npm - @datagrok-libraries/bio - Versions diffs - 5.48.3 → 5.49.1 - Mend

@datagrok-libraries/bio 5.48.3 → 5.49.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (24) hide show

package/CHANGELOG.md +8 -0
package/package.json +1 -1
package/src/monomer-works/monomer-hover.d.ts.map +1 -1
package/src/monomer-works/monomer-hover.js +33 -19
package/src/monomer-works/monomer-hover.js.map +1 -1
package/src/monomer-works/seq-to-molfile.js +4 -4
package/src/monomer-works/seq-to-molfile.js.map +1 -1
package/src/monomer-works/to-atomic-level-utils.js +2 -2
package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level.js +14 -4
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/utils/cell-renderer-back-base.d.ts.map +1 -1
package/src/utils/cell-renderer-back-base.js +10 -0
package/src/utils/cell-renderer-back-base.js.map +1 -1
package/src/utils/macromolecule/seq-handler.d.ts +5 -0
package/src/utils/macromolecule/seq-handler.d.ts.map +1 -1
package/src/utils/macromolecule/seq-handler.js +23 -0
package/src/utils/macromolecule/seq-handler.js.map +1 -1
package/src/utils/macromolecule/utils.d.ts +1 -0
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +12 -1
package/src/utils/macromolecule/utils.js.map +1 -1
package/tsconfig.json +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,13 @@
 # bio changelog
+## 5.49.1 (2025-02-17)
+Fix helm splitter for marginal cases
+## 5.49.0 (2025-02-17)
+To-Tomic-level support for RNA/DNA sequences
 ## 5.48.3 (2025-02-05)
 Remove healthCheck method from the IAutoDockService interface

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.48.3",
+  "version": "5.49.1",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

package/src/monomer-works/monomer-hover.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"monomer-hover.d.ts","sourceRoot":"","sources":["monomer-hover.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAMtC,OAAO,EAAC,QAAQ,EAAC,MAAM,6CAA6C,CAAC;AAIrE,OAAO,EAAC,eAAe,EAAC,MAAM,gBAAgB,CAAC;AAC/C,OAAO,EAAC,WAAW,EAAC,MAAM,eAAe,CAAC;AAK1C,OAAO,EAAC,gBAAgB,EAAC,MAAM,SAAS,CAAC;AAGzC,OAAO,EAAC,UAAU,EAAC,MAAM,qBAAqB,CAAC;AAE/C,eAAO,MAAM,qBAAqB,sBAAsB,CAAC;AAEzD,wBAAgB,mBAAmB,CAAC,UAAU,EAAE,GAAG,EAAE,OAAO,EAAE,gBAAgB,QAM7E;AAED,wBAAgB,qBAAqB,CACnC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EACpD,UAAU,EAAE,eAAe,EAAE,SAAS,EAAE,UAAU,EAAE,WAAW,EAAE,QAAQ,GACxE,gBAAgB,CAyGlB;AAED,wBAAgB,qBAAqB,CACnC,WAAW,EAAE,EAAE,CAAC,QAAQ,EAAE,UAAU,EAAE,WAAW,GAAG,IAAI,GACvD,IAAI,CAkBN;AAED,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,gBAAgB,EAAE,CAElF"}

