@datagrok/peptides 1.17.25 → 1.17.26

package/CHANGELOG.md

@@ -1,5 +1,9 @@
 # Peptides changelog
 
+## 1.17.26 (2024-08-07)
+
+Rename monomer position viewer to sequence variability map
+
 ## 1.17.25 (2024-08-06)
 
 Update MCLalgorytm and Add params to starting menu

package/dist/501.js

@@ -1,2 +1,2 @@
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d={gapOpen:1,gapExtend:.6,scoringMatrix:[[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0,-4],[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1,-4],[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1,-4],[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1,-4],[0,-3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4],[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1,-4],[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1,-4],[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1,-4],[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1,-4],[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,1,-4,-3,-1,-4],[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1,-4],[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1,-4],[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1,-4],[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2,-4],[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0,-4],[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0,-4],[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,1,-4,-3,-2,11,2,-3,-4,-3,-2,-4],[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1,-4],[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1,-4],[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1,-4],[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1,-4],[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1]],alphabetIndexes:{A:0,R:1,N:2,D:3,C:4,Q:5,E:6,G:7,H:8,I:9,L:10,K:11,M:12,F:13,P:14,S:15,T:16,W:17,Y:18,V:19,B:20,Z:21,X:22,"*":23}};var m;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(m||(m={}));const C={[m.HAMMING]:_,[m.LEVENSHTEIN]:function(){return(t,e)=>c(t,e)/Math.max(t.length,e.length)},[m.NEEDLEMANN_WUNSCH]:function(t){const e=new Uint16Array(65536),{gapOpen:n,gapExtend:r,scoringMatrix:i,alphabetIndexes:s}={...d,...t};Object.entries(s).forEach((([t,n])=>e[t.charCodeAt(0)]=n));const o=[new Float32Array(1e4),new Float32Array(1e4)];return(t,s)=>{const h=new Array(t.length+1).fill(!1),a=new Array(t.length+1).fill(!1);let l=0,u=1;for(let e=1;e<t.length+1;e++)o[0][e]=-r-(e-1)*r,o[1][e]=0;o[0][0]=0;for(let c=1;c<s.length+1;c++){o[u][0]=-r-(c-1)*r;for(let g=1;g<t.length+1;g++){const f=o[l][g-1]+i[e[t.charCodeAt(g-1)]][e[s.charCodeAt(c-1)]],_=o[l][g]-(h[g]||1===c||c===s.length?r:n),d=o[u][g-1]-(a[g-1]||1===g||g===t.length?r:n);o[u][g]=Math.max(f,d,_),o[u][g]===f?(h[g]=!1,a[g]=!1):o[u][g]===d?(h[g]=!1,a[g]=!0):(h[g]=!0,a[g]=!1)}l=u,u=(u+1)%2}const c=Math.min(t.length,s.length);return(c-o[l][t.length])/c}},[m.MONOMER_CHEMICAL_DISTANCE]:_};function A(t,e){const n=t.trueCount()+e.trueCount();if(0==n)return 1;const r=t.andWithCountBits(e,!0);return r/(n-r)}function M(t){return 0===t?3402823e32:1/t-1}s.Tanimoto,s.Dice,s.Asymmetric,s.BraunBlanquet,s.Cosine,s.Kulczynski,s.McConnaughey,s.RogotGoldberg,s.Russel,s.Sokal,s.Hamming,s.Euclidean,s.Tanimoto,s.Dice,s.Asymmetric,s.BraunBlanquet,s.Cosine,s.Kulczynski,s.McConnaughey,s.RogotGoldberg,s.Russel,s.Sokal,s.Hamming,s.Euclidean,s.Tanimoto,s.Dice,s.Cosine,s.Tanimoto,s.Asymmetric,s.Cosine,s.Sokal,m.HAMMING,m.LEVENSHTEIN,m.MONOMER_CHEMICAL_DISTANCE,m.NEEDLEMANN_WUNSCH;const I={[i.Euclidean]:function(t,e){let n=0;const r=t.length;if(r!==e.length)throw new Error("The dimensionality of the vectors must match");for(let i=0;i<r;++i)n+=Math.pow(t[i]-e[i],2);return Math.sqrt(n)}},y={[r.Levenshtein]:c,[r.JaroWinkler]:g.Vb,[r.Manhattan]:function(t,e){if(t.length!