openchemlib-utils - npm Package Compare versions

Comparing version 1.6.0 to 1.7.0

CHANGELOG.md

 # Changelog
 
+## [1.7.0](https://www.github.com/cheminfo/openchemlib-utils/compare/v1.6.0...v1.7.0) (2021-12-14)
+
+
+### Features
+
+* add getHoseCodesForPath ([3584377](https://www.github.com/cheminfo/openchemlib-utils/commit/358437790716b6dcf7bb2e197d8702956061e9a0))
+
+
+### Bug Fixes
+
+* getMF return type ([7ac70ea](https://www.github.com/cheminfo/openchemlib-utils/commit/7ac70ea2a0a4be3296a6f682e87fd082892b1d56))
+* rename SimpleBonds to SingleBonds ([d2ff8ed](https://www.github.com/cheminfo/openchemlib-utils/commit/d2ff8ed4001ded1678e04570219ca408c530962f))
+
 ## [1.6.0](https://www.github.com/cheminfo/openchemlib-utils/compare/v1.5.1...v1.6.0) (2021-10-14)
@@ -4,0 +17,0 @@

lib/index.js

@@ -418,2 +418,106 @@ 'use strict';
 
+let fragment$1;
+
+/**
+ * Returns the hose code for a specific atom number
+ * @param {OCL.Molecule} molecule
+ */
+function getHoseCodesForPath(molecule, from, to, maxLength) {
+  const OCL = molecule.getOCL();
+  const originalFrom = from;
+  const originalTo = to;
+  molecule = molecule.getCompactCopy();
+
+  let originalAtoms = []; // path before renumbering
+  molecule.getPath(originalAtoms, from, to, maxLength + 1);
+  let torsion;
+  if (originalAtoms.length === 4) {
+    torsion = molecule.calculateTorsion(originalAtoms);
+  }
+
+  const tag1 = tagAtom(molecule, from);
+  const tag2 = tagAtom(molecule, to);
+
+  molecule.addImplicitHydrogens();
+  molecule.addMissingChirality();
+
+  molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);
+
+  from = -1;
+  to = -1;
+  for (let i = 0; i < molecule.getAllAtoms(); i++) {
+    if (tag1 === tag2) {
+      if (molecule.getAtomCustomLabel(i) === tag1) {
+        if (from === -1) {
+          from = i;
+        } else {
+          to = i;
+        }
+      }
+    } else {
+      if (tag1 === molecule.getAtomCustomLabel(i)) {
+        from = i;
+      }
+      if (tag2 === molecule.getAtomCustomLabel(i)) {
+        to = i;
+      }
+    }
+  }
+
+  if (!fragment$1) fragment$1 = new OCL.Molecule(0, 0);
+
+  let atoms = [];
+  molecule.getPath(atoms, from, to, maxLength + 1);
+
+  let min = 0;
+  let max = 0;
+  let atomMask = new Array(molecule.getAllAtoms()).fill(false);
+  let atomList = new Array(molecule.getAllAtoms()).fill(-1);
+  let hoses = [];
+
+  for (let sphere = 0; sphere <= 2; sphere++) {
+    if (max === 0) {
+      for (let atom of atoms) {
+        atomMask[atom] = true;
+        atomList[max++] = atom;
+      }
+    } 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;
+    }
+    let atomMap = [];
+
+    molecule.copyMoleculeByAtoms(fragment$1, atomMask, true, atomMap);
+    makeRacemic(fragment$1);
+    let oclID = fragment$1.getCanonizedIDCode(
+      OCL.Molecule.CANONIZER_ENCODE_ATOM_CUSTOM_LABELS,
+    );
+
+    hoses.push({
+      sphere,
+      oclID,
+    });
+  }
+
+  return {
+    atoms: originalAtoms,
+    from: originalFrom,
+    to: originalTo,
+    torsion,
+    hoses,
+    length: originalAtoms.length - 1,
+  };
+}
+
 const MAX_R = 10;
@@ -770,3 +874,3 @@
  * {OCL.Molecule} [molecule] an instance of OCL.Molecule
- * @returns {String}
+ * @returns {object}
  */
@@ -853,106 +957,2 @@
 
