feat: add getProperties

src/db/utils/search.js

@@ -189,7 +189,7 @@ function similaritySearch(moleculesDB, query) {
           queryIndex,
           entry.index,
         ) *
-        1000000 -
+          1000000 -
         Math.abs(queryMW - entry.properties.mw) / 10000;
     }
     searchResult.push({ similarity, entry });
@@ -221,7 +221,7 @@ function processResult(entries, options = {}) {
           data,
           idCode: entry.idCode,
           properties: entry.properties,
-        }
+        };
         if (keepMolecule) {
           result.molecule = entry.molecule;
         }

src/index.js

@@ -20,6 +20,7 @@ export * from './util/tagAtom';
 export * from './util/isCsp3';
 export * from './util/getMF';
 export * from './util/getCharge';
+export * from './util/getProperties';
 export * from './util/getAtoms';
 export * from './util/nbOH';
 export * from './util/nbCOOH';

src/util/__tests__/getProperties.test.js

@@ -0,0 +1,64 @@
+import { Molecule } from 'openchemlib';
+
+import { getProperties } from '../getProperties';
+
+test('getProperties, default options', () => {
+  let molecule = Molecule.fromSmiles('[NH3+]CC(=O)[O-]');
+  let properties = getProperties(molecule);
+  expect(properties).toStrictEqual({
+    acceptorCount: 3,
+    donorCount: 1,
+    logP: -6.870399981737137,
+    logS: -0.027999980375170708,
+    polarSurfaceArea: 67.76999855041504,
+    rotatableBondCount: 1,
+    stereoCenterCount: 0,
+    mf: 'C2H5NO2',
+    mw: 75.0667,
+  });
+});
+
+test('getProperties, includeToxicities', () => {
+  let molecule = Molecule.fromSmiles('[NH3+]CC(=O)[O-]');
+  let properties = getProperties(molecule, { includeToxicities: true });
+  expect(properties).toStrictEqual({
+    acceptorCount: 3,
+    donorCount: 1,
+    logP: -6.870399981737137,
+    logS: -0.027999980375170708,
+    polarSurfaceArea: 67.76999855041504,
+    rotatableBondCount: 1,
+    stereoCenterCount: 0,
+    mf: 'C2H5NO2',
+    mw: 75.0667,
+    mutagenic: 1,
+    tumorigenic: 1,
+    irritant: 1,
+    reproductiveEffective: 1,
+  });
+});
+
+test('getProperties, include all', () => {
+  let molecule = Molecule.fromSmiles('[NH3+]CC(=O)[O-]');
+  let properties = getProperties(molecule, {
+    includeToxicities: true,
+    includeDruglikeness: true,
+  });
+  expect(properties).toStrictEqual({
+    acceptorCount: 3,
+    donorCount: 1,
+    logP: -6.870399981737137,
+    logS: -0.027999980375170708,
+    polarSurfaceArea: 67.76999855041504,
+    rotatableBondCount: 1,
+    stereoCenterCount: 0,
+    mf: 'C2H5NO2',
+    mw: 75.0667,
+    mutagenic: 1,
+    tumorigenic: 1,
+    irritant: 1,
+    reproductiveEffective: 1,
+    drugLikeness: -3.0141666666666667,
+    drugScore: 0.5218060573381611,
+  });
+});

src/util/getProperties.js

@@ -0,0 +1,84 @@
+let toxicityPredictor;
+let druglikenessPredictor;
+
+/**
+ *
+ * @param {import('openchemlib').Molecule} molecule
+ * @param {object} [options={}]
+ * @param {boolean} [options.includeToxicities=false]
+ * @param {boolean} [options.includeDruglikeness=false]
+ */
+export function getProperties(molecule, options = {}) {
+  const { includeToxicities = false, includeDruglikeness = false } = options;
+  const OCL = molecule.getOCL();
+  if (!OCL.MoleculeProperties) {
+    throw new Error('OCL.MoleculeProperties is not defined');
+  }
+  const props = new OCL.MoleculeProperties(molecule);
+  const moleculeFormula = molecule.getMolecularFormula();
+  const result = {
+    acceptorCount: props.acceptorCount,
+    donorCount: props.donorCount,
+    logP: props.logP,
+    logS: props.logS,
+    polarSurfaceArea: props.polarSurfaceArea,
+    rotatableBondCount: props.rotatableBondCount,
+    stereoCenterCount: props.stereoCenterCount,
+    mw: moleculeFormula.relativeWeight,
+    mf: moleculeFormula.formula,
+  };
+
+  if (includeToxicities) {
+    const { ToxicityPredictor } = molecule.getOCL();
+    if (!ToxicityPredictor) {
+      throw new Error('OCL.ToxicityPredictor is not defined');
+    }
+    if (!toxicityPredictor) {
+      toxicityPredictor = new ToxicityPredictor();
+    }
+    result.mutagenic = toxicityPredictor.assessRisk(
+      molecule,
+      ToxicityPredictor.TYPE_MUTAGENIC,
+    );
+    result.tumorigenic = toxicityPredictor.assessRisk(
+      molecule,
+      ToxicityPredictor.TYPE_TUMORIGENIC,
+    );
+    result.irritant = toxicityPredictor.assessRisk(
+      molecule,
+      ToxicityPredictor.TYPE_IRRITANT,
+    );
+    result.reproductiveEffective = toxicityPredictor.assessRisk(
+      molecule,
+      ToxicityPredictor.TYPE_REPRODUCTIVE_EFFECTIVE,
+    );
+  }
+
+  if (includeDruglikeness) {
+    const { DruglikenessPredictor } = molecule.getOCL();
+    if (!DruglikenessPredictor) {
+      throw new Error('OCL.DruglikenessPredictor is not defined');
+    }
+    if (!druglikenessPredictor) {
+      druglikenessPredictor = new DruglikenessPredictor();
+    }
+    result.drugLikeness = druglikenessPredictor.assessDruglikeness(molecule);
+  }
+
+  if (result.drugLikeness !== undefined && result.mutagenic !== undefined) {
+    result.drugScore = OCL.DrugScoreCalculator.calculate(
+      result.logP,
+      result.polarSurfaceArea,
+      result.mw,
+      result.drugLikeness,
+      [
+        result.mutagenic,
+        result.tumurogenic,
+        result.irritant,
+        result.reproductiveEffective,
+      ],
+    );
+  }
+
+  return result;
+}