openchemlib-utils - npm Package Compare versions

Comparing version 0.7.0 to 0.7.1

CHANGELOG.md

 # Changelog
 
+### [0.7.1](https://www.github.com/cheminfo/openchemlib-utils/compare/v0.7.0...v0.7.1) (2021-03-24)
+
+
+### Bug Fixes
+
+* use molecule.getOCL where possible ([936c791](https://www.github.com/cheminfo/openchemlib-utils/commit/936c791a5d393fc4c3aa1372418a29c270d0e5f9))
+
 ## [0.7.0](https://www.github.com/cheminfo/openchemlib-utils/compare/v0.6.1...v0.7.0) (2021-03-01)
@@ -4,0 +11,0 @@

lib/index.js

@@ -14,25 +14,2 @@ 'use strict';
 
-let OCL;
-
-function getOCL() {
-  if (!OCL) {
-    throw new Error('OCL has to be initialized using initOCL(OCL)');
-  }
-  return OCL;
-}
-/**
- *
- * @param {OCL} newOCL
- * @param {object} [options={}]
- * @param {boolean} [options.keepExisting=false] Will keep current OCL if we initialize more than once
- */
-function initOCL(newOCL, options = {}) {
-  const { keepExisting = false } = options;
-  if (OCL && keepExisting) return;
-  if (OCL && OCL !== newOCL) {
-    throw new Error('OCL-utils was already initialized with a different OCL');
-  }
-  OCL = newOCL;
-}
-
 let xAtomicNumber = 0;
@@ -49,3 +26,3 @@
   if (molecule.getAtomicNo(iAtom) === 1) {
-    molecule.setAtomicNo(iAtom, getXAtomicNumber());
+    molecule.setAtomicNo(iAtom, getXAtomicNumber(molecule));
   } else {
@@ -60,5 +37,5 @@ // we can not use X because we would have problems with valencies if it is
 
-function getXAtomicNumber() {
+function getXAtomicNumber(molecule) {
   if (!xAtomicNumber) {
-    const OCL = getOCL();
+    const OCL = molecule.getOCL();
     xAtomicNumber = OCL.Molecule.getAtomicNoFromLabel('X');
@@ -78,3 +55,3 @@ }
 function addDiastereotopicMissingChirality(molecule, options = {}) {
-  const { Molecule } = getOCL();
+  const { Molecule } = molecule.getOCL();
   const { esrType = Molecule.cESRTypeAnd } = options;
@@ -118,3 +95,3 @@
 function makeRacemic(molecule) {
-  const { Molecule } = getOCL();
+  const { Molecule } = molecule.getOCL();
 
@@ -137,3 +114,3 @@ // if we don't calculate this we have 2 epimers
 function getDiastereotopicAtomIDs(molecule) {
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
   addDiastereotopicMissingChirality(molecule);
@@ -162,3 +139,3 @@
 function getDiastereotopicAtomIDsAndH(originalMolecule) {
-  const OCL = getOCL();
+  const OCL = originalMolecule.getOCL();
   const molecule = originalMolecule.getCompactCopy();
@@ -282,3 +259,26 @@ molecule.addImplicitHydrogens();
 
+let OCL;
+
+function getOCL() {
+  if (!OCL) {
+    throw new Error('OCL has to be initialized using initOCL(OCL)');
+  }
+  return OCL;
+}
 /**
+ *
+ * @param {OCL} newOCL
+ * @param {object} [options={}]
+ * @param {boolean} [options.keepExisting=false] Will keep current OCL if we initialize more than once
+ */
+function initOCL(newOCL, options = {}) {
+  const { keepExisting = false } = options;
+  if (OCL && keepExisting) return;
+  if (OCL && OCL !== newOCL) {
+    throw new Error('OCL-utils was already initialized with a different OCL');
+  }
+  OCL = newOCL;
+}
+
+/**
  * Check if a specific atom is a sp3 carbon
@@ -312,3 +312,3 @@ * @param {OCL.Molecule} molecule
 function getHoseCodesForAtom(originalMolecule, rootAtom, options = {}) {
-  const OCL = getOCL();
+  const OCL = originalMolecule.getOCL();
   const {
@@ -554,3 +554,3 @@ minSphereSize = 0,
     originalSmiles: coreSmiles,
-    smiles: coreSmiles.replace(/\[R([1-4])\]/g, '%5$1'),
+    smiles: coreSmiles.replace(/\[R(?<group>[1-4])\]/g, '%5$<group>'),
   };
@@ -621,3 +621,3 @@
 function getAtomsInfo(molecule) {
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
   molecule.ensureHelperArrays(OCL.Molecule.cHelperRings);
@@ -734,3 +734,3 @@
 function getConnectivityMatrix(molecule, options = {}) {
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
   molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);
@@ -891,3 +891,3 @@ let nbAtoms = molecule.getAllAtoms();
 function getHoseCodesForPath(molecule, from, to, maxLength) {
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
   const originalFrom = from;
@@ -1009,3 +1009,3 @@ const originalTo = to;
 
