@datagrok-libraries/bio 5.41.0 → 5.41.2

package/CHANGELOG.md

@@ -1,5 +1,24 @@
 # bio changelog
 
+## 5.41.2 (2024-05-13)
+
+### Bug fixes
+
+Fix MonomerLib.getSummary for backward compatibility
+Fix cell renderer async base for sync rendering
+
+## 5.41.1 (2024-05-13)
+
+### Features
+
+* Add types for Helm Web Editor
+
+### Bug fixes
+
+* Unveil cell renderer errors for tests
+* Fix cell renderer for StackOverflow error on long seqs
+* Optimize SeqHandler.getSplitter for split limit (separator)
+
 ## 5.41.0 (2024-05-01)
 
 Optimize cell renderer on async renderer base

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.41.0",
+  "version": "5.41.2",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.71",

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

@@ -1,3 +1,4 @@
+import '../types/helm';
 import * as org from 'org';
 import { IHelmWebEditor } from './types';
 export interface IHelmHelper {

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

@@ -1 +1 @@
-{"version":3,"file":"helm-helper.d.ts","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,GAAG,MAAM,KAAK,CAAC;AAE3B,OAAO,EAAC,cAAc,EAAC,MAAM,SAAS,CAAC;AAEvC,MAAM,WAAW,WAAW;IAC1B,mBAAmB,IAAI,cAAc,CAAC;IAEtC,kBAAkB,CAAC,IAAI,EAAE,cAAc,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,GAAG,CAAC,IAAI,CAAC,aAAa,CAAC;CACjF;AAED,wBAAsB,aAAa,IAAI,OAAO,CAAC,WAAW,CAAC,CAO1D"}
+{"version":3,"file":"helm-helper.d.ts","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AAIA,OAAO,eAAe,CAAC;AACvB,OAAO,KAAK,GAAG,MAAM,KAAK,CAAC;AAE3B,OAAO,EAAC,cAAc,EAAC,MAAM,SAAS,CAAC;AAEvC,MAAM,WAAW,WAAW;IAC1B,mBAAmB,IAAI,cAAc,CAAC;IAEtC,kBAAkB,CAAC,IAAI,EAAE,cAAc,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,GAAG,CAAC,IAAI,CAAC,aAAa,CAAC;CACjF;AAED,wBAAsB,aAAa,IAAI,OAAO,CAAC,WAAW,CAAC,CAO1D"}

package/src/helm/helm-helper.js

@@ -1,4 +1,5 @@
 import * as DG from 'datagrok-api/dg';
+import '../types/helm';
 export async function getHelmHelper() {
     const packageName = 'Helm';
     const funcList = DG.Func.find({ package: packageName, name: `getHelmHelper` });

package/src/helm/helm-helper.js.map

@@ -1 +1 @@
-{"version":3,"file":"helm-helper.js","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAatC,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,MAAM,WAAW,GAAG,MAAM,CAAC;IAC3B,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,eAAe,EAAC,CAAC,CAAC;IAC7E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,qCAAqC,CAAC,CAAC;IAChF,MAAM,GAAG,GAAG,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAiB,CAAC;IACtF,OAAO,GAAG,CAAC;AACb,CAAC"}
+{"version":3,"file":"helm-helper.js","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,eAAe,CAAC;AAWvB,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,MAAM,WAAW,GAAG,MAAM,CAAC;IAC3B,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,eAAe,EAAC,CAAC,CAAC;IAC7E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,qCAAqC,CAAC,CAAC;IAChF,MAAM,GAAG,GAAG,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAiB,CAAC;IACtF,OAAO,GAAG,CAAC;AACb,CAAC"}

