@datagrok-libraries/bio 5.43.1 → 5.44.0

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

@@ -6,57 +6,48 @@ import { ALPHABET, NOTATION } from '../utils/macromolecule/consts';
 import { SeqHandler } from '../utils/seq-handler';
 import { getFormattedMonomerLib, keepPrecision } from './to-atomic-level-utils';
 import { seqToMolFileWorker } from './seq-to-molfile';
+import { hasMolGraph, setMolGraph } from './types';
+import { errInfo } from '../utils/err-info';
+import { alphabetToPolymerType } from './utils';
 import { monomerWorksConsts as C } from './consts';
+import { HelmTypes } from '../helm/consts';
 // todo: verify that all functions have return types
 /** Convert Macromolecule column into Molecule column storing molfile V3000 with the help of a monomer library
  * @param {DG.DataFrame} df - DataFrame containing the column to be converted
  * @param {DG.Column} seqCol - Column containing the macromolecule sequence
  * @param {IMonomerLib} monomerLib - Monomer library
  */
-export async function _toAtomicLevel(df, seqCol, monomerLib) {
-    // todo: remove this from the library
-    if (DG.Func.find({ package: 'Chem', name: 'getRdKitModule' }).length === 0) {
-        const msg = 'Transformation to atomic level requires the package "Chem" installed.';
-        return { col: null, warnings: [msg] };
-    }
+export async function _toAtomicLevel(df, seqCol, monomerLib, rdKitModule) {
     if (seqCol.semType !== DG.SEMTYPE.MACROMOLECULE) {
         const msg = `Only the ${DG.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, ` +
             `the chosen column has semType '${seqCol.semType}'`;
-        return { col: null, warnings: [msg] };
+        return { molCol: null, warnings: [msg] };
     }
     let srcCol = seqCol;
     const seqUh = SeqHandler.forColumn(seqCol);
     // convert 'helm' to 'separator' units
-    if (seqUh.isHelm()) {
+    if (seqUh.notation !== NOTATION.SEPARATOR) {
         srcCol = seqUh.convert(NOTATION.SEPARATOR, '.');
         srcCol.name = seqCol.name; // Replace converted col name 'separator(<original>)' to '<original>';
     }
-    const srcSh = SeqHandler.forColumn(srcCol);
-    const alphabet = srcSh.alphabet;
-    // determine the polymer type according to HELM specifications
     let polymerType;
-    // todo: an exception from dart comes before this check if the alphabet is UN
-    if (alphabet === ALPHABET.PT || alphabet === ALPHABET.UN)
-        polymerType = "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */;
-    else if (alphabet === ALPHABET.RNA || alphabet === ALPHABET.DNA)
-        polymerType = "RNA" /* HELM_POLYMER_TYPE.RNA */;
-    else {
-        const msg = `Unexpected column's '${srcCol.name}' alphabet '${alphabet}'.`;
-        return { col: null, warnings: [msg] };
+    let alphabet;
+    try {
+        const srcSh = SeqHandler.forColumn(srcCol);
+        alphabet = srcSh.alphabet;
+        polymerType = alphabetToPolymerType(alphabet);
+    }
+    catch (err) {
+        const [errMsg, _errStack] = errInfo(err);
+        return { molCol: null, warnings: [errMsg] };
     }
     const monomerSequencesArray = getMonomerSequencesArray(srcCol);
-    const monomersDict = await getMonomersDictFromLib(monomerSequencesArray, monomerLib, polymerType, alphabet);
+    const monomersDict = getMonomersDictFromLib(monomerSequencesArray, polymerType, alphabet, monomerLib, rdKitModule);
     const srcColLength = srcCol.length;
-    const { molfileList, molfileWarningList } = await seqToMolFileWorker(monomerSequencesArray, monomersDict, alphabet, polymerType, srcColLength);
-    if (molfileWarningList.length > 0.05 * srcColLength)
+    const res = await seqToMolFileWorker(srcCol, monomersDict, alphabet, polymerType, monomerLib, rdKitModule);
+    if (res.warnings.length > 0.05 * srcColLength)
         throw new Error('Too many errors getting molfiles.');
-    // exclude name collisions
-    const name = `molfile(${srcCol.name})`;
-    const resColName = df.columns.getUnusedName(name);
