...Object.keys(e).map((t=>t.charCodeAt(0))))+1,s=new Float32Array((n.length+r)*(n.length+r));return 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r=null,i=null;const o=new d.Subject;await(0,e.SG)(o,(()=>{}),(()=>{const e={name:"test1",props:{helm:"PEPTIDE1{I.H.A.N.T.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",backColor:t.Color.fromHtml("#FFFFFF"),width:300,height:100},onAfterRender:(t,e)=>{i=e,o.next()}};s.reset(),r=s.render(r,e,0)}),7e3),(0,e.ct)(null!==i,!0,"Helm task aux is null"),(0,e.ct)(i.mol.atoms.length>0,!0,"Polymer mol atoms empty"),(0,e.ct)(i.mol.atoms.length,8),(0,e.ct)(i.mol.bonds.length,7),(0,e.ct)(s.errorCount,0,"There was errors in NglGlService."),(0,e.ct)(null!==r,!0,"consumerId not assigned"),V.logger.debug(`${n}, end`)}),{timeout:1e4})}));var p,f=n(304),C=n(592),y=n.n(C),b=n(736);async function A(t,n=5e3){await(0,e.oL)(100),await(0,e.SG)(t.onAfterDrawContent,(()=>{}),(()=>{t.invalidate()}),n)}(0,e.Gu)("renderers",(()=>{let n,r;(0,e.a8)((async()=>{n=await(0,i.wW)(),r=await h(),await g(),await n.loadLibraries(!0)})),(0,e.iV)((async()=>{await c(r),await n.loadLibraries(!0)})),(0,e.GM)("missedInLib",(async()=>{await async 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MouseEvent("mousemove",{cancelable:!0,bubbles:!0,view:window,button:0,clientX:l.left+a.x,clientY:l.top+a.y}),h=y()(i.root).find("canvas").get()[0];await(0,e.SG)((0,d.fromEvent)(h,"mousemove"),(()=>{V.logger.debug(`Test: event, currentRowIdx=${n.currentRowIdx}`),(0,e.ct)(y()(f.tooltip.root).find("div table.d4-row-tooltip-table tr td canvas").length,1),(0,e.ct)(i.hitTest(a.x,a.y),1)}),(()=>{h.dispatchEvent(u)}),500),await A(r.grid,500)}()}));const s="seq,x,y\nPEPTIDE1{I.H.A.N.T.Thr_PO3H2.Aca.D-Tyr_Et}$$$$,0,0\nRNA1{r(A)p.r(C)p.r(G)p.r(U)p}$$$$,1,0\nRNA1{d(A)p.d(C)p.d(G)p.d(U)p}|PEPTIDE1{I.H.A.N.T.Thr_PO3H2}$$$$,0,1\n"})),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"}(p||(p={}));class x{constructor(t){this.init(t)}init(t){this.fileContent=t.replace(/\r/g,""),this._atomCount=void 0,this._atomTypes=void 0,this._bondCount=void 0,this._bondTypes=void 0,this.xyzAtomCoordinates=void 0,this._pairsOfBondedAtoms=void 0}get atomCount(){return void 0===this._atomCount&&this.setAtomAndBondCounts(),this._atomCount}get bondCount(){return void 0===this._bondCount&&this.setAtomAndBondCounts(),this._bondCount}get x(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var t;return null!==(t=this._atomTypes)&&void 0!==t||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var t;return null!==(t=this._pairsOfBondedAtoms)&&void 0!==t||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var t;return null!==(t=this._bondTypes)&&void 0!==t||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:t,bondCount:e}=this.parseAtomAndBondCounts();this._atomCount=t,this._bondCount=e}getNextColumnIdx(t){for(;!this.isWhitespace(t);)++t;for(;this.isWhitespace(t);)++t;return t}shiftIdxToSpecifiedColumn(t,e){let n=t;const r=this.isWhitespace(n)?e:e-1;for(let t=0;t<r;t++)n=this.getNextColumnIdx(n);return n}parseAtomTypes(){const t=this.atomCount,e=new Array(t);let n=this.getAtomBlockIdx();for(let r=0;r<t;r++)n=this.shiftIdxToAtomType(n),e[r]=this.parseAtomType(n),n=this.getNextLineIdx(n);return e}parseAtomCoordinates(){const t=new Float32Array(this.atomCount),e=new Float32Array(this.atomCount),n=new Float32Array(this.atomCount);let r=this.getAtomBlockIdx();for(let s=0;s<this.atomCount;s++){r=this.shiftIdxToXColumn(r);for(const i of[t,e,n])i[s]=this.parseFloatValue(r),r=this.getNextColumnIdx(r);r=this.getNextLineIdx(r)}return{x:t,y:e,z:n}}parseBondedAtomPairs(){const t=new Array(this.bondCount);let e=this.getBondBlockIdx();for(let n=0;n<this.bondCount;n++){e=this.shiftIdxToBondedAtomsPair(e);const r=new Uint16Array(2);r[0]=this.parseIntValue(e),e=this.getNextColumnIdx(e),r[1]=this.parseIntValue(e),t[n]=r,e=this.getNextLineIdx(e)}return t}parseBondTypes(){const t=this.bondCount,e=new Uint16Array(t);let n=this.getBondBlockIdx();for(let r=0;r<t;r++)n=this.shiftIdxToBondType(n),e[r]=this.parseIntValue(n),n=this.getNextLineIdx(n);return e}isWhitespace(t){const e=this.fileContent[t];return" "===e||"\t"===e}getNextLineIdx(t){return"\n"!==this.fileContent[t]?this.fileContent.indexOf("\n",t)+1:t+1}parseFloatValue(t){return this.parseNumericValue(parseFloat,t)}parseIntValue(t){return this.parseNumericValue(parseInt,t)}parseNumericValue(t,e){let n=e+1;for(;!this.isWhitespace(n);)++n;return t(this.fileContent.substring(e,n))}}class E extends x{constructor(t){super(t),this.init(t)}init(t){super.init(t)}parseAtomType(t){let e=t,n=e;return this.isQuote(e)?(n=this.getNextIdenticalChar(e),e++):n=this.fileContent.indexOf(" ",n),this.fileContent.substring(e,n)}isQuote(t){const e=this.fileContent[t].charCodeAt(0);return 39===e||34===e}getNextIdenticalChar(t){const e=this.fileContent[t];return e?this.fileContent.indexOf(e,t+1):-1}isQuery(){return this.isQueryOrFragment(((t,e)=>{return 39===t||34===t||76===t&&!((n=this.fileContent.charCodeAt(e+1))>64&&n<91||n>96&&n<123);var n}))}isFragment(){return this.isQueryOrFragment((t=>82===t||42===t))}isQueryOrFragment(t){const e=this.atomCount;let n=this.getAtomBlockIdx();for(let r=0;r<e;r++){if(n=this.shiftIdxToAtomType(n),t(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}class _ extends E{constructor(t){super(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map,e=this.fileContent.split("\n");e.filter((t=>t.startsWith(p.RGP_LINE_START))).forEach((e=>{const n=this.getAtomIdxToRgpIdxList(e);for(const[e,r]of n){if(t.has(e))throw new Error(`R group ${e} is already in the map`);t.set(e,r)}}));const n=e.map(((t,e)=>{if(t.startsWith(p.ATOM_ALIAS_LINE_START))return e})).filter((t=>void 0!