openchemlib-utils - npm Package Compare versions

Comparing version 0.2.0 to 0.2.1

lib/index.js

@@ -9,2 +9,3 @@ 'use strict';
 var mlMatrix = require('ml-matrix');
+var atomSorter = _interopDefault(require('atom-sorter'));
 
@@ -552,2 +553,87 @@ let OCL;
 
+/**
+ * Calculate the molecular formula in 'chemcalc' notation taking into account fragments, isotopes and charges
+ * {OCL.Molecule} [molecule] an instance of OCL.Molecule
+ * @returns {String}
+ */
+
+function getMF(molecule) {
+  let entries = molecule.getFragments();
+  let result = {};
+  let parts = [];
+  let allAtoms = [];
+
+  entries.forEach(function(entry) {
+    let mf = getFragmentMF(entry, allAtoms);
+    parts.push(mf);
+  });
+
+  let counts = {};
+  for (let part of parts) {
+    if (!counts[part]) counts[part] = 0;
+    counts[part]++;
+  }
+  parts = [];
+  for (let key of Object.keys(counts).sort()) {
+    if (counts[key] > 1) {
+      parts.push(counts[key] + key);
+    } else {
+      parts.push(key);
+    }
+  }
+
+  result.parts = parts;
+  result.mf = toMFString(allAtoms);
+  return result;
+}
+
+function getFragmentMF(molecule, allAtoms) {
+  let atoms = [];
+  for (let i = 0; i < molecule.getAllAtoms(); i++) {
+    let atom = {};
+    atom.charge = molecule.getAtomCharge(i);
+    atom.label = molecule.getAtomLabel(i);
+    atom.mass = molecule.getAtomMass(i);
+    atom.implicitHydrogens = molecule.getImplicitHydrogens(i);
+    atoms.push(atom);
+    allAtoms.push(atom);
+  }
+  return toMFString(atoms);
+}
+
+function toMFString(atoms) {
+  let charge = 0;
+  let mfs = {};
+  for (let atom of atoms) {
+    let label = atom.label;
+    charge += atom.charge;
+    if (atom.mass) {
+      label = `[${atom.mass}${label}]`;
+    }
+    let mfAtom = mfs[label];
+    if (!mfAtom) {
+      mfs[label] = 0;
+    }
+    mfs[label] += 1;
+    if (atom.implicitHydrogens) {
+      if (!mfs.H) mfs.H = 0;
+      mfs.H += atom.implicitHydrogens;
+    }
+  }
+
+  let mf = '';
+  let keys = Object.keys(mfs).sort(atomSorter);
+  for (let key of keys) {
+    mf += key;
+    if (mfs[key] > 1) mf += mfs[key];
+  }
+
+  if (charge > 0) {
+    mf += `(+${charge > 1 ? charge : ''})`;
+  } else if (charge < 0) {
+    mf += `(${charge < -1 ? charge : '-'})`;
+  }
+  return mf;
+}
+
 let fragment;
@@ -780,2 +866,3 @@
 exports.getHoseCodesFromDiastereotopicID = getHoseCodesFromDiastereotopicID;
+exports.getMF = getMF;
 exports.getOCL = getOCL;
@@ -782,0 +869,0 @@ exports.getPathsInfo = getPathsInfo;

package.json

 {
   "name": "openchemlib-utils",
-  "version": "0.2.0",
+  "version": "0.2.1",
   "description": "",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/index.js

@@ -15,2 +15,3 @@ export * from './diastereotopic/addDiastereotopicMissingChirality';
 export * from './util/isCsp3';
+export * from './util/getMF';
 
@@ -17,0 +18,0 @@ export * from './path/getPathsInfo';

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Improved metrics

Total package byte prevSize

59831

increased by3.54%

Lines of code

1641

increased by5.06%

No dependency changes