@datagrok-libraries/bio 5.39.28 → 5.40.0

package/.eslintrc.json

@@ -15,7 +15,7 @@
     "@typescript-eslint"
   ],
   "rules": {
-    "indent": ["error", 2, {"SwitchCase": 1}],
+    "indent": ["error", 2, {"SwitchCase": 0}],
     "max-len": ["error", 120],
     "no-unused-vars": "off",
     "@typescript-eslint/no-unused-vars": [

package/CHANGELOG.md

@@ -1,5 +1,26 @@
 # bio changelog
 
+## 5.40.0 (2024-03-30)
+
+### Features
+
+* #2707: Add original and canonical to ISeqSplitted
+
+### Bug fixes
+
+* Bio: Fix SeqHandler.splitted cache for changing data
+* Bio: Fix SeqHandler.forColumn temp cache for changing column
+
+### Breaking changes
+
+* Rename UnitsHandler to SeqHandler, .getOrCreate() to forColumn()
+
+## 5.39.29 (2024-03-07)
+
+### Features
+
+* Add NEWICK_EMPTY const
+
 ## 5.39.28 (2024-03-04)
 
 ### Bug fixes

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.39.28",
+  "version": "5.40.0",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.68",
@@ -48,4 +48,4 @@
     "lint": "eslint \"./src/**/*.ts\"",
     "lint-fix": "eslint \"./src/**/*.ts\" --fix"
   }
-}
+}

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

@@ -1 +1 @@
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+{"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,CA8BpE;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"}