-let fragment$1;
-
-/**
- * Returns the hose code for a specific atom number
- * @param {OCL.Molecule} molecule
- */
-function getHoseCodesForPath(molecule, from, to, maxLength) {
-  const OCL = molecule.getOCL();
-  const originalFrom = from;
-  const originalTo = to;
-  molecule = molecule.getCompactCopy();
-
-  let originalAtoms = []; // path before renumbering
-  molecule.getPath(originalAtoms, from, to, maxLength + 1);
-  let torsion;
-  if (originalAtoms.length === 4) {
-    torsion = molecule.calculateTorsion(originalAtoms);
-  }
-
-  const tag1 = tagAtom(molecule, from);
-  const tag2 = tagAtom(molecule, to);
-
-  molecule.addImplicitHydrogens();
-  molecule.addMissingChirality();
-
-  molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);
-
-  from = -1;
-  to = -1;
-  for (let i = 0; i < molecule.getAllAtoms(); i++) {
-    if (tag1 === tag2) {
-      if (molecule.getAtomCustomLabel(i) === tag1) {
-        if (from === -1) {
-          from = i;
-        } else {
-          to = i;
-        }
-      }
-    } else {
-      if (tag1 === molecule.getAtomCustomLabel(i)) {
-        from = i;
-      }
-      if (tag2 === molecule.getAtomCustomLabel(i)) {
-        to = i;
-      }
-    }
-  }
-
-  if (!fragment$1) fragment$1 = new OCL.Molecule(0, 0);
-
-  let atoms = [];
-  molecule.getPath(atoms, from, to, maxLength + 1);
-
-  let min = 0;
-  let max = 0;
-  let atomMask = new Array(molecule.getAllAtoms()).fill(false);
-  let atomList = new Array(molecule.getAllAtoms()).fill(-1);
-  let hoses = [];
-
-  for (let sphere = 0; sphere <= 2; sphere++) {
-    if (max === 0) {
-      for (let atom of atoms) {
-        atomMask[atom] = true;
-        atomList[max++] = atom;
-      }
-    } 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;
-    }
-    let atomMap = [];
-
-    molecule.copyMoleculeByAtoms(fragment$1, atomMask, true, atomMap);
-    makeRacemic(fragment$1);
-    let oclID = fragment$1.getCanonizedIDCode(
-      OCL.Molecule.CANONIZER_ENCODE_ATOM_CUSTOM_LABELS,
-    );
-
-    hoses.push({
-      sphere,
-      oclID,
-    });
-  }
-
-  return {
-    atoms: originalAtoms,
-    from: originalFrom,
-    to: originalTo,
-    torsion,
-    hoses,
-    length: originalAtoms.length - 1,
-  };
-}
-
 let fragment;
@@ -1654,3 +1654,3 @@
 
-function fragmentAcyclicSimpleBonds(molecule) {
+function fragmentAcyclicSingleBonds(molecule) {
   const OCL = molecule.getOCL();
@@ -1730,3 +1730,3 @@ let atoms = [];
 exports.combineSmiles = combineSmiles;
-exports.fragmentAcyclicSimpleBonds = fragmentAcyclicSimpleBonds;
+exports.fragmentAcyclicSingleBonds = fragmentAcyclicSingleBonds;
 exports.getAtomsInfo = getAtomsInfo;
@@ -1739,2 +1739,3 @@ exports.getConnectivityMatrix = getConnectivityMatrix;
 exports.getHoseCodesForAtom = getHoseCodesForAtom;
+exports.getHoseCodesForPath = getHoseCodesForPath;
 exports.getHoseCodesFromDiastereotopicID = getHoseCodesFromDiastereotopicID;
@@ -1741,0 +1742,0 @@ exports.getMF = getMF;

package.json

 {
   "name": "openchemlib-utils",
-  "version": "1.6.0",
+  "version": "1.7.0",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/index.js

@@ -10,2 +10,3 @@ export * from './diastereotopic/addDiastereotopicMissingChirality';
 export * from './hose/getHoseCodesFromDiastereotopicID';
+export * from './hose/getHoseCodesForPath';
 
@@ -27,2 +28,2 @@ export * from './util/combineSmiles';
 
-export * from './fragment/fragmentAcyclicSimpleBonds';
+export * from './fragment/fragmentAcyclicSingleBonds';

src/util/getMF.js

@@ -6,3 +6,3 @@ import atomSorter from 'atom-sorter';
  * {OCL.Molecule} [molecule] an instance of OCL.Molecule
- * @returns {String}
+ * @returns {object}
  */
@@ -9,0 +9,0 @@

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Improved metrics

Total package byte prevSize

122609

increased by0.53%

Lines of code

3306

increased by0.06%

No dependency changes