Merge pull request #1453 from ReactionMechanismGenerator/isotope_tran…

…slation

Improved isotope support in converter and translator modules

rmgpy/molecule/converter.py

@@ -69,6 +69,8 @@ def toRDKitMol(mol, removeHs=True, returnMapping=False, sanitize=True):
     rdkitmol = Chem.rdchem.EditableMol(Chem.rdchem.Mol())
     for index, atom in enumerate(mol.vertices):
         rdAtom = Chem.rdchem.Atom(atom.element.symbol)
+        if atom.element.isotope != -1:
+            rdAtom.SetIsotope(atom.element.isotope)
         rdAtom.SetNumRadicalElectrons(atom.radicalElectrons)
         rdAtom.SetFormalCharge(atom.charge)
         if atom.element.symbol == 'C' and atom.lonePairs == 1 and mol.multiplicity == 1: rdAtom.SetNumRadicalElectrons(2)
@@ -131,7 +133,8 @@ def fromRDKitMol(mol, rdkitmol):
 
         # Use atomic number as key for element
         number = rdkitatom.GetAtomicNum()
-        element = elements.getElement(number)
+        isotope = rdkitatom.GetIsotope()
+        element = elements.getElement(number, isotope or -1)
 
         # Process charge
         charge = rdkitatom.GetFormalCharge()
@@ -214,6 +217,8 @@ def toOBMol(mol, returnMapping=False):
     for atom in atoms:
         a = obmol.NewAtom()
         a.SetAtomicNum(atom.number)
+        if atom.element.isotope != -1:
+            a.SetIsotope(atom.element.isotope)
         a.SetFormalCharge(atom.charge)
         obAtomIds[atom] = a.GetId()
     orders = {1: 1, 2: 2, 3: 3, 1.5: 5}
@@ -255,7 +260,8 @@ def fromOBMol(mol, obmol):
     for obatom in openbabel.OBMolAtomIter(obmol):
         # Use atomic number as key for element
         number = obatom.GetAtomicNum()
-        element = elements.getElement(number)
+        isotope = obatom.GetIsotope()
+        element = elements.getElement(number, isotope or -1)
         # Process charge
         charge = obatom.GetFormalCharge()
         obatom_multiplicity = obatom.GetSpinMultiplicity()

rmgpy/molecule/converterTest.py

@@ -35,7 +35,7 @@
 import unittest
 
 from rmgpy.exceptions import AtomTypeError
-from rmgpy.molecule.converter import debugRDKitMol, toRDKitMol, fromRDKitMol
+from rmgpy.molecule.converter import debugRDKitMol, toRDKitMol, fromRDKitMol, toOBMol, fromOBMol
 from rmgpy.molecule.molecule import Molecule
 
 
@@ -123,3 +123,38 @@ def test_atom_mapping_2(self):
                         rdkitmol.GetBondBetweenAtoms(rdAtomIndices[at1], rdAtomIndices[at2])
                     except RuntimeError:
                         self.fail("RDKit failed in finding the bond in the original atom!")
+
+class ConverterTest(unittest.TestCase):
+
+    def setUp(self):
+        """Function run before each test in this class."""
+        self.test_mols = [
+            Molecule().fromSMILES('C'),
+            Molecule().fromSMILES('O'),
+            Molecule().fromSMILES('N'),
+            Molecule().fromSMILES('S'),
+            Molecule().fromSMILES('[CH2]C'),
+            Molecule().fromSMILES('[CH]C'),
+            Molecule().fromSMILES('C=CC=C'),
+            Molecule().fromSMILES('C#C[CH2]'),
+            Molecule().fromSMILES('c1ccccc1'),
+            Molecule().fromSMILES('[13CH3]C')
+        ]
+
+    def test_rdkit_round_trip(self):
+        """Test conversion to and from RDKitMol"""
+        for mol in self.test_mols:
+            rdkit_mol = toRDKitMol(mol)
+            new_mol = fromRDKitMol(Molecule(), rdkit_mol)
+
+            self.assertTrue(mol.isIsomorphic(new_mol))
+            self.assertEqual(mol.get_element_count(), new_mol.get_element_count())
+
+    def test_ob_round_trip(self):
+        """Test conversion to and from OBMol"""
+        for mol in self.test_mols:
+            ob_mol = toOBMol(mol)
+            new_mol = fromOBMol(Molecule(), ob_mol)
+
+            self.assertTrue(mol.isIsomorphic(new_mol))
+            self.assertEqual(mol.get_element_count(), new_mol.get_element_count())

rmgpy/molecule/translatorTest.py

@@ -414,6 +414,22 @@ def test_disconnected_molecule(self):
 
         self.assertEqual(mol.toInChI(), inchi)
 
+    def test_isotopic_molecule_1(self):
+        """Test that we can generate an InChI for an isotopic molecule."""
+        mol = Molecule().fromSMILES('[13CH4]')
+
+        inchi = 'InChI=1S/CH4/h1H4/i1+1'
+
+        self.assertEqual(mol.toInChI(), inchi)
+
+    def test_isotopic_molecule_2(self):
+        """Test that we can generate an InChI for an isotopic molecule."""
+        mol = Molecule().fromSMILES('[13CH3]C')
+
+        inchi = 'InChI=1S/C2H6/c1-2/h1-2H3/i1+1'
+
+        self.assertEqual(mol.toInChI(), inchi)
+
 
 class SMILESGenerationTest(unittest.TestCase):
     def compare(self, adjlist, smiles):
@@ -1372,3 +1388,17 @@ def test_NO(self):
         inchi = 'InChI=1S/NO/c1-2'
         u_indices = [1]
         self.compare(inchi, u_indices)
+
+    def test_isotopic_molecule_1(self):
+        """Test that we can parse an InChI for an isotopic molecule."""
+        mol = Molecule().fromInChI('InChI=1S/CH4/h1H4/i1+1')
+
+        self.assertTrue(len(mol.atoms), 4)
+        self.assertEqual([atom.element.isotope for atom in mol.atoms].count(13), 1)
+
+    def test_isotopic_molecule_2(self):
+        """Test that we can parse an InChI for an isotopic molecule."""
+        mol = Molecule().fromInChI('InChI=1S/C2H6/c1-2/h1-2H3/i1+1')
+
+        self.assertTrue(len(mol.atoms), 6)
+        self.assertEqual([atom.element.isotope for atom in mol.atoms].count(13), 1)