==e.length)return 1;{let n=0;for(let r=1;r<t.length;r++)n+=t[r]==e[r]?0:1;return n/t.length}},[r.Onehot]:function(t,e){return t===e?0:1}},E={[s.Tanimoto]:function(t,e){return 1-A(t,e)},[s.Dice]:function(t,e){return 1-function(t,e){const n=t.trueCount()+e.trueCount();return 0==n?0:2*t.andWithCountBits(e,!0)/n}(t,e)},[s.Asymmetric]:function(t,e){return 1-function(t,e){const n=Math.min(t.trueCount(),e.trueCount());return 0==n?0:t.andWithCountBits(e,!0)/n}(t,e)},[s.BraunBlanquet]:function(t,e){return M(function(t,e){const n=Math.max(t.trueCount(),e.trueCount());return 0==n?0:t.andWithCountBits(e,!0)/n}(t,e))},[s.Cosine]:function(t,e){return 1-function(t,e){const n=t.trueCount()*e.trueCount();return 0==n?0:t.andWithCountBits(e,!0)/Math.sqrt(n)}(t,e)},[s.Kulczynski]:function(t,e){return M(function(t,e){const n=t.trueCount()+e.trueCount(),r=t.trueCount()*e.trueCount();return 0==r?0:t.andWithCountBits(e,!0)*n/(2*r)}(t,e))},[s.McConnaughey]:function(t,e){return M(function(t,e){const n=t.trueCount()+e.trueCount(),r=t.trueCount()*e.trueCount();return 0==r?0:(t.andWithCountBits(e,!0)*n-r)/r}(t,e))},[s.RogotGoldberg]:function(t,e){return M(function(t,e){const n=t.andWithCountBits(e,!0),r=t.countBits(!0)+e.countBits(!0),i=t.length,s=i-r+n;return n==i||s==i?1:n/r+s/(2*i-r)}(t,e))},[s.Russel]:function(t,e){return M(function(t,e){return 0==t.length?0:t.andWithCountBits(e,!0)/t.length}(t,e))},[s.Sokal]:function(t,e){return 1-function(t,e){const n=t.trueCount()+e.trueCount(),r=t.andWithCountBits(e,!0);return r/(2*n-3*r)}(t,e)},[s.Hamming]:function(t,e){return t.trueCount()+e.trueCount()-2*t.andWithCountBits(e,!0)},[s.Euclidean]:function(t,e){return Math.sqrt(t.trueCount()+e.trueCount()-2*t.andWithCountBits(e,!0))}},N={[o.TanimotoIntArray]:function(t,e){return M(A(new f.A(t,32*t.length),new f.A(e,32*e.length)))}},B={[a.Difference]:function(t){if(t&&null!=t.range&&t.range>0){const e=t.range;return(t,n)=>Math.abs(t-n)/e}return(t,e)=>Math.abs(t-e)}},w={[l.CommonItems]:function(t){const e=function(t){const e=t?.mostCommon??new Set;return(t,n)=>{const r=t.length,i=n.length;let s=0,o=0,h=0;for(;o<r&&h<i;)t[o]===n[h]?(e?.has(t[o])||++s,++o,++h):t[o]<n[h]?++o:++h;return s}}(t);return(t,n)=>0===n.length||0===t.length?1e4:Math.min(t.length,n.length)/(e(t,n)+1e-4)}},v={[h.Vector]:{[i.Euclidean]:I[i.Euclidean]},[h.String]:{[r.Levenshtein]:y[r.Levenshtein],[r.JaroWinkler]:y[r.JaroWinkler],[r.Manhattan]:y[r.Manhattan],[r.Onehot]:y[r.Onehot]},[h.BitArray]:{[s.Tanimoto]:E[s.Tanimoto],[s.Dice]:E[s.Dice],[s.Asymmetric]:E[s.Asymmetric],[s.BraunBlanquet]:E[s.BraunBlanquet],[s.Cosine]:E[s.Cosine],[s.Kulczynski]:E[s.Kulczynski],[s.McConnaughey]:E[s.McConnaughey],[s.RogotGoldberg]:E[s.RogotGoldberg],[s.Russel]:E[s.Russel],[s.Sokal]:E[s.Sokal]},[h.MacroMolecule]:{[m.HAMMING]:C[m.HAMMING],[m.LEVENSHTEIN]:C[m.LEVENSHTEIN],[m.NEEDLEMANN_WUNSCH]:C[m.NEEDLEMANN_WUNSCH],[m.MONOMER_CHEMICAL_DISTANCE]:C[m.MONOMER_CHEMICAL_DISTANCE]},[h.Number]:{[a.Difference]:B[a.Difference]},[h.IntArray]:{[o.TanimotoIntArray]:N[o.TanimotoIntArray]},[h.NumberArray]:{[l.CommonItems]:w[l.CommonItems]}},b=Object.keys(v).reduce(((t,e)=>{for(const n of Object.keys(v[e]))t[n]=e;return t}),{});function p(t){return"BitArray"==b[t]}class T{constructor(t){this.method=t,this.dataType=b[t]}metricNeedsArgs(t){return b[t]==h.MacroMolecule.toString()||b[t]==h.Number.toString()||function(t){return b[t]==h.NumberArray.toString()}(t)}getMeasure(t){const e=v;if(!e.hasOwnProperty(this.dataType)||!e[this.dataType].hasOwnProperty(this.method))throw new Error(`Unknown measure ${this.method} for data type ${this.dataType}`);return this.metricNeedsArgs(this.method)?e[this.dataType][this.method](t):e[this.dataType][this.method]}static getMetricByDataType(t){return Object.keys(v[t])}static get availableMeasures(){return Object.keys(v)}}},8774:(t,e,n)=>{n.d(e,{A:()=>r});class r{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,i=r._createBuffer(n);if(e)for(let 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versionedName(t){this._versionedName=t,this._versionedNameVersion=this._version}get self(){return this}setLength(t){if(t<0)throw new Error("should be >= 0");if(t==this._length)return;const e=Math.floor((t+31)/32);if(e>this._data.length||e+this.SHRINK_THRESHOLD<this._data.length){const t=new Uint32Array(e);this.copy(this._data,t,e>this._data.length?this._data.length:e),this._data=t}t>this._length&&(this._length%32>0&&(this._data[this.lengthInInts-1]&=(1<<(this._length%32&31))-1),this._data.fill(0,this.lengthInInts,e)),this._length=t,this._version++}static fromAnd(t,e){if(t._length!