@datagrok-libraries/bio 5.16.3 → 5.16.5

package/index.d.ts

@@ -22,6 +22,7 @@ export { ALIGNMENT, ALPHABET, NOTATION, TAGS, getSplitter, splitterAsFasta, getS
 export { IMonomerLib, Monomer } from './src/types';
 export { NodeType, NodeCuttedType } from './src/trees';
 export { ITreeHelper, getTreeHelper } from './src/trees/tree-helper';
+export { IPdbHelper, getPdbHelper } from './src/pdb/pdb-helper';
 export { TreeCutOptions, IDendrogramService, getDendrogramService } from './src/trees/dendrogram';
 export { Shapes, TreeTypes } from './src/trees/phylocanvas';
 export { NotationConverter, splitAlignedSequences, SeqPalette, SeqPaletteBase, Aminoacids, AminoacidsPalettes, Nucleotides, NucleotidesPalettes, UnknownSeqPalettes, UnknownSeqPalette, PositionHeight, PositionInfo, PositionMonomerInfo, WebLogoViewer, UnitsHandler, DrawStyle, printLeftOrCentered, FastaFileHandler, VdRegionType, VdRegion, IVdRegionsViewer, isLeaf, PhylocanvasTreeNode, NodeStyleType, StylesType, IPhylocanvasGlViewer, TreeTypesNames, PhylocanvasGlServiceBase, CanvasCallback, PhylocanvasGlTask, getPhylocanvasGlService, parseNewick, getNglGlService, NglGlServiceBase, NglGlTask, MonomerWorks, MonomerLib, readLibrary };

package/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,UAAU,EAAE,kBAAkB,EAAC,MAAM,kBAAkB,CAAC;AAChE,OAAO,EAAC,YAAY,EAAC,MAAM,mCAAmC,CAAC;AAC/D,OAAO,EAAC,WAAW,EAAE,mBAAmB,EAAC,MAAM,mBAAmB,CAAC;AACnE,OAAO,EAAC,UAAU,EAAE,cAAc,EAAC,MAAM,oBAAoB,CAAC;AAC9D,OAAO,EAAC,iBAAiB,EAAE,kBAAkB,EAAC,MAAM,eAAe,CAAC;AACpE,OAAO,EAAC,SAAS,EAAE,mBAAmB,EAAC,MAAM,2BAA2B,CAAC;AACzE,OAAO,EAAC,gBAAgB,EAAC,MAAM,2BAA2B,CAAC;AAC3D,OAAO,EAAC,iBAAiB,EAAC,MAAM,gCAAgC,CAAC;AACjE,OAAO,EAAC,qBAAqB,EAAC,MAAM,sBAAsB,CAAC;AAE3D,OAAO,EAAC,YAAY,EAAC,MAAM,2BAA2B,CAAC;AACvD,OAAO,EAAC,QAAQ,EAAE,YAAY,EAAC,MAAM,kBAAkB,CAAC;AACxD,OAAO,EACL,cAAc,EACd,uBAAuB,EACvB,oBAAoB,EACpB,aAAa,EACb,wBAAwB,EACxB,iBAAiB,EACjB,UAAU,EACV,cAAc,EACf,MAAM,qCAAqC,CAAC;AAC7C,OAAO,EAAC,gBAAgB,EAAC,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAC,cAAc,EAAE,YAAY,EAAE,mBAAmB,EAAE,aAAa,EAAC,MAAM,+BAA+B,CAAC;AAC/G,OAAO,EAAC,UAAU,EAAC,MAAM,iCAAiC,CAAC;AAC3D,OAAO,EAAC,WAAW,EAAC,MAAM,mCAAmC,CAAC;AAC9D,OAAO,EACL,eAAe,EACf,gBAAgB,EAChB,SAAS,EACV,MAAM,6BAA6B,CAAC;AAErC,OAAO,EAAC,WAAW,EAAE,mBAAmB,EAAC,MAAM,yBAAyB,CAAC;AACzE,OAAO,EAAC,MAAM,EAAC,MAAM,aAAa,CAAC;AAEnC,OAAO,EACL,cAAc,EACf,MAAM,6BAA6B,CAAC;AAErC,OAAO,EACL,SAAS,EACT,QAAQ,EACR,QAAQ,EACR,IAAI,EACJ,WAAW,EACX,eAAe,EACf,oBAAoB,EACpB,YAAY,EACZ,cAAc,EACd,cAAc,EACd,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,WAAW,EACX,qBAAqB,EACtB,MAAM,2BAA2B,CAAC;AAEnC,OAAO,EACL,WAAW,EACX,OAAO,EACR,MAAM,aAAa,CAAC;AAErB,OAAO,EACL,QAAQ,EACR,cAAc,EACf,MAAM,aAAa,CAAC;AAErB,OAAO,EACL,WAAW,EACX,aAAa,EACd,MAAM,yBAAyB,CAAC;AAEjC,OAAO,EACL,UAAU,EACV,YAAY,EACb,MAAM,sBAAsB,CAAC;AAE9B,OAAO,EACL,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACrB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EACL,MAAM,EACN,SAAS,EACV,MAAM,yBAAyB,CAAC;AAEjC,OAAO,EACL,iBAAiB,EACjB,qBAAqB,EACrB,UAAU,EACV,cAAc,EACd,UAAU,EACV,kBAAkB,EAClB,WAAW,EACX,mBAAmB,EACnB,kBAAkB,EAClB,iBAAiB,EACjB,cAAc,EACd,YAAY,EACZ,mBAAmB,EACnB,aAAa,EACb,YAAY,EACZ,SAAS,EACT,mBAAmB,EACnB,gBAAgB,EAChB,YAAY,EACZ,QAAQ,EACR,gBAAgB,EAEhB,MAAM,EACN,mBAAmB,EAEnB,aAAa,EAAE,UAAU,EAEzB,oBAAoB,EACpB,cAAc,EACd,wBAAwB,EACxB,cAAc,EACd,iBAAiB,EACjB,uBAAuB,EAEvB,WAAW,EAIX,eAAe,EACf,gBAAgB,EAChB,SAAS,EAGT,YAAY,EACZ,UAAU,EACV,WAAW,EACZ,CAAC"}