package/src/monomer-works/monomer-hover.js CHANGED Viewed

@@ -14,6 +14,8 @@ export function addMonomerHoverLink(seqColTemp, resLink) {
     seqColTemp[MonomerHoverLinksTemp] = mhhList;
 }
 export function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelper, rdKitModule) {
+    const seqSH = seqHelper.getSeqHandler(seqCol);
+    const isNucleotideHelmSequence = seqSH.isHelm() && (seqSH.alphabet == ALPHABET.RNA || seqSH.alphabet == ALPHABET.DNA);
     function buildMonomerMap(seqCol, tableRowIdx) {
         const seqSH = seqHelper.getSeqHandler(seqCol);
         const seqSS = seqSH.getSplitted(tableRowIdx);
@@ -34,9 +36,8 @@ export function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelper, rdK
         if (seq == null)
             return null;
         let resMonomerMap = monomerMapLruCache.get(seq);
-        if (!resMonomerMap) {
+        if (!resMonomerMap)
             monomerMapLruCache.set(seq, resMonomerMap = buildMonomerMap(seqCol, tableRowIdx));
-        }
         return resMonomerMap;
     }
     const resLink = {
@@ -51,26 +52,34 @@ export function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelper, rdK
                 prev.seqColName != seqCol.name || prev.seqPosition != seqMonomer?.position))) {
                 if (prev) {
                     setMonomerHover(null);
-                    prev.gridCell.grid?.invalidate();
-                    // prev.gridCell.render();
+                    //prev.gridCell.grid?.invalidate();
+                    prev.gridCell.render();
                 }
                 if (!seqMonomer) {
                     setMonomerHover(null);
                     return true;
                 }
+                const getSeqMonomerCorrectedPosition = () => {
+                    if (!seqMonomer)
+                        return null;
+                    // if its dna or rna, we need to correct position as it will contain sugar and phosphate
+                    if (isNucleotideHelmSequence)
+                        return Math.floor(seqMonomer.position / 3);
+                    return seqMonomer.position;
+                };
                 setMonomerHover({
                     gridCell: targetGridCell,
                     dataFrameId: seqCol.dataFrame.id,
                     gridRowIdx: gridRowIdx,
                     seqColName: seqCol.name,
-                    seqPosition: seqMonomer ? seqMonomer.position : -1,
+                    seqPosition: getSeqMonomerCorrectedPosition() ?? -1,
                     getSubstruct: () => {
                         if (!seqMonomer || seqMonomer.symbol === '*')
                             return undefined;
                         const molMonomerMap = getMonomerMap(seqCol, tableRowIdx);
                         if (!molMonomerMap)
                             return undefined;
-                        const monomerMap = molMonomerMap.get(seqMonomer.position); // single monomer
+                        const monomerMap = molMonomerMap.get(getSeqMonomerCorrectedPosition()); // single monomer
                         if (!monomerMap)
                             return { atoms: [], bonds: [], highlightAtomColors: [], highlightBondColors: [] };
                         const res = getMolHighlight([monomerMap], monomerLib);
@@ -78,8 +87,8 @@ export function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelper, rdK
                     }
                 });
                 // TODO: Invalidate targetGridCell
-                grid.invalidate();
-                // targetGridCell.render();
+                //grid.invalidate();
+                targetGridCell.render();
             }
             return true;
         },
@@ -103,19 +112,24 @@ export function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelper, rdK
     return resLink;
 }
 export function execMonomerHoverLinks(seqGridCell, seqMonomer) {
-    const seqCol = seqGridCell.tableColumn;
-    if (!seqCol)
-        return;
-    const mhlList = getMonomerHoverLinks(seqCol);
-    for (let mhlI = mhlList.length - 1; mhlI >= 0; --mhlI) {
-        const mhl = mhlList[mhlI];
-        const molGridCol = seqGridCell.grid.col(mhl.targetCol.name);
-        if (molGridCol) {
-            const handlerRes = mhl.handler(seqGridCell, seqMonomer, molGridCol);
-            if (!handlerRes)
-                break;
+    try {
+        const seqCol = seqGridCell.tableColumn;
+        if (!seqCol)
+            return;
+        const mhlList = getMonomerHoverLinks(seqCol);
+        for (let mhlI = mhlList.length - 1; mhlI >= 0; --mhlI) {
+            const mhl = mhlList[mhlI];
+            const molGridCol = seqGridCell.grid.col(mhl.targetCol.name);
+            if (molGridCol) {
+                const handlerRes = mhl.handler(seqGridCell, seqMonomer, molGridCol);
+                if (!handlerRes)
+                    break;
+            }
         }
     }
+    catch (e) {
+        console.error(e);
+    }
 }
 export function getMonomerHoverLinks(seqCol) {
     return seqCol.temp[MonomerHoverLinksTemp] ?? [];

package/src/monomer-works/monomer-hover.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/src/monomer-works/seq-to-molfile.js CHANGED Viewed

