openchemlib-utils - npm Package Compare versions

Comparing version 1.7.0 to 1.8.0

CHANGELOG.md

 # Changelog
 
+## [1.8.0](https://www.github.com/cheminfo/openchemlib-utils/compare/v1.7.0...v1.8.0) (2021-12-14)
+
+
+### Features
+
+* add getHoseCodesForAtoms ([b0f2b6b](https://www.github.com/cheminfo/openchemlib-utils/commit/b0f2b6bf2dab7e6a184225eb27612aa89f659ddb))
+
 ## [1.7.0](https://www.github.com/cheminfo/openchemlib-utils/compare/v1.6.0...v1.7.0) (2021-12-14)
@@ -4,0 +11,0 @@

lib/index.js

@@ -280,7 +280,14 @@ 'use strict';
  * @param {OCL.Molecule} originalMolecule
- * @param {number} rootAtom
+ * @param {array<number>} rootAtoms
  * @param {object} [options={}]
- * @param {boolean} [options.isTagged] Specify is the atom is already tagged
+ * @param {boolean} [options.isTagged] Specify is the atoms are already tagged
+ * @param {number} [options.minSphereSize=0] Smallest hose code sphere
+ * @param {number} [options.maxSphereSize=4] Largest hose code sphere
+ * @param {number} [options.kind=FULL_HOSE_CODE] Kind of hose code, default usual sphere
  */
-function getHoseCodesForAtom(originalMolecule, rootAtom, options = {}) {
+function getHoseCodesForAtoms(
+  originalMolecule,
+  rootAtoms = [],
+  options = {},
+) {
   const OCL = originalMolecule.getOCL();
@@ -297,11 +304,15 @@ const {
   if (!isTagged) {
-    let tag = tagAtom(molecule, rootAtom);
-    molecule.addImplicitHydrogens();
-    molecule.addMissingChirality();
-    molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);
-    // because ensuring helper reorder atoms we need to look again for it
-    for (let i = 0; i < molecule.getAllAtoms(); i++) {
-      if (tag === molecule.getAtomCustomLabel(i)) {
-        rootAtom = i;
-        break;
+    const tags = [];
+    for (let i = 0; i < rootAtoms.length; i++) {
+      let rootAtom = rootAtoms[i];
+      tags.push(tagAtom(molecule, rootAtom));
+      molecule.addImplicitHydrogens();
+      molecule.addMissingChirality();
+      molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);
+      // because ensuring helper reorder atoms we need to look again for it
+    }
+    rootAtoms.length = 0;
+    for (let j = 0; j < molecule.getAllAtoms(); j++) {
+      if (tags.includes(molecule.getAtomCustomLabel(j))) {
+        rootAtoms.push(j);
       }
@@ -320,5 +331,7 @@ }
     if (max === 0) {
-      atomList[0] = rootAtom;
-      atomMask[rootAtom] = true;
-      max = 1;
+      for (let rootAtom of rootAtoms) {
+        atomList[max] = rootAtom;
+        atomMask[rootAtom] = true;
+        max++;
+      }
     } else {
@@ -365,2 +378,16 @@ let newMax = max;
 /**
+ * Returns the hose code for a specific atom number
+ * @param {OCL.Molecule} originalMolecule
+ * @param {number} rootAtom
+ * @param {object} [options={}]
+ * @param {boolean} [options.isTagged] Specify is the atom is already tagged
+ * @param {number} [options.minSphereSize=0] Smallest hose code sphere
+ * @param {number} [options.maxSphereSize=4] Largest hose code sphere
+ * @param {number} [options.kind=FULL_HOSE_CODE] Kind of hose code, default usual sphere
+ */
+function getHoseCodesForAtom(originalMolecule, rootAtom, options = {}) {
+  return getHoseCodesForAtoms(originalMolecule, [rootAtom], options);
+}
+
+/**
  * Returns the hose code for a specific marked atom
@@ -1738,2 +1765,3 @@ * @param {OCL.Molecule} diastereotopicID
 exports.getHoseCodesForAtom = getHoseCodesForAtom;
+exports.getHoseCodesForAtoms = getHoseCodesForAtoms;
 exports.getHoseCodesForPath = getHoseCodesForPath;
@@ -1740,0 +1768,0 @@ exports.getHoseCodesFromDiastereotopicID = getHoseCodesFromDiastereotopicID;

