openchemlib-utils - npm Package Compare versions

Comparing version 2.7.1 to 2.8.0

package.json

 {
   "name": "openchemlib-utils",
-  "version": "2.7.1",
+  "version": "2.8.0",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -33,13 +33,13 @@ "main": "lib/index.js",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.20.11",
-    "@types/jest": "^29.4.0",
-    "cheminfo-build": "^1.1.11",
-    "eslint": "^8.32.0",
-    "eslint-config-cheminfo": "^8.1.3",
+    "@babel/plugin-transform-modules-commonjs": "^7.22.5",
+    "@types/jest": "^29.5.3",
+    "cheminfo-build": "^1.2.0",
+    "eslint": "^8.45.0",
+    "eslint-config-cheminfo": "^9.0.2",
     "eslint-plugin-import": "^2.27.5",
-    "jest": "^29.4.0",
+    "jest": "^29.6.1",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "openchemlib": "^8.2.0",
-    "prettier": "^2.8.3",
-    "rollup": "^3.10.1"
+    "openchemlib": "^8.3.0",
+    "prettier": "^3.0.0",
+    "rollup": "^3.26.3"
   },
@@ -49,10 +49,11 @@ "dependencies": {
     "ensure-string": "^1.2.0",
-    "ml-floyd-warshall": "^2.0.1",
+    "get-value": "^3.0.1",
+    "ml-floyd-warshall": "^3.0.1",
     "ml-matrix": "^6.10.4",
-    "papaparse": "^5.3.2",
+    "papaparse": "^5.4.1",
     "sdf-parser": "^6.0.1"
   },
   "peerDependencies": {
-    "openchemlib": ">=8.0.0"
+    "openchemlib": ">=8.3.0"
   }
 }

src/db/MoleculesDB.js

 import appendCSV from './utils/appendCSV';
 import appendColor from './utils/appendColor';
+import appendEntries from './utils/appendEntries.js';
 import appendSDF from './utils/appendSDF';
@@ -34,2 +35,22 @@ import appendSmilesList from './utils/appendSmilesList';
   /**
+   * Append an array of entries to the current database. An entry is an object that by default should contain a 'ocl' property containing idCode and optionally index and coordinates
+   * @param {*} moleculesDB
+   * @param {object[]} entries
+   * @param {object} [options={}]
+   * @param {string} [options.idCodePath='ocl.idCode']
+   * @param {string} [options.indexPath='ocl.index']
+   * @param {string} [options.coordinatesPath='ocl.coordinates']
+   * @param {string} [options.mwPath='mw']
+   * @param {string} [options.smilesPath]
+   * @param {string} [options.molfilePath]
+   * @param {function} [options.onStep] call back to execute after each molecule
+   */
+  appendEntries(entries, options) {
+    return appendEntries(this, entries, {
+      computeProperties: this.computeProperties,
+      ...options,
+    });
+  }
+
+  /**
    * append to the current database a CSV file
@@ -43,3 +64,2 @@ * @param {string|ArrayBuffer} csv - text file containing the comma separated value file
    */
-
   appendCSV(csv, options) {
@@ -59,3 +79,2 @@ return appendCSV(this, csv, {
    */
-
   appendSDF(sdf, options) {
@@ -75,3 +94,2 @@ return appendSDF(this, sdf, {
    */
-
   appendSmilesList(text, options) {
@@ -109,3 +127,3 @@ return appendSmilesList(this, text, {
    * @param {object} [options={}]
-   * @param {string} [options.format='idCode'] - query is in the format 'smiles', 'oclid' or 'molfile'
+   * @param {'smiles'|'idCode'|'smarts'|'molfile'} [options.format='idCode'] - query format
    * @param {string} [options.mode='substructure'] - search by 'substructure', 'exact' or 'similarity'
@@ -126,3 +144,3 @@ * @param {boolean} [options.flattenResult=true] - The database group the data for the same product. This allows to flatten the result
    * @param {object} [options={}]
-   * @param {string} [options.format='idCode'] - query is in the format 'smiles', 'oclid' or 'molfile'
+   * @param {'smiles'|'idCode'|'smarts'|'molfile'} [options.format='idCode'] - query format
    * @param {string} [options.mode='substructure'] - search by 'substructure', 'exact' or 'similarity'
@@ -129,0 +147,0 @@ * @param {boolean} [options.flattenResult=true] - The database group the data for the same product. This allows to flatten the result

src/db/utils/appendCSV.js

@@ -15,3 +15,3 @@ import { ensureString } from 'ensure-string';
   csv = ensureString(csv);
-  const moleculeCreators = getMoleculeCreators(moleculesDB.OCL.Molecule);
+  const moleculeCreators = getMoleculeCreators(moleculesDB.OCL);
 
@@ -18,0 +18,0 @@ if (typeof csv !== 'string') {

src/db/utils/getMoleculeCreators.js

@@ -1,10 +0,14 @@
-export default function getMoleculeCreators(Molecule) {
+export default function getMoleculeCreators(OCL) {
   const fields = new Map();
 