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

@@ -2,50 +2,51 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 import { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME, } from '../utils/const';
-import { UnitsHandler } from '../utils/units-handler';
+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 = {};
-    const uh = UnitsHandler.getOrCreate(col);
-    const splitterFunc = uh.getSplitter();
+    const sh = SeqHandler.forColumn(col);
     const encodedStringArray = [];
-    for (let i = 0; i < col.length; ++i) {
+    const rowCount = col.length;
+    for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
         let encodedMonomerStr = '';
-        const monomers = splitterFunc(col.get(i));
-        for (const m of monomers) {
-            if (!monomerSymbolDict[m]) {
+        const monomers = sh.getSplitted(rowIdx);
+        for (const cm of monomers.canonicals) {
+            if (!monomerSymbolDict[cm]) {
                 if (encodeSymbol > MONOMER_ENCODE_MAX) {
                     grok.shell.error(`Not enough symbols to encode monomers`);
                     return null;
                 }
-                monomerSymbolDict[m] = encodeSymbol;
+                monomerSymbolDict[cm] = encodeSymbol;
                 encodeSymbol++;
             }
-            encodedMonomerStr += String.fromCodePoint(monomerSymbolDict[m]);
+            encodedMonomerStr += String.fromCodePoint(monomerSymbolDict[cm]);
         }
         encodedStringArray.push(encodedMonomerStr);
     }
     return DG.Column.fromStrings('encodedMolecules', encodedStringArray);
 }
 export function getMolfilesFromSeq(col, monomersLibObject) {
-    const uh = UnitsHandler.getOrCreate(col);
-    const splitter = uh.getSplitter();
+    const sh = SeqHandler.forColumn(col);
     const monomersDict = createMomomersMolDict(monomersLibObject);
     const molFiles = [];
-    for (let i = 0; i < col.length; ++i) {
-        const macroMolecule = col.get(i);
-        const monomers = splitter(macroMolecule);
+    const rowCount = col.length;
+    for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
+        const monomers = sh.getSplitted(rowIdx);
         const molFilesForSeq = [];
         for (let j = 0; j < monomers.length; ++j) {
-            if (monomers[j]) {
-                if (!monomersDict[monomers[j]]) {
-                    grok.shell.warning(`Monomer ${monomers[j]} is missing in HELM library. Structure cannot be created`);
+            const cm = monomers.getCanonical(j);
+            if (cm) {
+                if (!monomersDict[cm]) {
+                    grok.shell.warning(`Monomer ${cm} is missing in HELM library. Structure cannot be created`);
                     return null;
                 }
                 // what is the reason of double conversion?
-                molFilesForSeq.push(JSON.parse(JSON.stringify(monomersDict[monomers[j]])));
+                molFilesForSeq.push(JSON.parse(JSON.stringify(monomersDict[cm])));
             }
         }
         molFiles.push(molFilesForSeq);
@@ -53,20 +54,19 @@ export function getMolfilesFromSeq(col, monomersLibObject) {
     return molFiles;
 }
 export function getMolfilesFromSingleSeq(cell, monomersLibObject) {
-    const uh = UnitsHandler.getOrCreate(cell.column);
-    const splitterFunc = uh.getSplitter();
+    const sh = SeqHandler.forColumn(cell.column);
     const monomersDict = createMomomersMolDict(monomersLibObject);
     const molFiles = [];
-    const macroMolecule = cell.value;
-    const monomers = splitterFunc(macroMolecule);
+    const monomers = sh.getSplitted(cell.rowIndex);
     const molFilesForSeq = [];
     for (let j = 0; j < monomers.length; ++j) {
-        if (monomers[j]) {
-            if (!monomersDict[monomers[j]]) {
-                grok.shell.warning(`Monomer ${monomers[j]} is missing in HELM library. Structure cannot be created`);
+        const cm = monomers.getCanonical(j);
+        if (cm) {
+            if (!monomersDict[cm]) {
+                grok.shell.warning(`Monomer ${cm} is missing in HELM library. Structure cannot be created`);
                 return null;
             }
-            molFilesForSeq.push(JSON.parse(JSON.stringify(monomersDict[monomers[j]])));
+            molFilesForSeq.push(JSON.parse(JSON.stringify(monomersDict[cm])));
         }
     }
     molFiles.push(molFilesForSeq);
@@ -126,6 +126,7 @@ export async function getMonomerLibHelper() {
     return res;
 }
 export async function sequenceChemSimilarity(positionColumns, referenceSequence) {
+    /* eslint-enable max-len */
     if (positionColumns instanceof DG.Column)
         positionColumns = splitAlignedSequences(positionColumns).columns.toList();
     const libHelper = await getMonomerLibHelper();
@@ -136,14 +137,14 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
     const totalSimilarity = new Float32Array(rowCount);
     // Calculate base similarity
     for (let position = 0; position < positionColumns.length; ++position) {
-        const referenceMonomer = referenceSequence[position];
-        const referenceMol = monomerLib.getMonomer('PEPTIDE', referenceMonomer)?.smiles ?? '';
+        const referenceMonomerCanonical = referenceSequence.getCanonical(position);
+        const referenceMol = monomerLib.getMonomer('PEPTIDE', referenceMonomerCanonical)?.smiles ?? '';
         const monomerCol = positionColumns[position];
         const monomerColData = monomerCol.getRawData();
         const monomerColCategories = monomerCol.categories;
         const emptyCategoryIdx = monomerColCategories.indexOf('');
         rawCols[position] = { categories: monomerColCategories, data: monomerColData, emptyIndex: emptyCategoryIdx };
-        if (typeof referenceMonomer === 'undefined')
+        if (typeof referenceMonomerCanonical === 'undefined')
             continue;
         // Calculating similarity for
         const molCol = DG.Column.fromStrings('smiles', monomerColCategories.map((cat) => monomerLib.getMonomer('PEPTIDE', cat)?.smiles ?? ''));
@@ -152,9 +153,9 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
         const similarityColData = similarityCol.getRawData();
         for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
             const monomerCategoryIdx = monomerColData[rowIdx];
-            totalSimilarity[rowIdx] += referenceMonomer !== '' && monomerCategoryIdx !== emptyCategoryIdx ?
+            totalSimilarity[rowIdx] += referenceMonomerCanonical !== GAP_SYMBOL && monomerCategoryIdx !== emptyCategoryIdx ?
                 similarityColData[monomerCategoryIdx] :
-                referenceMonomer === '' && monomerCategoryIdx === emptyCategoryIdx ? 1 : 0;
+                referenceMonomerCanonical === GAP_SYMBOL && monomerCategoryIdx === emptyCategoryIdx ? 1 : 0;
         }
     }
     for (let similarityIndex = 0; similarityIndex < totalSimilarity.length; ++similarityIndex) {
@@ -172,10 +173,12 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
     const similarityCol = DG.Column.fromFloat32Array('Similarity', totalSimilarity);
     return similarityCol;
 }
+/* eslint-disable max-len */
 /** Calculates chemical similarity between each pair of monomers.
  * @param {string[]} monomerSet Set of unique monomers.
  * @returns {Promise<{scoringMatrix: number[][], alphabetIndexes: {[monomerId: string]: number}}>} Ojbect containing similarity scoring matrix and monomer to index mapping. */
 export async function calculateMonomerSimilarity(monomerSet) {
+    /* eslint-enable max-len */
     const libHelper = await getMonomerLibHelper();
     const monomerLib = libHelper.getBioLib();
     const scoringMatrix = [];