==t)),r=n.map((t=>e[t])),s=n.map((t=>e[t+1]));r.forEach(((e,n)=>{const r=parseInt(e.split(/\s+/)[1])-1,i=parseInt(s[n].substring(1));if(t.has(i))throw new Error(`R group ${i} is already in the map`);t.set(i,r)}));const i=this.getRGroupAtomicIndices().filter((e=>!Array.from(t.values()).includes(e)));if(0!==i.length)throw new Error(`Unaccounted R group indices: ${i}`);return t}getAtomIdxToRgpIdxList(t){const e=t.split(/\s+/).filter((t=>t)).slice(3).map((t=>parseInt(t))),n=new Array(e.length/2);for(let t=0;t<e.length;t+=2)n[t/2]=[e[t+1],e[t]-1];return n}getRGroupAtomicIndices(){return this.atomTypes.map(((t,e)=>{if(t.includes("R#"))return e})).filter((t=>void 0!==t))}static isValidMolfile(t){return-1!==t.indexOf(p.TYPE)&&-1!==t.indexOf(p.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,p.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<p.NUM_OF_HEADER_LINES;++e)t=this.getNextLineIdx(t);return t}getAtomBlockIdx(){let t=this.getCountsLineIdx();return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){return this.getNextColumnIdx(t)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,p.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,p.BOND_TYPE_COL)}getBondBlockIdx(){let t=this.getAtomBlockIdx();for(let e=0;e<this.atomCount;e++)t=this.getNextLineIdx(t);return t}parseAtomAndBondCounts(){let t=this.getCountsLineIdx(),e=t+p.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=p.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class w extends E{constructor(t){super(t),this.init(t)}getAtomLines(){const t=this.getAtomBlockIdx(),e=this.getBondBlockIdx();return this.fileContent.substring(t,e).split("\n").slice(0,this.atomCount)}getBondLines(){const t=this.getBondBlockIdx();return this.fileContent.substring(t).split("\n").slice(0,this.bondCount)}getRGroupIdToAtomicIdxMap(){const t=new Map;return this.getAtomLines().forEach(((e,n)=>{const r=e.match(/RGROUPS=\(([\d\s]+)\)/);if(r){const e=r[1].split(/\s+/).map((t=>parseInt(t)));if(e.length>2)throw new Error(`R group data ${e} has more than 2 elements`);const s=e[1];if(t.has(s))throw new Error(`R group ${s} is already in the map`);t.set(s,n)}})),t}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M V30 BEGIN BOND"))}static isValidMolfile(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M V30 COUNTS ")+14,e=this.fileContent.indexOf(" ",t+1);const n=parseInt(this.fileContent.substring(t,e));return t=e+1,e=this.fileContent.indexOf(" ",t+1),{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class T{constructor(){}static getInstance(t){if(T.isMolfileV2K(t))return new _(t);if(T.isMolfileV3K(t))return new w(t);throw new Error("Malformed molfile")}static isMolfileV2K(t){return _.isValidMolfile(t)}static isMolfileV3K(t){return w.isValidMolfile(t)}}(0,e.Gu)("getMolfiles",(()=>{let n,r;(0,e.a8)((async()=>{n=await(0,i.wW)(),r=await h(),await g(),await n.loadLibraries(!0)})),(0,e.iV)((async()=>{await c(r),await n.loadLibraries(!0)})),(0,e.GM)("linear1",(async()=>{const n=t.DataFrame.fromCsv("Helm, atoms, bonds\nPEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV}$$$$,11,10\nPEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV}$$$$,11,10\nPEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$$,9,8"),r=n.getCol("Helm"),s=o.shell.addTableView(n);V.logger.debug("Helm/getMolfiles/linear1, grid awaiting 1"),await A(s.grid,5e3),V.logger.debug("Helm/getMolfiles/linear1, grid awaited 1");const i=await o.functions.call("Helm:getMolfiles",{col:r});(0,e.ct)(i.length,r.length);const l=i.toList().map((t=>T.getInstance(t)));(0,e.gz)(l.map((t=>t.atomCount)),n.getCol("atoms").toList()),(0,e.gz)(l.map((t=>t.bondCount)),n.getCol("bonds").toList()),V.logger.debug("Helm/getMolfiles/linear1, grid awaiting 2"),await A(s.grid,5e3),V.logger.debug("Helm/getMolfiles/linear1, grid awaited 2")}))}));var O=n(688),M=n(980);const N={Helm:{seq:"PEPTIDE1{I.H.A.C.T.[Thr_PO3H2].[Aca].[D-Tyr_Et]}|PEPTIDE2{E.A.[meG]}$PEPTIDE1,PEPTIDE2,4:R3-1:R1$$$V2.0",units:b.qD.HELM,res:{formula:"C58H94N13O21SP","molecular weight":1372.48,"extinction coefficient":1.55}},separator:{seq:"I/H/A/C/T/Thr_PO3H2/Aca/D-Tyr_Et",units:b.qD.SEPARATOR,separator:"/",alphabet:"UN",res:{formula:"C47H77N10O15SP","molecular weight":1085.21,"extinction coefficient":1.55}},separator2:{seq:"meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Aze/dV/E/N////Phe_4Me",units:b.qD.SEPARATOR,separator:"/",alphabet:"UN",res:{formula:"C91H146N19O25P","molecular weight":1937.21,"extinction coefficient":1.49}},"separator-gaps":{seq:"I/H/A//T/Thr_PO3H2/Aca/D-Tyr_Et",units:b.qD.SEPARATOR,separator:"/",alphabet:"UN",res:{formula:"C44H72N9O14P","molecular weight":982.07,"extinction coefficient":1.49}},"fasta-PT":{seq:"IHACTTAY",units:b.qD.FASTA,alphabet:"PT",res:{formula:"C38H58N10O12S","molecular weight":878.99,"extinction coefficient":1.55}},"fasta-DNA":{seq:"ACGTATTCC",units:b.qD.FASTA,alphabet:"DNA",res:{formula:"C87H113N30O56P9","molecular weight":2753.76,"extinction coefficient":91.74}}};function R(n,r,s,i,o){const l=t.Column.fromStrings("seq",[n]);l.semType=t.SEMTYPE.MACROMOLECULE,l.setTag(t.TAGS.UNITS,r),s&&l.setTag("separator",s),i&&l.setTag("alphabet",i);const a=O.YL.forColumn(l),u=(0,M.C)(n,a);(0,e.o1)(u,o)}(0,e.Gu)("properties-widget",(()=>{let t,n=null;(0,e.a8)((async()=>{t=await(0,i.wW)(),n=h(),await g(),await t.loadLibraries(!0)})),(0,e.iV)((async()=>{await c(n),await t.loadLibraries(!0)}));for(const[t,n]of Object.entries(N))(0,e.GM)(t,(async()=>{R(n.seq,n.units,n.separator,n.alphabet,n.res)}))}));var I=n(848),L=n.n(I),S=n(544);async function v(t,n){const r=function(t){const e=t?(0,s.a6)(t):[];return t?(0,s.kR)(e,t):[]}(t);(0,e.gz)(r,n)}n(368),S.W,(0,e.Gu)("getAllParts",(()=>{const t={peptideSimpleSingleChar:{seq:"PEPTIDE1{L.V.A}$$$$",tgt:["PEPTIDE1{","L",".","V",".","A","}$$$$"]},peptideSimpleMultiChar:{seq:"PEPTIDE1{[Ac].V.A}$$$$",tgt:["PEPTIDE1{[","Ac","].","V",".","A","}$$$$"]}};for(const[n,r]of Object.entries(t))(0,e.GM)(`${n}`,(async()=>{await v(r.seq,r.tgt)}))}));var H=n(372),D=n(924),P=n(872);const $={PEPTIDE:322,RNA:383,CHEM:0};function k(t,n){const r=n??