package.json

 {
   "name": "openchemlib-utils",
-  "version": "1.7.0",
+  "version": "1.8.0",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -43,2 +43,3 @@ "main": "lib/index.js",
     "@babel/plugin-transform-modules-commonjs": "^7.15.4",
+    "@types/jest": "^27.0.3",
     "cheminfo-build": "^1.1.11",
@@ -45,0 +46,0 @@ "eslint": "^7.32.0",

src/hose/getHoseCodesForAtom.js

@@ -1,8 +0,3 @@
-import { isCsp3 } from '../util/isCsp3';
-import { makeRacemic } from '../util/makeRacemic';
-import { tagAtom } from '../util/tagAtom';
+import { getHoseCodesForAtoms } from './getHoseCodesForAtoms.js';
 
-export const FULL_HOSE_CODE = 1;
-export const HOSE_CODE_CUT_C_SP3_SP3 = 2;
-
 /**
@@ -14,78 +9,8 @@ * Returns the hose code for a specific atom number
  * @param {boolean} [options.isTagged] Specify is the atom is already tagged
+ * @param {number} [options.minSphereSize=0] Smallest hose code sphere
+ * @param {number} [options.maxSphereSize=4] Largest hose code sphere
+ * @param {number} [options.kind=FULL_HOSE_CODE] Kind of hose code, default usual sphere
  */
 export function getHoseCodesForAtom(originalMolecule, rootAtom, options = {}) {
-  const OCL = originalMolecule.getOCL();
-  const {
-    minSphereSize = 0,
-    maxSphereSize = 4,
-    kind = FULL_HOSE_CODE,
-    isTagged = false,
-  } = options;
-
-  const molecule = originalMolecule.getCompactCopy();
-
-  if (!isTagged) {
-    let tag = tagAtom(molecule, rootAtom);
-    molecule.addImplicitHydrogens();
-    molecule.addMissingChirality();
-    molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);
-    // because ensuring helper reorder atoms we need to look again for it
-    for (let i = 0; i < molecule.getAllAtoms(); i++) {
-      if (tag === molecule.getAtomCustomLabel(i)) {
-        rootAtom = i;
-        break;
-      }
-    }
-  }
-
-  let fragment = new OCL.Molecule(0, 0);
-  let results = [];
-  let min = 0;
-  let max = 0;
-  let atomMask = new Array(molecule.getAllAtoms());
-  let atomList = new Array(molecule.getAllAtoms());
-
-  for (let sphere = 0; sphere <= maxSphereSize; sphere++) {
-    if (max === 0) {
-      atomList[0] = rootAtom;
-      atomMask[rootAtom] = true;
-      max = 1;
-    } 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]) {
-            switch (kind) {
-              case FULL_HOSE_CODE:
-                atomMask[connAtom] = true;
-                atomList[newMax++] = connAtom;
-                break;
-              case HOSE_CODE_CUT_C_SP3_SP3:
-                if (!(isCsp3(molecule, atom) && isCsp3(molecule, connAtom))) {
-                  atomMask[connAtom] = true;
-                  atomList[newMax++] = connAtom;
-                }
-                break;
-              default:
-                throw new Error('getHoseCoesForAtom unknown kind');
-            }
-          }
-        }
-      }
-      min = max;
-      max = newMax;
-    }
-    molecule.copyMoleculeByAtoms(fragment, atomMask, true, null);
-    if (sphere >= minSphereSize) {
-      makeRacemic(fragment);
-      results.push(
-        fragment.getCanonizedIDCode(
-          OCL.Molecule.CANONIZER_ENCODE_ATOM_CUSTOM_LABELS,
-        ),
-      );
-    }
-  }
-  return results;
+  return getHoseCodesForAtoms(originalMolecule, [rootAtom], options);
 }

src/index.js

@@ -9,2 +9,3 @@ export * from './diastereotopic/addDiastereotopicMissingChirality';
 export * from './hose/getHoseCodesForAtom';
+export * from './hose/getHoseCodesForAtoms';
 export * from './hose/getHoseCodesFromDiastereotopicID';
@@ -11,0 +12,0 @@ export * from './hose/getHoseCodesForPath';

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Improved metrics

Total package byte prevSize

125204

increased by2.12%

Number of package files

44

increased by2.33%

Lines of code

3361

increased by1.66%

Worsened metrics

Dev dependency count

11

increased by10%

No dependency changes