openchemlib-utils - npm Package Compare versions

Comparing version 2.1.0 to 2.1.1-pre.1669644163

package.json

 {
   "name": "openchemlib-utils",
-  "version": "2.1.0",
+  "version": "2.1.1-pre.1669644163",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -36,3 +36,3 @@ "main": "lib/index.js",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^8.27.0",
+    "eslint": "^8.28.0",
     "eslint-config-cheminfo": "^8.1.3",
@@ -44,3 +44,3 @@ "eslint-plugin-import": "^2.26.0",
     "prettier": "^2.7.1",
-    "rollup": "^3.3.0"
+    "rollup": "^3.4.0"
   },
@@ -50,3 +50,3 @@ "dependencies": {
     "ensure-string": "^1.2.0",
-    "ml-floyd-warshall": "^1.0.4",
+    "ml-floyd-warshall": "^2.0.1",
     "ml-matrix": "^6.10.4",
@@ -53,0 +53,0 @@ "papaparse": "^5.3.2",

src/diastereotopic/__tests/getDiastereotopicAtomIDsFromMolfile.test.js

@@ -73,1 +73,64 @@ import OCL from 'openchemlib';
 });
+
+test('getDiastereotopicAtomIDsFromMolfile with H', () => {
+  const molfile = `Empty String
+  ACD/Labs09022211502D
+  $$ Empty String
+ 21 23  0  0  0  0  0  0  0  0 22 V2000
+    1.1400   -1.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3282   -1.8626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3282   -3.1793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.1400   -3.8536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -3.1793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.8626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.4843   -1.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.6244   -1.8626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.8447   -1.3167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.7118   -2.2961    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    6.0695   -3.4362    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.7528   -3.1793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.1016    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    6.6154   -4.6565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.9321   -4.6565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.6065   -5.8126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.9321   -6.9526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.6154   -6.9526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.9410   -5.8126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7734   -4.0784    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    3.5164   -2.6975    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  6  2  0  0  0  0
+  2  3  2  0  0  0  0
+  2  7  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  2  0  0  0  0
+  5  6  1  0  0  0  0
+  7  8  2  0  0  0  0
+  8  9  1  0  0  0  0
+  8 12  1  0  0  0  0
+  9 10  1  0  0  0  0
+  9 13  2  0  0  0  0
+ 10 11  1  0  0  0  0
+ 11 12  1  0  0  0  0
+ 11 14  1  0  0  0  0
+ 12 21  1  0  0  0  0
+ 12 20  1  0  0  0  0
+ 14 15  1  0  0  0  0
+ 14 19  2  0  0  0  0
+ 15 16  2  0  0  0  0
+ 16 17  1  0  0  0  0
+ 17 18  2  0  0  0  0
+ 18 19  1  0  0  0  0
+M  END`;
+
+  const result = getDiastereotopicAtomIDsFromMolfile(OCL, molfile);
+
+  expect(result.diaIDs[20]).toMatchInlineSnapshot(`
+    {
+      "heavyAtom": "flu@\`@@HRYYvYU\\eGQBejf\`@@BBAJHTfHThOt\`eGBj@",
+      "hydrogenOCLIDs": [],
+      "nbHydrogens": 0,
+      "oclID": "fbm@b@FBALiLsKwJkdYyL\\uSS@@@DBHDXh\`Q_iA@HeT",
+    }
+  `);
+});

src/diastereotopic/getGroupedDiastereotopicAtomIDs.js

 import { getDiastereotopicAtomIDs } from './getDiastereotopicAtomIDs';
+import { groupDiastereotopicAtomIDs } from './groupDiastereotopicAtomIDs';
 /**
@@ -12,22 +13,4 @@ * This function groups the diasterotopic atomIds of the molecule based on equivalence of atoms. The output object contains
 export function getGroupedDiastereotopicAtomIDs(molecule, options = {}) {
-  const { atomLabel } = options;
-  let diaIDs = getDiastereotopicAtomIDs(molecule, options);
-  let diaIDsObject = {};
-  for (let i = 0; i < diaIDs.length; i++) {
-    if (!atomLabel || molecule.getAtomLabel(i) === atomLabel) {
-      let diaID = diaIDs[i];
-      if (!diaIDsObject[diaID]) {
-        diaIDsObject[diaID] = {
-          counter: 0,
-          atoms: [],
-          oclID: diaID,
-          atomLabel: molecule.getAtomLabel(i),
-        };
-      }
-      diaIDsObject[diaID].counter++;
-      diaIDsObject[diaID].atoms.push(i);
-    }
-  }
-
-  return Object.values(diaIDsObject);
+  let diaIDs = getDiastereotopicAtomIDs(molecule);
+  return groupDiastereotopicAtomIDs(diaIDs, molecule, options);
 }

src/index.js

@@ -7,2 +7,3 @@ export * from './diastereotopic/addDiastereotopicMissingChirality';
 export * from './diastereotopic/getDiastereotopicAtomIDsFromMolfile';
+export * from './diastereotopic/groupDiastereotopicAtomIDs';
 
@@ -9,0 +10,0 @@ export * from './hose/getHoseCodesAndDiastereotopicIDs';

src/util/getConnectivityMatrix.js

@@ -1,2 +0,2 @@
-import floydWarshall from 'ml-floyd-warshall';
+import { floydWarshall } from 'ml-floyd-warshall';
 import { Matrix } from 'ml-matrix';
@@ -3,0 +3,0 @@

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

No v1

Quality

Package is not semver >=1. This means it is not stable and does not support ^ ranges.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

144009

increased by2.16%

Number of package files

51

increased by2%

Lines of code

4094

increased by1.71%

Worsened metrics

Number of low quality alerts

1

increased byInfinity%

Dependency changes

• + Addedml-floyd-warshall@2.0.1(transitive)

• - Removedml-floyd-warshall@1.0.4(transitive)

• Updatedml-floyd-warshall@^2.0.1