@@ -29,15 +29,15 @@ export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymer
         });
         worker.postMessage({ seqList, monomersDict, alphabet, polymerType, start, end });
     }
-    let molList = [];
-    let warnings = [];
+    const molList = [];
+    const warnings = [];
     await Promise.all(promises).then((resArray) => {
         for (const resItem of resArray) {
             molList.push(...resItem.molfiles);
             warnings.push(...resItem.warnings);
         }
     });
-    const molHlList = molList.map((item) => getMolHighlight(item.monomers.values(), monomerLib));
+    //const molHlList = molList.map((item: MolfileWithMap) => getMolHighlight(item.monomers.values(), monomerLib));
     setTimeout(() => {
         workers.forEach((worker) => {
             worker.terminate();
@@ -45,7 +45,7 @@ export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymer
     }, 0);
     const molColName = getMolColName(df, seqCol.name);
     const molCol = DG.Column.fromType(DG.COLUMN_TYPE.STRING, molColName, seqCol.length)
-        .init((rowIdx) => molList[rowIdx].molfile);
+        .init((rowIdx) => molList[rowIdx]?.molfile);
     molCol.semType = DG.SEMTYPE.MOLECULE;
     molCol.meta.units = DG.UNITS.Molecule.MOLBLOCK;
     molCol.setTag(".sequence-src-col" /* ChemTags.SEQUENCE_SRC_COL */, seqCol.name);

package/src/monomer-works/seq-to-molfile.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/monomer-works/to-atomic-level-utils.js CHANGED Viewed

@@ -210,8 +210,8 @@ function updateChainExtendingVariables(monomer, v) {
     v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];
     v.bondShift += monomer.bonds.atomPairs.length + 1;
     v.nodeShift += monomer.atoms.atomTypes.length;
-    v.backbonePositionShift[0] += monomer.meta.backboneShift[0]; // todo: non-null check
-    v.backbonePositionShift[1] += v.flipFactor * monomer.meta.backboneShift[1];
+    v.backbonePositionShift[0] += monomer.meta.backboneShift?.[0] ?? 0; // todo: non-null check
+    v.backbonePositionShift[1] += v.flipFactor * (monomer.meta.backboneShift?.[1] ?? 0);
 }
 function updateBranchVariables(monomer, v) {
     v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];

package/src/monomer-works/to-atomic-level-utils.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/src/monomer-works/to-atomic-level.js CHANGED Viewed

