openchemlib-utils - npm Package Compare versions

Comparing version 1.10.0 to 1.11.0

lib/index.js

@@ -1904,2 +1904,60 @@ 'use strict';
 
+function getAtomFeatures(originalMolecule) {
+  const OCL = originalMolecule.getOCL();
+
+  let sphere = 1;
+  let fragment = new OCL.Molecule(0, 0);
+  let results = [];
+
+  for (
+    let rootAtom = 0;
+    rootAtom < originalMolecule.getAllAtoms();
+    rootAtom++
+  ) {
+    let min = 0;
+    let max = 0;
+    let atomMask = new Array(originalMolecule.getAtoms());
+    let atomList = new Array(originalMolecule.getAtoms());
+
+    const molecule = originalMolecule.getCompactCopy();
+    for (let currentSphere = 0; currentSphere <= sphere; currentSphere++) {
+      if (max === 0) {
+        atomList[max] = rootAtom;
+        atomMask[rootAtom] = true;
+        max++;
+      } else {
+        let newMax = max;
+        for (let i = min; i < max; i++) {
+          let atom = atomList[i];
+          for (let j = 0; j < molecule.getAllConnAtoms(atom); j++) {
+            let connAtom = molecule.getConnAtom(atom, j);
+            if (!atomMask[connAtom]) {
+              atomMask[connAtom] = true;
+              atomList[newMax++] = connAtom;
+            }
+          }
+        }
+        min = max;
+        max = newMax;
+      }
+      molecule.copyMoleculeByAtoms(fragment, atomMask, true, null);
+      if (currentSphere === sphere) {
+        makeRacemic(fragment);
+        results.push(fragment.getCanonizedIDCode());
+      }
+    }
+  }
+
+  const atoms = {};
+  for (let result of results) {
+    if (!atoms[result]) {
+      atoms[result] = 1;
+    } else {
+      atoms[result]++;
+    }
+  }
+
+  return atoms;
+}
+
 function toVisualizerMolfile(molecule, options = {}) {
@@ -2025,2 +2083,3 @@ const { diastereotopic, heavyAtomHydrogen } = options;
 exports.fragmentAcyclicSingleBonds = fragmentAcyclicSingleBonds;
+exports.getAtomFeatures = getAtomFeatures;
 exports.getAtomsInfo = getAtomsInfo;
@@ -2027,0 +2086,0 @@ exports.getConnectivityMatrix = getConnectivityMatrix;

package.json

 {
   "name": "openchemlib-utils",
-  "version": "1.10.0",
+  "version": "1.11.0",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -42,22 +42,22 @@ "main": "lib/index.js",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.16.8",
-    "@types/jest": "^27.4.0",
+    "@babel/plugin-transform-modules-commonjs": "^7.17.9",
+    "@types/jest": "^27.4.1",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^8.8.0",
-    "eslint-config-cheminfo": "^7.2.2",
-    "eslint-plugin-import": "^2.25.4",
+    "eslint": "^8.13.0",
+    "eslint-config-cheminfo": "^7.3.0",
+    "eslint-plugin-import": "^2.26.0",
     "esm": "^3.2.25",
-    "jest": "^27.5.0",
+    "jest": "^27.5.1",
     "jest-matcher-deep-close-to": "^3.0.2",
     "openchemlib": "7.4.0",
-    "prettier": "^2.5.1",
-    "rollup": "^2.67.1"
+    "prettier": "^2.6.2",
+    "rollup": "^2.70.2"
   },
   "dependencies": {
-    "atom-sorter": "^1.1.9",
-    "ensure-string": "^1.1.0",
-    "ml-floyd-warshall": "^1.0.3",
-    "ml-matrix": "^6.8.2",
-    "papaparse": "^5.3.1",
-    "sdf-parser": "^5.0.0"
+    "atom-sorter": "^1.1.10",
+    "ensure-string": "^1.2.0",
+    "ml-floyd-warshall": "^1.0.4",
+    "ml-matrix": "^6.9.0",
+    "papaparse": "^5.3.2",
+    "sdf-parser": "^5.0.1"
   },
@@ -64,0 +64,0 @@ "peerDependencies": {

src/index.js

@@ -32,4 +32,6 @@ export * from './diastereotopic/addDiastereotopicMissingChirality';
 
+export * from './features/getAtomFeatures';
+
 export * from './misc/toVisualizerMolfile';
 
 export * from './fragment/fragmentAcyclicSingleBonds';

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Improved metrics

Total package byte prevSize

139014

increased by2.3%

Number of package files

50

increased by2.04%

Lines of code

3973

increased by2.77%

Dependency changes

• Updatedatom-sorter@^1.1.10

• Updatedensure-string@^1.2.0

• Updatedml-floyd-warshall@^1.0.4

• Updatedml-matrix@^6.9.0

• Updatedpapaparse@^5.3.2

• Updatedsdf-parser@^5.0.1