@datagrok/sequence-translator 1.9.6 → 1.9.7

package/dist/package-test.js

@@ -1179,11 +1179,13 @@ function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {
     const monomers = new _types__WEBPACK_IMPORTED_MODULE_1__.MonomerMap();
     const steabsCollection = [];
     let nAtoms = 0;
+    let lastMonomerCappingAtom = undefined;
     for (v.i = 0; v.i < LC.seqLength; ++v.i) {
         const seqMonomer = monomerSeq[v.i];
         if (seqMonomer.symbol === _utils_macromolecule_consts__WEBPACK_IMPORTED_MODULE_3__.GAP_SYMBOL)
             continue;
         const monomer = (0,_types__WEBPACK_IMPORTED_MODULE_1__.getMolGraph)(monomersDict, { symbol: seqMonomer.symbol, polymerType: (0,_monomer_works__WEBPACK_IMPORTED_MODULE_4__.helmTypeToPolymerType)(seqMonomer.biotype) });
+        lastMonomerCappingAtom = monomer.terminalR2Atom;
         const mAtomFirst = v.nodeShift;
         const mBondFirst = v.bondShift;
         addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);
@@ -1206,7 +1208,7 @@ function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {
     }
     // if the last monomer needs to be capped, add the terminal OH to the resulting molfile
     if (needsCapping)
-        capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC);
+        capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, lastMonomerCappingAtom ?? _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.OXYGEN);
     const molfileCountsLine = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_COUNTS_LINE_ENDING;
     // todo: possible optimization may be achieved by replacing .join('') with +=
     // since counterintuitively joining an array into a new string is reportedly
@@ -1254,11 +1256,11 @@ function getCollectionBlock(collection) {
  * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block
  * @param {LoopVariables} v - Loop variables
  * @param {LoopConstants} LC - Loop constants*/
-function capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC) {
+function capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.OXYGEN) {
     // add terminal oxygen
     const atomIdx = v.nodeShift + 1;
     molfileAtomBlock[LC.atomCount] = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +
-        _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.OXYGEN + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +
+        (cappingAtomType ?? _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.OXYGEN) + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +
         v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\n';
     // add terminal bond
     const firstAtom = v.backboneAttachNode;
@@ -1411,8 +1413,10 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
         // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)
         bondCount += monomerCount;
         // if the last monomer is something like NH2, which only has R1, there is no need to cap it
+        // although, this should never happen, but hey... in other bits of code, there is a chunk that adds pseudo-R2 as hydrogen
+        // we should also check, if the R2 of the last monomer is not hydrogen, that case should also be omitted
         if (monomerCount > 0) {
-            if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2) {
+            if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2 || lastMonomerGraph?.terminalR2Atom?.toLowerCase() === _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.HYDROGEN.toLowerCase()) {
                 needsCapping = false;
                 atomCount -= 1; // remove the last atom (the terminal 'O')
                 bondCount -= 1; // remove the last bond (the terminal C-OH)
@@ -1691,7 +1695,9 @@ function setShiftsAndTerminalNodes(polymerType, monomerGraph, monomerSymbol) {
     // remove the 'rightmost' chain-extending r-group node in the backbone
     if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */) {
         setShifts(monomerGraph, polymerType);
-        removeNodeAndBonds(monomerGraph, monomerGraph.meta.rNodes[1]);
+        const removedR2Atom = removeNodeAndBonds(monomerGraph, monomerGraph.meta.rNodes[1]);
+        if (removedR2Atom?.removedAtom)
+            monomerGraph.terminalR2Atom = removedR2Atom.removedAtom; // store the removed R2 Atom type, if any
     }
     else { // nucleotides
         if (monomerSymbol === _consts__WEBPACK_IMPORTED_MODULE_9__.monomerWorksConsts.RIBOSE.symbol || monomerSymbol === _consts__WEBPACK_IMPORTED_MODULE_9__.monomerWorksConsts.DEOXYRIBOSE.symbol) {
@@ -1742,14 +1748,30 @@ function getMonomerMetadata(atoms, bonds, capGroups, capGroupIdxMap) {
         const existingRgroupIdx = Array.from(capGroupIdxMap.keys()).find((i) => capGroupIdxMap.get(i) === existingRgroup) - 1; // -1 because molfile indexing starts from 1
         const existingRgroupX = atoms.x[existingRgroupIdx];
         const existingRgroupY = atoms.y[existingRgroupIdx];
-        const furthestAtomIdx = atoms.x.reduce((furthestIdx, x, idx) => {
+        const atomBondedToExistingRgroupIdx = bonds.atomPairs.find((pair) => pair.includes(existingRgroupIdx + 1)).
+            find((i) => i !== existingRgroupIdx + 1) - 1; // -1 because molfile indexing starts from 1
+        let furthestAtomIdx = atoms.x.reduce((furthestIdx, x, idx) => {
             if (idx === existingRgroupIdx)
                 return furthestIdx; // skip existing r-group
+            // also skip the atom bonded to the existing r-group
+            if (idx === atomBondedToExistingRgroupIdx)
+                return furthestIdx;
             const y = atoms.y[idx];
             const dist = Math.sqrt((x - existingRgroupX) ** 2 + (y - existingRgroupY) ** 2);
