npm - @datagrok-libraries/bio - Versions diffs - 5.49.1 → 5.50.1 - Mend

@datagrok-libraries/bio 5.49.1 → 5.50.1

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Files changed (18) hide show

package/CHANGELOG.md +8 -0
package/package.json +1 -1
package/src/monomer-works/monomer-hover.d.ts +5 -1
package/src/monomer-works/monomer-hover.d.ts.map +1 -1
package/src/monomer-works/monomer-hover.js +42 -23
package/src/monomer-works/monomer-hover.js.map +1 -1
package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level.js +33 -7
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/utils/macromolecule/seq-handler.d.ts.map +1 -1
package/src/utils/macromolecule/seq-handler.js +7 -4
package/src/utils/macromolecule/seq-handler.js.map +1 -1
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +11 -3
package/src/utils/macromolecule/utils.js.map +1 -1
package/src/utils/seq-helper.d.ts +12 -0
package/src/utils/seq-helper.d.ts.map +1 -1
package/src/utils/seq-helper.js.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,13 @@
 # bio changelog
+## 5.50.1 (2025-02-20)
+Remove helm dependency in toAtomicLevel for Linear sequences
+## 5.50.0 (2025-02-20)
+Support toAtomicLevel and POM conversion for all notations
 ## 5.49.1 (2025-02-17)
 Fix helm splitter for marginal cases

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.49.1",
+  "version": "5.50.1",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

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

@@ -6,7 +6,11 @@ import { MonomerHoverLink } from './utils';
 import { ISeqHelper } from '../utils/seq-helper';
 export declare const MonomerHoverLinksTemp = "MonomerHoverLinks";
 export declare function addMonomerHoverLink(seqColTemp: any, resLink: MonomerHoverLink): void;
-export declare function buildMonomerHoverLink(seqCol: DG.Column<string>, molCol: DG.Column<string>, monomerLib: IMonomerLibBase, seqHelper: ISeqHelper, rdKitModule: RDModule): MonomerHoverLink;
+/**
+ * Builds a monomer hover link between sequence and molecule columns
+ * throughPOM specifies if the sequence is translated through seqhelper using POM (default is false)
+ */
+export declare function buildMonomerHoverLink(seqCol: DG.Column<string>, molCol: DG.Column<string>, monomerLib: IMonomerLibBase, seqHelper: ISeqHelper, rdKitModule: RDModule, throughPOM?: boolean): Promise<MonomerHoverLink>;
 export declare function execMonomerHoverLinks(seqGridCell: DG.GridCell, seqMonomer: ISeqMonomer | null): void;
 export declare function getMonomerHoverLinks(seqCol: DG.Column<string>): MonomerHoverLink[];
 //# sourceMappingURL=monomer-hover.d.ts.map

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

	@@ -1 +1 @@
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package/src/monomer-works/monomer-hover.js CHANGED Viewed