@@ -44,7 +44,7 @@ export async function _toAtomicLevel(df, seqCol, monomerLib, seqHelper, rdKitMod
     const srcColLength = srcCol.length;
     const res = await seqToMolFileWorker(srcCol, monomersDict, alphabet, polymerType, monomerLib, seqHelper, rdKitModule);
     if (res.warnings.length > 0.05 * srcColLength)
-        throw new Error('Too many errors getting molfiles.');
+        grok.shell.warning(`Molfile conversion resulted in ${res.warnings.length} errors`);
     return res;
 }
 /** Get jagged array of monomer symbols for the dataframe
@@ -97,7 +97,16 @@ export function getMonomersDictFromLib(monomerSequencesArray, polymerType, alpha
             if (sym === '')
                 continue; // Skip gap/empty monomer for MSA
             try {
-                addMonomerToDict(monomersDict, sym, formattedMonomerLib, rdKitModule, polymerType, pointerToBranchAngle);
+                if (polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ && sym[1] == '(' && sym[sym.length - 2] == ')') {
+                    // special case for nucleobases
+                    const nsym = sym.substring(2, sym.length - 2);
+                    addMonomerToDict(monomersDict, nsym, formattedMonomerLib, rdKitModule, polymerType, pointerToBranchAngle);
+                    if (monomersDict[polymerType]?.[nsym])
+                        monomersDict[polymerType][sym] = monomersDict[polymerType][nsym];
+                }
+                else {
+                    addMonomerToDict(monomersDict, sym, formattedMonomerLib, rdKitModule, polymerType, pointerToBranchAngle);
+                }
             }
             catch (err) {
                 const errTxt = err instanceof Error ? err.message : err.toString();
@@ -442,9 +451,8 @@ export function parseCapGroupIdxMapV3K(molfileV3K) {
     let res;
     while ((res = regex.exec(molfileV3K)) !== null) {
         // This is necessary to avoid infinite loops with zero-width matches
-        if (res.index === regex.lastIndex) {
+        if (res.index === regex.lastIndex)
             regex.lastIndex++;
-        }
         // index 1 matches array is the atom number, index 3 is R group number
         capGroupIdxMap.set(parseInt(res[1]), parseInt(res[3]));
     }
@@ -797,6 +805,8 @@ function findDoubleBondedCarbonylOxygen(monomer) {
     let doubleBondedOxygen = 0;
     const sentinel = monomer.atoms.atomTypes.length;
     let i = 0;
+    if (monomer.meta.terminalNodes.length < 2)
+        return null;
     // iterate over the nodes bonded to the carbon and find the double one
     while (doubleBondedOxygen === 0) {
         const node = bondsMap.get(monomer.meta.terminalNodes[1])[i];

package/src/monomer-works/to-atomic-level.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/cell-renderer-back-base.d.ts.map CHANGED Viewed

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package/src/utils/cell-renderer-back-base.js CHANGED Viewed

@@ -50,6 +50,16 @@ export class CellRendererBackBase extends CellRendererBackStub {
             this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe(() => {
                 this.dirty = true;
             }));
+            this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe((_) => {
+                try {
+                    // this way we can check if the column is still in the dataframe
+                    if (!this.destroyed && this.tableCol && !this.tableCol.dataFrame)
+                        this.destroy();
+                }
+                catch (err) {
+                    this.logger.error(err);
+                }
+            }));
         }
         if (this.tableCol) {
             this.subs.push(grok.events.onTableRemoved.subscribe((eventData) => {

package/src/utils/cell-renderer-back-base.js.map CHANGED Viewed

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package/src/utils/macromolecule/seq-handler.d.ts CHANGED Viewed

@@ -17,8 +17,13 @@ export declare class SeqValueBase extends DG.SemanticValue<string> {
     get value(): string;
     set value(v: string);
     get helm(): string;
+    isDna(): boolean;
+    isRna(): boolean;
+    isNaturalPeptide(): boolean;
+    isHelm(): boolean;
     constructor(rowIdx: number, seqHandler: ISeqHandler);
     getSplitted(): ISeqSplitted;
+    getSplittedWithSugarsAndPhosphates(): ISeqSplitted;
 }
 export interface ISeqHandler {
     get column(): DG.Column<string>;