package/src/monomer-works/monomer-utils.d.ts

@@ -1,4 +1,5 @@
 import * as DG from 'datagrok-api/dg';
+import { Observable } from 'rxjs';
 import { IMonomerLib } from '../types/index';
 import { ISeqSplitted } from '../utils/macromolecule/types';
 export declare function encodeMonomers(col: DG.Column): DG.Column | null;
@@ -8,9 +9,27 @@ export declare function createMomomersMolDict(lib: any[]): {
     [key: string]: string | any;
 };
 export declare function createJsonMonomerLibFromSdf(table: DG.DataFrame): any;
+export interface IMonomerLibFileEventManager {
+    get addLibraryFileRequested$(): Observable<void>;
+    get updateUIControlsRequested$(): Observable<string[]>;
+    get librarySelectionRequested$(): Observable<[string, boolean]>;
+    updateLibrarySelectionStatus(libFileName: string, isSelected: boolean): void;
+}
+export interface IMonomerLibFileManager {
+    get eventManager(): IMonomerLibFileEventManager;
+    getValidLibraryPaths(): string[];
+    getValidLibraryPathsAsynchronously(): Promise<string[]>;
+    addLibraryFile(fileContent: string, fileName: string): Promise<void>;
+    deleteLibraryFile(fileName: string): Promise<void>;
+    loadLibraryFromFile(path: string, fileName: string): Promise<IMonomerLib>;
+}
 export interface IMonomerLibHelper {
+    get eventManager(): IMonomerLibFileEventManager;
+    /** Ensures files are loaded and validated, throws error after timeout */
+    awaitLoaded(timeout?: number): Promise<void>;
     /** Singleton monomer library */
     getBioLib(): IMonomerLib;
+    getFileManager(): Promise<IMonomerLibFileManager>;
     /** (Re)Loads libraries based on settings in user storage {@link LIB_STORAGE_NAME} to singleton.
      * @param {boolean} reload Clean {@link monomerLib} before load libraries [false]
      */

package/src/monomer-works/monomer-utils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAOtC,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAa,YAAY,EAAC,MAAM,8BAA8B,CAAC;AAMtE,wBAAgB,cAAc,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,GAAG,IAAI,CAuB/D;AAED,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAsB3F;AAED,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAkBhG;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,GAAG,CAAA;CAAE,CAYjF;AAGD,wBAAgB,2BAA2B,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,GAAG,GAAG,CAoCpE;AAED,MAAM,WAAW,iBAAiB;IAChC,gCAAgC;IAChC,SAAS,IAAI,WAAW,CAAC;IAEzB;;OAEG;IACH,aAAa,CAAC,MAAM,CAAC,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE/C,6DAA6D;IAC7D,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CACnE;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,iBAAiB,CAAC,CAOtE;AAED;;;;;0EAK0E;AAG1E,wBAAsB,sBAAsB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAC1I,wBAAsB,sBAAsB,CAAC,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AA6DhJ;;+KAE+K;AAC/K,wBAAsB,0BAA0B,CAAC,UAAU,EAAE,MAAM,EAAE,GAClE,OAAO,CAAC;IAAE,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAE,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,CAAA;CAAE,CAAC,CAqB1F;AAED,wBAAsB,4BAA4B,CAAC,UAAU,EAAE,MAAM,EAAE,EAAE,eAAe,GAAE,MAAiB,GACxG,OAAO,CAAC;IAAE,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAE,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,CAAA;CAAE,CAAC,CAmC1F"}
+{"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAShC,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAa,YAAY,EAAC,MAAM,8BAA8B,CAAC;AAItE,wBAAgB,cAAc,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,GAAG,IAAI,CAuB/D;AAED,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAsB3F;AAED,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAkBhG;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,GAAG,CAAA;CAAE,CAYjF;AAGD,wBAAgB,2BAA2B,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,GAAG,GAAG,CAoCpE;AAED,MAAM,WAAW,2BAA2B;IAC1C,IAAI,wBAAwB,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC;IACjD,IAAI,0BAA0B,IAAI,UAAU,CAAC,MAAM,EAAE,CAAC,CAAC;IACvD,IAAI,0BAA0B,IAAI,UAAU,CAAC,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;IAEhE,4BAA4B,CAAC,WAAW,EAAE,MAAM,EAAE,UAAU,EAAE,OAAO,GAAG,IAAI,CAAC;CAC9E;AAED,MAAM,WAAW,sBAAsB;IACrC,IAAI,YAAY,IAAI,2BAA2B,CAAC;IAEhD,oBAAoB,IAAI,MAAM,EAAE,CAAC;IACjC,kCAAkC,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IAExD,cAAc,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IACrE,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAEnD,mBAAmB,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CAC3E;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,YAAY,IAAI,2BAA2B,CAAC;IAEhD,yEAAyE;IACzE,WAAW,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE7C,gCAAgC;IAChC,SAAS,IAAI,WAAW,CAAC;IAEzB,cAAc,IAAI,OAAO,CAAC,sBAAsB,CAAC,CAAC;IAElD;;OAEG;IACH,aAAa,CAAC,MAAM,CAAC,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE/C,6DAA6D;IAC7D,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CACnE;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,iBAAiB,CAAC,CAOtE;AAED;;;;;0EAK0E;AAG1E,wBAAsB,sBAAsB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAC1I,wBAAsB,sBAAsB,CAAC,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AA6DhJ;;+KAE+K;AAC/K,wBAAsB,0BAA0B,CAAC,UAAU,EAAE,MAAM,EAAE,GAClE,OAAO,CAAC;IAAE,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAE,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,CAAA;CAAE,CAAC,CAqB1F;AAED,wBAAsB,4BAA4B,CAAC,UAAU,EAAE,MAAM,EAAE,EAAE,eAAe,GAAE,MAAiB,GACxG,OAAO,CAAC;IAAE,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAE,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,CAAA;CAAE,CAAC,CAmC1F"}