-    const resCol = DG.Column.fromStrings(resColName, molfileList);
-    resCol.semType = DG.SEMTYPE.MOLECULE;
-    resCol.meta.units = DG.UNITS.Molecule.MOLBLOCK;
-    return { col: resCol, warnings: molfileWarningList };
+    return res;
 }
 /** Get jagged array of monomer symbols for the dataframe
  * @param {DG.Column} macroMolCol - Column with macro-molecules
@@ -67,11 +58,12 @@ export function getMonomerSequencesArray(macroMolCol) {
     // split the string into monomers
     const sh = SeqHandler.forColumn(macroMolCol);
     let containsEmptyValues = false;
+    const biotype = sh.alphabet === ALPHABET.RNA || sh.alphabet === ALPHABET.DNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
     for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
         const seqSS = sh.getSplitted(rowIdx);
         containsEmptyValues || (containsEmptyValues = seqSS.length === 0);
-        result[rowIdx] = wu(seqSS.canonicals)
-            .filter((cm) => !sh.isGap(cm)).map((cm) => cm).toArray();
+        result[rowIdx] = wu.count(0).take(seqSS.length).filter((posIdx) => !seqSS.isGap(posIdx))
+            .map((posIdx) => { return { position: posIdx, biotype: biotype, symbol: seqSS.getCanonical(posIdx) }; }).toArray();
     }
     if (containsEmptyValues)
         grok.shell.warning(`Some values in the "${macroMolCol.name}" column are empty`);
@@ -82,14 +74,13 @@ export function getMonomerSequencesArray(macroMolCol) {
  * with the help of async function call from Chem (RdKit module)
  * @param {string[]} monomerSequencesArray - Jagged array of monomer symbols for the dataframe
  * @param {IMonomerLib} monomerLib - Monomer library
- * @param {HELM_POLYMER_TYPE} polymerType - Polymer type
+ * @param {PolymerType} polymerType - Polymer type
  * @param {ALPHABET} alphabet - Alphabet
  * @return {Map<string, MolGraph>} - Mapping of monomer symbols to MolGraph objects*/
-export async function getMonomersDictFromLib(monomerSequencesArray, monomerLib, polymerType, alphabet) {
+export function getMonomersDictFromLib(monomerSequencesArray, polymerType, alphabet, monomerLib, rdKitModule) {
     // todo: exception - no gaps, no empty string monomers
     const formattedMonomerLib = getFormattedMonomerLib(monomerLib, polymerType, alphabet);
-    const monomersDict = new Map();
-    const moduleRdkit = await grok.functions.call('Chem:getRdKitModule');
+    const monomersDict = {};
     const pointerToBranchAngle = {
         value: null
     };
@@ -99,15 +90,16 @@ export async function getMonomersDictFromLib(monomerSequencesArray, monomerLib,
         const symbols = (alphabet === ALPHABET.RNA) ?
             [C.RIBOSE, C.PHOSPHATE] : [C.DEOXYRIBOSE, C.PHOSPHATE];
         for (const sym of symbols)
-            addMonomerToDict(monomersDict, sym, formattedMonomerLib, moduleRdkit, polymerType, pointerToBranchAngle);
+            addMonomerToDict(monomersDict, sym.symbol, formattedMonomerLib, rdKitModule, polymerType, pointerToBranchAngle);
     }
     for (let rowI = 0; rowI < monomerSequencesArray.length; ++rowI) {
         const monomerSeq = monomerSequencesArray[rowI];
-        for (const sym of monomerSeq) {
+        for (const seqMonomer of monomerSeq) {
+            const sym = seqMonomer.symbol;
             if (sym === '')
                 continue; // Skip gap/empty monomer for MSA
             try {
-                addMonomerToDict(monomersDict, sym, formattedMonomerLib, moduleRdkit, polymerType, pointerToBranchAngle);
+                addMonomerToDict(monomersDict, sym, formattedMonomerLib, rdKitModule, polymerType, pointerToBranchAngle);
             }
             catch (err) {
                 const errTxt = err instanceof Error ? err.message : err.toString();
@@ -125,13 +117,14 @@ export async function getMonomersDictFromLib(monomerSequencesArray, monomerLib,
  * @param {string} sym - Monomer symbol
  * @param {Map<string, any>} formattedMonomerLib - Formatted monomer library