$,s=t.getSummaryObj();for(const t in r)r[t]||delete r[t];for(const t in s)s[t]||delete s[t];if(0==Object.keys(r).length&&0!=Object.keys(s).length)throw new Error("Expected empty monomer lib, actual is not.");if(0!=Object.keys(r).length&&0==Object.keys(s).length)throw new Error("Expected non-empty monomer lib, actual is empty.");try{(0,e.o1)(s,r),(0,e.o1)(r,s)}catch(t){throw new Error(`Expected monomer lib ${JSON.stringify(r)} does not match actual ${JSON.stringify(s)}.`)}}var F=n(696);const G={t0:{args:{a:"HELM_BASE",name:"A"},tgt:{id:"A",m:"HELM Core Monomer library\n Ketcher 10131612512D 1 1.00000 0.00000 0\n\n 11 12 0 0 0 999 V2000\n 0.9632 -3.5449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0970 -4.0450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0970 -5.0451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9630 -5.5451 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8291 -5.0452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8293 -4.0451 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8536 -5.3539 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4413 -4.5449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8535 -3.7357 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9632 -2.5448 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -1.1626 -6.3051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 10 1 0 0 0\n 1 6 2 0 0 0\n 1 2 1 0 0 0\n 9 2 1 0 0 0\n 2 3 2 0 0 0\n 7 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 2 0 0 0\n 5 6 1 0 0 0\n 7 8 1 0 0 0\n 7 11 1 0 0 0\n 8 9 2 0 0 0\nA 11\nR1\nM END\n",n:"Adenine",na:"A",rs:1,at:{R1:"H"}}},t1:{args:{a:"HELM_BASE",name:"C"},tgt:{id:"C",m:"HELM Core Monomer library\nHELMMonomers071816.sdf \n\n 9 9 0 0 0 0 0 0 0 0999 V2000\n 10.7683 -10.8385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 10.7683 -12.3385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -13.0885 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.1683 -12.3385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.1683 -10.8385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -10.0885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -8.5885 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -14.5885 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0\n 12.0673 -13.0885 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0\n 2 3 1 0 0\n 3 4 1 0 0\n 4 5 2 0 0\n 5 6 1 0 0\n 1 6 2 0 0\n 6 7 1 0 0\n 3 8 1 0 0\n 2 9 2 0 0\nA 8\nR1\nM END\n",n:"Cytosine",na:"C",rs:1,at:{R1:"H"}}},t2:{args:{a:"HELM_BASE",name:"G"},tgt:{id:"G",m:"HELM Core Monomer library\nHELMMonomers071816.sdf \n\n 12 13 0 0 0 0 0 0 0 0999 V2000\n 12.7698 -10.2854 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 12.7698 -11.7854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 11.4733 -12.5380 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 10.1698 -11.7854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 10.1698 -10.2854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 11.4748 -9.5354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.8623 -11.0354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.7448 -9.8154 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 11.4748 -8.0354 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.0689 -12.5354 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.7448 -12.2479 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.2789 -13.6737 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0\n 2 3 2 0 0\n 3 4 1 0 0\n 4 5 2 0 0\n 5 6 1 0 0\n 1 6 1 0 0\n 7 8 2 0 0\n 5 8 1 0 0\n 6 9 2 0 0\n 2 10 1 0 0\n 4 11 1 0 0\n 7 11 1 0 0\n 11 12 1 0 0\nA 12\nR1\nM END\n",n:"Guanine",na:"G",rs:1,at:{R1:"H"}}},t3:{args:{a:"HELM_LINKER",name:"p"},tgt:{id:"p",m:"HELM Core Monomer library\n Ketcher 10061618102D 1 1.00000 0.00000 0\n\n 5 4 0 0 0 999 V2000\n 15.7527 -12.0837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.7527 -13.0837 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 16.6188 -13.5837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.2527 -13.9496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.7868 -12.8248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 2 4 2 0 0 0\n 2 5 1 0 0 0\nA 1\nR1\nA 3\nR2\nM END\n",n:"Phosphate",na:"p",rs:2,at:{R1:"OH",R2:"OH"}}},t4:{args:{a:"HELM_SUGAR",name:"p"},tgt:null},t5:{args:{a:"HELM_SUGAR",name:"r"},tgt:{id:"r",m:"HELM Core Monomer library\n Ketcher 10111608242D 1 1.00000 0.00000 0\n\n 12 12 0 0 0 999 V2000\n -31.2431 12.8416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.9523 11.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.9523 11.8659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.6254 12.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.4231 13.4140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -32.1882 13.1686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5552 11.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5220 10.0877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.3803 11.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -28.6686 13.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -32.3775 14.1506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -33.2435 14.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\n 1 6 1 1 0 0\n 2 7 1 6 0 0\n 7 8 1 0 0 0\n 3 9 1 6 0 0\n 4 10 1 1 0 0\n 6 11 1 0 0 0\n 11 12 1 0 0 0\nA 8\nR2\nA 10\nR3\nA 12\nR1\nM END\n",n:"Ribose",na:"r",rs:3,at:{R1:"H",R2:"H",R3:"OH"}}},t6:{args:{a:{T:"ATOM",p:{x:144,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_SUGAR",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"r",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:4}},tgt:{id:"r",m:"HELM Core Monomer library\n Ketcher 10111608242D 1 1.00000 0.00000 0\n\n 12 12 0 0 0 999 V2000\n -31.2431 12.8416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.9523 11.