             return dist > Math.sqrt((atoms.x[furthestIdx] - existingRgroupX) ** 2 +
                 (atoms.y[furthestIdx] - existingRgroupY) ** 2) ? idx : furthestIdx;
-        }, 0);
+        }, -1);
+        if (furthestAtomIdx === -1) {
+            furthestAtomIdx = atoms.x.length;
+            // add pseudo-hydrogen atom, very relevant for stuff like NH2-R
+            atoms.x = new Float32Array([...atoms.x, -existingRgroupX]);
+            atoms.y = new Float32Array([...atoms.y, -existingRgroupY]);
+            atoms.atomTypes = [...atoms.atomTypes, 'H'];
+            atoms.kwargs = [...atoms.kwargs, ''];
+            bonds.atomPairs.push([atomBondedToExistingRgroupIdx + 1, furthestAtomIdx + 1]); // +1 because molfile indexing starts from 1
+            bonds.bondTypes = new Uint32Array([...bonds.bondTypes, 1]); // single bond
+            bonds.kwargs.set(bonds.atomPairs.length - 1, ''); // empty kwargs for the new bond
+        }
         capGroupIdxMap.set(furthestAtomIdx + 1, missingRGroup); // +1 because molfile indexing starts from 1
         // finaly splice the capGroups array in correct place
         if (missingRGroup === 1)
@@ -2096,7 +2118,9 @@ function removeRgroupKwargs(monomerGraph) {
 /** Remove node 'removedNode' and the associated bonds. Notice, numeration of
  * nodes in molfiles starts from 1, not 0
  * @param {MolGraph} monomerGraph - monomer graph
- * @param {number} removedNode - node to be removed*/
+ * @param {number} removedNode - node to be removed
+ * @return {{removedAtom: string} | undefined} - removed atom type, if any
+ * */
 function removeNodeAndBonds(monomerGraph, removedNode) {
     if (typeof removedNode !== 'undefined') {
         const removedNodeIdx = removedNode - 1;
@@ -2104,7 +2128,7 @@ function removeNodeAndBonds(monomerGraph, removedNode) {
         const bonds = monomerGraph.bonds;
         const meta = monomerGraph.meta;
         // remove the node from atoms
-        atoms.atomTypes.splice(removedNodeIdx, 1);
+        const removedAtomType = atoms.atomTypes.splice(removedNodeIdx, 1)[0];
         atoms.x = spliceTypedArray(Float32Array, atoms.x, removedNodeIdx, 1);
         atoms.y = spliceTypedArray(Float32Array, atoms.y, removedNodeIdx, 1);
         atoms.kwargs.splice(removedNodeIdx, 1);
@@ -2158,6 +2182,7 @@ function removeNodeAndBonds(monomerGraph, removedNode) {
                 bonds.kwargs.set(key - 1, value);
             }
         });
+        return removedAtomType ? { removedAtom: removedAtomType } : undefined;
     }
 }
 // todo: rewrite the following two functions using templates,
@@ -3230,6 +3255,15 @@ class MonomerPlacer extends _cell_renderer_back_base__WEBPACK_IMPORTED_MODULE_5_
         return renderMultiline === 'true';
     }
     calculateMultiLineLayoutDynamic(g, w, h, subParts, positionShift, maxLengthOfMonomer) {
+        if (this.dirty) {
+            try {
+                this.reset();
+            }
+            catch (err) {
+                const [errMsg, errStack] = (0,_err_info__WEBPACK_IMPORTED_MODULE_7__.errInfo)(err);
+                this.logger.error(errMsg, undefined, errStack);
+            }
+        }
         // --- 1. Setup ---
         const { lineHeight, monomerSpacing } = this.calculateFontBasedSpacing(g);
         const availableWidth = w - (this.padding * 2);
@@ -3507,6 +3541,7 @@ class MonomerPlacer extends _cell_renderer_back_base__WEBPACK_IMPORTED_MODULE_5_
                 this.setMonomerLengthLimit(maxLengthOfMonomer);
                 this.setSeparatorWidth(sh.isMsa() ? msaGapLength : gapLength);
                 tableCol.temp[".mm.cellRenderer.settingsChanged" /* MmcrTemps.rendererSettingsChanged */] = _cell_renderer_consts__WEBPACK_IMPORTED_MODULE_9__.rendererSettingsChangedState.false;
+                this.dirty = true;
             }
             const rowIdx = gridCell.cell.rowIndex;
             const value = gridCell.cell.value;
@@ -3533,7 +3568,7 @@ class MonomerPlacer extends _cell_renderer_back_base__WEBPACK_IMPORTED_MODULE_5_
                 return wu__WEBPACK_IMPORTED_MODULE_2___default().count(0).take(seqSS.length).slice(positionShift).map((posIdx) => seqSS.getCanonical(posIdx)).toArray();
             })();
             const selectedPosition = Number.parseInt(tableCol.getTag(_macromolecule__WEBPACK_IMPORTED_MODULE_4__.TAGS.selectedPosition) ?? '-200');
-            const shouldUseMultiLine = this.shouldUseMultilineRendering(tableCol) && drawStyle !== _cell_renderer__WEBPACK_IMPORTED_MODULE_8__.DrawStyle.MSA;
+            const shouldUseMultiLine = this.shouldUseMultilineRendering(tableCol);
             if (shouldUseMultiLine) {
                 const currentCellBounds = [];
                 const layout = this.calculateMultiLineLayoutDynamic(g, w, h, subParts, positionShift, maxLengthOfMonomer);
@@ -4028,6 +4063,7 @@ __webpack_require__.r(__webpack_exports__);
 /* harmony export */   BioTags: () => (/* binding */ TAGS),
 /* harmony export */   GAP_SYMBOL: () => (/* binding */ GAP_SYMBOL),
 /* harmony export */   GapOriginals: () => (/* binding */ GapOriginals),
+/* harmony export */   MONOMER_MOTIF_SPLITTER: () => (/* binding */ MONOMER_MOTIF_SPLITTER),
 /* harmony export */   NOTATION: () => (/* binding */ NOTATION),
 /* harmony export */   TAGS: () => (/* binding */ TAGS),
 /* harmony export */   candidateAlphabets: () => (/* binding */ candidateAlphabets),
@@ -4097,6 +4133,7 @@ const GapOriginals = {
     [NOTATION.SEPARATOR]: '',
     [NOTATION.HELM]: '*',
 };
+const MONOMER_MOTIF_SPLITTER = ' , ';
 //# sourceMappingURL=consts.js.map
 