package/src/monomer-works/monomer-utils.js

@@ -1,11 +1,11 @@
 // import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
+import { tanimotoSimilarity } from '@datagrok-libraries/ml/src/distance-metrics-methods';
 import { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME, } from '../utils/const';
 import { GAP_SYMBOL } from '../utils/macromolecule/types';
 import { SeqHandler } from '../utils/seq-handler';
 import { splitAlignedSequences } from '../utils/splitter';
-import { tanimotoSimilarity } from '@datagrok-libraries/ml/src/distance-metrics-methods';
 export function encodeMonomers(col) {
     let encodeSymbol = MONOMER_ENCODE_MIN;
     const monomerSymbolDict = {};
@@ -102,7 +102,7 @@ export function createJsonMonomerLibFromSdf(table) {
                     const rgroup = {};
                     const altAtom = g.substring(g.lastIndexOf(']') + 1);
                     const radicalNum = g.match(/\[R(\d+)\]/)[1];
-                    rgroup["capGroupSMILES" /* HELM_RGROUP_FIELDS.CAP_GROUP_SMILES */] = altAtom === 'H' ? `[*:${radicalNum}][H]` : `O[*:${radicalNum}]`;
+                    rgroup["capGroupSmiles" /* HELM_RGROUP_FIELDS.CAP_GROUP_SMILES */] = altAtom === 'H' ? `[*:${radicalNum}][H]` : `O[*:${radicalNum}]`;
                     rgroup["alternateId" /* HELM_RGROUP_FIELDS.ALTERNATE_ID */] = altAtom === 'H' ? `R${radicalNum}-H` : `R${radicalNum}-OH`;
                     rgroup["capGroupName" /* HELM_RGROUP_FIELDS.CAP_GROUP_NAME */] = altAtom === 'H' ? `H` : `OH`;
                     rgroup["label" /* HELM_RGROUP_FIELDS.LABEL */] = `R${radicalNum}`;

package/src/monomer-works/monomer-utils.js.map

@@ -1 +1 @@
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package/src/monomer-works/monomer-works.d.ts

@@ -1,4 +1,4 @@
-import { IMonomerLib } from '../types';
+import { IMonomerLib, HelmType, PolymerType } from '../types';
 /** Hypothetical interface to convert mol block notation.
  * It should be placed in the chem-meta package, and have an implementation in the Chem package.
  * So dependency of MonomerWorks on molfile conversion operation becomes explicit.
@@ -10,6 +10,7 @@ export interface IMolfileConverter {
 export declare class MonomerWorks {
     private monomerLib;
     constructor(monomerLib: IMonomerLib);
-    getCappedRotatedMonomer(monomerType: string, monomerName: string): string | null;
+    getCappedRotatedMonomer(monomerType: PolymerType, monomerName: string): string | null;
 }
+export declare function helmTypeToPolymerType(helmType: HelmType): PolymerType;
 //# sourceMappingURL=monomer-works.d.ts.map

package/src/monomer-works/monomer-works.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"monomer-works.d.ts","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,WAAW,EAAC,MAAM,UAAU,CAAC;AAGrC;;;GAGG;AACH,MAAM,WAAW,iBAAiB;IAChC,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAAC;IAEzC,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAAC;CAC1C;AAED,qBAAa,YAAY;IACvB,OAAO,CAAC,UAAU,CAAc;gBAIpB,UAAU,EAAE,WAAW;IAM5B,uBAAuB,CAAC,WAAW,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;CAOxF"}
+{"version":3,"file":"monomer-works.d.ts","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,WAAW,EAAE,QAAQ,EAAE,WAAW,EAAC,MAAM,UAAU,CAAC;AAG5D;;;GAGG;AACH,MAAM,WAAW,iBAAiB;IAChC,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAAC;IAEzC,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAAC;CAC1C;AAED,qBAAa,YAAY;IACvB,OAAO,CAAC,UAAU,CAAc;gBAIpB,UAAU,EAAE,WAAW;IAM5B,uBAAuB,CAAC,WAAW,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;CAQ7F;AAED,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,QAAQ,GAAG,WAAW,CAyBrE"}