package/src/utils/macromolecule/seq-handler.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"seq-handler.d.ts","sourceRoot":"","sources":["seq-handler.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,wBAAwB,EAAC,MAAM,6DAA6D,CAAC;AAErG,OAAO,EAAC,YAAY,EAAE,WAAW,EAAE,YAAY,EAAC,MAAM,SAAS,CAAC;AAChE,OAAO,EAAW,QAAQ,EAAC,MAAM,UAAU,CAAC;AAC5C,OAAO,EAAC,QAAQ,EAAC,MAAM,kBAAkB,CAAC;AAC1C,OAAO,EAAC,oBAAoB,EAAC,MAAM,4BAA4B,CAAC;AAGhE,eAAO,MAAM,QAAQ;IACnB,sDAAsD;;;CAGrD,CAAC;AACJ,MAAM,MAAM,WAAW,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,CAAC;AAClD,MAAM,MAAM,UAAU,GAAG,CAAC,GAAG,EAAE,YAAY,KAAK,MAAM,CAAC;AAEvD,qBAAa,YAAa,SAAQ,EAAE,CAAC,aAAa,CAAC,MAAM,CAAC;IAgBtD,OAAO,CAAC,MAAM;IACd,OAAO,CAAC,UAAU;IAhBpB,IAAa,KAAK,IAAI,MAAM,CAAqD;IAEjF,IAAa,KAAK,CAAC,CAAC,EAAE,MAAM,EAAiD;IAE7E,IAAI,IAAI,IAAI,MAAM,CAAiD;IAEnE,KAAK,IAAI,OAAO;IAEhB,KAAK,IAAI,OAAO;IAEhB,gBAAgB,IAAI,OAAO;IAE3B,MAAM,IAAI,OAAO;gBAGP,MAAM,EAAE,MAAM,EACd,UAAU,EAAE,WAAW;IAUjC,WAAW,IAAI,YAAY;IAI3B,kCAAkC,IAAI,YAAY;CAiBnD;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,MAAM,IAAI,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IAEhC,IAAI,QAAQ,IAAI,MAAM,CAAC;IACvB,IAAI,QAAQ,IAAI,QAAQ,CAAC;IACzB,IAAI,SAAS,IAAI,MAAM,GAAG,SAAS,CAAC;IAEpC,IAAI,OAAO,IAAI,MAAM,CAAC;IACtB,IAAI,KAAK,IAAI,MAAM,CAAC;IACpB,IAAI,cAAc,IAAI,QAAQ,CAAC;IAC/B,IAAI,SAAS,IAAI,MAAM,CAAC;IACxB,IAAI,MAAM,IAAI,MAAM,CAAC;IACrB,IAAI,kBAAkB,IAAI,MAAM,CAAC;IACjC,IAAI,KAAK,IAAI,WAAW,CAAC;IACzB,IAAI,QAAQ,IAAI,YAAY,CAAC;IAC7B,IAAI,MAAM,IAAI,UAAU,CAAC;IAEzB,IAAI,OAAO,IAAI,MAAM,EAAE,CAAC;IAExB,OAAO,IAAI,OAAO,CAAC;IACnB,KAAK,IAAI,OAAO,CAAC;IACjB,MAAM,IAAI,OAAO,CAAC;IAClB,WAAW,IAAI,OAAO,CAAC;IAEvB,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,MAAM,GAAG,YAAY,CAAC;IAC1D,QAAQ,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,GAAG,GAAG,YAAY,CAAC;IACtD,OAAO,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAEhC,eAAe,IAAI,MAAM,CAAC;IAC1B,sBAAsB,IAAI,OAAO,CAAC;IAClC,oBAAoB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IACzE,OAAO,CAAC,WAAW,EAAE,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IACzE,2BAA2B,CAAC,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAC7D,YAAY,CAAC,EAAE,MAAM,EAAE,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC1D,SAAS,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,EAAE,IAAI,EAAE,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IAC3F,SAAS,CAAC,IAAI,CAAC,EAAE;QAAE,QAAQ,EAAE,QAAQ,CAAC;QAAC,SAAS,CAAC,EAAE,MAAM,CAAA;KAAE,GAAG,UAAU,CAAC;IAEzE,uBAAuB,IAAI,wBAAwB,CAAC;IACpD,YAAY,CAAC,QAAQ,EAAE,QAAQ,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,WAAW,CAAC;IACrE,eAAe,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAAE,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC;CAC3G"}

