@openchemistry/cjson-utils - npm Package Compare versions

Comparing version 0.0.5 to 0.1.0

CHANGELOG.md

@@ -6,2 +6,13 @@ # Change Log
 
+<a name="0.1.0"></a>
+# [0.1.0](https://github.com/OpenChemistry/oc-web-components/compare/@openchemistry/cjson-utils@0.0.5...@openchemistry/cjson-utils@0.1.0) (2018-06-18)
+
+
+### Features
+
+* Add animation of a molecule's normal modes ([f4517f7](https://github.com/OpenChemistry/oc-web-components/commit/f4517f7))
+
+
+
+
 <a name="0.0.5"></a>
@@ -8,0 +19,0 @@ ## [0.0.5](https://github.com/OpenChemistry/oc-web-components/compare/@openchemistry/cjson-utils@0.0.4...@openchemistry/cjson-utils@0.0.5) (2018-06-17)

dist/cjsonToMoljs.js

 import { numberOfAtoms } from './validation';
+import { isNil } from "lodash-es";
 export { cjsonToMoljs };
@@ -19,3 +20,3 @@ var elementSymbols = [
     var atoms = atomsToMoljs(cjson.atoms);
-    if (cjson.bonds) {
+    if (!isNil(cjson.bonds)) {
         atoms = bondsToMoljs(cjson.atoms, cjson.bonds, atoms);
@@ -51,3 +52,3 @@ }
         var jAtom = bondsIn.connections.index[i * 2 + 1];
-        if (atoms[iAtom].bonds === undefined) {
+        if (isNil(atoms[iAtom].bonds)) {
             atoms[iAtom].bonds = [];
@@ -57,3 +58,3 @@ }
         if (bondsIn.order) {
-            if (atoms[iAtom].bondOrder === undefined) {
+            if (isNil(atoms[iAtom].bondOrder)) {
                 atoms[iAtom].bondOrder = [];
@@ -60,0 +61,0 @@ }

dist/validation.js

@@ -0,1 +1,2 @@
+import { isNil } from "lodash-es";
 export { validateChemJson, isChemJson, numberOfAtoms };
@@ -9,3 +10,3 @@ function isChemJson(obj) {
     }
-    if (obj.bonds) {
+    if (!isNil(obj.bonds)) {
         // If bonds are invalid, throw them out but still keep the atoms
@@ -16,3 +17,3 @@ if (!validateBonds(obj.atoms, obj.bonds)) {
     }
-    if (obj.cube) {
+    if (!isNil(obj.cube)) {
         // If cube data is invalid, throw it out but still keep the rest
@@ -23,2 +24,8 @@ if (!validateCube(obj.cube)) {
     }
+    if (!isNil(obj.vibrations)) {
+        // If vibration data is invalid, throw it out but still keep the rest
+        if (!validateVibrations(obj.atoms, obj.vibrations)) {
+            obj.vibrations = undefined;
+        }
+    }
     return true;
@@ -38,3 +45,3 @@ }
     var nAtoms = numberOfAtoms(atoms);
-    if (bonds.order) {
+    if (!isNil(bonds.order)) {
         if (bonds.order.length * 2 !== bonds.connections.index.length) {
@@ -63,4 +70,29 @@ return false;
 }
+function validateVibrations(atoms, vibrations) {
+    if (isNil(vibrations.modes)) {
+        return false;
+    }
+    var nModes = vibrations.modes.length;
+    if (vibrations.frequencies && vibrations.frequencies.length !== nModes) {
+        return false;
+    }
+    if (!isNil(vibrations.intensities) && vibrations.intensities.length !== nModes) {
+        return false;
+    }
+    if (!isNil(vibrations.eigenVectors)) {
+        if (vibrations.eigenVectors.length !== nModes) {
+            return false;
+        }
+        var nAtoms = numberOfAtoms(atoms);
+        for (var _i = 0, _a = vibrations.eigenVectors; _i < _a.length; _i++) {
+            var eigenVector = _a[_i];
+            if (eigenVector.length !== nAtoms * 3) {
+                return false;
+            }
+        }
+    }
+    return true;
+}
 function numberOfAtoms(atoms) {
-    if (atoms.elements.number && atoms.elements.symbol) {
+    if (!isNil(atoms.elements.number) && !isNil(atoms.elements.symbol)) {
         if (atoms.elements.number.length !== atoms.elements.symbol.length) {
@@ -71,6 +103,6 @@ return -1;
     }
-    else if (atoms.elements.number) {
+    else if (!isNil(atoms.elements.number)) {
         return atoms.elements.number.length;
     }
-    else if (atoms.elements.symbol) {
+    else if (!isNil(atoms.elements.symbol)) {
         return atoms.elements.symbol.length;
@@ -77,0 +109,0 @@ }

package.json

 {
   "name": "@openchemistry/cjson-utils",
-  "version": "0.0.5",
+  "version": "0.1.0",
   "description": "Utilities to validate and convert cjson chemical data",
@@ -22,3 +22,5 @@ "main": "dist/index.js",
   "dependencies": {
-    "@openchemistry/types": "^0.0.6"
+    "@openchemistry/types": "^0.1.0",
+    "@types/lodash-es": "^4.17.0",
+    "lodash-es": "^4.17.10"
   },
@@ -25,0 +27,0 @@ "devDependencies": {

src/cjsonToMoljs.ts

 import { IChemJson, IAtoms, IBonds, IAtomSpec } from '@openchemistry/types';
 import { numberOfAtoms } from './validation';
+import { isNil } from "lodash-es";
 