@@ -13,22 +13,49 @@ export function addMonomerHoverLink(seqColTemp, resLink) {
     mhhList.push(resLink);
     seqColTemp[MonomerHoverLinksTemp] = mhhList;
 }
-export function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelper, rdKitModule) {
+/**
+ * Builds a monomer hover link between sequence and molecule columns
+ * throughPOM specifies if the sequence is translated through seqhelper using POM (default is false)
+ */
+export async function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelper, rdKitModule, throughPOM = false) {
     const seqSH = seqHelper.getSeqHandler(seqCol);
-    const isNucleotideHelmSequence = seqSH.isHelm() && (seqSH.alphabet == ALPHABET.RNA || seqSH.alphabet == ALPHABET.DNA);
+    const isNucleotide = (seqSH.alphabet == ALPHABET.RNA || seqSH.alphabet == ALPHABET.DNA);
+    const isNucleotideHelmSequence = seqSH.isHelm() && isNucleotide;
+    // if the conversion goes through polymer object model, it is aware that DNA/RNA need sugars and phosphates, therefore, for fasta
+    // of length 15, it will return 45 monomers. so we need to handle this case separately
+    const isNucleotideNonHelmSequence = !seqSH.isHelm() && isNucleotide;
+    const getSeqMonomerCorrectedPosition = (pos) => {
+        if (pos == undefined)
+            return null;
+        // if its dna or rna, we need to correct position as it will contain sugar and phosphate
+        // toAtomicLevel returns 15 monomers for 15 nucleotides (r(n)p is one monmer), while helm converter returns 45
+        if (isNucleotideHelmSequence)
+            return throughPOM ? pos : Math.floor(pos / 3);
+        if (isNucleotideNonHelmSequence)
+            return throughPOM ? pos * 3 + 1 : pos;
+        return pos;
+    };
+    const helmToMolfileConverter = throughPOM ? await seqHelper.getHelmToMolfileConverter(monomerLib) : null;
     function buildMonomerMap(seqCol, tableRowIdx) {
         const seqSH = seqHelper.getSeqHandler(seqCol);
-        const seqSS = seqSH.getSplitted(tableRowIdx);
-        const biotype = seqSH.defaultBiotype;
-        const seqMList = wu.count(0).take(seqSS.length)
-            .map((posIdx) => { return { position: posIdx, symbol: seqSS.getCanonical(posIdx), biotype: biotype }; })
-            .toArray();
-        const alphabet = seqSH.alphabet;
-        const polymerType = alphabet == ALPHABET.RNA || alphabet == ALPHABET.DNA ? "RNA" /* PolymerTypes.RNA */ : "PEPTIDE" /* PolymerTypes.PEPTIDE */;
-        const monomersDict = getMonomersDictFromLib([seqMList], polymerType, alphabet, monomerLib, rdKitModule);
-        // Call seq-to-molfile worker core directly
-        const molWM = monomerSeqToMolfile(seqMList, monomersDict, alphabet, polymerType);
-        return molWM.monomers;
+        if (!throughPOM) {
+            const seqSS = seqSH.getSplitted(tableRowIdx);
+            const biotype = seqSH.defaultBiotype;
+            const seqMList = wu.count(0).take(seqSS.length)
+                .map((posIdx) => { return { position: posIdx, symbol: seqSS.getCanonical(posIdx), biotype: biotype }; })
+                .toArray();
+            const alphabet = seqSH.alphabet;
+            const polymerType = alphabet == ALPHABET.RNA || alphabet == ALPHABET.DNA ? "RNA" /* PolymerTypes.RNA */ : "PEPTIDE" /* PolymerTypes.PEPTIDE */;
+            const monomersDict = getMonomersDictFromLib([seqMList], polymerType, alphabet, monomerLib, rdKitModule);
+            // Call seq-to-molfile worker core directly
+            const molWM = monomerSeqToMolfile(seqMList, monomersDict, alphabet, polymerType);
+            return molWM.monomers;
+        }
+        else {
+            const helm = seqSH.getHelm(tableRowIdx);
+            const molWM = seqHelper.helmToAtomicLevelSingle(helm, helmToMolfileConverter, false, false); // skip mol beautification step. not needed.
+            return molWM.monomers;
+        }
     }
     const monomerMapLruCache = new LRUCache({ max: 100 });
     function getMonomerMap(seqCol, tableRowIdx) {
@@ -59,27 +86,19 @@ export function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelper, rdK
                     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: getSeqMonomerCorrectedPosition() ?? -1,
+                    seqPosition: getSeqMonomerCorrectedPosition(seqMonomer?.position) ?? -1,
                     getSubstruct: () => {
                         if (!seqMonomer || seqMonomer.symbol === '*')
                             return undefined;
                         const molMonomerMap = getMonomerMap(seqCol, tableRowIdx);
                         if (!molMonomerMap)
                             return undefined;
-                        const monomerMap = molMonomerMap.get(getSeqMonomerCorrectedPosition()); // single monomer
+                        const monomerMap = molMonomerMap.get(getSeqMonomerCorrectedPosition(seqMonomer?.position)); // single monomer
                         if (!monomerMap)
                             return { atoms: [], bonds: [], highlightAtomColors: [], highlightBondColors: [] };
                         const res = getMolHighlight([monomerMap], monomerLib);

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/to-atomic-level.d.ts.map CHANGED Viewed