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.9523 11.8659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.6254 12.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.4231 13.4140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -32.1882 13.1686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5552 11.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5220 10.0877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.3803 11.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -28.6686 13.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -32.3775 14.1506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -33.2435 14.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\n 1 6 1 1 0 0\n 2 7 1 6 0 0\n 7 8 1 0 0 0\n 3 9 1 6 0 0\n 4 10 1 1 0 0\n 6 11 1 0 0 0\n 11 12 1 0 0 0\nA 8\nR2\nA 10\nR3\nA 12\nR1\nM END\n",n:"Ribose",na:"r",rs:3,at:{R1:"H",R2:"H",R3:"OH"}}},t7:{args:{a:{T:"ATOM",p:{x:144,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_SUGAR",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"r",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:4}},tgt:{id:"r",m:"HELM Core Monomer library\n Ketcher 10111608242D 1 1.00000 0.00000 0\n\n 12 12 0 0 0 999 V2000\n -31.2431 12.8416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.9523 11.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.9523 11.8659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.6254 12.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.4231 13.4140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -32.1882 13.1686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5552 11.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5220 10.0877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.3803 11.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -28.6686 13.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -32.3775 14.1506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -33.2435 14.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\n 1 6 1 1 0 0\n 2 7 1 6 0 0\n 7 8 1 0 0 0\n 3 9 1 6 0 0\n 4 10 1 1 0 0\n 6 11 1 0 0 0\n 11 12 1 0 0 0\nA 8\nR2\nA 10\nR3\nA 12\nR1\nM END\n",n:"Ribose",na:"r",rs:3,at:{R1:"H",R2:"H",R3:"OH"}}},t8:{args:{a:{T:"ATOM",p:{x:144,y:48},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_BASE",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"G",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:5}},tgt:{id:"G",m:"HELM Core Monomer library\nHELMMonomers071816.sdf \n\n 12 13 0 0 0 0 0 0 0 0999 V2000\n 12.7698 -10.2854 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 12.7698 -11.7854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 11.4733 -12.5380 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 10.1698 -11.7854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 10.1698 -10.2854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 11.4748 -9.5354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.8623 -11.0354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.7448 -9.8154 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 11.4748 -8.0354 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.0689 -12.5354 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.7448 -12.2479 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.2789 -13.6737 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0\n 2 3 2 0 0\n 3 4 1 0 0\n 4 5 2 0 0\n 5 6 1 0 0\n 1 6 1 0 0\n 7 8 2 0 0\n 5 8 1 0 0\n 6 9 2 0 0\n 2 10 1 0 0\n 4 11 1 0 0\n 7 11 1 0 0\n 11 12 1 0 0\nA 12\nR1\nM END\n",n:"Guanine",na:"G",rs:1,at:{R1:"H"}}},t9:{args:{a:{T:"ATOM",p:{x:192,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_LINKER",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"p",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:6}},tgt:{id:"p",m:"HELM Core Monomer library\n Ketcher 10061618102D 1 1.00000 0.00000 0\n\n 5 4 0 0 0 999 V2000\n 15.7527 -12.0837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.7527 -13.0837 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 16.6188 -13.5837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.2527 -13.9496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.7868 -12.8248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 2 4 2 0 0 0\n 2 5 1 0 0 0\nA 1\nR1\nA 3\nR2\nM END\n",n:"Phosphate",na:"p",rs:2,at:{R1:"OH",R2:"OH"}}},t10:{args:{a:{T:"ATOM",p:{x:192,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_LINKER",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"p",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:6}},tgt:{id:"p",m:"HELM Core Monomer library\n Ketcher 10061618102D 1 1.00000 0.00000 0\n\n 5 4 0 0 0 999 V2000\n 15.7527 -12.0837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.7527 -13.0837 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 16.6188 -13.5837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.2527 -13.9496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.7868 -12.8248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 2 4 2 0 0 0\n 2 5 1 0 0 0\nA 1\nR1\nA 3\nR2\nM END\n",n:"Phosphate",na:"p",rs:2,at:{R1:"OH",R2:"OH"}}},t11:{args:{a:{T:"ATOM",p:{x:205,y:136},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_SUGAR",id:null,ambiguity:null,annotation:"5'",annotationshowright:null},locked:!1,hidden:null,_rect:null,elem:"r",color:null,hcount:null,selected:!1,f:0,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:1,ringclosures:null,_outside:!1,_haslabel:!1},name:"r"},tgt:{id:"r",m:"HELM Core Monomer library\n Ketcher 10111608242D 1 1.00000 0.00000 0\n\n 12 12 0 0 0 999 V2000\n -31.2431 12.8416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.9523 11.