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Merged
alongd merged 6 commits into from
Mar 20, 2018
Merged

Adding Iodine as a new reactive element in RMG #1321

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94760de
Added Iodine atomType to documentation
sarahkha Mar 15, 2018
7e9cb09
Added 'I1s' iodine atomType
sarahkha Mar 15, 2018
5b90cd4
Added a iodine atomType Test
sarahkha Mar 15, 2018
5f7e063
Added I to group updateFingerprint()
sarahkha Mar 15, 2018
3465eb9
Added I to generatePairs() in reaction.py
sarahkha Mar 15, 2018
98bce38
Avoid generating a charged iodine atomType in isomorphismTest
sarahkha Mar 15, 2018
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4 changes: 4 additions & 0 deletions documentation/source/reference/molecule/atomtype.rst
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Expand Up @@ -119,4 +119,8 @@ Atom type Description
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
``Cl`` chlorine atom with any local bond structure
``Cl1s`` chlorine atom with three lone pairs and zero to one single bonds
*Iodine atom types*
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
``I`` iodine atom with any local bond structure
``I1s`` iodine atom with three lone pairs and zero to one single bonds
=============== ==============================================================================================================================================================
4 changes: 4 additions & 0 deletions documentation/source/users/rmg/database/introduction.rst
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Expand Up @@ -193,6 +193,10 @@ table below shows all atoms types in RMG.
+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
|Cl1s |Chlorine |Three lone pairs, zero to one single bonds |
+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
|I |Iodine |No requirements |
+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
|I1s |Iodine |Three lone pairs, zero to one single bonds |
+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
|He |Helium |No requirements, nonreactive |
+----------+-------------------+------------------------------------------------------------------------------------------------------------------+
|Ne |Neon |No requirements, nonreactive |
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16 changes: 12 additions & 4 deletions rmgpy/molecule/atomtype.py
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Expand Up @@ -239,10 +239,10 @@ def getFeatures(self):
'C','Ca','Cs','Csc','Cd','CO','CS','Cdd','Cdc','Ct','Cb','Cbf','C2s','C2sc','C2d','C2dc','C2tc',
'N','N0sc','N1s','N1sc','N1dc','N3s','N3sc','N3d','N3t','N3b','N5sc','N5dc','N5ddc','N5dddc','N5t','N5tc','N5b','N5bd',
'O','Oa','O0sc','O2s','O2sc','O2d','O4sc','O4dc','O4tc','O4b',

'Si','Sis','Sid','Sidd','Sit','SiO','Sib','Sibf',
'S','Sa','S0sc','S2s','S2sc','S2d','S2dc','S2tc','S4s','S4sc','S4d','S4dd','S4dc','S4b','S4t','S4tdc','S6s','S6sc','S6d','S6dd','S6ddd','S6dc','S6t','S6td','S6tt','S6tdc',
'Cl','Cl1s'])
'Cl','Cl1s',
'I','I1s'])

atomTypes['R!H'] = AtomType(label='R!H', generic=['R'], specific=[
'Val4','Val5','Val6','Val7',
Expand All @@ -252,7 +252,8 @@ def getFeatures(self):
'O','Oa','O0sc','O2s','O2sc','O2d','O4sc','O4dc','O4tc','O4b',
'Si','Sis','Sid','Sidd','Sit','SiO','Sib','Sibf',
'S','Sa','S0sc','S2s','S2sc','S2d','S2dc','S2tc','S4s','S4sc','S4d','S4dd','S4dc','S4b','S4t','S4tdc','S6s','S6sc','S6d','S6dd','S6ddd','S6dc','S6t','S6td','S6tt','S6tdc',
'Cl','Cl1s'])
'Cl','Cl1s',
'I','I1s'])

atomTypes['Val4'] = AtomType(label='Val4', generic=['R','R!H'], specific=[
'C','Ca','Cs','Csc','Cd','CO','CS','Cdd','Cdc','Ct','Cb','Cbf','C2s','C2sc','C2d','C2dc','C2tc',
Expand All @@ -266,7 +267,8 @@ def getFeatures(self):
'S','Sa','S0sc','S2s','S2sc','S2d','S2dc','S2tc','S4s','S4sc','S4d','S4dd','S4dc','S4b','S4t','S4tdc','S6s','S6sc','S6d','S6dd','S6ddd','S6dc','S6t','S6td','S6tt','S6tdc'])

atomTypes['Val7'] = AtomType(label='Val7', generic=['R','R!H'], specific=[
'Cl','Cl1s'])
'Cl','Cl1s',
'I','I1s'])

atomTypes['H' ] = AtomType('H', generic=['R'], specific=[])

