openchemlib-utils - npm Package Compare versions

Comparing version 0.7.1 to 1.0.0

CHANGELOG.md

 # Changelog
 
+## [1.0.0](https://www.github.com/cheminfo/openchemlib-utils/compare/v0.7.1...v1.0.0) (2021-03-24)
+
+
+### ⚠ BREAKING CHANGES
+
+* 
+
+### Features
+
+* combineSmiles requires to pass OCL ([aa9218a](https://www.github.com/cheminfo/openchemlib-utils/commit/aa9218ad530d5a1a98d90d7215c97e7ed4e35edb))
+* getHoseCodesFromDiastereotopicID requires an OCL.Molecule ([00b8845](https://www.github.com/cheminfo/openchemlib-utils/commit/00b8845682c86dfb45cafc3c195840f285c783c4))
+
+
+### Bug Fixes
+
+* add openchemlib to peer dependencies ([c856127](https://www.github.com/cheminfo/openchemlib-utils/commit/c8561273dc0a224a03949853ace5067c03ecc0e9))
+
 ### [0.7.1](https://www.github.com/cheminfo/openchemlib-utils/compare/v0.7.0...v0.7.1) (2021-03-24)
@@ -4,0 +21,0 @@

lib/index.js

@@ -252,26 +252,3 @@ '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;
-}
-
-/**
  * Check if a specific atom is a sp3 carbon
@@ -383,12 +360,7 @@ * @param {OCL.Molecule} molecule
  * Returns the hose code for a specific marked atom
- * @param {string} diastereotopicID
+ * @param {OCL.Molecule} diastereotopicID
  * @param {object} options
  */
 
-function getHoseCodesFromDiastereotopicID(
-  diastereotopicID,
-  options = {},
-) {
-  const OCL = getOCL();
-  const molecule = OCL.Molecule.fromIDCode(diastereotopicID);
+function getHoseCodesFromDiastereotopicID(molecule, options = {}) {
   molecule.addImplicitHydrogens();
@@ -425,5 +397,9 @@ molecule.addMissingChirality();
   }));
+  const OCL = molecule.getOCL();
   // TODO: seems like a very slow approach
   diaIDs.forEach(function (diaID) {
-    const hoses = getHoseCodesFromDiastereotopicID(diaID.oclID, options);
+    const hoses = getHoseCodesFromDiastereotopicID(
+      OCL.Molecule.fromIDCode(diaID.oclID),
+      options,
+    );
     diaID.hoses = [];
@@ -452,3 +428,3 @@ let sphere = 0;
  */
-async function combineSmiles(coreSmiles, fragments, options = {}) {
+async function combineSmiles(coreSmiles, fragments, OCL, options = {}) {
   const { complexity = false } = options;
@@ -460,3 +436,3 @@ const core = getCore(coreSmiles);
   }
-  return generate(core, rGroups, options);
+  return generate(core, rGroups, OCL, options);
 }
@@ -472,3 +448,3 @@
 
-async function generate(core, rGroups, options = {}) {
+async function generate(core, rGroups, OCL, options = {}) {
   const { onStep } = options;
@@ -492,3 +468,3 @@ const molecules = {};
         }
-        appendMolecule(molecules, core, rGroups, currents);
+        appendMolecule(molecules, core, rGroups, currents, OCL);
         currents[position]++;
@@ -507,3 +483,3 @@ for (let i = 0; i < position; i++) {
       }
-      appendMolecule(molecules, core, rGroups, currents);
+      appendMolecule(molecules, core, rGroups, currents, OCL);
       break;
@@ -517,3 +493,3 @@ }
 
-function appendMolecule(molecules, core, rGroups, currents) {
+function appendMolecule(molecules, core, rGroups, currents, OCL) {
   let newSmiles = core.smiles;
@@ -524,4 +500,2 @@ for (let i = 0; i < currents.length; i++) {
 
-  const OCL = getOCL();
-
   const currentMol = OCL.Molecule.fromSmiles(newSmiles);
@@ -1111,6 +1085,4 @@ const idCode = currentMol.getIDCode();
 exports.getMF = getMF;
-exports.getOCL = getOCL;
 exports.getPathsInfo = getPathsInfo;
 exports.getShortestPaths = getShortestPaths;
-exports.initOCL = initOCL;
 exports.isCsp3 = isCsp3;
@@ -1117,0 +1089,0 @@ exports.makeRacemic = makeRacemic;

package.json

 {
   "name": "openchemlib-utils",
-  "version": "0.7.1",
+  "version": "1.0.0",
   "description": "",
@@ -48,3 +48,3 @@ "main": "lib/index.js",
     "jest": "^26.6.3",
-    "openchemlib": "^7.4.0",
+    "openchemlib": "7.4.0",
     "prettier": "^2.2.1",
@@ -57,3 +57,6 @@ "rollup": "^2.42.3"
     "ml-matrix": "^6.7.0"
+  },
+  "peerDependencies": {
+    "openchemlib": ">=7.4.0"
   }
 }