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.9523 11.8659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.6254 12.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.4231 13.4140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -32.1882 13.1686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5552 11.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5220 10.0877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.3803 11.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -28.6686 13.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -32.3775 14.1506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -33.2435 14.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\n 1 6 1 1 0 0\n 2 7 1 6 0 0\n 7 8 1 0 0 0\n 3 9 1 6 0 0\n 4 10 1 1 0 0\n 6 11 1 0 0 0\n 11 12 1 0 0 0\nA 8\nR2\nA 10\nR3\nA 12\nR1\nM END\n",n:"Ribose",na:"r",rs:3,at:{R1:"H",R2:"H",R3:"OH"}}},t12:{args:{a:{T:"ATOM",p:{x:205,y:184},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_BASE",id:1,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"A",color:null,hcount:null,selected:!1,f:0,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:2,ringclosures:null,_outside:!1,_haslabel:!1},name:"A"},tgt:{id:"A",m:"HELM Core Monomer library\n Ketcher 10131612512D 1 1.00000 0.00000 0\n\n 11 12 0 0 0 999 V2000\n 0.9632 -3.5449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0970 -4.0450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0970 -5.0451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9630 -5.5451 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8291 -5.0452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8293 -4.0451 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8536 -5.3539 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4413 -4.5449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8535 -3.7357 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9632 -2.5448 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -1.1626 -6.3051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 10 1 0 0 0\n 1 6 2 0 0 0\n 1 2 1 0 0 0\n 9 2 1 0 0 0\n 2 3 2 0 0 0\n 7 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 2 0 0 0\n 5 6 1 0 0 0\n 7 8 1 0 0 0\n 7 11 1 0 0 0\n 8 9 2 0 0 0\nA 11\nR1\nM END\n",n:"Adenine",na:"A",rs:1,at:{R1:"H"}}},t13:{args:{a:{T:"ATOM",p:{x:240,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_SUGAR",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"r",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:7}},tgt:{id:"r",m:"HELM Core Monomer library\n Ketcher 10111608242D 1 1.00000 0.00000 0\n\n 12 12 0 0 0 999 V2000\n -31.2431 12.8416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.9523 11.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.9523 11.8659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.6254 12.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.4231 13.4140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -32.1882 13.1686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5552 11.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5220 10.0877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.3803 11.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -28.6686 13.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -32.3775 14.1506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -33.2435 14.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\n 1 6 1 1 0 0\n 2 7 1 6 0 0\n 7 8 1 0 0 0\n 3 9 1 6 0 0\n 4 10 1 1 0 0\n 6 11 1 0 0 0\n 11 12 1 0 0 0\nA 8\nR2\nA 10\nR3\nA 12\nR1\nM END\n",n:"Ribose",na:"r",rs:3,at:{R1:"H",R2:"H",R3:"OH"}}},t14:{args:{a:{T:"ATOM",p:{x:240,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_SUGAR",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"r",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:7}},tgt:{id:"r",m:"HELM Core Monomer library\n Ketcher 10111608242D 1 1.00000 0.00000 0\n\n 12 12 0 0 0 999 V2000\n -31.2431 12.8416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.9523 11.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.9523 11.8659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.6254 12.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.4231 13.4140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -32.1882 13.1686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5552 11.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5220 10.0877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.3803 11.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -28.6686 13.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -32.3775 14.1506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -33.2435 14.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\n 1 6 1 1 0 0\n 2 7 1 6 0 0\n 7 8 1 0 0 0\n 3 9 1 6 0 0\n 4 10 1 1 0 0\n 6 11 1 0 0 0\n 11 12 1 0 0 0\nA 8\nR2\nA 10\nR3\nA 12\nR1\nM END\n",n:"Ribose",na:"r",rs:3,at:{R1:"H",R2:"H",R3:"OH"}}},t15:{args:{a:{T:"ATOM",p:{x:240,y:48},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_BASE",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"C",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:8}},tgt:{id:"C",m:"HELM Core Monomer library\nHELMMonomers071816.sdf \n\n 9 9 0 0 0 0 0 0 0 0999 V2000\n 10.7683 -10.8385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 10.7683 -12.3385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -13.0885 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.1683 -12.3385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.1683 -10.8385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -10.0885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -8.5885 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -14.5885 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0\n 12.0673 -13.0885 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0\n 