  * @param {any} moduleRdkit - RDKit module
- * @param {HELM_POLYMER_TYPE} polymerType - Polymer type
+ * @param {PolymerType} polymerType - Polymer type
  * @param {NumberWrapper} pointerToBranchAngle - Pointer to branch angle*/
 function addMonomerToDict(monomersDict, sym, formattedMonomerLib, moduleRdkit, polymerType, pointerToBranchAngle) {
-    if (!monomersDict.has(sym)) {
+    const symKey = { polymerType, symbol: sym };
+    if (!hasMolGraph(monomersDict, symKey)) {
         const monomerData = getMolGraph(sym, formattedMonomerLib, moduleRdkit, polymerType, pointerToBranchAngle);
         if (monomerData)
-            monomersDict.set(sym, monomerData);
+            setMolGraph(monomersDict, symKey, monomerData);
         else {
             // todo: handle exception
             throw new Error(`Monomer with symbol '${sym}' is absent the monomer library`);
@@ -143,7 +136,7 @@ function addMonomerToDict(monomersDict, sym, formattedMonomerLib, moduleRdkit, p
  * @param {string} monomerSymbol - Monomer symbol
  * @param {Map<string, any>} formattedMonomerLib - Formatted monomer library
  * @param {any} moduleRdkit - RDKit module
- * @param {HELM_POLYMER_TYPE} polymerType - Polymer type
+ * @param {PolymerType} polymerType - Polymer type
  * @param {NumberWrapper} pointerToBranchAngle - Pointer to branch angle
  * @return {MolGraph | null} - MolGraph object or null if monomerSymbol is absent in the library*/
 function getMolGraph(monomerSymbol, formattedMonomerLib, moduleRdkit, polymerType, pointerToBranchAngle) {
@@ -165,9 +158,9 @@ function getMolGraph(monomerSymbol, formattedMonomerLib, moduleRdkit, polymerTyp
         if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */)
             adjustPeptideMonomerGraph(monomerGraph);
         else { // nucleotides
-            if (monomerSymbol === C.RIBOSE || monomerSymbol === C.DEOXYRIBOSE)
+            if (monomerSymbol === C.RIBOSE.symbol || monomerSymbol === C.DEOXYRIBOSE.symbol)
                 adjustSugarMonomerGraph(monomerGraph, pointerToBranchAngle);
-            else if (monomerSymbol === C.PHOSPHATE)
+            else if (monomerSymbol === C.PHOSPHATE.symbol)
                 adjustPhosphateMonomerGraph(monomerGraph);
             else
                 adjustBaseMonomerGraph(monomerGraph, pointerToBranchAngle);
@@ -199,7 +192,7 @@ function setShiftsAndTerminalNodes(polymerType, monomerGraph, monomerSymbol) {
         removeNodeAndBonds(monomerGraph, monomerGraph.meta.rNodes[1]);
     }
     else { // nucleotides
-        if (monomerSymbol === C.RIBOSE || monomerSymbol === C.DEOXYRIBOSE) {
+        if (monomerSymbol === C.RIBOSE.symbol || monomerSymbol === C.DEOXYRIBOSE.symbol) {
             // remove R2
             removeNodeAndBonds(monomerGraph, monomerGraph.meta.rNodes[1]);
             // set terminalNode2 (oxygen) as new R2
@@ -213,7 +206,7 @@ function setShiftsAndTerminalNodes(polymerType, monomerGraph, monomerSymbol) {
             // remove the branching r-group
             removeNodeAndBonds(monomerGraph, monomerGraph.meta.rNodes[2]);
         }
-        else if (monomerSymbol === C.PHOSPHATE) {
+        else if (monomerSymbol === C.PHOSPHATE.symbol) {
             monomerGraph.meta.terminalNodes[0] = monomerGraph.meta.rNodes[0];
             shiftCoordinates(monomerGraph, -monomerGraph.atoms.x[monomerGraph.meta.terminalNodes[0] - 1], -monomerGraph.atoms.y[monomerGraph.meta.terminalNodes[0] - 1]);
             setShifts(monomerGraph, polymerType);
@@ -308,7 +301,7 @@ function setTerminalNodes(bonds, meta) {
 }
 /** Sets shifts in 'meta' attribute of MolGraph
  * @param {MolGraph} molGraph - MolGraph object
- * @param {HELM_POLYMER_TYPE} polymerType - Polymer type*/
+ * @param {PolymerType} polymerType - Polymer type*/
 function setShifts(molGraph, polymerType) {
     if (molGraph.meta.rNodes.length > 1) {
         molGraph.meta.backboneShift = getShiftBetweenNodes(molGraph, molGraph.meta.rNodes[1] - 1, molGraph.meta.terminalNodes[0] - 1);