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

@@ -61,7 +61,9 @@ export function getMonomerSequencesArray(macroMolCol, seqHelper) {
         const seqSS = sh.getSplitted(rowIdx);
         containsEmptyValues || (containsEmptyValues = seqSS.length === 0);
         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();
+            .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`);
@@ -97,9 +99,9 @@ export function getMonomersDictFromLib(monomerSequencesArray, polymerType, alpha
             if (sym === '')
                 continue; // Skip gap/empty monomer for MSA
             try {
-                if (polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ && sym[1] == '(' && sym[sym.length - 2] == ')') {
+                if (polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ && sym.split(/\(|\)/).filter((e) => !!e).length === 3) {
                     // special case for nucleobases
-                    const nsym = sym.substring(2, sym.length - 2);
+                    const nsym = sym.split(/\(|\)/)[1];
                     addMonomerToDict(monomersDict, nsym, formattedMonomerLib, rdKitModule, polymerType, pointerToBranchAngle);
                     if (monomersDict[polymerType]?.[nsym])
                         monomersDict[polymerType][sym] = monomersDict[polymerType][nsym];
@@ -175,6 +177,7 @@ function getMolGraph(monomerSymbol, formattedMonomerLib, moduleRdkit, polymerTyp
         setShiftsAndTerminalNodes(polymerType, monomerGraph, monomerSymbol);
         // todo: restore after debugging
         removeHydrogen(monomerGraph);
+        removeRgroupKwargs(monomerGraph);
         return monomerGraph;
     }
 }
@@ -525,6 +528,17 @@ function removeHydrogen(monomerGraph) {
         ++i;
     }
 }
+/** After processing and removing r-groups, the KWARGS property might still contain RGROUPS lines.
+ * this needs to be removed
+ * @param {MolGraph} monomerGraph - monomer graph*/
+function removeRgroupKwargs(monomerGraph) {
+    const molv3kRGroupKwargLine = ' RGROUPS=(1 1)';
+    for (let i = 0; i < (monomerGraph.atoms.kwargs?.length ?? 0); i++) {
+        const kwarg = monomerGraph.atoms.kwargs[i];
+        if (kwarg && kwarg.includes(molv3kRGroupKwargLine))
+            monomerGraph.atoms.kwargs[i] = kwarg.replace(molv3kRGroupKwargLine, ''); // remove the line
+    }
+}
 /** Remove node 'removedNode' and the associated bonds. Notice, numeration of
  * nodes in molfiles starts from 1, not 0
  * @param {MolGraph} monomerGraph - monomer graph
@@ -630,24 +644,36 @@ function adjustPeptideMonomerGraph(monomer) {
     }
 }
 function adjustPhosphateMonomerGraph(monomer) {
-    const centeredNode = monomer.meta.terminalNodes[0] - 1; // Phosphorus
+    //need to rotate phosphate so that O-P-O is on OX axis, this is not always possible, but we can always
+    // make sure both O's are on the OX axis
+    const centeredNode = monomer.meta.rNodes[1] - 1; // Oxigen 1
     const rotatedNode = monomer.meta.rNodes[0] - 1; // Oxygen
-    // const nodeTwoIdx = monomer.meta.rNodes[0] - 1;
     const x = monomer.atoms.x;
     const y = monomer.atoms.y;
     // place nodeOne at origin
     shiftCoordinates(monomer, -x[centeredNode], -y[centeredNode]);
     // angle is measured between OY and the rotated node
     const angle = findAngleWithOY(x[rotatedNode], y[rotatedNode]);
-    // rotate the centered graph so that P-O is on OX
+    // rotate the centered graph so that O-P-O is on OX
     rotateCenteredGraph(monomer.atoms, Math.PI / 2 - angle);
 }
 function adjustSugarMonomerGraph(monomer, pointerToBranchAngle) {
+    // eslint-disable-next-line max-len
+    // sugars connect with R1 to previous nucleotide phosphate, R3 to the nucleobase and R2 to the next nucleotide phosphate
+    // need to adjust the graph so that R1 is looking left, R2 is looking right and R3 is looking up
     const x = monomer.atoms.x;
     const y = monomer.atoms.y;
     let centeredNode = monomer.meta.terminalNodes[0] - 1;
     const rotatedNode = monomer.meta.rNodes[1] - 1;
     shiftCoordinates(monomer, -x[centeredNode], -y[centeredNode]);
+    // check if the sugar needs to be flipped around (mirrored)
+    // orient sugar with R3 pointing up
+    const r3Angle = findAngleWithOY(x[monomer.meta.rNodes[2] - 1], y[monomer.meta.rNodes[2] - 1]);
+    rotateCenteredGraph(monomer.atoms, -r3Angle);
+    // console.log(x[monomer.meta.rNodes[0] - 1], x[monomer.meta.rNodes[1] - 1]);
+    // if r1 is to the right of r2, flip the sugar around OY
+    if (x[monomer.meta.rNodes[0] - 1] > x[monomer.meta.rNodes[1] - 1])
+        flipMonomerAroundOY(monomer);
     // angle is measured between OX and the rotated node
     const angle = findAngleWithOY(x[rotatedNode], y[rotatedNode]);
     // rotate the centered graph so that the rotated node in on OX
@@ -783,7 +809,7 @@ function getAngleBetweenSugarBranchAndOY(molGraph) {
     const terminalNode = molGraph.meta.terminalNodes[2] - 1;
     const xShift = x[rNode] - x[terminalNode];
     const yShift = y[rNode] - y[terminalNode];
-    return Math.atan(yShift / xShift) + Math.PI / 2;
+    return Math.atan2(xShift, yShift); // notice the fliped order of arguments
 }
 /** Flips double-bonded 'O' in carbonyl group with 'OH' in order for the monomers
  * to have standard representation simplifying their concatenation. The