package/src/monomer-works/monomer-works.js

@@ -6,10 +6,37 @@ export class MonomerWorks {
     }
     //types according to Monomer possible
     getCappedRotatedMonomer(monomerType, monomerName) {
+        // TODO: Check type of monomerType arg
         const monomer = this.monomerLib.getMonomer(monomerType, monomerName);
         if (monomer)
             return monomer.molfile; //TODO cap
         return null;
     }
 }
+export function helmTypeToPolymerType(helmType) {
+    let polymerType = undefined;
+    switch (helmType) {
+        case "HELM_BASE" /* HelmTypes.BASE */:
+        case "HELM_SUGAR" /* HelmTypes.SUGAR */: // r - ribose, d - deoxyribose
+        case "HELM_LINKER" /* HelmTypes.LINKER */: // p - phosphate
+        case "HELM_NUCLETIDE" /* HelmTypes.NUCLEOTIDE */:
+        // @ts-ignore
+        case 'nucleotide':
+            polymerType = "RNA" /* PolymerTypes.RNA */;
+            break;
+        case "HELM_AA" /* HelmTypes.AA */:
+            polymerType = "PEPTIDE" /* PolymerTypes.PEPTIDE */;
+            break;
+        case "HELM_CHEM" /* HelmTypes.CHEM */:
+            polymerType = "CHEM" /* PolymerTypes.CHEM */;
+            break;
+        case "HELM_BLOB" /* HelmTypes.BLOB */:
+            polymerType = "BLOB" /* PolymerTypes.BLOB */;
+            break;
+        default:
+            polymerType = "PEPTIDE" /* PolymerTypes.PEPTIDE */;
+            console.warn(`Unexpected HelmType '${helmType}'`);
+    }
+    return polymerType;
+}
 //# sourceMappingURL=monomer-works.js.map

package/src/monomer-works/monomer-works.js.map

@@ -1 +1 @@
-{"version":3,"file":"monomer-works.js","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAiBA,MAAM,OAAO,YAAY;IAGvB,8CAA8C;IAE9C,YAAY,UAAuB,CAAA,yCAAyC;QAC1E,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;QAC7B,2CAA2C;IAC7C,CAAC;IAED,qCAAqC;IAC9B,uBAAuB,CAAC,WAAmB,EAAE,WAAmB;QACrE,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QACrE,IAAI,OAAO;YACT,OAAO,OAAO,CAAC,OAAO,CAAC,CAAC,UAAU;QAEpC,OAAO,IAAI,CAAC;IACd,CAAC;CACF"}
+{"version":3,"file":"monomer-works.js","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAiBA,MAAM,OAAO,YAAY;IAGvB,8CAA8C;IAE9C,YAAY,UAAuB,CAAA,yCAAyC;QAC1E,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;QAC7B,2CAA2C;IAC7C,CAAC;IAED,qCAAqC;IAC9B,uBAAuB,CAAC,WAAwB,EAAE,WAAmB;QAC1E,sCAAsC;QACtC,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QACrE,IAAI,OAAO;YACT,OAAO,OAAO,CAAC,OAAO,CAAC,CAAC,UAAU;QAEpC,OAAO,IAAI,CAAC;IACd,CAAC;CACF;AAED,MAAM,UAAU,qBAAqB,CAAC,QAAkB;IACtD,IAAI,WAAW,GAA4B,SAAS,CAAC;IACrD,QAAQ,QAAQ,EAAE;QAClB,sCAAoB;QACpB,wCAAqB,CAAC,8BAA8B;QACpD,0CAAsB,CAAC,gBAAgB;QACvC,iDAA0B;QACxB,aAAa;QACf,KAAK,YAAY;YACf,WAAW,+BAAmB,CAAC;YAC/B,MAAM;QACR;YACE,WAAW,uCAAuB,CAAC;YACnC,MAAM;QACR;YACE,WAAW,iCAAoB,CAAC;YAChC,MAAM;QACR;YACE,WAAW,iCAAoB,CAAC;YAChC,MAAM;QACR;YACE,WAAW,uCAAuB,CAAC;YACnC,OAAO,CAAC,IAAI,CAAC,wBAAwB,QAAQ,GAAG,CAAC,CAAC;KACnD;IACD,OAAO,WAAW,CAAC;AACrB,CAAC"}