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

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

@@ -40,10 +40,10 @@ export declare function convertMolfileToV3K(molfileV2K: string, moduleRdkit: any
  * @return {Bonds} - Bonds object*/
 export declare function parseBondBlock(molfileV3K: string, bondCount: number): Bonds;
 /** Constructs mapping of r-group nodes to default capGroups, all numeration starting from 1.
-  * According to https://pubs.acs.org/doi/10.1021/ci3001925, R1 and R2 are the chain extending attachment points,
-  * while R3 is the branching attachment point.
-  * @param {string} molfileV2K - V2000 molfile
-  * @return {Map<number, number>} - Map of r-group nodes to default capGroups*/
+ * According to https://pubs.acs.org/doi/10.1021/ci3001925, R1 and R2 are the chain extending attachment points,
+ * while R3 is the branching attachment point.
+ * @param {string} molfileV2K - V2000 molfile
+ * @return {Map<number, number>} - Map of r-group nodes to default capGroups*/
 export declare function parseCapGroupIdxMap(molfileV2K: string): Map<number, number>;
 export declare function parseAtomAndBondCounts(molfileV3K: string): {
     atomCount: number;

package/src/monomer-works/to-atomic-level.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"to-atomic-level.d.ts","sourceRoot":"","sources":["to-atomic-level.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAMtC,OAAO,EAAc,iBAAiB,EAAqB,MAAM,gBAAgB,CAAC;AAClF,OAAO,EAAC,QAAQ,EAAW,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAC,WAAW,EAAE,OAAO,EAAC,MAAM,UAAU,CAAC;AAO9C,OAAO,EAAQ,KAAK,EAAe,QAAQ,EAAwC,MAAM,SAAS,CAAC;AAOnG;;;;GAIG;AACH,wBAAsB,cAAc,CAClC,EAAE,EAAE,EAAE,CAAC,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,WAAW,GACnE,OAAO,CAAC;IAAE,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,IAAI,CAAC;IAAC,QAAQ,EAAE,MAAM,EAAG,CAAA;CAAE,CAAC,CAsDzD;AAED;;4EAE4E;AAC5E,wBAAgB,wBAAwB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,MAAM,EAAE,EAAE,CAoBnF;AAGD;;;;;;;qFAOqF;AACrF,wBAAsB,sBAAsB,CAC1C,qBAAqB,EAAE,MAAM,EAAE,EAAE,EAAE,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,iBAAiB,EAAE,QAAQ,EAAE,QAAQ,GAC7G,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC,CAsChC;AAqID;;wDAEwD;AACxD,wBAAgB,cAAc,CAAC,aAAa,EAAE,GAAG,EAAE,GAAG,MAAM,EAAE,CAe7D;AAmGD;;;qCAGqC;AACrC,wBAAgB,mBAAmB,CAAC,UAAU,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,GAAG,MAAM,CAMhF;AAED;;;mCAGmC;AACnC,wBAAgB,cAAc,CAAC,UAAU,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,GAAG,KAAK,CA8C3E;AAED;;;;8EAI8E;AAC9E,wBAAgB,mBAAmB,CAAC,UAAU,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAyC3E;AAED,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,MAAM,GAAG;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,SAAS,EAAE,MAAM,CAAA;CAAE,CAcnG;AA6cD,wBAAgB,2BAA2B,CAAC,QAAQ,EAAE,QAAQ,GAAG,MAAM,CAmEtE;AAED,wBAAsB,2BAA2B,CAAC,eAAe,EAAE,GAAG,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,CAAC,CA6BlH;AAED;;iCAEiC;AACjC,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,OAAO,GAAG,MAAM,CAmB1D"}