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

	@@ -1 +1 @@
1	- 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package/src/utils/macromolecule/seq-handler.d.ts.map CHANGED Viewed

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

@@ -34,12 +34,15 @@ export class SeqValueBase extends DG.SemanticValue {
             return this.getSplitted();
         const originalSplit = splitterAsHelm(this.helm);
         const fullArray = [];
+        // heuristic for detecting dna/rna
+        const helmNucleotideFullRe = /\(|\)/;
         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]);
+            const splitM = m.split(helmNucleotideFullRe).filter((el) => !!el);
+            if (splitM.length === 3) {
+                fullArray.push(splitM[0]);
+                fullArray.push(splitM[1]);
+                fullArray.push(splitM[2]);
             }
             else
                 fullArray.push(m);

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

	@@ -1 +1 @@
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package/src/utils/macromolecule/utils.d.ts.map CHANGED Viewed

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

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { Vector } from '@datagrok-libraries/utils/src/type-declarations';
@@ -220,10 +221,17 @@ export function detectAlphabet(freq, candidates, gapSymbol = '-') {
 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 helmNucleotideFullRe = /\(|\)/;
+    // heuristic for detecting dna/rna
+    const hasBranching = mons.filter((m) => m.split(helmNucleotideFullRe).filter((p) => !!p).length === 3).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;
+        .reduce((acc, [m, f]) => {
+        const split = m.split(helmNucleotideFullRe);
+        const actualMonomer = split[1]; // the inside part is the actual monomer (for example r(A)p)
+        if (actualMonomer)
+            acc[actualMonomer] = f;
+        return acc;
+    }, {}) : freq;
     return detectAlphabet(correctedFreqs, candidates, gapSymbol);
 }
 /** Selects a suitable palette based on column data

package/src/utils/macromolecule/utils.js.map CHANGED Viewed

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package/src/utils/seq-helper.d.ts CHANGED Viewed

@@ -1,10 +1,20 @@
 import * as DG from 'datagrok-api/dg';
 import { IMonomerLibBase } from '../types';
 import { ISeqHandler } from './macromolecule/seq-handler';
+import { MolfileWithMap } from '../monomer-works/types';
+import { RDModule, RDMol } from '@datagrok-libraries/chem-meta/src/rdkit-api';
 export type ToAtomicLevelRes = {
     molCol: DG.Column<string> | null;
     warnings: string[];
 };
+export interface IHelmToMolfileConverter {
+    convertToSmiles(helmCol: DG.Column<string>): DG.Column<string>;
+    molV3KtoMolV3KOCL(molV3k: string): string;
+    getMolV3000ViaOCL(beautifiedMols: (RDMol | null)[], columnName: string): DG.Column<string>;
+    convertToRdKitBeautifiedMolfileColumn(helmCol: DG.Column<string>, chiralityEngine: boolean, rdKitModule: RDModule, monomerLib: IMonomerLibBase): DG.Column<string>;
+    convertToMolfileV3KColumn(helmCol: DG.Column<string>): DG.Column<string>;
+    convertToMolfileV3K(helmList: string[]): MolfileWithMap[];
+}
 export interface ISeqHelper {
     /**
      * @param helmCol {DG.Column<string>} Macromolecules in Helm format
@@ -13,11 +23,13 @@ export interface ISeqHelper {
      * @param overrideMonomerLib {IMonomerLibBase} [null] Override monomer library for monomers from reactions
      **/
     helmToAtomicLevel(helmCol: DG.Column<string>, chiralityEngine?: boolean, highlight?: boolean, overrideMonomerLib?: IMonomerLibBase): Promise<ToAtomicLevelRes>;
+    helmToAtomicLevelSingle(helm: string, converter: IHelmToMolfileConverter, chiralityEngine?: boolean, beautifyMol?: boolean): MolfileWithMap;
     getSeqHandler(seqCol: DG.Column<string>): ISeqHandler;
     getSeqMonomers(seqCol: DG.Column<string>): string[];
     setUnitsToFastaColumn(sh: ISeqHandler): void;
     setUnitsToSeparatorColumn(sh: ISeqHandler): void;
     setUnitsToHelmColumn(sh: ISeqHandler): void;
+    getHelmToMolfileConverter(monomerLib: IMonomerLibBase): Promise<IHelmToMolfileConverter>;
 }
 export declare function getSeqHelper(): Promise<ISeqHelper>;
 //# sourceMappingURL=seq-helper.d.ts.map

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

	@@ -1 +1 @@
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