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

@@ -1,3 +1,6 @@
+import { ALPHABET } from '../utils/macromolecule';
+import { HELM_POLYMER_TYPE } from '../utils/const';
+import { HelmType, ISeqMonomer } from '../helm/types';
 export interface ITypedArray {
     length: number;
     [key: number]: any;
@@ -53,6 +56,18 @@ export type MolGraph = {
     meta: MonomerMetadata;
     stereoAtoms?: number[];
 };
+export type MonomerMolGraphMap = {
+    [polymerType: string]: {
+        [symbol: string]: MolGraph;
+    };
+};
+export type LibMonomerKey = {
+    polymerType: string;
+    symbol: string;
+};
+export declare function getMolGraph(dict: MonomerMolGraphMap, libKey: LibMonomerKey): MolGraph | undefined;
+export declare function hasMolGraph(dict: MonomerMolGraphMap, libKey: LibMonomerKey): boolean;
+export declare function setMolGraph(dict: MonomerMolGraphMap, libKey: LibMonomerKey, value: MolGraph): void;
 export type Point = {
     x: number;
     y: number;
@@ -80,4 +95,33 @@ export type LoopConstants = {
 export type NumberWrapper = {
     value: number | null;
 };
+export type MonomerMapValue = {
+    biotype: HelmType;
+    symbol: string;
+    atoms: number[];
+    bonds: number[];
+};
+export declare class MonomerMap extends Map<number, MonomerMapValue> {
+    constructor(entries?: [number, MonomerMapValue][] | null);
+}
+/** @property monomers key - helm seq position, */
+export declare class MolfileWithMap {
+    readonly molfile: string;
+    readonly monomers: MonomerMap;
+    constructor(molfile: string, monomers: MonomerMap);
+    static createEmpty(): MolfileWithMap;
+}
+/** Only simple types allowed for worker data, avoid classes with methods */
+export type SeqToMolfileWorkerData = {
+    seqList: ISeqMonomer[][];
+    monomersDict: MonomerMolGraphMap;
+    alphabet: ALPHABET;
+    polymerType: HELM_POLYMER_TYPE;
+    start: number;
+    end: number;
+};
+export type SeqToMolfileWorkerRes = {
+    molfiles: MolfileWithMap[];
+    warnings: string[];
+};
 //# sourceMappingURL=types.d.ts.map

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

@@ -1 +1 @@
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package/src/monomer-works/types.js

@@ -1,2 +1,26 @@
-export {};
+export function getMolGraph(dict, libKey) {
+    return dict[libKey.polymerType]?.[libKey.symbol];
+}
+export function hasMolGraph(dict, libKey) {
+    return !!dict[libKey.polymerType]?.[libKey.symbol];
+}
+export function setMolGraph(dict, libKey, value) {
+    let pt = dict[libKey.polymerType];
+    if (!pt)
+        pt = dict[libKey.polymerType] = {};
+    pt[libKey.symbol] = value;
+}
+export class MonomerMap extends Map {
+    constructor(entries) {
+        super(entries);
+    }
+}
+/** @property monomers key - helm seq position, */
+export class MolfileWithMap {
+    constructor(molfile, monomers) {
+        this.molfile = molfile;
+        this.monomers = monomers;
+    }
+    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }
+}
 //# sourceMappingURL=types.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":""}
+{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAkEA,MAAM,UAAU,WAAW,CAAC,IAAwB,EAAE,MAAqB;IACzE,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;AACnD,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,IAAwB,EAAE,MAAqB;IACzE,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;AACrD,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,IAAwB,EAAE,MAAqB,EAAE,KAAe;IAC1F,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC;IAClC,IAAI,CAAC,EAAE;QACL,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,GAAG,EAAE,CAAC;IACrC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,KAAK,CAAC;AAC5B,CAAC;AA0CD,MAAM,OAAO,UAAW,SAAQ,GAA4B;IAC1D,YAAY,OAA4C;QACtD,KAAK,CAAC,OAAO,CAAC,CAAC;IACjB,CAAC;CACF;AAED,kDAAkD;AAClD,MAAM,OAAO,cAAc;IACzB,YACkB,OAAe,EACf,QAAoB;QADpB,YAAO,GAAP,OAAO,CAAQ;QACf,aAAQ,GAAR,QAAQ,CAAY;IACnC,CAAC;IAEJ,MAAM,CAAC,WAAW,KAAK,OAAO,IAAI,cAAc,CAAC,EAAE,EAAE,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;CAC9E"}

