openchemlib-utils - npm Package Compare versions

Comparing version 0.2.1 to 0.3.0

History.md

@@ -0,1 +1,11 @@
+# [0.3.0](https://github.com/cheminfo/openchemlib-utils/compare/v0.2.1...v0.3.0) (2020-02-21)
+
+
+### Features
+
+* add negative atomicNo option ([44f812f](https://github.com/cheminfo/openchemlib-utils/commit/44f812fbd237240592f89485e4f39e655af6281b))
+* add sdta for getConnectivityMatrix ([9fe9640](https://github.com/cheminfo/openchemlib-utils/commit/9fe9640f4e5ab23e2f5837249eff528a2da8bdd6))
+
+
+
 ## 0.0.1 (2020-01-21)
@@ -2,0 +12,0 @@

lib/index.js

@@ -504,3 +504,5 @@ 'use strict';
  * @param {boolean} [options.atomicNo=false] set the atomic number of the atom on diagonal
+ * @param {boolean} [options.negativeAtomicNo=false] set the atomic number * -1 of the atom on diagonal
  * @param {boolean} [options.sdt=false] set 1, 2 or 3 depending if single, double or triple bond
+ * @param {boolean} [options.sdta=false] set 1, 2, 3 or 4 depending if single, double, triple or aromatic  bond
  */
@@ -520,2 +522,6 @@ function getConnectivityMatrix(molecule, options = {}) {
       }
+    } else if (options.negativeAtomicNo) {
+      for (let i = 0; i < nbAtoms; i++) {
+        result[i][i] = -molecule.getAtomicNo(i);
+      }
     } else if (options.mass) {
@@ -539,2 +545,17 @@ for (let i = 0; i < nbAtoms; i++) {
     }
+  } else if (options.sdta) {
+    for (let i = 0; i < nbAtoms; i++) {
+      let l = molecule.getAllConnAtoms(i);
+      for (let j = 0; j < l; j++) {
+        let bondNumber = molecule.getConnBond(i, j);
+        if (molecule.isAromaticBond(bondNumber)) {
+          result[i][molecule.getConnAtom(i, j)] = 4;
+        } else {
+          result[i][molecule.getConnAtom(i, j)] = molecule.getConnBondOrder(
+            i,
+            j,
+          );
+        }
+      }
+    }
   } else {
@@ -541,0 +562,0 @@ for (let i = 0; i < nbAtoms; i++) {

package.json

 {
   "name": "openchemlib-utils",
-  "version": "0.2.1",
+  "version": "0.3.0",
   "description": "",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/util/getConnectivityMatrix.js

@@ -13,3 +13,5 @@ import floydWarshall from 'ml-floyd-warshall';
  * @param {boolean} [options.atomicNo=false] set the atomic number of the atom on diagonal
+ * @param {boolean} [options.negativeAtomicNo=false] set the atomic number * -1 of the atom on diagonal
  * @param {boolean} [options.sdt=false] set 1, 2 or 3 depending if single, double or triple bond
+ * @param {boolean} [options.sdta=false] set 1, 2, 3 or 4 depending if single, double, triple or aromatic  bond
  */
@@ -29,2 +31,6 @@ export function getConnectivityMatrix(molecule, options = {}) {
       }
+    } else if (options.negativeAtomicNo) {
+      for (let i = 0; i < nbAtoms; i++) {
+        result[i][i] = -molecule.getAtomicNo(i);
+      }
     } else if (options.mass) {
@@ -48,2 +54,17 @@ for (let i = 0; i < nbAtoms; i++) {
     }
+  } else if (options.sdta) {
+    for (let i = 0; i < nbAtoms; i++) {
+      let l = molecule.getAllConnAtoms(i);
+      for (let j = 0; j < l; j++) {
+        let bondNumber = molecule.getConnBond(i, j);
+        if (molecule.isAromaticBond(bondNumber)) {
+          result[i][molecule.getConnAtom(i, j)] = 4;
+        } else {
+          result[i][molecule.getConnAtom(i, j)] = molecule.getConnBondOrder(
+            i,
+            j,
+          );
+        }
+      }
+    }
   } else {
@@ -50,0 +71,0 @@ for (let i = 0; i < nbAtoms; i++) {

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