package/index.js

@@ -19,6 +19,7 @@ import { isLeaf } from './src/trees';
 export { DistanceMatrix } from './src/trees/distance-matrix';
 export { getSplitter, splitterAsFasta, getSplitterForColumn, monomerToShort, splitterAsHelm, getStats, pickUpPalette, getPaletteByType, getAlphabet, getAlphabetSimilarity } from './src/utils/macromolecule';
 export { getTreeHelper } from './src/trees/tree-helper';
+export { getPdbHelper } from './src/pdb/pdb-helper';
 export { getDendrogramService } from './src/trees/dendrogram';
 export { Shapes, TreeTypes } from './src/trees/phylocanvas';
 export { NotationConverter, splitAlignedSequences, SeqPaletteBase, Aminoacids, AminoacidsPalettes, Nucleotides, NucleotidesPalettes, UnknownSeqPalettes, UnknownSeqPalette, PositionHeight, PositionInfo, PositionMonomerInfo, WebLogoViewer, UnitsHandler, DrawStyle, printLeftOrCentered, FastaFileHandler, VdRegionType, VdRegion, isLeaf, TreeTypesNames, PhylocanvasGlServiceBase, getPhylocanvasGlService, parseNewick, 
@@ -27,4 +28,4 @@ export { NotationConverter, splitAlignedSequences, SeqPaletteBase, Aminoacids, A
 getNglGlService, NglGlServiceBase, 
 //Monomer lib and features
 MonomerWorks, MonomerLib, readLibrary };
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1lclxufSBmcm9tICcuL3NyYy90eXBlcyc7XG5cbmV4cG9ydCB7XG4gIE5vZGVUeXBlLFxuICBOb2RlQ3V0dGVkVHlwZVxufSBmcm9tICcuL3NyYy90cmVlcyc7XG5cbmV4cG9ydCB7XG4gIElUcmVlSGVscGVyLFxuICBnZXRUcmVlSGVscGVyXG59IGZyb20gJy4vc3JjL3RyZWVzL3RyZWUtaGVscGVyJztcblxuZXhwb3J0IHtcbiAgSVBkYkhlbHBlcixcbiAgZ2V0UGRiSGVscGVyXG59IGZyb20gJy4vc3JjL3BkYi9wZGItaGVscGVyJztcblxuZXhwb3J0IHtcbiAgVHJlZUN1dE9wdGlvbnMsXG4gIElEZW5kcm9ncmFtU2VydmljZSxcbiAgZ2V0RGVuZHJvZ3JhbVNlcnZpY2Vcbn0gZnJvbSAnLi9zcmMvdHJlZXMvZGVuZHJvZ3JhbSc7XG5cbmV4cG9ydCB7XG4gIFNoYXBlcyxcbiAgVHJlZVR5cGVzXG59IGZyb20gJy4vc3JjL3RyZWVzL3BoeWxvY2FudmFzJztcblxuZXhwb3J0IHtcbiAgTm90YXRpb25Db252ZXJ0ZXIsXG4gIHNwbGl0QWxpZ25lZFNlcXVlbmNlcyxcbiAgU2VxUGFsZXR0ZSxcbiAgU2VxUGFsZXR0ZUJhc2UsXG4gIEFtaW5vYWNpZHMsXG4gIEFtaW5vYWNpZHNQYWxldHRlcyxcbiAgTnVjbGVvdGlkZXMsXG4gIE51Y2xlb3RpZGVzUGFsZXR0ZXMsXG4gIFVua25vd25TZXFQYWxldHRlcyxcbiAgVW5rbm93blNlcVBhbGV0dGUsXG4gIFBvc2l0aW9uSGVpZ2h0LFxuICBQb3NpdGlvbkluZm8sXG4gIFBvc2l0aW9uTW9ub21lckluZm8sXG4gIFdlYkxvZ29WaWV3ZXIsXG4gIFVuaXRzSGFuZGxlcixcbiAgRHJhd1N0eWxlLFxuICBwcmludExlZnRPckNlbnRlcmVkLFxuICBGYXN0YUZpbGVIYW5kbGVyLFxuICBWZFJlZ2lvblR5cGUsXG4gIFZkUmVnaW9uLFxuICBJVmRSZWdpb25zVmlld2VyLFxuXG4gIGlzTGVhZixcbiAgUGh5bG9jYW52YXNUcmVlTm9kZSxcbiAgLy8gdHJlZVRyYXZlcnNhbCxcbiAgTm9kZVN0eWxlVHlwZSwgU3R5bGVzVHlwZSxcblxuICBJUGh5bG9jYW52YXNHbFZpZXdlcixcbiAgVHJlZVR5cGVzTmFtZXMsXG4gIFBoeWxvY2FudmFzR2xTZXJ2aWNlQmFzZSxcbiAgQ2FudmFzQ2FsbGJhY2ssXG4gIFBoeWxvY2FudmFzR2xUYXNrLFxuICBnZXRQaHlsb2NhbnZhc0dsU2VydmljZSxcblxuICBwYXJzZU5ld2ljayxcbiAgLy8gVXRpbHMsXG4gIC8vIE5ld2ljayxcblxuICBnZXROZ2xHbFNlcnZpY2UsXG4gIE5nbEdsU2VydmljZUJhc2UsXG4gIE5nbEdsVGFzayxcblxuICAvL01vbm9tZXIgbGliIGFuZCBmZWF0dXJlc1xuICBNb25vbWVyV29ya3MsXG4gIE1vbm9tZXJMaWIsXG4gIHJlYWRMaWJyYXJ5XG59O1xuIl19