2 3 1 0 0\n 3 4 1 0 0\n 4 5 2 0 0\n 5 6 1 0 0\n 1 6 2 0 0\n 6 7 1 0 0\n 3 8 1 0 0\n 2 9 2 0 0\nA 8\nR1\nM END\n",n:"Cytosine",na:"C",rs:1,at:{R1:"H"}}},t16:{args:{a:{T:"ATOM",p:{x:253,y:136},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_LINKER",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"p",color:null,hcount:null,selected:!1,f:0,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:3,ringclosures:null,_outside:!1,_haslabel:!1},name:"p"},tgt:{id:"p",m:"HELM Core Monomer library\n Ketcher 10061618102D 1 1.00000 0.00000 0\n\n 5 4 0 0 0 999 V2000\n 15.7527 -12.0837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.7527 -13.0837 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 16.6188 -13.5837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.2527 -13.9496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.7868 -12.8248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 2 4 2 0 0 0\n 2 5 1 0 0 0\nA 1\nR1\nA 3\nR2\nM END\n",n:"Phosphate",na:"p",rs:2,at:{R1:"OH",R2:"OH"}}},t17:{args:{a:{T:"ATOM",p:{x:288,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_LINKER",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"p",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:9}},tgt:{id:"p",m:"HELM Core Monomer library\n Ketcher 10061618102D 1 1.00000 0.00000 0\n\n 5 4 0 0 0 999 V2000\n 15.7527 -12.0837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.7527 -13.0837 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 16.6188 -13.5837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.2527 -13.9496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.7868 -12.8248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 2 4 2 0 0 0\n 2 5 1 0 0 0\nA 1\nR1\nA 3\nR2\nM END\n",n:"Phosphate",na:"p",rs:2,at:{R1:"OH",R2:"OH"}}},t18:{args:{a:{T:"ATOM",p:{x:301,y:136},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_SUGAR",id:null,ambiguity:null,annotation:null},locked:!1,hidden:null,_rect:null,elem:"r",color:null,hcount:null,selected:!1,f:0,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:1,ringclosures:null,_outside:!1,_haslabel:!1},name:"r"},tgt:{id:"r",m:"HELM Core Monomer library\n Ketcher 10111608242D 1 1.00000 0.00000 0\n\n 12 12 0 0 0 999 V2000\n -31.2431 12.8416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.9523 11.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.9523 11.8659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.6254 12.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.4231 13.4140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -32.1882 13.1686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5552 11.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5220 10.0877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.3803 11.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -28.6686 13.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -32.3775 14.1506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -33.2435 14.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\n 1 6 1 1 0 0\n 2 7 1 6 0 0\n 7 8 1 0 0 0\n 3 9 1 6 0 0\n 4 10 1 1 0 0\n 6 11 1 0 0 0\n 11 12 1 0 0 0\nA 8\nR2\nA 10\nR3\nA 12\nR1\nM END\n",n:"Ribose",na:"r",rs:3,at:{R1:"H",R2:"H",R3:"OH"}}},t19:{args:{a:{T:"ATOM",p:{x:301,y:184},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_BASE",id:2,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"G",color:null,hcount:null,selected:!1,f:0,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:2,ringclosures:null,_outside:!1,_haslabel:!1},name:"G"},tgt:{id:"G",m:"HELM Core Monomer library\nHELMMonomers071816.sdf \n\n 12 13 0 0 0 0 0 0 0 0999 V2000\n 12.7698 -10.2854 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 12.7698 -11.7854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 11.4733 -12.5380 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 10.1698 -11.7854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 10.1698 -10.2854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 11.4748 -9.5354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7.8623 -11.0354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.7448 -9.8154 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 11.4748 -8.0354 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.0689 -12.5354 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.7448 -12.2479 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.2789 -13.6737 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0\n 2 3 2 0 0\n 3 4 1 0 0\n 4 5 2 0 0\n 5 6 1 0 0\n 1 6 1 0 0\n 7 8 2 0 0\n 5 8 1 0 0\n 6 9 2 0 0\n 2 10 1 0 0\n 4 11 1 0 0\n 7 11 1 0 0\n 11 12 1 0 0\nA 12\nR1\nM END\n",n:"Guanine",na:"G",rs:1,at:{R1:"H"}}},t20:{args:{a:{T:"ATOM",p:{x:349,y:136},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_LINKER",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"p",color:null,hcount:null,selected:!1,f:0,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:6,ringclosures:null,_outside:!1,_haslabel:!1},name:"p"},tgt:{id:"p",m:"HELM Core Monomer library\n Ketcher 10061618102D 1 1.00000 0.00000 0\n\n 5 4 0 0 0 999 V2000\n 15.7527 -12.0837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.7527 -13.0837 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 16.6188 -13.5837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.2527 -13.9496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.7868 -12.8248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 2 4 2 0 0 0\n 2 5 1 0 0 0\nA 1\nR1\nA 3\nR2\nM END\n",n:"Phosphate",na:"p",rs:2,at:{R1:"OH",R2:"OH"}}},t21:{args:{a:{T:"ATOM",p:{x:397,y:136},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_SUGAR",id:null,ambiguity:null,annotation:null},locked:!1,hidden:null,_rect:null,elem:"r",color:null,hcount:null,selected:!1,f:0,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:1,ringclosures:null,_outside:!1,_haslabel:!1},name:"r"},tgt:{id:"r",m:"HELM Core Monomer library\n Ketcher 10111608242D 1 1.00000 0.00000 0\n\n 12 12 0 0 0 999 V2000\n -31.2431 12.8416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.9523 11.