=e._length)throw new Error(`Lengths differ (${t._length} != ${e._length})`);const n=new r(t._length);n._length=t._length,n._data=r._createBuffer(n._length),n._version=0;const i=t.lengthInInts;for(let r=0;r<i;r++)n._data[r]=t._data[r]&e._data[r];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new r(t.length);e._version=0;for(let 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t=Math.floor(Math.random()*this._length);this.getBit(t)!=e&&(this.setFast(t,e),n++)}this.incrementVersion(n)}and(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]&=t._data[e];return this.incrementVersion(e),this}andNot(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");const n=this.lengthInInts;for(let e=0;e<n;e++)this._data[e]&=~t._data[e];return this.incrementVersion(e),this}notAnd(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]=~this._data[e]&t._data[e];return this.incrementVersion(e),this}not(t=!0){for(let t=0,e=this.lengthInInts;t<e;t++)this._data[t]=~this._data[t];return this.incrementVersion(t),this}or(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]|=t._data[e];return this.incrementVersion(e),this}xor(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]^=t._data[e];return this.incrementVersion(e),this}insertAt(t,e,n=!1){if(this.assureInRange(t,0,this._length,"pos"),0==e)return;const r=this._length;this.setLength(this._length+e);for(let n=r-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let r=t;r<t+e;r++)this.setBit(r,n)}removeAt(t,e=1){if(e<0)throw new Error("n cannot be negative");if(this.assureInRange(t,0,this._length-e,"pos"),this.contains(!0))for(let n=t;n<this._length-e;n++)this.setBit(n,this.getBit(n+e));this.setLength(this._length-e)}removeByMask(t,e=!0){if(this._length!=t.length)throw new Error("length != mask.length");if(t==this)this.setLength(t.countBits(!e)),this.setAll(!e);else{let n=0;for(let r=-1;-1!=(r=t.findNext(r,!e));)this.setFast(n++,this.getBit(r));this._length=n,this._version++}return this}getBit(t){return!!(this._data[Math.floor(t/32)]&1<<(31&t))}setBit(t,e,n=!0){this.setFast(t,e),this._version++}setFast(t,e){e?this._data[Math.floor(t/32)]|=1<<(31&t):this._data[Math.floor(t/32)]&=~(1<<(31&t))}setTrue(t){this._data[Math.floor(t/32)]|=1<<(31&t)}setFalse(t){this._data[Math.floor(t/32)]&=~(1<<(31&t))}trueCount(){return this.countBits(!0)}falseCount(){return this.countBits(!1)}countBits(t){if(0==this._length)return 0;if(this._selectedCountVersion!=this._version){this._selectedCount=0;const t=this.lengthInInts;let e=0;for(;e<t-1;e++)for(let t=this._data[e];0!=t;t>>>=8)this._selectedCount+=r._onBitCount[255&t];let n=this._data[e];const i=31&this._length;for(0!=i&&(n&=~(4294967295<<i));0!=n;n>>>=8)this._selectedCount+=r._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 i=this.lengthInInts;let s=0;for(;s<i-1;s++)for(let e=this._data[s]&t._data[s];0!=e;e>>>=8)n+=r._onBitCount[255&e];let o=this._data[s]&t._data[s];const h=31&this._length;for(0!=h&&(o&=~(4294967295<<h));0!=o;o>>>=8)n+=r._onBitCount[255&o];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 i=this.lengthInInts;for(let s=Math.floor(t/32);s<i;s++){let i=e?this._data[s]:~this._data[s];if(0!=n)i&=4294967295<<n&4294967295,n=0;else if(!e&&-4294967296==i)continue;for(let e=0;0!=i;e+=8,i>>>=8){const n=r._firstOnBit[255&i];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 i=Math.floor(t/32);i>=0;i--){let t=e?this._data[i]:~this._data[i];0!=n&&(t&=~(4294967295<<n),n=0);for(let e=24;0!=t;e-=8,t<<=8){const n=r._lastOnBit[t>>>24];if(n>=0)return n+32*i+e}}return-1}}r._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]),r._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]),r._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])},944:(t,e)=>{e.Vb=void 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