package/index.ts

@@ -70,6 +70,11 @@ export {
   getTreeHelper
 } from './src/trees/tree-helper';
 
+export {
+  IPdbHelper,
+  getPdbHelper
+} from './src/pdb/pdb-helper';
+
 export {
   TreeCutOptions,
   IDendrogramService,

package/package.json

@@ -4,7 +4,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.16.3",
+  "version": "5.16.5",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.22",

package/src/pdb/index.d.ts

@@ -0,0 +1,4 @@
+export declare enum TAGS {
+    PDB = ".pdb"
+}
+//# sourceMappingURL=index.d.ts.map

package/src/pdb/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,oBAAY,IAAI;IACd,GAAG,SAAS;CACb"}

package/src/pdb/index.js

@@ -0,0 +1,5 @@
+export var TAGS;
+(function (TAGS) {
+    TAGS["PDB"] = ".pdb";
+})(TAGS || (TAGS = {}));
+//# sourceMappingURL=data:application/json;base64,eyJ2ZXJzaW9uIjozLCJmaWxlIjoiaW5kZXguanMiLCJzb3VyY2VSb290IjoiIiwic291cmNlcyI6WyJpbmRleC50cyJdLCJuYW1lcyI6W10sIm1hcHBpbmdzIjoiQUFJQSxNQUFNLENBQU4sSUFBWSxJQUVYO0FBRkQsV0FBWSxJQUFJO0lBQ2Qsb0JBQVksQ0FBQTtBQUNkLENBQUMsRUFGVyxJQUFJLEtBQUosSUFBSSxRQUVmIiwic291cmNlc0NvbnRlbnQiOlsiaW1wb3J0ICogYXMgdWkgZnJvbSAnZGF0YWdyb2stYXBpL3VpJztcbmltcG9ydCAqIGFzIGdyb2sgZnJvbSAnZGF0YWdyb2stYXBpL2dyb2snO1xuaW1wb3J0ICogYXMgREcgZnJvbSAnZGF0YWdyb2stYXBpL2RnJztcblxuZXhwb3J0IGVudW0gVEFHUyB7XG4gIFBEQiA9ICcucGRiJ1xufVxuIl19