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.9523 11.8659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.6254 12.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.4231 13.4140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -32.1882 13.1686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5552 11.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5220 10.0877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.3803 11.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -28.6686 13.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -32.3775 14.1506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -33.2435 14.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\n 1 6 1 1 0 0\n 2 7 1 6 0 0\n 7 8 1 0 0 0\n 3 9 1 6 0 0\n 4 10 1 1 0 0\n 6 11 1 0 0 0\n 11 12 1 0 0 0\nA 8\nR2\nA 10\nR3\nA 12\nR1\nM END\n",n:"Ribose",na:"r",rs:3,at:{R1:"H",R2:"H",R3:"OH"}}},t22:{args:{a:{T:"ATOM",p:{x:397,y:184},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_BASE",id:3,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"C",color:null,hcount:null,selected:!1,f:0,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:2,ringclosures:null,_outside:!1,_haslabel:!1},name:"C"},tgt:{id:"C",m:"HELM Core Monomer library\nHELMMonomers071816.sdf \n\n 9 9 0 0 0 0 0 0 0 0999 V2000\n 10.7683 -10.8385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 10.7683 -12.3385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -13.0885 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 8.1683 -12.3385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 8.1683 -10.8385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -10.0885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -8.5885 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 9.4733 -14.5885 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0\n 12.0673 -13.0885 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0\n 2 3 1 0 0\n 3 4 1 0 0\n 4 5 2 0 0\n 5 6 1 0 0\n 1 6 2 0 0\n 6 7 1 0 0\n 3 8 1 0 0\n 2 9 2 0 0\nA 8\nR1\nM END\n",n:"Cytosine",na:"C",rs:1,at:{R1:"H"}}},t23:{args:{a:{T:"ATOM",p:{x:445,y:136},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_LINKER",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"p",color:null,hcount:null,selected:!1,f:0,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:9,ringclosures:null,_outside:!1,_haslabel:!1},name:"p"},tgt:{id:"p",m:"HELM Core Monomer library\n Ketcher 10061618102D 1 1.00000 0.00000 0\n\n 5 4 0 0 0 999 V2000\n 15.7527 -12.0837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.7527 -13.0837 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 16.6188 -13.5837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.2527 -13.9496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.7868 -12.8248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 2 4 2 0 0 0\n 2 5 1 0 0 0\nA 1\nR1\nA 3\nR2\nM END\n",n:"Phosphate",na:"p",rs:2,at:{R1:"OH",R2:"OH"}}},t24:{args:{a:{T:"ATOM",p:{x:48,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_SUGAR",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"r",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:1}},tgt:{id:"r",m:"HELM Core Monomer library\n Ketcher 10111608242D 1 1.00000 0.00000 0\n\n 12 12 0 0 0 999 V2000\n -31.2431 12.8416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.9523 11.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.9523 11.8659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.6254 12.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.4231 13.4140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -32.1882 13.1686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5552 11.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5220 10.0877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.3803 11.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -28.6686 13.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -32.3775 14.1506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -33.2435 14.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\n 1 6 1 1 0 0\n 2 7 1 6 0 0\n 7 8 1 0 0 0\n 3 9 1 6 0 0\n 4 10 1 1 0 0\n 6 11 1 0 0 0\n 11 12 1 0 0 0\nA 8\nR2\nA 10\nR3\nA 12\nR1\nM END\n",n:"Ribose",na:"r",rs:3,at:{R1:"H",R2:"H",R3:"OH"}}},t25:{args:{a:{T:"ATOM",p:{x:48,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_SUGAR",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"r",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:1}},tgt:{id:"r",m:"HELM Core Monomer library\n Ketcher 10111608242D 1 1.00000 0.00000 0\n\n 12 12 0 0 0 999 V2000\n -31.2431 12.8416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.9523 11.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.9523 11.8659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.6254 12.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -30.4231 13.4140 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -32.1882 13.1686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5552 11.0872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -31.5220 10.0877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -29.3803 11.