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Enable Species instantiation by SMILES or InChI argument
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Add SMILES property and unit tests
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@mliu49
mliu49 committed Apr 5, 2019
1 parent 920e501 commit db7edd5
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Showing 3 changed files with 65 additions and 58 deletions.
1 change: 1 addition & 0 deletions rmgpy/species.pxd
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ cdef class Species:
cdef public bint explicitlyAllowed
cdef str _fingerprint
cdef str _inchi
cdef str _smiles

cpdef generate_resonance_structures(self, bint keep_isomorphic=?, bint filter_structures=?)

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35 changes: 28 additions & 7 deletions rmgpy/species.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,16 +81,16 @@ class Species(object):
always considered regardless of this variable
`props` A generic 'properties' dictionary to store user-defined flags
`aug_inchi` Unique augmented inchi
`isSolvent` Boolean describing whether this species is the solvent
`symmetryNumber` Estimated symmetry number of the species, using the resonance hybrid
`creationIteration` Iteration which the species is created within the reaction mechanism generation algorithm
`explicitlyAllowed` Flag to exempt species from forbidden structure checks
======================= ====================================================
"""

def __init__(self, index=-1, label='', thermo=None, conformer=None,
molecule=None, transportData=None, molecularWeight=None,
energyTransferModel=None, reactive=True, props=None, aug_inchi=None,
symmetryNumber = -1, creationIteration = 0, explicitlyAllowed=False):
def __init__(self, index=-1, label='', thermo=None, conformer=None, molecule=None, transportData=None,
molecularWeight=None, energyTransferModel=None, reactive=True, props=None, SMILES='', InChI='',
aug_inchi=None, symmetryNumber = -1, creationIteration = 0, explicitlyAllowed=False):
self.index = index
self.label = label
self.thermo = thermo
Expand All @@ -108,14 +108,23 @@ def __init__(self, index=-1, label='', thermo=None, conformer=None,
self.explicitlyAllowed = explicitlyAllowed
self._fingerprint = None
self._inchi = None
self._smiles = None

if InChI and SMILES:
logging.warning('Both InChI and SMILES provided for Species instantiation, using InChI and ignoring SMILES.')
if InChI:
self.molecule = [Molecule(InChI=InChI)]
self._inchi = InChI
elif SMILES:
self.molecule = [Molecule(SMILES=SMILES)]
self._smiles = SMILES

# Check multiplicity of each molecule is the same
if molecule is not None and len(molecule)>1:
mult = molecule[0].multiplicity
for m in molecule[1:]:
if mult != m.multiplicity:
raise SpeciesError('Multiplicities of molecules in species {species} do not match.'.format(species=label))



def __repr__(self):
"""
Expand Down Expand Up @@ -172,6 +181,18 @@ def InChI(self):
self._inchi = self.molecule[0].InChI
return self._inchi

@property
def SMILES(self):
"""
SMILES string representation of this species. Read-only.
Note that SMILES representations for different resonance structures of the same species may be different.
"""
if self._smiles is None:
if self.molecule:
self._smiles = self.molecule[0].SMILES
return self._smiles

@property
def multiplicity(self):
"""Fingerprint of this species, taken from molecule attribute. Read-only."""
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87 changes: 36 additions & 51 deletions rmgpy/speciesTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,23 @@ def setUp(self):
molecularWeight=(28.03,'amu'),
reactive=True,
)


self.species2 = Species().fromAdjacencyList(
"""
1 C u0 p0 c0 {2,D} {6,S} {7,S}
2 C u0 p0 c0 {1,D} {3,S} {8,S}
3 C u0 p0 c0 {2,S} {4,D} {9,S}
4 C u0 p0 c0 {3,D} {5,S} {10,S}
5 C u0 p0 c0 {4,S} {6,D} {11,S}
6 C u0 p0 c0 {1,S} {5,D} {12,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {4,S}
11 H u0 p0 c0 {5,S}
12 H u0 p0 c0 {6,S}
""")

def testPickle(self):
"""
Test that a Species object can be pickled and unpickled.
Expand Down Expand Up @@ -324,63 +340,32 @@ def testGetTransportData(self):

def test_fingerprint_property(self):
"""Test that the fingerprint property works"""
spc = Species().fromAdjacencyList(
"""
1 C u0 p0 c0 {2,D} {6,S} {7,S}
2 C u0 p0 c0 {1,D} {3,S} {8,S}
3 C u0 p0 c0 {2,S} {4,D} {9,S}
4 C u0 p0 c0 {3,D} {5,S} {10,S}
5 C u0 p0 c0 {4,S} {6,D} {11,S}
6 C u0 p0 c0 {1,S} {5,D} {12,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {4,S}
11 H u0 p0 c0 {5,S}
12 H u0 p0 c0 {6,S}
""")

self.assertEqual(spc.fingerprint, 'C6H6')
self.assertEqual(self.species2.fingerprint, 'C6H6')

def test_inchi_property(self):
"""Test that the InChI property works"""
spc = Species().fromAdjacencyList(
"""
1 C u0 p0 c0 {2,D} {6,S} {7,S}
2 C u0 p0 c0 {1,D} {3,S} {8,S}
3 C u0 p0 c0 {2,S} {4,D} {9,S}
4 C u0 p0 c0 {3,D} {5,S} {10,S}
5 C u0 p0 c0 {4,S} {6,D} {11,S}
6 C u0 p0 c0 {1,S} {5,D} {12,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {4,S}
11 H u0 p0 c0 {5,S}
12 H u0 p0 c0 {6,S}
""")

self.assertEqual(spc.InChI, 'InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H')
self.assertEqual(self.species2.InChI, 'InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H')

def test_multiplicity_property(self):
"""Test that the fingerprint property works"""
spc = Species().fromAdjacencyList(
"""
1 C u0 p0 c0 {2,D} {6,S} {7,S}
2 C u0 p0 c0 {1,D} {3,S} {8,S}
3 C u0 p0 c0 {2,S} {4,D} {9,S}
4 C u0 p0 c0 {3,D} {5,S} {10,S}
5 C u0 p0 c0 {4,S} {6,D} {11,S}
6 C u0 p0 c0 {1,S} {5,D} {12,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {4,S}
11 H u0 p0 c0 {5,S}
12 H u0 p0 c0 {6,S}
""")
self.assertEqual(self.species2.multiplicity, 1)

def test_smiles_property(self):
"""Test that the InChI property works"""
self.assertEqual(self.species2.SMILES, 'C1=CC=CC=C1')

def test_inchi_instantiation(self):
"""Test that we can create a species using the InChI argument"""
test = Species(InChI='InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H')

self.assertTrue(test.isIsomorphic(self.species2))

def test_smiles_instantiation(self):
"""Test that we can create a species using the SMILES argument"""
test = Species(SMILES='C1=CC=CC=C1')

self.assertTrue(test.isIsomorphic(self.species2))

self.assertEqual(spc.multiplicity, 1)

################################################################################

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