package/src/monomer-works/to-atomic-level.js

@@ -252,7 +252,7 @@ export function parseCapGroups(rGroupObjList) {
     // supposing that elements in rGroupObjList are sorted w.r.t. the rgroups idx
     const capGroupsArray = [];
     for (const obj of rGroupObjList) {
-        let capGroup = obj["capGroupSMILES" /* HELM_RGROUP_FIELDS.CAP_GROUP_SMILES */];
+        let capGroup = obj["capGroupSmiles" /* HELM_RGROUP_FIELDS.CAP_GROUP_SMILES */];
         // in some cases the smiles field is written with uppercase
         if (!capGroup)
             capGroup = obj["capGroupSMILES" /* HELM_RGROUP_FIELDS.CAP_GROUP_SMILES_UPPERCASE */];

package/src/tests/monomer-lib-tests.d.ts

@@ -0,0 +1,7 @@
+import { IMonomerLib, MonomerLibSummaryType } from '../types/index';
+/** Summary for HELMCoreLibrary.json */
+export declare const defaultMonomerLibSummary: MonomerLibSummaryType;
+export declare function expectMonomerLib(lib: IMonomerLib, summary?: {
+    [polymerType: string]: number;
+}): void;
+//# sourceMappingURL=monomer-lib-tests.d.ts.map

package/src/tests/monomer-lib-tests.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"monomer-lib-tests.d.ts","sourceRoot":"","sources":["monomer-lib-tests.ts"],"names":[],"mappings":"AAMA,OAAO,EAAC,WAAW,EAAE,qBAAqB,EAAC,MAAM,gBAAgB,CAAC;AAElE,uCAAuC;AACvC,eAAO,MAAM,wBAAwB,EAAE,qBAA+D,CAAC;AAEvG,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,WAAW,EAAE,OAAO,CAAC,EAAE;IAAE,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,GAAG,IAAI,CAqBpG"}

package/src/tests/monomer-lib-tests.js

@@ -0,0 +1,27 @@
+import { expectObject } from '@datagrok-libraries/utils/src/test';
+/** Summary for HELMCoreLibrary.json */
+export const defaultMonomerLibSummary = { 'PEPTIDE': 322, 'RNA': 383, 'CHEM': 0 };
+export function expectMonomerLib(lib, summary) {
+    const exp = summary ?? defaultMonomerLibSummary;
+    const act = lib.getSummaryObj();
+    for (const pt in exp)
+        if (!exp[pt])
+            delete exp[pt];
+    for (const pt in act)
+        if (!act[pt])
+            delete act[pt];
+    if (Object.keys(exp).length == 0 && Object.keys(act).length != 0)
+        throw new Error('Expected empty monomer lib, actual is not.');
+    else if (Object.keys(exp).length != 0 && Object.keys(act).length == 0)
+        throw new Error('Expected non-empty monomer lib, actual is empty.');
+    else {
+        try {
+            expectObject(act, exp);
+            expectObject(exp, act);
+        }
+        catch (err) {
+            throw new Error(`Expected monomer lib ${JSON.stringify(exp)} does not match actual ${JSON.stringify(act)}.`);
+        }
+    }
+}
+//# sourceMappingURL=monomer-lib-tests.js.map

package/src/tests/monomer-lib-tests.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"monomer-lib-tests.js","sourceRoot":"","sources":["monomer-lib-tests.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,YAAY,EAAC,MAAM,oCAAoC,CAAC;AAIhE,uCAAuC;AACvC,MAAM,CAAC,MAAM,wBAAwB,GAA0B,EAAC,SAAS,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAC,CAAC;AAEvG,MAAM,UAAU,gBAAgB,CAAC,GAAgB,EAAE,OAA2C;IAC5F,MAAM,GAAG,GAA0B,OAAO,IAAI,wBAAwB,CAAC;IACvE,MAAM,GAAG,GAA0B,GAAG,CAAC,aAAa,EAAE,CAAC;IAEvD,KAAK,MAAM,EAAE,IAAI,GAAG;QAClB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YAAE,OAAO,GAAG,CAAC,EAAE,CAAC,CAAC;IAC/B,KAAK,MAAM,EAAE,IAAI,GAAG;QAClB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YAAE,OAAO,GAAG,CAAC,EAAE,CAAC,CAAC;IAE/B,IAAI,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,MAAM,IAAI,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,MAAM,IAAI,CAAC;QAC9D,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAC;SAC3D,IAAI,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,MAAM,IAAI,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,MAAM,IAAI,CAAC;QACnE,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAC;SACjE;QACH,IAAI;YACF,YAAY,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC;YACvB,YAAY,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC;SACxB;QAAC,OAAO,GAAG,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,wBAAwB,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,0BAA0B,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;SAC9G;KACF;AACH,CAAC"}