package/src/pdb/pdb-helper.d.ts

@@ -0,0 +1,6 @@
+import * as DG from 'datagrok-api/dg';
+export interface IPdbHelper {
+    pdbToDf(pdb: string, name: string): Promise<DG.DataFrame>;
+}
+export declare function getPdbHelper(): Promise<IPdbHelper>;
+//# sourceMappingURL=pdb-helper.d.ts.map

package/src/pdb/pdb-helper.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"pdb-helper.d.ts","sourceRoot":"","sources":["pdb-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,MAAM,WAAW,UAAU;IACzB,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC;CAC3D;AAED,wBAAsB,YAAY,IAAI,OAAO,CAAC,UAAU,CAAC,CAQxD"}

package/src/pdb/pdb-helper.js

@@ -0,0 +1,21 @@
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+import * as DG from 'datagrok-api/dg';
+export function getPdbHelper() {
+    return __awaiter(this, void 0, void 0, function* () {
+        const packageName = 'BiostructureViewer';
+        const funcList = DG.Func.find({ package: packageName, name: 'getPdbHelper' });
+        if (funcList.length === 0)
+            throw new Error(`Package '${packageName}' must be installed for PdbHelper.`);
+        const res = (yield funcList[0].prepare().call()).getOutputParamValue();
+        return res;
+    });
+}
+//# sourceMappingURL=data:application/json;base64,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

package/src/trees/dendrogram.d.ts

@@ -1,9 +1,13 @@
 import * as DG from 'datagrok-api/dg';
 import { GridNeighbor } from '@datagrok-libraries/gridext/src/ui/GridNeighbor';
 import { NodeType } from '.';
+/**
+ * min - undefined for root at 0
+ * max - undefined for total length of the tree
+ */
 export type TreeCutOptions = {
-    min: number;
-    max: number;
+    min?: number;
+    max?: number;
     dataDf: DG.DataFrame;
     clusterDf: DG.DataFrame;
     clusterColName: string;

package/src/trees/dendrogram.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dendrogram.d.ts","sourceRoot":"","sources":["dendrogram.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iDAAiD,CAAC;AAC7E,OAAO,EAAC,QAAQ,EAAC,MAAM,GAAG,CAAC;AAE3B,MAAM,MAAM,cAAc,GAAG;IAC3B,GAAG,EAAE,MAAM,CAAC;IAAC,GAAG,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,EAAE,CAAC,SAAS,CAAC;IAC/C,SAAS,EAAE,EAAE,CAAC,SAAS,CAAC;IAAC,cAAc,EAAE,MAAM,CAAC;CACjD,CAAA;AAED,MAAM,WAAW,kBAAkB;IACjC,0EAA0E;IAC1E,iBAAiB,CACf,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,QAAQ,EAAE,QAAQ,GAAG,IAAI,EAAE,WAAW,CAAC,EAAE,MAAM,EAAE,aAAa,CAAC,EAAE,MAAM,EAAE,GAAG,CAAC,EAAE,cAAc,GAC3G,YAAY,CAAC;CACjB;AAED,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,kBAAkB,CAAC,CAExE"}
+{"version":3,"file":"dendrogram.d.ts","sourceRoot":"","sources":["dendrogram.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iDAAiD,CAAC;AAC7E,OAAO,EAAC,QAAQ,EAAC,MAAM,GAAG,CAAC;AAE3B;;;GAGG;AACH,MAAM,MAAM,cAAc,GAAG;IAC3B,GAAG,CAAC,EAAE,MAAM,CAAC;IAAC,GAAG,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,EAAE,CAAC,SAAS,CAAC;IACjD,SAAS,EAAE,EAAE,CAAC,SAAS,CAAC;IAAC,cAAc,EAAE,MAAM,CAAC;CACjD,CAAA;AAED,MAAM,WAAW,kBAAkB;IACjC,0EAA0E;IAC1E,iBAAiB,CACf,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,QAAQ,EAAE,QAAQ,GAAG,IAAI,EAAE,WAAW,CAAC,EAAE,MAAM,EAAE,aAAa,CAAC,EAAE,MAAM,EAAE,GAAG,CAAC,EAAE,cAAc,GAC3G,YAAY,CAAC;CACjB;AAED,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,kBAAkB,CAAC,CAExE"}

package/src/trees/dendrogram.js

@@ -13,4 +13,4 @@ export function getDendrogramService() {
         return yield grok.functions.call('Dendrogram:getDendrogramService', {});
     });
 }
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