openchemlib-utils - npm Package Compare versions

Comparing version 2.0.0 to 2.1.0

lib/index.js

 'use strict';
 
-Object.defineProperty(exports, '__esModule', { value: true });
-
 var floydWarshall = require('ml-floyd-warshall');
@@ -12,8 +10,2 @@ var mlMatrix = require('ml-matrix');
 
-function _interopDefaultLegacy (e) { return e && typeof e === 'object' && 'default' in e ? e : { 'default': e }; }
-
-var floydWarshall__default = /*#__PURE__*/_interopDefaultLegacy(floydWarshall);
-var atomSorter__default = /*#__PURE__*/_interopDefaultLegacy(atomSorter);
-var Papa__default = /*#__PURE__*/_interopDefaultLegacy(Papa);
-
 let xAtomicNumber = 0;
@@ -256,2 +248,23 @@
 /**
+ * Parse a molfile and returns an object containing the molecule, the map and the diaIDs
+ * The map allows to reload properties assigned to the atom molfile
+ * Pelase take care than numbering of atoms starts at 0 !
+ * @param {object} OCL - openchemlib library
+ * @param {string} molfile
+ * @returns
+ */
+function getDiastereotopicAtomIDsFromMolfile(OCL, molfile) {
+  const { map, molecule } = OCL.Molecule.fromMolfileWithAtomMap(molfile);
+
+  const diaIDsArray = getDiastereotopicAtomIDsAndH(molecule);
+  const diaIDs = {};
+
+  for (let i = 0; i < map.length; i++) {
+    diaIDs[map[i]] = { source: map[i], destination: i, ...diaIDsArray[i] };
+  }
+
+  return { map: diaIDs, molecule, diaIDs: diaIDsArray };
+}
+
+/**
  * Check if a specific atom is a sp3 carbon
@@ -892,3 +905,3 @@ * @param {OCL.Molecule} molecule
   if (options.pathLength) {
-    result = floydWarshall__default["default"](new mlMatrix.Matrix(result)).to2DArray();
+    result = floydWarshall(new mlMatrix.Matrix(result)).to2DArray();
   }
@@ -969,3 +982,3 @@ return result;
   let mf = '';
-  let keys = Object.keys(mfs).sort(atomSorter__default["default"]);
+  let keys = Object.keys(mfs).sort(atomSorter);
   for (let key of keys) {
@@ -1393,3 +1406,3 @@ mf += key;
 
-  const parsed = Papa__default["default"].parse(csv, options);
+  const parsed = Papa.parse(csv, options);
   const fields = parsed.meta.fields;
@@ -1538,2 +1551,12 @@ const stats = new Array(fields.length);
 
+/**
+ *
+ * @param {MoleculesDB} moleculesDB
+ * @param {OCL.Molecule} molecule
+ * @param {object} data
+ * @param {object} [moleculeInfo]
+ * @param {string} [moleculeInfo.idCode]
+ * @param {number[]} [moleculeInfo.index]
+ */
+
 function pushEntry(
@@ -2084,2 +2107,3 @@ moleculesDB,
 exports.getDiastereotopicAtomIDsAndH = getDiastereotopicAtomIDsAndH;
+exports.getDiastereotopicAtomIDsFromMolfile = getDiastereotopicAtomIDsFromMolfile;
 exports.getGroupedDiastereotopicAtomIDs = getGroupedDiastereotopicAtomIDs;
@@ -2086,0 +2110,0 @@ exports.getHoseCodesAndDiastereotopicIDs = getHoseCodesAndDiastereotopicIDs;

