Chemical identity comparison for Molecules and Species

rmgpy/molecule/group.py

@@ -1010,9 +1010,18 @@ def draw(self, format):
         img = graph.create(prog='neato', format=format)
         return img
 
-    def __getAtoms(self): return self.vertices
-    def __setAtoms(self, atoms): self.vertices = atoms
-    atoms = property(__getAtoms, __setAtoms)
+    @property
+    def atoms(self):
+        """
+        List of atoms contained in the current molecule.
+
+        Renames the inherited vertices attribute of :class:`Graph`.
+        """
+        return self.vertices
+
+    @atoms.setter
+    def atoms(self, atoms):
+        self.vertices = atoms
 
     def addAtom(self, atom):
         """

rmgpy/molecule/molecule.pxd

@@ -139,10 +139,11 @@ cdef class Molecule(Graph):
     cdef public bint reactive
     cdef public object rdMol
     cdef public int rdMolConfId
-    cdef str _fingerprint
-    cdef public str InChI
     cdef public dict props
-
+    cdef str _fingerprint
+    cdef str _inchi
+    cdef str _smiles
+
     cpdef addAtom(self, Atom atom)
 
     cpdef addBond(self, Bond bond)

rmgpy/molecule/molecule.py

@@ -780,33 +780,44 @@ class Molecule(Graph):
     ======================= =========== ========================================
     Attribute               Type        Description
     ======================= =========== ========================================
+    `atoms`                 ``list``    A list of Atom objects in the molecule
     `symmetryNumber`        ``float``   The (estimated) external + internal symmetry number of the molecule, modified for chirality
     `multiplicity`          ``int``     The multiplicity of this species, multiplicity = 2*total_spin+1
     `reactive`              ``bool``    ``True`` (by default) if the molecule participates in reaction families.
                                             It is set to ``False`` by the filtration functions if a non
                                             representative resonance structure was generated by a template reaction
     `props`                 ``dict``    A list of properties describing the state of the molecule.
     `InChI`                 ``str``     A string representation of the molecule in InChI
-    `atoms`                 ``list``    A list of Atom objects in the molecule
+    `SMILES`                ``str``     A string representation of the molecule in SMILES
     `fingerprint`           ``str``     A representation for fast comparison, set as molecular formula
     ======================= =========== ========================================
 
     A new molecule object can be easily instantiated by passing the `SMILES` or
     `InChI` string representing the molecular structure.
     """
 
-    def __init__(self, atoms=None, symmetry=-1, multiplicity=-187, reactive=True, props=None, SMILES=''):
+    def __init__(self, atoms=None, symmetry=-1, multiplicity=-187, reactive=True, props=None, InChI='', SMILES=''):
         Graph.__init__(self, atoms)
         self.symmetryNumber = symmetry
         self.multiplicity = multiplicity
         self.reactive = reactive
         self._fingerprint = None
-        self.InChI = ''
-        if SMILES != '': self.fromSMILES(SMILES)
+        self._inchi = None
+        self._smiles = None
         self.props = props or {}
+
+        if InChI and SMILES:
+            logging.warning('Both InChI and SMILES provided for Molecule instantiation, using InChI and ignoring SMILES.')
+        if InChI:
+            self.fromInChI(InChI)
+            self._inchi = InChI
+        elif SMILES:
+            self.fromSMILES(SMILES)
+            self._smiles = SMILES
+
         if multiplicity != -187:  # it was set explicitly, so re-set it (fromSMILES etc may have changed it)
             self.multiplicity = multiplicity
-    
+
     def __deepcopy__(self, memo):
         return self.copy(deep=True)
 
@@ -857,37 +868,65 @@ def __reduce__(self):
         """
         return (Molecule, (self.vertices, self.symmetryNumber, self.multiplicity, self.reactive, self.props))
 
-    def __getAtoms(self): return self.vertices
-    def __setAtoms(self, atoms): self.vertices = atoms
-    atoms = property(__getAtoms, __setAtoms)
+    @property
+    def atoms(self):
+        """
+        List of atoms contained in the current molecule.
+
+        Renames the inherited vertices attribute of :class:`Graph`.
+        """
+        return self.vertices
+
+    @atoms.setter
+    def atoms(self, atoms):
+        self.vertices = atoms
 
-    def __getFingerprint(self):
+    @property
+    def fingerprint(self):
         """
-        Return a string containing the "fingerprint" used to accelerate graph
-        isomorphism comparisons with other molecules. The fingerprint is a
-        short string containing a summary of selected information about the 
-        molecule. Two fingerprint strings matching is a necessary (but not
-        sufficient) condition for the associated molecules to be isomorphic.
+        Fingerprint used to accelerate graph isomorphism comparisons with
+        other molecules. The fingerprint is a short string containing a
+        summary of selected information about the molecule. Two fingerprint
+        strings matching is a necessary (but not sufficient) condition for
+        the associated molecules to be isomorphic.
+
+        Currently, the fingerprint is simply the chemical formula.
         """
         if self._fingerprint is None:
             self.fingerprint = self.getFormula()
         return self._fingerprint
-    def __setFingerprint(self, fingerprint): self._fingerprint = fingerprint
-    fingerprint = property(__getFingerprint, __setFingerprint)
+
+    @fingerprint.setter
+    def fingerprint(self, fingerprint):
+        self._fingerprint = fingerprint
+
+    @property
+    def InChI(self):
+        """InChI string for this molecule. Read-only."""
+        if self._inchi is None:
+            self._inchi = self.toInChI()
+        return self._inchi
+
+    @property
+    def SMILES(self):
+        """SMILES string for this molecule. Read-only."""
+        if self._smiles is None:
+            self._smiles = self.toSMILES()
+        return self._smiles
 