package/src/types/helm-web-editor.d.ts

@@ -0,0 +1,26 @@
+export interface IEditorOptions {
+    width: number;
+    height: number;
+}
+export interface IEditor {
+    get options(): IEditorOptions;
+    get div(): HTMLDivElement;
+    get m(): IEditorMol;
+    resize(width: number, height: number): void;
+    /** Clear all contents */ clear(redraw: boolean, fireevents: boolean): void;
+    /** Resets and clears undo and redo buffers */ reset(): void;
+    setData(data: string, format: string): void;
+}
+export interface IEditorMol {
+    get atoms(): IEditorMolAtom[];
+    clone(selectedOnly: boolean): IEditorMol;
+}
+export interface IEditorMolAtom {
+    get p(): IEditorPoint;
+    get elem(): string;
+}
+export interface IEditorPoint {
+    get x(): number;
+    get y(): number;
+}
+//# sourceMappingURL=helm-web-editor.d.ts.map

package/src/types/helm-web-editor.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"helm-web-editor.d.ts","sourceRoot":"","sources":["helm-web-editor.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,cAAc;IAC7B,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,OAAO;IACtB,IAAI,OAAO,IAAI,cAAc,CAAC;IAE9B,IAAI,GAAG,IAAI,cAAc,CAAC;IAC1B,IAAI,CAAC,IAAI,UAAU,CAAC;IAEpB,MAAM,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5C,yBAAyB,CAAC,KAAK,CAAC,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,OAAO,GAAG,IAAI,CAAC;IAC5E,8CAA8C,CAAC,KAAK,IAAI,IAAI,CAAC;IAC7D,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;CAC7C;AAED,MAAM,WAAW,UAAU;IACzB,IAAI,KAAK,IAAI,cAAc,EAAE,CAAC;IAE9B,KAAK,CAAC,YAAY,EAAE,OAAO,GAAG,UAAU,CAAC;CAC1C;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,CAAC,IAAI,YAAY,CAAC;IAEtB,IAAI,IAAI,IAAI,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,CAAC,IAAI,MAAM,CAAC;IAEhB,IAAI,CAAC,IAAI,MAAM,CAAC;CACjB"}

package/src/types/helm-web-editor.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=helm-web-editor.js.map

package/src/types/helm-web-editor.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"helm-web-editor.js","sourceRoot":"","sources":["helm-web-editor.ts"],"names":[],"mappings":""}