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
 
@@ -1063,3 +1063,3 @@ if (!fragment) {
 function getShortestPaths(molecule, options = {}) {
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
   const { fromLabel = '', toLabel = '', maxLength = 3 } = options;
@@ -1066,0 +1066,0 @@

package.json

 {
   "name": "openchemlib-utils",
-  "version": "0.7.0",
+  "version": "0.7.1",
   "description": "",
@@ -42,17 +42,17 @@ "main": "lib/index.js",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.12.1",
-    "cheminfo-build": "^1.1.8",
-    "eslint": "^7.18.0",
-    "eslint-config-cheminfo": "^5.2.2",
+    "@babel/plugin-transform-modules-commonjs": "^7.13.8",
+    "cheminfo-build": "^1.1.10",
+    "eslint": "^7.22.0",
+    "eslint-config-cheminfo": "^5.2.3",
     "esm": "^3.2.25",
     "jest": "^26.6.3",
-    "openchemlib": "^7.3.0",
+    "openchemlib": "^7.4.0",
     "prettier": "^2.2.1",
-    "rollup": "^2.36.2"
+    "rollup": "^2.42.3"
   },
   "dependencies": {
-    "atom-sorter": "^1.1.5",
+    "atom-sorter": "^1.1.9",
     "ml-floyd-warshall": "^1.0.3",
-    "ml-matrix": "^6.6.0"
+    "ml-matrix": "^6.7.0"
   }
 }

src/diastereotopic/addDiastereotopicMissingChirality.js

@@ -1,2 +0,1 @@
-import { getOCL } from '../OCL';
 import { tagAtom } from '../util/tagAtom';
@@ -13,3 +12,3 @@
 export function addDiastereotopicMissingChirality(molecule, options = {}) {
-  const { Molecule } = getOCL();
+  const { Molecule } = molecule.getOCL();
   const { esrType = Molecule.cESRTypeAnd } = options;
@@ -16,0 +15,0 @@

src/diastereotopic/getDiastereotopicAtomIDs.js

@@ -1,2 +0,1 @@
-import { getOCL } from '../OCL';
 import { makeRacemic } from '../util/makeRacemic';
@@ -12,3 +11,3 @@ import { tagAtom } from '../util/tagAtom';
 export function getDiastereotopicAtomIDs(molecule) {
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
   addDiastereotopicMissingChirality(molecule);
@@ -15,0 +14,0 @@

src/diastereotopic/getDiastereotopicAtomIDsAndH.js

@@ -1,3 +0,1 @@
-import { getOCL } from '../OCL';
-
 import { getDiastereotopicAtomIDs } from './getDiastereotopicAtomIDs';
@@ -11,3 +9,3 @@ // Previously getExtendedDiastereotopicAtomIDs
 export function getDiastereotopicAtomIDsAndH(originalMolecule) {
-  const OCL = getOCL();
+  const OCL = originalMolecule.getOCL();
   const molecule = originalMolecule.getCompactCopy();
@@ -14,0 +12,0 @@ molecule.addImplicitHydrogens();

src/hose/getHoseCodesForAtom.js

@@ -1,2 +0,1 @@
-import { getOCL } from '../OCL';
 import { isCsp3 } from '../util/isCsp3';
@@ -17,3 +16,3 @@ import { makeRacemic } from '../util/makeRacemic';
 export function getHoseCodesForAtom(originalMolecule, rootAtom, options = {}) {
-  const OCL = getOCL();
+  const OCL = originalMolecule.getOCL();
   const {
@@ -20,0 +19,0 @@ minSphereSize = 0,