     def addAtom(self, atom):
         """
         Add an `atom` to the graph. The atom is initialized with no bonds.
         """
-        self._fingerprint = None
+        self._fingerprint = self._inchi = self._smiles = None
         return self.addVertex(atom)
 
     def addBond(self, bond):
         """
         Add a `bond` to the graph as an edge connecting the two atoms `atom1`
         and `atom2`.
         """
-        self._fingerprint = None
+        self._fingerprint = self._inchi = self._smiles = None
         return self.addEdge(bond)
 
     def getBonds(self, atom):
@@ -936,7 +975,7 @@ def removeAtom(self, atom):
         not remove atoms that no longer have any bonds as a result of this
         removal.
         """
-        self._fingerprint = None
+        self._fingerprint = self._inchi = self._smiles = None
         return self.removeVertex(atom)
 
     def removeBond(self, bond):
@@ -945,7 +984,7 @@ def removeBond(self, bond):
         Does not remove atoms that no longer have any bonds as a result of
         this removal.
         """
-        self._fingerprint = None
+        self._fingerprint = self._inchi = self._smiles = None
         return self.removeEdge(bond)
 
     def removeVanDerWaalsBonds(self):

rmgpy/molecule/translator.py

@@ -260,8 +260,6 @@ def fromInChI(mol, inchistr, backend='try-all'):
     a user-specified backend for conversion, currently supporting
     rdkit (default) and openbabel.
     """
-    mol.InChI = inchistr
-
     if inchiutil.INCHI_PREFIX in inchistr:
         return _read(mol, inchistr, 'inchi', backend)
     else:

rmgpy/reaction.py

@@ -200,10 +200,19 @@ def __reduce__(self):
                            self.comment
                            ))
 
-    def __getDegneneracy(self):
+    @property
+    def degeneracy(self):
+        """
+        The reaction path degeneracy for this reaction.
+
+        If the reaction has kinetics, changing the degeneracy
+        will adjust the reaction rate by a ratio of the new
+        degeneracy to the old degeneracy.
+        """
         return self._degeneracy
 
-    def __setDegeneracy(self, new):
+    @degeneracy.setter
+    def degeneracy(self, new):
         # modify rate if kinetics exists
         if self.kinetics is not None:
             if self._degeneracy < 2:
@@ -220,7 +229,6 @@ def __setDegeneracy(self, new):
             self.kinetics.changeRate(degeneracyRatio)
         # set new degeneracy
         self._degeneracy = new
-    degeneracy = property(__getDegneneracy, __setDegeneracy)
 
     def toChemkin(self, speciesList=None, kinetics=True):
         """

rmgpy/species.pxd

@@ -53,6 +53,7 @@ cdef class Species:
     cdef public bint isSolvent
     cdef public int creationIteration
     cdef public bint explicitlyAllowed
+    cdef str _inchi
 
     cpdef generate_resonance_structures(self, bint keep_isomorphic=?, bint filter_structures=?)
 

rmgpy/species.py

@@ -106,6 +106,7 @@ def __init__(self, index=-1, label='', thermo=None, conformer=None,
         self.isSolvent = False
         self.creationIteration = creationIteration
         self.explicitlyAllowed = explicitlyAllowed
+        self._inchi = None
         # Check multiplicity of each molecule is the same
         if molecule is not None and len(molecule)>1:
             mult = molecule[0].multiplicity
@@ -154,6 +155,14 @@ def __reduce__(self):
         """
         return (Species, (self.index, self.label, self.thermo, self.conformer, self.molecule, self.transportData, self.molecularWeight, self.energyTransferModel, self.reactive, self.props))
 
+    @property
+    def InChI(self):
+        """InChI string representation of this species. Read-only."""
+        if self._inchi is None:
+            if self.molecule:
+                self._inchi = self.molecule[0].InChI
+        return self._inchi
+
     @property
     def molecularWeight(self):
         """The molecular weight of the species. (Note: value_si is in kg/molecule not kg/mol)"""
@@ -781,11 +790,14 @@ def __reduce__(self):
         """
         return (TransitionState, (self.label, self.conformer, self.frequency, self.tunneling, self.degeneracy))
 
-    def getFrequency(self):
+    @property
+    def frequency(self):
+        """The negative frequency of the first-order saddle point."""
         return self._frequency
-    def setFrequency(self, value):
+
+    @frequency.setter
+    def frequency(self, value):
         self._frequency = quantity.Frequency(value)
-    frequency = property(getFrequency, setFrequency, """The negative frequency of the first-order saddle point.""")
 
     def getPartitionFunction(self, T):
         """