package/src/utils/macromolecule/seq-handler.js CHANGED Viewed

@@ -1,4 +1,6 @@
 import * as DG from 'datagrok-api/dg';
+import { ALPHABET } from './consts';
+import { splitterAsHelm, StringListSeqSplitted } from './utils';
 export const SeqTemps = new class {
     constructor() {
         /** Column's temp slot name for a SeqHandler object */
@@ -10,6 +12,10 @@ export class SeqValueBase extends DG.SemanticValue {
     get value() { return this.seqHandler.column.get(this.rowIdx); }
     set value(v) { this.seqHandler.column.set(this.rowIdx, v); }
     get helm() { return this.seqHandler.getHelm(this.rowIdx); }
+    isDna() { return this.seqHandler.alphabet === ALPHABET.DNA; }
+    isRna() { return this.seqHandler.alphabet === ALPHABET.RNA; }
+    isNaturalPeptide() { return this.seqHandler.alphabet === ALPHABET.PT; }
+    isHelm() { return this.seqHandler.isHelm(); }
     constructor(rowIdx, seqHandler) {
         if (seqHandler.column.dataFrame == null)
             throw new Error('Attribute .dataFrame is required for SeqValueBase from cell');
@@ -23,5 +29,22 @@ export class SeqValueBase extends DG.SemanticValue {
     getSplitted() {
         return this.seqHandler.getSplitted(this.rowIdx);
     }
+    getSplittedWithSugarsAndPhosphates() {
+        if (!this.isDna() && !this.isRna())
+            return this.getSplitted();
+        const originalSplit = splitterAsHelm(this.helm);
+        const fullArray = [];
+        for (let i = 0; i < originalSplit.length; i++) {
+            const m = originalSplit.getOriginal(i);
+            if (m[1] === '(' && m[m.length - 2] === ')') {
+                fullArray.push(m[0]);
+                fullArray.push(m.substring(2, m.length - 2));
+                fullArray.push(m[m.length - 1]);
+            }
+            else
+                fullArray.push(m);
+        }
+        return new StringListSeqSplitted(fullArray, this.seqHandler.defaultGapOriginal);
+    }
 }
 //# sourceMappingURL=seq-handler.js.map

package/src/utils/macromolecule/seq-handler.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"seq-handler.js","sourceRoot":"","sources":["seq-handler.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAC,QAAQ,EAAW,MAAM,UAAU,CAAC;AAG5C,OAAO,EAAC,cAAc,EAAE,qBAAqB,EAAC,MAAM,SAAS,CAAC;AAE9D,MAAM,CAAC,MAAM,QAAQ,GAAG,IAAI;IAAA;QAC1B,sDAAsD;QACtD,eAAU,GAAG,aAAa,CAAC;QAC3B,qBAAgB,GAAG,+BAA+B,CAAC;IACrD,CAAC;CAAA,EAAE,CAAC;AAIJ,MAAM,OAAO,YAAa,SAAQ,EAAE,CAAC,aAAqB;IACxD,IAAa,KAAK,KAAa,OAAO,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,CAAE,CAAC,CAAC,CAAC;IAEjF,IAAa,KAAK,CAAC,CAAS,IAAI,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;IAE7E,IAAI,IAAI,KAAa,OAAO,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;IAEnE,KAAK,KAAc,OAAO,IAAI,CAAC,UAAU,CAAC,QAAQ,KAAK,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC;IAEtE,KAAK,KAAc,OAAO,IAAI,CAAC,UAAU,CAAC,QAAQ,KAAK,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC;IAEtE,gBAAgB,KAAc,OAAO,IAAI,CAAC,UAAU,CAAC,QAAQ,KAAK,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;IAEhF,MAAM,KAAc,OAAO,IAAI,CAAC,UAAU,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC;IAEtD,YACU,MAAc,EACd,UAAuB;QAE/B,IAAI,UAAU,CAAC,MAAM,CAAC,SAAS,IAAI,IAAI;YACrC,MAAM,IAAI,KAAK,CAAC,6DAA6D,CAAC,CAAC;QACjF,MAAM,SAAS,GAAG,UAAU,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QACnF,MAAM,CAAC,GAAG,EAAE,CAAC,aAAa,CAAC,aAAa,CAAC,SAAS,CAAC,CAAC;QACpD,aAAa;QACb,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;QARN,WAAM,GAAN,MAAM,CAAQ;QACd,eAAU,GAAV,UAAU,CAAa;IAQjC,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAClD,CAAC;IAED,kCAAkC;QAChC,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE;YAChC,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;QAC5B,MAAM,aAAa,GAAG,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAChD,MAAM,SAAS,GAAa,EAAE,CAAC;QAC/B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC9C,MAAM,CAAC,GAAG,aAAa,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;YACvC,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;gBAC5C,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gBACrB,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC;gBAC7C,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC;YAClC,CAAC;;gBACC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QACtB,CAAC;QAED,OAAO,IAAI,qBAAqB,CAAC,SAAS,EAAE,IAAI,CAAC,UAAU,CAAC,kBAAkB,CAAC,CAAC;IAClF,CAAC;CACF"}