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -28.6686 13.1017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -32.3775 14.1506 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -33.2435 14.6506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\n 1 6 1 1 0 0\n 2 7 1 6 0 0\n 7 8 1 0 0 0\n 3 9 1 6 0 0\n 4 10 1 1 0 0\n 6 11 1 0 0 0\n 11 12 1 0 0 0\nA 8\nR2\nA 10\nR3\nA 12\nR1\nM END\n",n:"Ribose",na:"r",rs:3,at:{R1:"H",R2:"H",R3:"OH"}}},t26:{args:{a:{T:"ATOM",p:{x:48,y:48},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_BASE",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"A",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:2}},tgt:{id:"A",m:"HELM Core Monomer library\n Ketcher 10131612512D 1 1.00000 0.00000 0\n\n 11 12 0 0 0 999 V2000\n 0.9632 -3.5449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0970 -4.0450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0970 -5.0451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9630 -5.5451 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8291 -5.0452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8293 -4.0451 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8536 -5.3539 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4413 -4.5449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8535 -3.7357 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9632 -2.5448 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -1.1626 -6.3051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 10 1 0 0 0\n 1 6 2 0 0 0\n 1 2 1 0 0 0\n 9 2 1 0 0 0\n 2 3 2 0 0 0\n 7 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 2 0 0 0\n 5 6 1 0 0 0\n 7 8 1 0 0 0\n 7 11 1 0 0 0\n 8 9 2 0 0 0\nA 11\nR1\nM END\n",n:"Adenine",na:"A",rs:1,at:{R1:"H"}}},t27:{args:{a:{T:"ATOM",p:{x:96,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_LINKER",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"p",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,_parent:"[object Object]",_aaid:3}},tgt:{id:"p",m:"HELM Core Monomer library\n Ketcher 10061618102D 1 1.00000 0.00000 0\n\n 5 4 0 0 0 999 V2000\n 15.7527 -12.0837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.7527 -13.0837 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 16.6188 -13.5837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.2527 -13.9496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.7868 -12.8248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 2 4 2 0 0 0\n 2 5 1 0 0 0\nA 1\nR1\nA 3\nR2\nM END\n",n:"Phosphate",na:"p",rs:2,at:{R1:"OH",R2:"OH"}}},t28:{args:{a:{T:"ATOM",p:{x:96,y:0},charge:0,isotope:null,radical:null,group:null,alias:null,superatom:null,attachpoints:[],rgroup:null,bio:{type:"HELM_LINKER",id:null,ambiguity:null},locked:!1,hidden:null,_rect:null,elem:"p",color:null,hcount:null,selected:!1,f:null,bonds:null,id:null,atommapid:null,query:null,hasError:null,hs:null,val:null,tag:null,_parent:"[object Object]",_aaid:3}},tgt:{id:"p",m:"HELM Core Monomer library\n Ketcher 10061618102D 1 1.00000 0.00000 0\n\n 5 4 0 0 0 999 V2000\n 15.7527 -12.0837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.7527 -13.0837 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 16.6188 -13.5837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 15.2527 -13.9496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 14.7868 -12.8248 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 2 4 2 0 0 0\n 2 5 1 0 0 0\nA 1\nR1\nA 3\nR2\nM END\n",n:"Phosphate",na:"p",rs:2,at:{R1:"OH",R2:"OH"}}}};function q(t){let e;const n=t;return e="ATOM"===n.T?new D.Atom(n.p,n.elem,n.bio):t,e}function B(t,n){if(null!=t||null!=n){if(null==t&&null!=n)throw new Error("actual is null, but expected is not null");if(null!=t&&null==n)throw new Error("actual is not null, but expected is null");for(const[r,s]of Object.entries(n)){if(!(r in t)&&!t.hasOwnProperty(r))throw new Error(`Expected property "${r}" not found`);const n=t[r];if(n instanceof Array&&s instanceof Array)(0,e.gz)(n,s);else if(n instanceof Object&&s instanceof Object)B(n,s);else if(Number.isFinite(n)&&Number.isFinite(s))(0,e.UZ)(n,s);else if(n!=s)throw new Error(`Expected (${s}) for key '${r}', got (${n})`)}}}(0,e.Gu)("getMonomer",(()=>{let n,r;function s(e,r){const s=t.DataFrame.fromColumns([t.Column.fromStrings("subTest",[]),t.Column.fromList(t.COLUMN_TYPE.BOOL,"success",[]),t.Column.fromStrings("res",[]),t.Column.fromStrings("tgt",[]),t.Column.fromStrings("error",[]),t.Column.fromStrings("stack",[])]),i=s.rows.addNew().idx;s.set("subTest",i,"Monomer lib"),s.set("res",i,""),s.set("tgt",i,"");try{k(n.getBioLib()),s.set("success",i,!0)}catch(t){const[e,n]=(0,P.g$)(t);s.set("error",i,e),s.set("stack",i,n),s.set("success",i,!1)}for(const[[t,n],i]of L().enumerate(Object.entries(G))){const i=q(n.args.a),[o,l]=(0,F.g7)(i,n.args.name),a=n.tgt,u=s.rows.addNew().idx;s.set("subTest",u,`${e}-${t}-${o}-${l}`),s.set("tgt",u,JSON.stringify(a?{id:a.id,n:a.n,rs:a.rs}:null));try{const t=r(i,n.args.name);s.set("res",u,JSON.stringify(t?{id:t.id,n:t.n,rs:t.rs}:null)),B(t,a),s.set("success",u,!0)}catch(t){const[e,n]=(0,P.g$)(t);s.set("error",u,e),s.set("stack",u,n),s.set("success",u,!1)}}return s}(0,e.a8)((async()=>{n=await(0,i.wW)(),r=await h(),await g(),await n.awaitLoaded(),await n.loadLibraries(!0)})),(0,e.iV)((async()=>{await c(r),await n.loadLibraries(!0)})),(0,e.GM)("original",(async()=>{const n=await async function(){const e="Helm",n=t.Func.find({package:e,name:"getHelmHelper"});if(0===n.length)throw new Error(`Package '${e}' must be installed for HelmHelper.`);return(await n[0].prepare().call()).getOutputParamValue()}();return(0,e.ct)(null!=n,!0),s("original",helm._package.getMonomerOriginal)}),{isAggregated:!0}),(0,e.GM)("monomerLib",(async()=>(k(n.getBioLib()),s("monomerLib",H.helm.webeditor.Monomers.getMonomer))),{isAggregated:!0}),(0,e.GM)("missing",(async()=>{k(n.getBioLib()),new D.Editor(f.div(),{viewonly:!0}).setHelm("PEPTIDE1{[mis1].R.[mis2].T.C.F}$$$$;");const t=JSON.parse(JSON.stringify($));t.PEPTIDE+=2,k(n.getBioLib(),t)}))}));const V=new t.Package;async function U(n,r,s){const i=await(0,e.Md)({category:n,test:r,testContext:s,verbose:!0});return t.DataFrame.fromObjects(i)}})(),helm_test=r})();
2
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