Expand Down Expand Up @@ -509,6 +511,10 @@ def getFeatures(self):
single=[0,1], allDouble=[0], rDouble=[], oDouble=[], sDouble=[], triple=[0], benzene=[0], lonePairs=[3], charge=[0])
# examples for Cl1s: HCl, [Cl]

atomTypes['I' ] = AtomType('I', generic=['R','R!H','Val7'], specific=['I1s'])
atomTypes['I1s'] = AtomType('I1s', generic=['R','R!H','I','Val7'], specific=[],
single=[0,1], allDouble=[0], rDouble=[], oDouble=[], sDouble=[], triple=[0], benzene=[0], lonePairs=[3], charge=[0])
# examples for I1s: HI, [I], IO, CH3I, I2

atomTypes['R' ].setActions(incrementBond=['R'], decrementBond=['R'], formBond=['R'], breakBond=['R'], incrementRadical=['R'], decrementRadical=['R'], incrementLonePair=['R'], decrementLonePair=['R'])
atomTypes['R!H' ].setActions(incrementBond=['R!H'], decrementBond=['R!H'], formBond=['R!H'], breakBond=['R!H'], incrementRadical=['R!H'], decrementRadical=['R!H'], incrementLonePair=['R!H'], decrementLonePair=['R!H'])
Expand Down Expand Up @@ -610,6 +616,8 @@ def getFeatures(self):
atomTypes['Cl' ].setActions(incrementBond=[], decrementBond=[], formBond=['Cl'], breakBond=['Cl'], incrementRadical=['Cl'], decrementRadical=['Cl'], incrementLonePair=[], decrementLonePair=[])
atomTypes['Cl1s'].setActions(incrementBond=[], decrementBond=[], formBond=['Cl1s'], breakBond=['Cl1s'], incrementRadical=['Cl1s'], decrementRadical=['Cl1s'], incrementLonePair=[], decrementLonePair=[])

atomTypes['I' ].setActions(incrementBond=[], decrementBond=[], formBond=['I'], breakBond=['I'], incrementRadical=['I'], decrementRadical=['I'], incrementLonePair=[], decrementLonePair=[])
atomTypes['I1s'].setActions(incrementBond=[], decrementBond=[], formBond=['I1s'], breakBond=['I1s'], incrementRadical=['I1s'], decrementRadical=['I1s'], incrementLonePair=[], decrementLonePair=[])

#list of elements that do not have more specific atomTypes
#these are ordered on priority of picking if we encounter a more general atomType for make
Expand Down
9 changes: 9 additions & 0 deletions rmgpy/molecule/atomtypeTest.py
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Expand Up @@ -489,6 +489,9 @@ def setUp(self):
self.mol73 = Molecule().fromAdjacencyList('''1 H u0 p0 c0 {2,S}
2 Cl u0 p3 c0 {1,S}''')

self.mol74 = Molecule().fromAdjacencyList('''1 H u0 p0 c0 {2,S}
2 I u0 p3 c0 {1,S}''')

def atomType(self, mol, atomID):
atom = mol.atoms[atomID]
type = getAtomType(atom, mol.getBonds(atom))
Expand Down Expand Up @@ -614,6 +617,12 @@ def testChlorineTypes(self):
"""
self.assertEqual(self.atomType(self.mol73, 1), 'Cl1s')

def testIodineTypes(self):
"""
Test that getAtomType() returns appropriate iodine atom types.
"""
self.assertEqual(self.atomType(self.mol74, 1), 'I1s')

def testOtherTypes(self):
"""
Test that getAtomType() returns appropriate types for other misc inerts.
Expand Down
1 change: 1 addition & 0 deletions rmgpy/molecule/group.pxd
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Expand Up @@ -119,6 +119,7 @@ cdef class Group(Graph):
cdef public short oxygenCount
cdef public short sulfurCount
cdef public short chlorineCount
cdef public short iodineCount
cdef public short siliconCount
cdef public short radicalCount

Expand Down
14 changes: 10 additions & 4 deletions rmgpy/molecule/group.py
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Expand Up @@ -1117,23 +1117,26 @@ def updateFingerprint(self):
isomorphism checks.
"""
cython.declare(atom=GroupAtom, atomType=AtomType)
cython.declare(carbon=AtomType, nitrogen=AtomType, oxygen=AtomType, sulfur=AtomType, chlorine=AtomType, silicon=AtomType)
cython.declare(carbon=AtomType, nitrogen=AtomType, oxygen=AtomType, sulfur=AtomType, chlorine=AtomType,
iodine=AtomType, silicon=AtomType)
cython.declare(isCarbon=cython.bint, isNitrogen=cython.bint, isOxygen=cython.bint, isSulfur=cython.bint,
isChlorine=cython.bint, isSilicon=cython.bint, radical=cython.int)
isChlorine=cython.bint, isIodine=cython.bint, isSilicon=cython.bint, radical=cython.int)