package/src/utils/macromolecule/utils.d.ts CHANGED Viewed

@@ -70,6 +70,7 @@ export declare function getAlphabet(alphabet: ALPHABET): Set<string>;
 export declare function getAlphabetSimilarity(freq: MonomerFreqs, alphabet: Set<string>, gapSymbol?: string): number;
 /** From detectMacromolecule */
 export declare function detectAlphabet(freq: MonomerFreqs, candidates: CandidateType[], gapSymbol?: string): string;
+export declare function detectHelmAlphabet(freq: MonomerFreqs, candidates: CandidateType[], gapSymbol?: string): string;
 /** Selects a suitable palette based on column data
  * @param {DG.Column} seqCol Column to look for a palette
  * @param {number}  minLength minimum length of sequence to detect palette (empty strings are allowed)

package/src/utils/macromolecule/utils.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/utils.js CHANGED Viewed

@@ -134,7 +134,9 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
 export const splitterAsHelm = (seq) => {
     const helmParts = seq.split('$');
     const spList = helmParts[0].split('|');
-    const mList = wu(spList.map((sp) => sp.match(/(?<=\{).+(?=})/)[0].split('.').map((m) => cleanupHelmSymbol(m))))
+    const mList = wu(spList
+        .map((sp) => (sp.match(/(?<=\{).+(?=})/)?.[0]?.split('.') ?? [])
+        .map((m) => cleanupHelmSymbol(m))))
         .flatten().toArray();
     return new StringListSeqSplitted(mList, GapOriginals[NOTATION.HELM]);
 };
@@ -215,6 +217,15 @@ export function detectAlphabet(freq, candidates, gapSymbol = '-') {
         alphabetName = ALPHABET.UN;
     return alphabetName;
 }
+export function detectHelmAlphabet(freq, candidates, gapSymbol = '-') {
+    // helm can contain DNA/RNA and other monomers. need to check that
+    const mons = Object.keys(freq);
+    // heuristic
+    const hasBranching = mons.filter((m) => m[1] === '(' && m[m.length - 2] === ')').length > mons.length * 0.8;
+    const correctedFreqs = hasBranching ? Object.entries(freq)
+        .reduce((acc, [m, f]) => { acc[m.substring(2, m.length - 2)] = f; return acc; }, {}) : freq;
+    return detectAlphabet(correctedFreqs, candidates, gapSymbol);
+}
 /** Selects a suitable palette based on column data
  * @param {DG.Column} seqCol Column to look for a palette
  * @param {number}  minLength minimum length of sequence to detect palette (empty strings are allowed)

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package/tsconfig.json CHANGED Viewed

@@ -30,7 +30,7 @@
     // "strictNullChecks": true,                    /* Enable strict null checks. */
     // "strictFunctionTypes": true,                 /* Enable strict checking of function types. */
     // "strictBindCallApply": true,                 /* Enable strict 'bind', 'call', and 'apply' methods on functions. */
-    // "strictPropertyInitialization": true,        /* Enable strict checking of property initialization in classes. */
+    "strictPropertyInitialization": false,        /* Enable strict checking of property initialization in classes. */
     // "noImplicitThis": true,                      /* Raise error on 'this' expressions with an implied 'any' type. */
     // "alwaysStrict": true,                        /* Parse in strict mode and emit "use strict" for each source file. */