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

@@ -0,0 +1,15 @@
+import * as DG from 'datagrok-api/dg';
+import { ISubstructProvider } from '@datagrok-libraries/chem-meta/src/types';
+import { PolymerType } from '@datagrok-libraries/js-draw-lite/src/types/org';
+import { ISeqMonomer } from '../helm/types';
+import { ALPHABET } from '../utils/macromolecule';
+export type MonomerHoverLink = {
+    targetCol: DG.Column;
+    handler(seqGridCell: DG.GridCell, monomer: ISeqMonomer | null, targetGridCol: DG.GridColumn): boolean;
+} & ISubstructProvider;
+export declare function getUnusedName(df: DG.DataFrame | undefined, colName: string): string;
+export declare function getMolColName(df: DG.DataFrame | undefined, seqColName: string): string;
+export declare function alphabetToPolymerType(alphabet: ALPHABET): PolymerType;
+/** @deprecated Use DG.Color.hexToPercentRgb */
+export declare function hexToPercentRgb(hex: string): number[] | null;
+//# sourceMappingURL=utils.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,kBAAkB,EAAC,MAAM,yCAAyC,CAAC;AAC3E,OAAO,EAAC,WAAW,EAAC,MAAM,gDAAgD,CAAC;AAG3E,OAAO,EAAC,WAAW,EAAC,MAAM,eAAe,CAAC;AAE1C,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAIhD,MAAM,MAAM,gBAAgB,GAAG;IAC7B,SAAS,EAAE,EAAE,CAAC,MAAM,CAAC;IACrB,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,GAAG,IAAI,EAAE,aAAa,EAAE,EAAE,CAAC,UAAU,GAAG,OAAO,CAAC;CACvG,GAAG,kBAAkB,CAAC;AAEvB,wBAAgB,aAAa,CAAC,EAAE,EAAE,EAAE,CAAC,SAAS,GAAG,SAAS,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAGnF;AAED,wBAAgB,aAAa,CAAC,EAAE,EAAE,EAAE,CAAC,SAAS,GAAG,SAAS,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,CAEtF;AAED,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,QAAQ,GAAG,WAAW,CAYrE;AAED,+CAA+C;AAC/C,wBAAgB,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,IAAI,CAS5D"}

package/src/monomer-works/utils.js

@@ -0,0 +1,34 @@
+import { ALPHABET } from '../utils/macromolecule';
+export function getUnusedName(df, colName) {
+    if (!df)
+        return colName;
+    return df.columns.getUnusedName(colName);
+}
+export function getMolColName(df, seqColName) {
+    return getUnusedName(df, `molfile(${seqColName})`);
+}
+export function alphabetToPolymerType(alphabet) {
+    // determine the polymer type according to HELM specifications
+    let resPolymerType;
+    // todo: an exception from dart comes before this check if the alphabet is UN
+    if (alphabet === ALPHABET.PT || alphabet === ALPHABET.UN)
+        resPolymerType = "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */;
+    else if (alphabet === ALPHABET.RNA || alphabet === ALPHABET.DNA)
+        resPolymerType = "RNA" /* HELM_POLYMER_TYPE.RNA */;
+    else {
+        throw new Error(`Unexpected alphabet '${alphabet}'.`);
+    }
+    return resPolymerType;
+}
+/** @deprecated Use DG.Color.hexToPercentRgb */
+export function hexToPercentRgb(hex) {
+    const result = hex.length === 7 ? /^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(hex) :
+        /^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(hex);
+    return result ? [
+        parseInt(result[1], 16) / 256,
+        parseInt(result[2], 16) / 256,
+        parseInt(result[3], 16) / 256,
+        result.length > 4 ? parseInt(result[4], 16) / 256 : 0.3
+    ] : null;
+}
+//# sourceMappingURL=utils.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"utils.js","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AAYA,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAShD,MAAM,UAAU,aAAa,CAAC,EAA4B,EAAE,OAAe;IACzE,IAAI,CAAC,EAAE;QAAE,OAAO,OAAO,CAAC;IACxB,OAAO,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC,OAAO,CAAC,CAAC;AAC3C,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,EAA4B,EAAE,UAAkB;IAC5E,OAAO,aAAa,CAAC,EAAE,EAAE,WAAW,UAAU,GAAG,CAAC,CAAC;AACrD,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,QAAkB;IACtD,8DAA8D;IAC9D,IAAI,cAAiC,CAAC;IACtC,6EAA6E;IAC7E,IAAI,QAAQ,KAAK,QAAQ,CAAC,EAAE,IAAI,QAAQ,KAAK,QAAQ,CAAC,EAAE;QACtD,cAAc,4CAA4B,CAAC;SACxC,IAAI,QAAQ,KAAK,QAAQ,CAAC,GAAG,IAAI,QAAQ,KAAK,QAAQ,CAAC,GAAG;QAC7D,cAAc,oCAAwB,CAAC;SACpC,CAAC;QACJ,MAAM,IAAI,KAAK,CAAC,wBAAwB,QAAQ,IAAI,CAAC,CAAC;IACxD,CAAC;IACD,OAAO,cAAc,CAAC;AACxB,CAAC;AAED,+CAA+C;AAC/C,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,2CAA2C,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;QACvF,uDAAuD,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACpE,OAAO,MAAM,CAAC,CAAC,CAAC;QACd,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG;KACxD,CAAC,CAAC,CAAC,IAAI,CAAC;AACX,CAAC"}