carbon = atomTypes['C']
nitrogen = atomTypes['N']
oxygen = atomTypes['O']
sulfur = atomTypes['S']
chlorine = atomTypes['Cl']
iodine = atomTypes['I']
silicon = atomTypes['Si']

self.carbonCount = 0
self.nitrogenCount = 0
self.oxygenCount = 0
self.sulfurCount = 0
self.chlorineCount = 0
self.siliconCount = 0
self.iodineCount = 0
self.siliconCount = 0
self.radicalCount = 0
for atom in self.vertices:
if len(atom.atomType) == 1:
Expand All @@ -1143,8 +1146,9 @@ def updateFingerprint(self):
isOxygen = atomType.equivalent(oxygen)
isSulfur = atomType.equivalent(sulfur)
isChlorine = atomType.equivalent(chlorine)
isIodine = atomType.equivalent(iodine)
isSilicon = atomType.equivalent(silicon)
sum_is_atom = isCarbon + isNitrogen + isOxygen + isSulfur + isChlorine + isSilicon
sum_is_atom = isCarbon + isNitrogen + isOxygen + isSulfur + isChlorine + isIodine + isSilicon
if sum_is_atom == 1:
if isCarbon:
self.carbonCount += 1
Expand All @@ -1156,6 +1160,8 @@ def updateFingerprint(self):
self.sulfurCount += 1
elif isChlorine:
self.chlorineCount += 1
elif isIodine:
self.iodineCount += 1
elif isSilicon:
self.siliconCount += 1
if len(atom.radicalElectrons) >= 1:
Expand Down
4 changes: 2 additions & 2 deletions rmgpy/molecule/isomorphismTest.py
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Expand Up @@ -40,7 +40,7 @@
from rmgpy.molecule.molecule import Molecule
from rmgpy.molecule.group import Group

molecule_atom_types = [ 'C', 'O', 'N', 'S', 'Si', 'Cl']
molecule_atom_types = [ 'C', 'O', 'N', 'S', 'Si', 'Cl', 'I']
group_atomtypes = {}

for item in create_atom_types() :
Expand Down Expand Up @@ -140,7 +140,7 @@ def load_cases_molecule_atom_types():
'''
output = []
a_types = list(itertools.product(molecule_atom_types, repeat=2))
uncharged_a_types = ['Cl']
uncharged_a_types = ['Cl','I']
unpaired_electrons = list(itertools.product(range(3), repeat=2))
cross_element_unpaired = list(itertools.product(a_types,unpaired_electrons))
for item in cross_element_unpaired:
Expand Down
14 changes: 8 additions & 6 deletions rmgpy/reaction.py
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Expand Up @@ -922,22 +922,24 @@ def generatePairs(self):
productSulfurs = [sum([1 for atom in product.molecule[0].atoms if atom.isSulfur()]) for product in products ]
reactantChlorines = [sum([1 for atom in reactant.molecule[0].atoms if atom.isChlorine()]) for reactant in reactants]
productChlorines = [sum([1 for atom in product.molecule[0].atoms if atom.isChlorine()]) for product in products ]
reactantIodines = [sum([1 for atom in reactant.molecule[0].atoms if atom.isChlorine()]) for reactant in reactants]
productIodines = [sum([1 for atom in product.molecule[0].atoms if atom.isChlorine()]) for product in products ]

# Sort the reactants and products by C/O/N/S numbers
reactants = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, reactant) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, reactant
in zip(reactantCarbons,reactantOxygens,reactantNitrogens,reactantSilicons,reactantSulfurs,reactantChlorines,reactants)]
reactants = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, reactant) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, reactant
in zip(reactantCarbons,reactantOxygens,reactantNitrogens,reactantSilicons,reactantSulfurs,reactantChlorines, reactantIodines, reactants)]
reactants.sort()
products = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, product) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, product
in zip(productCarbons,productOxygens,productNitrogens,productSilicons,productSulfurs,productChlorines,products)]
products = [(carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, product) for carbon, oxygen, nitrogen, silicon, sulfur, chlorine, iodine, product
in zip(productCarbons,productOxygens,productNitrogens,productSilicons,productSulfurs,productChlorines, productIodines, products)]
products.sort()

while len(reactants) > 1 and len(products) > 1:
self.pairs.append((reactants[-1][6], products[-1][6]))
self.pairs.append((reactants[-1][-1], products[-1][-1]))
reactants.pop()
products.pop()
for reactant in reactants:
for product in products:
self.pairs.append((reactant[6], product[6]))
self.pairs.append((reactant[-1], product[-1]))

def draw(self, path):
"""
Expand Down