Merge pull request #278 from nickvandewiele/props_species_refactor

Add props dictionary attribute to the Species class for storing various user-defined properties.

Author: connie

rmgpy/rmg/model.py

@@ -76,8 +76,8 @@ class Species(rmgpy.species.Species):
     def __init__(self, index=-1, label='', thermo=None, conformer=None, 
                  molecule=None, transportData=None, molecularWeight=None, 
                  dipoleMoment=None, polarizability=None, Zrot=None, 
-                 energyTransferModel=None, reactive=True, coreSizeAtCreation=0):
-        rmgpy.species.Species.__init__(self, index, label, thermo, conformer, molecule, transportData, molecularWeight, dipoleMoment, polarizability, Zrot, energyTransferModel, reactive)
+                 energyTransferModel=None, reactive=True, props={}, coreSizeAtCreation=0):
+        rmgpy.species.Species.__init__(self, index, label, thermo, conformer, molecule, transportData, molecularWeight, dipoleMoment, polarizability, Zrot, energyTransferModel, reactive, props)
         self.coreSizeAtCreation = coreSizeAtCreation
 
     def __reduce__(self):

rmgpy/species.pxd

@@ -48,6 +48,7 @@ cdef class Species:
     cdef public ScalarQuantity _Zrot
     cdef public bint reactive
     cdef public object energyTransferModel
+    cdef public dict props
 
     cpdef generateResonanceIsomers(self)
 

rmgpy/species.py

@@ -84,6 +84,7 @@ class Species(object):
     `Zrot`                  The rotational relaxation collision number
     `energyTransferModel`   The collisional energy transfer model to use
     `reactive`              ``True`` if the species participates in reactions, ``False`` if not
+    'props'                 A generic 'properties' dictionary to store user-defined flags
     ======================= ====================================================
 
     note::
@@ -94,7 +95,7 @@ class Species(object):
     def __init__(self, index=-1, label='', thermo=None, conformer=None, 
                  molecule=None, transportData=None, molecularWeight=None, 
                  dipoleMoment=None, polarizability=None, Zrot=None, 
-                 energyTransferModel=None, reactive=True):
+                 energyTransferModel=None, reactive=True, props={}):
         self.index = index
         self.label = label
         self.thermo = thermo
@@ -115,6 +116,8 @@ def __init__(self, index=-1, label='', thermo=None, conformer=None,
                 if mult != m.multiplicity:
                     raise SpeciesError('Multiplicities of molecules in species {species} do not match.'.format(species=label))
 
+        self.props = props
+
 
     def __repr__(self):
         """

rmgpy/speciesTest.py

@@ -109,7 +109,14 @@ def testToAdjacencyList(self):
         """
         string = self.species.toAdjacencyList()
         self.assertTrue(string.startswith(self.species.molecule[0].toAdjacencyList(label=self.species.label,removeH=False)),string)
-
+    
+    def testSpeciesProps(self):
+        '''
+        Create a test in which a key-value pair is added to the props attribute of Species.
+        '''
+        self.species.props['foo'] = 'bar'
+        self.assertIsInstance(self.species.props, dict)
+        self.assertEquals(self.species.props['foo'], 'bar')
 ################################################################################
 
 if __name__ == '__main__':