@@ -23,3 +24,3 @@ export { cjsonToMoljs };
   let atoms = atomsToMoljs(cjson.atoms);
-  if (cjson.bonds) {
+  if (!isNil(cjson.bonds)) {
     atoms = bondsToMoljs(cjson.atoms, cjson.bonds, atoms);
@@ -59,3 +60,3 @@ }
     let jAtom: number = bondsIn.connections.index[i * 2 + 1];
-    if (atoms[iAtom].bonds === undefined) {
+    if (isNil(atoms[iAtom].bonds)) {
       atoms[iAtom].bonds = [];
@@ -65,3 +66,3 @@ }
     if (bondsIn.order) {
-      if (atoms[iAtom].bondOrder === undefined) {
+      if (isNil(atoms[iAtom].bondOrder)) {
         atoms[iAtom].bondOrder = [];
@@ -68,0 +69,0 @@ }

src/validation.ts

@@ -1,2 +0,3 @@
-import { IChemJson, IAtoms, IBonds, ICube } from '@openchemistry/types';
+import { IChemJson, IAtoms, IBonds, ICube, IVibrations } from '@openchemistry/types';
+import { isNil } from "lodash-es";
 
@@ -13,3 +14,3 @@ export { validateChemJson, isChemJson, numberOfAtoms };
   }
-  if (obj.bonds) {
+  if (!isNil(obj.bonds)) {
     // If bonds are invalid, throw them out but still keep the atoms
@@ -20,3 +21,3 @@ if (!validateBonds(obj.atoms, obj.bonds)) {
   }
-  if (obj.cube) {
+  if (!isNil(obj.cube)) {
     // If cube data is invalid, throw it out but still keep the rest
@@ -27,2 +28,8 @@ if (!validateCube(obj.cube)) {
   }
+  if (!isNil(obj.vibrations)) {
+    // If vibration data is invalid, throw it out but still keep the rest
+    if (!validateVibrations(obj.atoms, obj.vibrations)) {
+      obj.vibrations = undefined;
+    }
+  }
   return true;
@@ -44,3 +51,3 @@ }
   let nAtoms: number = numberOfAtoms(atoms);
-  if (bonds.order) {
+  if (!isNil(bonds.order)) {
     if (bonds.order.length * 2 !== bonds.connections.index.length) {
@@ -69,4 +76,29 @@ return false;
 
+function validateVibrations(atoms: IAtoms, vibrations: IVibrations) : boolean {
+  if (isNil(vibrations.modes)) {
+    return false;
+  }
+  let nModes: number = vibrations.modes.length;
+  if (vibrations.frequencies && vibrations.frequencies.length !== nModes) {
+    return false;
+  }
+  if (!isNil(vibrations.intensities) && vibrations.intensities.length !== nModes) {
+    return false;
+  }
+  if (!isNil(vibrations.eigenVectors)) {
+    if (vibrations.eigenVectors.length !== nModes) {
+      return false;
+    }
+    let nAtoms: number = numberOfAtoms(atoms);
+    for (let eigenVector of vibrations.eigenVectors) {
+      if (eigenVector.length !== nAtoms * 3) {
+        return false;
+      }
+    }
+  }
+  return true;
+}
+
 function numberOfAtoms(atoms: IAtoms) : number {
-  if (atoms.elements.number && atoms.elements.symbol) {
+  if (!isNil(atoms.elements.number) && !isNil(atoms.elements.symbol)) {
     if (atoms.elements.number.length !== atoms.elements.symbol.length) {
@@ -76,5 +108,5 @@ return -1;
     return atoms.elements.number.length;
-  } else if (atoms.elements.number) {
+  } else if (!isNil(atoms.elements.number)) {
     return atoms.elements.number.length;
-  } else if (atoms.elements.symbol) {
+  } else if (!isNil(atoms.elements.symbol)) {
     return atoms.elements.symbol.length;
@@ -81,0 +113,0 @@ } else {

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Improved metrics

Total package byte prevSize

19461

increased by15.33%

Lines of code

405

increased by19.12%

Worsened metrics

Dependency count

3

increased by200%

Dependency changes

• + Added@types/lodash-es@^4.17.0

• + Addedlodash-es@^4.17.10

• + Added@openchemistry/types@0.1.0(transitive)

• + Added@types/lodash@4.17.13(transitive)

• + Added@types/lodash-es@4.17.12(transitive)

• + Addedlodash-es@4.17.21(transitive)

• - Removed@openchemistry/types@0.0.6(transitive)

• Updated@openchemistry/types@^0.1.0