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

@@ -3,7 +3,7 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { NOTATION } from '../utils/macromolecule/consts';
-import { UnitsHandler } from '../utils/units-handler';
+import { SeqHandler } from '../utils/seq-handler';
 import { getFormattedMonomerLib, keepPrecision } from './to-atomic-level-utils';
 import { seqToMolFileWorker } from './seq-to-molfile';
 import { monomerWorksConsts as C } from './consts';
@@ -25,14 +25,14 @@ export async function _toAtomicLevel(df, seqCol, monomerLib) {
         return { col: null, warnings: [msg] };
     }
     let srcCol = seqCol;
-    const seqUh = UnitsHandler.getOrCreate(seqCol);
+    const seqUh = SeqHandler.forColumn(seqCol);
     // convert 'helm' to 'separator' units
     if (seqUh.isHelm()) {
         srcCol = seqUh.convert(NOTATION.SEPARATOR, '.');
         srcCol.name = seqCol.name; // Replace converted col name 'separator(<original>)' to '<original>';
     }
-    const srcUh = UnitsHandler.getOrCreate(srcCol);
-    const alphabet = srcUh.alphabet;
+    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
@@ -62,17 +62,16 @@ export async function _toAtomicLevel(df, seqCol, monomerLib) {
  * @param {DG.Column} macroMolCol - Column with macro-molecules
  * @return {string[]} - Jagged array of monomer symbols for the dataframe */
 export function getMonomerSequencesArray(macroMolCol) {
-    const columnLength = macroMolCol.length;
-    const result = new Array(columnLength);
+    const rowCount = macroMolCol.length;
+    const result = new Array(rowCount);
     // split the string into monomers
-    const uh = UnitsHandler.getOrCreate(macroMolCol);
-    const splitter = uh.getSplitter();
+    const sh = SeqHandler.forColumn(macroMolCol);
     let containsEmptyValues = false;
-    for (let row = 0; row < columnLength; ++row) {
-        const macroMolecule = macroMolCol.get(row);
-        containsEmptyValues || (containsEmptyValues = macroMolecule === '');
-        result[row] = macroMolecule ? wu(splitter(macroMolecule))
-            .filter((monomerSymbol) => !uh.isGap(monomerSymbol)).toArray() : [];
+    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();
     }
     if (containsEmptyValues)
         grok.shell.warning(`Some values in the "${macroMolCol.name}" column are empty`);
@@ -313,9 +312,9 @@ function getShiftBetweenNodes(molGraph, rightNodeIdx, leftNodeIdx) {
     ];
 }
 /** Helper function necessary to build a correct V3000 molfile out of V2000 with
-  * specified r-groups
-  * @param {string} molfileV2K - V2000 molfile
-  * @return {string} - V2000 molfile without R-group lines*/
+ * specified r-groups
+ * @param {string} molfileV2K - V2000 molfile
+ * @return {string} - V2000 molfile without R-group lines*/
 function removeRGroupLines(molfileV2K) {
     let begin = molfileV2K.indexOf(C.V2K_A_LINE, 0);
     if (begin === -1)
@@ -383,10 +382,10 @@ export function parseBondBlock(molfileV3K, bondCount) {
     };
 }
 /** Constructs mapping of r-group nodes to default capGroups, all numeration starting from 1.
-  * According to https://pubs.acs.org/doi/10.1021/ci3001925, R1 and R2 are the chain extending attachment points,
-  * while R3 is the branching attachment point.
-  * @param {string} molfileV2K - V2000 molfile
-  * @return {Map<number, number>} - Map of r-group nodes to default capGroups*/
+ * According to https://pubs.acs.org/doi/10.1021/ci3001925, R1 and R2 are the chain extending attachment points,
+ * while R3 is the branching attachment point.
+ * @param {string} molfileV2K - V2000 molfile
+ * @return {Map<number, number>} - Map of r-group nodes to default capGroups*/
 export function parseCapGroupIdxMap(molfileV2K) {
     const capGroupIdxMap = new Map();
     // parse A-lines (RNA)
@@ -438,10 +437,10 @@ export function parseAtomAndBondCounts(molfileV3K) {
     return { atomCount: numOfAtoms, bondCount: numOfBonds };