package.json

 {
   "name": "openchemlib-utils",
-  "version": "2.0.0",
+  "version": "2.1.0",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -12,3 +12,3 @@ "main": "lib/index.js",
   "scripts": {
-    "build": "rollup -c && cheminfo-build --entry src/index.js --root OCLUtils",
+    "build": "rollup -c --bundleConfigAsCjs && cheminfo-build --entry src/index.js --root OCLUtils",
     "eslint": "eslint src",
@@ -18,3 +18,3 @@ "eslint-fix": "npm run eslint -- --fix",
     "prettier-write": "prettier --write src",
-    "prepare": "rollup -c",
+    "prepack": "rollup -c --bundleConfigAsCjs",
     "test": "npm run test-only && npm run eslint && npm run prettier",
@@ -35,13 +35,13 @@ "test-only": "jest --coverage"
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.18.6",
-    "@types/jest": "^28.1.6",
+    "@babel/plugin-transform-modules-commonjs": "^7.19.6",
+    "@types/jest": "^29.2.3",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^8.22.0",
-    "eslint-config-cheminfo": "^8.0.2",
+    "eslint": "^8.27.0",
+    "eslint-config-cheminfo": "^8.1.3",
     "eslint-plugin-import": "^2.26.0",
-    "jest": "^28.1.3",
+    "jest": "^29.3.1",
     "jest-matcher-deep-close-to": "^3.0.2",
     "openchemlib": "8.0.0",
     "prettier": "^2.7.1",
-    "rollup": "^2.78.0"
+    "rollup": "^3.3.0"
   },
@@ -52,5 +52,5 @@ "dependencies": {
     "ml-floyd-warshall": "^1.0.4",
-    "ml-matrix": "^6.10.2",
+    "ml-matrix": "^6.10.4",
     "papaparse": "^5.3.2",
-    "sdf-parser": "^5.0.1"
+    "sdf-parser": "^6.0.1"
   },
@@ -57,0 +57,0 @@ "peerDependencies": {

src/db/utils/pushEntry.js

@@ -0,1 +1,11 @@
+/**
+ *
+ * @param {MoleculesDB} moleculesDB
+ * @param {OCL.Molecule} molecule
+ * @param {object} data
+ * @param {object} [moleculeInfo]
+ * @param {string} [moleculeInfo.idCode]
+ * @param {number[]} [moleculeInfo.index]
+ */
+
 export default function pushEntry(
@@ -2,0 +12,0 @@ moleculesDB,

src/index.js

@@ -6,2 +6,3 @@ export * from './diastereotopic/addDiastereotopicMissingChirality';
 export * from './diastereotopic/getGroupedDiastereotopicAtomIDs';
+export * from './diastereotopic/getDiastereotopicAtomIDsFromMolfile';
 
@@ -8,0 +9,0 @@ export * from './hose/getHoseCodesAndDiastereotopicIDs';

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Found 1 instance in 1 package

Fixed alerts

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Improved metrics

Total package byte prevSize

140958

increased by3.03%

Number of package files

50

increased by4.17%

Lines of code

4025

increased by3.02%

Dependency changes

• + Addeddynamic-typing@1.0.1(transitive)

• + Addedsdf-parser@6.0.1(transitive)

• - Removedduplexify@4.1.3(transitive)

• - Removedend-of-stream@1.4.4(transitive)

• - Removedinherits@2.0.4(transitive)

• - Removedonce@1.4.0(transitive)

• - Removedpump@3.0.2(transitive)

• - Removedpumpify@2.0.1(transitive)

• - Removedreadable-stream@3.6.2(transitive)

• - Removedsafe-buffer@5.2.1(transitive)

• - Removedsdf-parser@5.0.2(transitive)

• - Removedsplit2@4.2.0(transitive)

• - Removedstream-shift@1.0.3(transitive)

• - Removedstring_decoder@1.3.0(transitive)

• - Removedthrough2@4.0.2(transitive)

• - Removedthrough2-filter@3.1.0(transitive)

• - Removedutil-deprecate@1.0.2(transitive)

• - Removedwrappy@1.0.2(transitive)

• Updatedml-matrix@^6.10.4

• Updatedsdf-parser@^6.0.1