 /***/ }),
@@ -4111,6 +4148,7 @@ const GapOriginals = {
 __webpack_require__.r(__webpack_exports__);
 /* harmony export */ __webpack_require__.d(__webpack_exports__, {
 /* harmony export */   ALPHABET: () => (/* reexport safe */ _consts__WEBPACK_IMPORTED_MODULE_0__.ALPHABET),
+/* harmony export */   MONOMER_MOTIF_SPLITTER: () => (/* reexport safe */ _consts__WEBPACK_IMPORTED_MODULE_0__.MONOMER_MOTIF_SPLITTER),
 /* harmony export */   NOTATION: () => (/* reexport safe */ _consts__WEBPACK_IMPORTED_MODULE_0__.NOTATION),
 /* harmony export */   TAGS: () => (/* reexport safe */ _consts__WEBPACK_IMPORTED_MODULE_0__.TAGS),
 /* harmony export */   candidateAlphabets: () => (/* reexport safe */ _consts__WEBPACK_IMPORTED_MODULE_0__.candidateAlphabets),
@@ -4129,6 +4167,7 @@ __webpack_require__.r(__webpack_exports__);
 /* harmony import */ var _utils__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! ./utils */ "./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/utils.js");
 
 
+
 //# sourceMappingURL=index.js.map
 
 /***/ }),