 }
 /** Parse V3000 atom block and return Atoms object. NOTICE: only atomTypes, x, y
-  * and kwargs fields are set in the return value, with other fields dummy initialized.
-  * @param {string} molfileV3K - V3000 molfile
-  * @param {number} atomCount - number of atoms in the molecule
-  * @return {Atoms} - Atoms object */
+ * and kwargs fields are set in the return value, with other fields dummy initialized.
+ * @param {string} molfileV3K - V3000 molfile
+ * @param {number} atomCount - number of atoms in the molecule
+ * @return {Atoms} - Atoms object */
 function parseAtomBlock(molfileV3K, atomCount) {
     const atomTypes = new Array(atomCount);
     const x = new Float32Array(atomCount);
@@ -493,9 +492,9 @@ function removeHydrogen(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*/
+ * nodes in molfiles starts from 1, not 0
+ * @param {MolGraph} monomerGraph - monomer graph
+ * @param {number} removedNode - node to be removed*/
 function removeNodeAndBonds(monomerGraph, removedNode) {
     if (typeof removedNode !== 'undefined') {
         const removedNodeIdx = removedNode - 1;
@@ -658,9 +657,9 @@ function getEuclideanDistance(p1, p2) {
     return keepPrecision(Math.sqrt((p1.x - p2.x) ** 2 + (p1.y - p2.y) ** 2));
 }
 /** Flip carboxyl group with the radical in a peptide monomer in case the
-  * carboxyl group is in the lower half-plane
-  * @param {MolGraph}monomer - peptide monomer
-  * @param {number}doubleBondedOxygen - index of the double-bonded oxygen atom*/
+ * carboxyl group is in the lower half-plane
+ * @param {MolGraph}monomer - peptide monomer
+ * @param {number}doubleBondedOxygen - index of the double-bonded oxygen atom*/
 function flipCarboxylAndRadical(monomer, doubleBondedOxygen) {
     // verify that the carboxyl group is in the lower half-plane
     if (monomer.atoms.y[monomer.meta.rNodes[1] - 1] < 0 &&
@@ -690,7 +689,7 @@ function findAngleWithOY(x, y) {
  * @param {number}x
  * @param {number}y
  * @return {number} angle in radians
-*/
+ */
 function findAngleWithOX(x, y) {
     return findAngleWithOY(x, y) + Math.PI / 2;
 }
@@ -751,10 +750,10 @@ function getAngleBetweenSugarBranchAndOY(molGraph) {
     return Math.atan(yShift / xShift) + Math.PI / 2;
 }
 /** Flips double-bonded 'O' in carbonyl group with 'OH' in order for the monomers
-  * to have standard representation simplifying their concatenation. The
-  * monomer must already be adjusted with adjustPeptideMonomerGraph in order for this function to be implemented
-  * @param {MolGraph}monomer - peptide monomer
-  * @param {number}doubleBondedOxygen - index of the double-bonded oxygen atom*/
+ * to have standard representation simplifying their concatenation. The
+ * monomer must already be adjusted with adjustPeptideMonomerGraph in order for this function to be implemented
+ * @param {MolGraph}monomer - peptide monomer
+ * @param {number}doubleBondedOxygen - index of the double-bonded oxygen atom*/
 function flipHydroxilGroup(monomer, doubleBondedOxygen) {
     const x = monomer.atoms.x;
     // -1 below because indexing of nodes in molfiles starts from 1, unlike arrays
@@ -762,9 +761,9 @@ function flipHydroxilGroup(monomer, doubleBondedOxygen) {
         swapNodes(monomer, doubleBondedOxygen, monomer.meta.rNodes[1]);
 }
 /** Determine the number of node (starting from 1) corresponding to the
-   * double-bonded oxygen of the carbonyl group
-   * @param {MolGraph}monomer - peptide monomer
-   * @return {number} index of the double-bonded oxygen atom*/
+ * double-bonded oxygen of the carbonyl group
+ * @param {MolGraph}monomer - peptide monomer
+ * @return {number} index of the double-bonded oxygen atom*/
 function findDoubleBondedCarbonylOxygen(monomer) {
     const bondsMap = constructBondsMap(monomer);
     let doubleBondedOxygen = 0;

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

@@ -1 +1 @@
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