package/src/types/helm.d.ts

@@ -1,21 +1,31 @@
 declare module 'scil' {
     function apply<T>(dest: T, atts: Partial<T>, defaults?: Partial<T>): void;
-    namespace Utils {
-        function alert(s: string): void;
-        function isNullOrEmpty(s: string): boolean;
-        function endswith(s: string, token: string, casesensitive?: boolean): boolean;
+    interface IUtils {
+        alert: (s: string) => void;
+        isNullOrEmpty(s: string): boolean;
+        endswith(s: string, token: string, casesensitive?: boolean): boolean;
     }
+    const Utils: IUtils;
 }
 declare module 'org' {
+    import * as JSDraw2 from 'JSDraw2';
     namespace helm {
+        type WebEditorRGroups = {
+            [group: string]: string;
+        };
+        type WebEditorMonomer = {
+            /** symbol */ id: string;
+            /** name */ n?: string;
+            /** natural analog */ na?: string;
+            /** polymer type */ type?: PolymerType;
+            /** monomer type */ mt?: MonomerType;
+            /** molfile */ m?: string;
+            /** substituents */ at: WebEditorRGroups;
+            /** number of substituents */ get rs(): number;
+        };
         interface IPistoiaBase {
             get T(): string;
         }
-        interface IAtom extends IPistoiaBase {
-            get T(): 'ATOM';
-            get elem(): string;
-            biotype(): string;
-        }
         interface IMonomer {
         }
         interface IAppOptions {
@@ -62,19 +72,48 @@ declare module 'org' {
         }
         interface IMonomers {
             addOneMonomer(monomer: IMonomer): void;
-            getMonomer(a: IAtom | string, elem: string): IAtom | null;
+            getMonomer(a: JSDraw2.Atom<HelmType> | HelmType, elem: string | undefined): WebEditorMonomer | null;
             getMonomerSet(biotype: string): any;
             clear(): void;
         }
         interface IWebEditorIO {
             trimBracket(s: string): string;
         }
+        const enum MonomerTypes {
+            BACKBONE = "Backbone",
+            BRANCH = "Branch",
+            TERMINAL = "Terminal"
+        }
+        /** 'Backbone' | 'Branch' | 'Terminal' */
+        type MonomerType = `${MonomerTypes}`;
+        const enum PolymerTypes {
+            RNA = "RNA",
+            PEPTIDE = "PEPTIDE",
+            CHEM = "CHEM",
+            BLOB = "BLOB",
+            G = "G"
+        }
+        /** 'RNA' | 'PEPTIDE' | 'CHEM' | 'BLOB' | 'G' */
+        type PolymerType = `${PolymerTypes}`;
+        const enum HelmTypes {
+            BASE = "HELM_BASE",
+            SUGAR = "HELM_SUGAR",
+            LINKER = "HELM_LINKER",
+            AA = "HELM_AA",
+            CHEM = "HELM_CHEM",
+            BLOB = "HELM_BLOB",
+            NUCLEOTIDE = "HELM_NUCLETIDE"
+        }
+        /** 'HELM_BASE' | 'HELM_SUGAR' | 'HELM_LINKER' | 'HELM_AA' | 'HELM_CHEM' | 'HELM_BLOB' | 'HELM_NUCLETIDE' */
+        type HelmType = `${HelmTypes}`;
+        type IHelmTypes = Record<HelmTypes, HelmType>;
         interface IOrgHelmWebEditor {
-            App: IApp;
-            Monomers: IMonomers;
-            MolViewer: IMolViewer;
-            IO: IWebEditorIO;
+            readonly App: IApp;
+            readonly Monomers: IMonomers;
+            readonly MolViewer: IMolViewer;
+            readonly IO: IWebEditorIO;
             kCaseSensitive: boolean;
+            readonly HELM: IHelmTypes;
             monomerTypeList(): string[];
         }
         const webeditor: IOrgHelmWebEditor;

package/src/types/helm.d.ts.map

@@ -1 +1 @@
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package/src/types/index.d.ts

@@ -1,3 +1,11 @@
+import * as DG from 'datagrok-api/dg';
+import './helm';
+import * as org from 'org';
+import PolymerType = org.helm.PolymerType;
+import HelmType = org.helm.HelmType;
+import MonomerType = org.helm.MonomerType;
+import WebEditorMonomer = org.helm.WebEditorMonomer;
+export { WebEditorMonomer, PolymerType, HelmType, MonomerType };
 import { Observable } from 'rxjs';
 import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT, HELM_POLYMER_TYPE } from '../utils/const';
 export type RGroup = {
@@ -6,6 +14,7 @@ export type RGroup = {
     [RGP.CAP_GROUP_NAME]: string;
     [RGP.LABEL]: string;
 };
+/** https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */
 export type Monomer = {
     [REQ.SYMBOL]: string;
     [REQ.NAME]: string;
@@ -14,30 +23,40 @@ export type Monomer = {
     [REQ.ID]: number;
     [REQ.RGROUPS]: RGroup[];
     [REQ.SMILES]: string;
-    [REQ.POLYMER_TYPE]: string;
-    [REQ.MONOMER_TYPE]: string;
+    [REQ.POLYMER_TYPE]: PolymerType;
+    [REQ.MONOMER_TYPE]: MonomerType;
     [REQ.CREATE_DATE]: string | null;
     [OPT.NATURAL_ANALOG]?: string;
     [OPT.META]?: {
         [property: string]: any;
     };
     lib?: IMonomerLib;
+    wem?: WebEditorMonomer;
+};
+export type MonomerLibSummaryType = {
+    [polymerType: string]: number;
 };
 export interface IMonomerLib {
     get source(): string | undefined;
     get error(): string | undefined;
-    getMonomer(polymerType: string, monomerSymbol: string): Monomer | null;
-    getMonomerMolsByPolymerType(polymerType: string): {
+    getMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer | null;
+    addMissingMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer;
+    getMonomerMolsByPolymerType(polymerType: PolymerType): {
         [monomerSymbol: string]: string;
     } | null;
-    getMonomerSymbolsByRGroup(rGroupNumber: number, polymerType: string, element?: string): string[];
-    getMonomerSymbolsByType(polymerType: string): string[];
-    getPolymerTypes(): string[];
+    getMonomerSymbolsByRGroup(rGroupNumber: number, polymerType: PolymerType, element?: string): string[];
+    getMonomerSymbolsByType(polymerType: PolymerType): string[];
+    getPolymerTypes(): PolymerType[];
     update(lib: IMonomerLib): void;
     get onChanged(): Observable<any>;
-    /** Summary with lib monomer count by type, csv */
+    /** Summary string with lib monomer count by type
+     * @deprecated Keep for backward compatibility */
     getSummary(): string;
-    getTooltip(polymerType: string, monomerSymbol: string): HTMLElement;
+    /** Summary with lib monomer count by type */
+    getSummaryObj(): MonomerLibSummaryType;
+    /** Gets dataframe with columns 'polymerType', 'count'. */
+    getSummaryDf(): DG.DataFrame;
+    getTooltip(polymerType: PolymerType, monomerSymbol: string): HTMLElement;
 }
 export declare const alphabetPolymerTypes: {
     DNA: HELM_POLYMER_TYPE;