package/src/types/index.d.ts

@@ -1,7 +1,8 @@
 import * as DG from 'datagrok-api/dg';
 import { Observable } from 'rxjs';
+import { HelmAtom } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
 import { HelmType, IWebEditorMonomer, MonomerSetType, MonomerType, PolymerType } from '../helm/types';
-import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT, HELM_POLYMER_TYPE } from '../utils/const';
+import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT } from '../utils/const';
 export type RGroup = {
     [RGP.CAP_GROUP_SMILES]: string;
     [RGP.ALTERNATE_ID]: string;
@@ -55,8 +56,8 @@ export type MonomerLibSummaryType = {
 export interface IMonomerLib {
     get source(): string | undefined;
     get error(): string | undefined;
-    getMonomer(polymerType: PolymerType | null, monomerSymbol: string): Monomer | null;
     addMissingMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer;
+    getMonomer(polymerType: PolymerType | null, monomerSymbol: string): Monomer | null;
     getMonomerMolsByPolymerType(polymerType: PolymerType): {
         [monomerSymbol: string]: string;
     } | null;
@@ -73,13 +74,12 @@ export interface IMonomerLib {
     getSummaryObj(): MonomerLibSummaryType;
     /** Gets dataframe with columns 'polymerType', 'count'. */
     getSummaryDf(): DG.DataFrame;
-    getTooltip(polymerType: PolymerType, monomerSymbol: string): HTMLElement;
-    getMonomerSet(type: HelmType): MonomerSetType | null;
+    getTooltip(biotype: HelmType, monomerSymbol: string): HTMLElement;
+    getMonomerSet(biotype: HelmType): MonomerSetType | null;
+    /** HELMWebEditor expects null for HelmTypes.LINKER and R-Group count != 2 */
+    getWebEditorMonomer(a: HelmAtom | HelmType, symbol?: string): IWebEditorMonomer | null;
+    getRS(smiles: string): {
+        [r: string]: string;
+    };
 }
-export declare const alphabetPolymerTypes: {
-    DNA: HELM_POLYMER_TYPE;
-    RNA: HELM_POLYMER_TYPE;
-    PT: HELM_POLYMER_TYPE;
-    UN: HELM_POLYMER_TYPE;
-};
 //# sourceMappingURL=index.d.ts.map

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

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

@@ -1,8 +1,2 @@
-import { ALPHABET } from '../utils/macromolecule';
-export const alphabetPolymerTypes = {
-    [ALPHABET.DNA]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
-    [ALPHABET.RNA]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
-    [ALPHABET.PT]: "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */,
-    [ALPHABET.UN]: "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */,
-};
+export {};
 //# sourceMappingURL=index.js.map

package/src/types/index.js.map

@@ -1 +1 @@
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