-  fields.set('oclid', Molecule.fromIDCode);
-  fields.set('idcode', Molecule.fromIDCode);
-  fields.set('smiles', Molecule.fromSmiles);
-  fields.set('molfile', Molecule.fromMolfile);
+  fields.set('oclid', OCL.Molecule.fromIDCode);
+  fields.set('idcode', OCL.Molecule.fromIDCode);
+  fields.set('smiles', OCL.Molecule.fromSmiles);
+  fields.set('molfile', OCL.Molecule.fromMolfile);
+  fields.set('smarts', (smarts) => {
+    const smilesParser = new OCL.SmilesParser({ smartsMode: 'smarts' });
+    return smilesParser.parseMolecule(smarts);
+  });
 
   return fields;
 }

src/db/utils/pushEntry.js

@@ -20,5 +20,3 @@ /**
 
-  let moleculeIDCode = moleculeInfo.idCode
-    ? moleculeInfo.idCode
-    : molecule.getIDCode();
+  let moleculeIDCode = getMoleculeIDCode(molecule, moleculeInfo);
   let entry = moleculesDB.db[moleculeIDCode];
@@ -64,1 +62,6 @@ if (!entry) {
 }
+
+function getMoleculeIDCode(molecule, moleculeInfo) {
+  if (moleculeInfo.idCode) return moleculeInfo.idCode;
+  return molecule.getIDCode();
+}

src/db/utils/search.js

@@ -14,3 +14,3 @@ import { noWait } from '../../util/noWait.js';
   if (typeof query === 'string') {
-    const moleculeCreators = getMoleculeCreators(moleculesDB.OCL.Molecule);
+    const moleculeCreators = getMoleculeCreators(moleculesDB.OCL);
     query = moleculeCreators.get(format.toLowerCase())(query);
@@ -17,0 +17,0 @@ } else if (!(query instanceof moleculesDB.OCL.Molecule)) {

src/index.js

@@ -22,2 +22,3 @@ export * from './diastereotopic/addDiastereotopicMissingChirality';
 export * from './util/getMF';
+export * from './util/getCharge';
 export * from './util/getAtoms';
@@ -24,0 +25,0 @@ export * from './util/nbOH';

src/util/getAtoms.js

@@ -1,2 +0,1 @@
-
 /**
@@ -10,11 +9,11 @@ * Calculate the molecular formula in 'chemcalc' notation taking into account fragments, isotopes and charges
   let entries = molecule.getFragments();
-  const atoms = {}
+  const atoms = {};
   const result = { atoms, parts: [] };
 
   entries.forEach((entry) => {
-    const part = {}
-    result.parts.push(part)
+    const part = {};
+    result.parts.push(part);
     appendAtomPart(entry, atoms, part);
   });
-  return result
+  return result;
 }
@@ -28,7 +27,7 @@
     }
-    atoms[label] += 1
+    atoms[label] += 1;
     if (!part[label]) {
       part[label] = 0;
     }
-    part[label] += 1
+    part[label] += 1;
     let implicitHydrogens = molecule.getImplicitHydrogens(i);
@@ -39,10 +38,9 @@ if (implicitHydrogens) {
       }
-      atoms.H += implicitHydrogens
+      atoms.H += implicitHydrogens;
       if (!part.H) {
         part.H = 0;
       }
-      part.H += implicitHydrogens
+      part.H += implicitHydrogens;
     }
   }
 }
-

src/util/getMF.js

@@ -5,3 +5,3 @@ import { atomSorter } from 'atom-sorter';
  * Calculate the molecular formula in 'chemcalc' notation taking into account fragments, isotopes and charges
- * @param {OCL.Molecule} [molecule] an instance of OCL.Molecule
+ * @param {import('openchemlib').Molecule} molecule an instance of OCL.Molecule
  * @returns {object}
@@ -8,0 +8,0 @@ */

src/util/makeRacemic.js

 /**
  *
- * @param {import('openchemlib').Molecule} [molecule] An instance of a molecule
+ * @param {import('openchemlib').Molecule} molecule An instance of a molecule
  * @param {object} [options={}]
@@ -5,0 +5,0 @@ * @param {object} [options.OCL] openchemlib library

src/util/nbLabileH.js

@@ -14,3 +14,3 @@ /**
     if (atomicNumbers.includes(molecule.getAtomicNo(i))) {
-      counter += molecule.getAllHydrogens(i)
+      counter += molecule.getAllHydrogens(i);
     }
@@ -17,0 +17,0 @@ }

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Improved metrics

Total package byte prevSize

195039

increased by3.44%

Number of package files

67

increased by3.08%

Lines of code

5564

increased by3.55%

Worsened metrics

Dependency count

8

increased by14.29%

Dependency changes

• + Addedget-value@^3.0.1

• + Addedget-value@3.0.1(transitive)

• + Addedisobject@3.0.1(transitive)

• + Addedml-floyd-warshall@3.0.1(transitive)

• - Removedml-floyd-warshall@2.0.1(transitive)

• Updatedml-floyd-warshall@^3.0.1

• Updatedpapaparse@^5.4.1