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

@@ -1 +1 @@
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package/src/types/index.js

@@ -1,3 +1,4 @@
+import './helm';
 export const alphabetPolymerTypes = {
     ["DNA" /* ALPHABET.DNA */]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
     ["RNA" /* ALPHABET.RNA */]: "RNA" /* HELM_POLYMER_TYPE.RNA */,

package/src/types/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAkDA,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,0BAAc,mCAAuB;IACrC,0BAAc,mCAAuB;IACrC,wBAAa,2CAA2B;IACxC,wBAAa,2CAA2B;CACzC,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,QAAQ,CAAC;AAuEhB,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,0BAAc,mCAAuB;IACrC,0BAAc,mCAAuB;IACrC,wBAAa,2CAA2B;IACxC,wBAAa,2CAA2B;CACzC,CAAC"}

package/src/types/jsdraw2.d.ts

@@ -40,5 +40,41 @@ declare module 'JSDraw2' {
         getMolfile(): string;
         constructor(host: HTMLElement, options?: Partial<IEditorOptions>);
     }
+    interface IPistoiaBase {
+        get T(): string;
+    }
+    const enum BioTypes {
+        AA = "AA",
+        ANTIBODY = "ANTIBODY",
+        PROTEIN = "PROTEIN",
+        GENE = "GENE",
+        DNA = "DNA",
+        RNA = "RNA",
+        BASE_DNA = "BASEDNA",
+        BASE_RNA = "BASERNA"
+    }
+    type BioType = `${BioTypes}`;
+    interface IBio<TBio> {
+        id?: number | null;
+        type: TBio;
+        ambiguity?: string | null;
+        annotation?: string | null;
+        annotationshowright?: string | null;
+    }
+    abstract class JsAtom<TBio> implements IPistoiaBase {
+        get T(): 'ATOM';
+        get p(): Point;
+        get elem(): string;
+        get bio(): IBio<TBio>;
+    }
+    class Atom<TBio> extends JsAtom<TBio> {
+        biotype(): TBio;
+        constructor(p: Point, elem: string, bio: IBio<TBio>);
+    }
+    class Point {
+        x: number;
+        y: number;
+        constructor(x: number, y: number);
+    }
 }
 //# sourceMappingURL=jsdraw2.d.ts.map

package/src/types/jsdraw2.d.ts.map

@@ -1 +1 @@
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package/src/types/renderer.d.ts

@@ -5,6 +5,6 @@ export interface IRenderer {
     /** @param timeout  Default 5000 ms */
     awaitRendered(timeout?: number): Promise<void>;
 }
-export declare function isIRenderer(value: IRenderer): value is IRenderer;
-export declare function asIRenderer(o: any): IRenderer | null;
+export declare function isRenderer(value: IRenderer): value is IRenderer;
+export declare function asRenderer(o: any): IRenderer | null;
 //# sourceMappingURL=renderer.d.ts.map