src/hose/getHoseCodesForPath.js

@@ -1,2 +0,1 @@
-import { getOCL } from '../OCL';
 import { makeRacemic } from '../util/makeRacemic';
@@ -12,3 +11,3 @@ import { tagAtom } from '../util/tagAtom';
 export function getHoseCodesForPath(molecule, from, to, maxLength) {
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
   const originalFrom = from;
@@ -15,0 +14,0 @@ const originalTo = to;

src/path/getPathsInfo.js

@@ -1,2 +0,1 @@
-import { getOCL } from '../OCL';
 import { getHoseCodesForPath } from '../hose/getHoseCodesForPath';
@@ -26,3 +25,3 @@ import { getAtomsInfo } from '../util/getAtomsInfo';
 
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
 
@@ -29,0 +28,0 @@ if (!fragment) {

src/path/getShortestPaths.js

@@ -1,3 +0,1 @@
-import { getOCL } from '../OCL';
-
 /**
@@ -13,3 +11,3 @@ * Get the shortest path between each pair of atoms in the molecule
 export function getShortestPaths(molecule, options = {}) {
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
   const { fromLabel = '', toLabel = '', maxLength = 3 } = options;
@@ -16,0 +14,0 @@

src/util/combineSmiles.js

@@ -110,3 +110,3 @@ import { getOCL } from '../OCL';
     originalSmiles: coreSmiles,
-    smiles: coreSmiles.replace(/\[R([1-4])\]/g, '%5$1'),
+    smiles: coreSmiles.replace(/\[R(?<group>[1-4])\]/g, '%5$<group>'),
   };
@@ -113,0 +113,0 @@

src/util/getAtomsInfo.js

@@ -1,2 +0,1 @@
-import { getOCL } from '../OCL';
 import { getDiastereotopicAtomIDs } from '../diastereotopic/getDiastereotopicAtomIDs';
@@ -9,3 +8,3 @@
 export function getAtomsInfo(molecule) {
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
   molecule.ensureHelperArrays(OCL.Molecule.cHelperRings);
@@ -12,0 +11,0 @@

src/util/getConnectivityMatrix.js

 import floydWarshall from 'ml-floyd-warshall';
 import { Matrix } from 'ml-matrix';
 
-import { getOCL } from '../OCL';
-
 /**
@@ -18,3 +16,3 @@ * Returns a connectivity matrix
 export function getConnectivityMatrix(molecule, options = {}) {
-  const OCL = getOCL();
+  const OCL = molecule.getOCL();
   molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);
@@ -21,0 +19,0 @@ let nbAtoms = molecule.getAllAtoms();

src/util/makeRacemic.js

@@ -1,3 +0,1 @@
-import { getOCL } from '../OCL';
-
 /**
@@ -10,3 +8,3 @@ *
 export function makeRacemic(molecule) {
-  const { Molecule } = getOCL();
+  const { Molecule } = molecule.getOCL();
 
@@ -13,0 +11,0 @@ // if we don't calculate this we have 2 epimers

src/util/tagAtom.js

@@ -1,3 +0,1 @@
-import { getOCL } from '../OCL';
-
 let xAtomicNumber = 0;
@@ -14,3 +12,3 @@
   if (molecule.getAtomicNo(iAtom) === 1) {
-    molecule.setAtomicNo(iAtom, getXAtomicNumber());
+    molecule.setAtomicNo(iAtom, getXAtomicNumber(molecule));
   } else {
@@ -25,5 +23,5 @@ // we can not use X because we would have problems with valencies if it is
 
-function getXAtomicNumber() {
+function getXAtomicNumber(molecule) {
   if (!xAtomicNumber) {
-    const OCL = getOCL();
+    const OCL = molecule.getOCL();
     xAtomicNumber = OCL.Molecule.getAtomicNoFromLabel('X');
@@ -30,0 +28,0 @@ }

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Found 1 instance in 1 package

Fixed alerts

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Improved metrics

Total package byte prevSize

79487

increased by0.24%

Worsened metrics

Lines of code

2106

decreased by-0.52%

Dependency changes

• Updatedatom-sorter@^1.1.9

• Updatedml-matrix@^6.7.0