README.md

@@ -16,3 +16,3 @@ # openchemlib-utils
 ```js
-import OCL from 'openchemlib';
+import OCL from 'openchemlib'; // version should be greater than 7.4
 
@@ -36,3 +36,2 @@ import { getPathsInfo, initOCL } from 'openchemlib-utils';
 
-
 ## [API Documentation](https://cheminfo.github.io/openchemlib-utils/)
@@ -39,0 +38,0 @@

src/diastereotopic/__tests/addDiastereotopicMissingChirality.test.js

 import OCL from 'openchemlib';
 
-import { initOCL } from '../../OCL';
 import { addDiastereotopicMissingChirality } from '../addDiastereotopicMissingChirality';
 
-initOCL(OCL);
 describe('addDiastereotopicMissingChirality', () => {
@@ -8,0 +6,0 @@ it('CC(Cl)CC', () => {

src/diastereotopic/__tests/getDiastereotopicAtomIDs.test.js

 import OCL from 'openchemlib';
 
-import { initOCL } from '../../OCL';
 import { getDiastereotopicAtomIDs } from '../getDiastereotopicAtomIDs';
 
-initOCL(OCL);
 describe('getDiastereotopicAtomIDs', () => {
@@ -8,0 +6,0 @@ it('CC(Cl)CC', () => {

src/diastereotopic/__tests/getDiastereotopicAtomIDsAndH.test.js

 import OCL from 'openchemlib';
 
-import { initOCL } from '../../OCL';
 import { getDiastereotopicAtomIDsAndH } from '../getDiastereotopicAtomIDsAndH';
 
-initOCL(OCL);
 describe('getDiastereotopicAtomIDsAndH', () => {
@@ -8,0 +6,0 @@ it('propane', () => {

src/diastereotopic/__tests/getGroupedDiastereotopicAtomIDs.test.js

 import OCL from 'openchemlib';
 
-import { initOCL } from '../../OCL';
 import { getGroupedDiastereotopicAtomIDs } from '../getGroupedDiastereotopicAtomIDs';
 
-initOCL(OCL);
-
 describe('getGroupedDiastereotopicIDs test propane', () => {
@@ -9,0 +6,0 @@ it('should yield the right table for all atoms', () => {

src/diastereotopic/__tests/toDiastereotopicSVG.test.js

 import OCL from 'openchemlib';
 
-import { initOCL } from '../../OCL';
 import { toDiastereotopicSVG } from '../toDiastereotopicSVG';
 
-initOCL(OCL);
 describe('toDiastereotopicSVG', () => {
@@ -8,0 +6,0 @@ it('CCC', () => {

src/hose/getHoseCodesAndDiastereotopicIDs.js

@@ -15,5 +15,9 @@ import { getDiastereotopicAtomIDs } from '../diastereotopic/getDiastereotopicAtomIDs';
   }));
+  const OCL = molecule.getOCL();
   // TODO: seems like a very slow approach
   diaIDs.forEach(function (diaID) {
-    const hoses = getHoseCodesFromDiastereotopicID(diaID.oclID, options);
+    const hoses = getHoseCodesFromDiastereotopicID(
+      OCL.Molecule.fromIDCode(diaID.oclID),
+      options,
+    );
     diaID.hoses = [];
@@ -20,0 +24,0 @@ let sphere = 0;

src/hose/getHoseCodesFromDiastereotopicID.js

@@ -1,16 +0,9 @@
-import { getOCL } from '../OCL';
-
 import { getHoseCodesForAtom } from './getHoseCodesForAtom';
 /**
  * Returns the hose code for a specific marked atom
- * @param {string} diastereotopicID
+ * @param {OCL.Molecule} diastereotopicID
  * @param {object} options
  */
 
-export function getHoseCodesFromDiastereotopicID(
-  diastereotopicID,
-  options = {},
-) {
-  const OCL = getOCL();
-  const molecule = OCL.Molecule.fromIDCode(diastereotopicID);
+export function getHoseCodesFromDiastereotopicID(molecule, options = {}) {
   molecule.addImplicitHydrogens();
@@ -17,0 +10,0 @@ molecule.addMissingChirality();

src/index.js

@@ -21,3 +21,1 @@ export * from './diastereotopic/addDiastereotopicMissingChirality';
 export * from './path/getShortestPaths';
-
-export * from './OCL';

src/util/combineSmiles.js

@@ -1,3 +0,1 @@
-import { getOCL } from '../OCL';
-
 const MAX_R = 10;
@@ -14,3 +12,3 @@
  */
-export async function combineSmiles(coreSmiles, fragments, options = {}) {
+export async function combineSmiles(coreSmiles, fragments, OCL, options = {}) {
   const { complexity = false } = options;
@@ -22,3 +20,3 @@ const core = getCore(coreSmiles);
   }
-  return generate(core, rGroups, options);
+  return generate(core, rGroups, OCL, options);
 }
@@ -34,3 +32,3 @@
 
-async function generate(core, rGroups, options = {}) {
+async function generate(core, rGroups, OCL, options = {}) {
   const { onStep } = options;
@@ -54,3 +52,3 @@ const molecules = {};
         }
-        appendMolecule(molecules, core, rGroups, currents);
+        appendMolecule(molecules, core, rGroups, currents, OCL);
         currents[position]++;
@@ -69,3 +67,3 @@ for (let i = 0; i < position; i++) {
       }
-      appendMolecule(molecules, core, rGroups, currents);
+      appendMolecule(molecules, core, rGroups, currents, OCL);
       break;
@@ -79,3 +77,3 @@ }
 
-function appendMolecule(molecules, core, rGroups, currents) {
+function appendMolecule(molecules, core, rGroups, currents, OCL) {
   let newSmiles = core.smiles;
@@ -86,4 +84,2 @@ for (let i = 0; i < currents.length; i++) {
 
-  const OCL = getOCL();
-
   const currentMol = OCL.Molecule.fromSmiles(newSmiles);
@@ -90,0 +86,0 @@ const idCode = currentMol.getIDCode();

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78664

decreased by-1.04%

Dependency count

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increased by33.33%

Number of package files

30

decreased by-3.23%

Lines of code

2045

decreased by-2.9%

Number of lines in readme file

47

decreased by-2.08%

No dependency changes