Compare names¶

import sys
import os
import re
import numpy
import csv
import cPickle as pickle
import itertools
import logging
from collections import Counter, defaultdict, OrderedDict
import IPython
from IPython.display import display, Markdown, HTML
def mprint(s):
    "A convenience to format things in Jupyter notebooks via MarkDown syntax"
    display(Markdown(s))
    
#import ck2cti  # the customized one stored alongside this notebook
from cantera import ck2cti  # we'll monkey-patch it if needed

# Add $RMGpy to front of your $PYTHONPATH in case you didn't already
sys.path.insert(1,os.getenv('RMGpy',os.path.expanduser('~/Code/RMG-Py')))
from rmgpy.molecule import Molecule
import rmgpy.kinetics
from rmgpy.data.rmg import RMGDatabase
from rmgpy.data.kinetics.library import KineticsLibrary

First, read in the chemkin file to the Cantera ck2cti parser.

model_name = 'butanol'
model_path = 'butanol-sarathy2012'

get_species_dict = KineticsLibrary().getSpecies
species_dict = get_species_dict(os.path.join(model_path, 'RMG-Py-kinetics-library', 'dictionary.txt'))
species_dict

{'ac3h5ooh': Species(label="ac3h5ooh", molecule=[Molecule(SMILES="C=CCOO")]),
 'ar': Species(label="ar", molecule=[Molecule(SMILES="[Ar]")]),
 'c': Species(label="c", molecule=[Molecule(SMILES="[C]")]),
 'c2h': Species(label="c2h", molecule=[Molecule(SMILES="[C]#C")]),
 'c2h2': Species(label="c2h2", molecule=[Molecule(SMILES="C#C")]),
 'c2h2oh': Species(label="c2h2oh", molecule=[Molecule(SMILES="[CH]=CO")]),
 'c2h3': Species(label="c2h3", molecule=[Molecule(SMILES="[CH]=C")]),
 'c2h3cho': Species(label="c2h3cho", molecule=[Molecule(SMILES="C=CC=O")]),
 'c2h3choch2': Species(label="c2h3choch2", molecule=[Molecule(SMILES="[CH2]C=CO[CH2]"), Molecule(SMILES="[CH2]O[CH]C=C")]),
 'c2h3co': Species(label="c2h3co", molecule=[Molecule(SMILES="C=C[C]=O"), Molecule(SMILES="[CH2]C=C=O")]),
 'c2h3coch3': Species(label="c2h3coch3", molecule=[Molecule(SMILES="C=CC(C)=O")]),
 'c2h3o1-2': Species(label="c2h3o1-2", molecule=[Molecule(SMILES="[CH]1CO1")]),
 'c2h3oh': Species(label="c2h3oh", molecule=[Molecule(SMILES="C=CO")]),
 'c2h3ooh': Species(label="c2h3ooh", molecule=[Molecule(SMILES="C=COO")]),
 'c2h4': Species(label="c2h4", molecule=[Molecule(SMILES="C=C")]),
 'c2h4o1-2': Species(label="c2h4o1-2", molecule=[Molecule(SMILES="C1CO1")]),
 'c2h4o2h': Species(label="c2h4o2h", molecule=[Molecule(SMILES="[CH2]COO")]),
 'c2h5': Species(label="c2h5", molecule=[Molecule(SMILES="C[CH2]")]),
 'c2h5chco': Species(label="c2h5chco", molecule=[Molecule(SMILES="CCC=C=O")]),
 'c2h5cho': Species(label="c2h5cho", molecule=[Molecule(SMILES="CCC=O")]),
 'c2h5co': Species(label="c2h5co", molecule=[Molecule(SMILES="CC[C]=O")]),
 'c2h5coch2': Species(label="c2h5coch2", molecule=[Molecule(SMILES="[CH2]C(=O)CC"), Molecule(SMILES="C=C([O])CC")]),
 'c2h5coch3': Species(label="c2h5coch3", molecule=[Molecule(SMILES="CCC(C)=O")]),
 'c2h5o': Species(label="c2h5o", molecule=[Molecule(SMILES="CC[O]")]),
 'c2h5o2': Species(label="c2h5o2", molecule=[Molecule(SMILES="CCO[O]")]),
 'c2h5o2h': Species(label="c2h5o2h", molecule=[Molecule(SMILES="CCOO")]),
 'c2h5oh': Species(label="c2h5oh", molecule=[Molecule(SMILES="CCO")]),
 'c2h6': Species(label="c2h6", molecule=[Molecule(SMILES="CC")]),
 'c3h3': Species(label="c3h3", molecule=[Molecule(SMILES="C#C[CH2]"), Molecule(SMILES="[CH]=C=C")]),
 'c3h4-a': Species(label="c3h4-a", molecule=[Molecule(SMILES="C=C=C")]),
 'c3h4-p': Species(label="c3h4-p", molecule=[Molecule(SMILES="C#CC")]),
 'c3h5-a': Species(label="c3h5-a", molecule=[Molecule(SMILES="[CH2]C=C"), Molecule(SMILES="[CH2]C=C")]),
 'c3h5-s': Species(label="c3h5-s", molecule=[Molecule(SMILES="[CH]=CC")]),
 'c3h5-t': Species(label="c3h5-t", molecule=[Molecule(SMILES="C=[C]C")]),
 'c3h51-2,3ooh': Species(label="c3h51-2,3ooh", molecule=[Molecule(SMILES="[CH2]C(COO)OO")]),
 'c3h52-1,3ooh': Species(label="c3h52-1,3ooh", molecule=[Molecule(SMILES="OOC[CH]COO")]),
 'c3h5o': Species(label="c3h5o", molecule=[Molecule(SMILES="C=CC[O]")]),
 'c3h5oh': Species(label="c3h5oh", molecule=[Molecule(SMILES="C=CCO")]),
 'c3h6': Species(label="c3h6", molecule=[Molecule(SMILES="C=CC")]),
 'c3h6cho-1': Species(label="c3h6cho-1", molecule=[Molecule(SMILES="[CH2]CCC=O")]),
 'c3h6cho-2': Species(label="c3h6cho-2", molecule=[Molecule(SMILES="C[CH]CC=O")]),
 'c3h6cho-3': Species(label="c3h6cho-3", molecule=[Molecule(SMILES="CC[CH]C=O"), Molecule(SMILES="CCC=C[O]")]),
 'c3h6o1-2': Species(label="c3h6o1-2", molecule=[Molecule(SMILES="CC1CO1")]),
 'c3h6o1-3': Species(label="c3h6o1-3", molecule=[Molecule(SMILES="C1COC1")]),
 'c3h6oh': Species(label="c3h6oh", molecule=[Molecule(SMILES="[CH2]CCO")]),
 'c3h6oh-1': Species(label="c3h6oh-1", molecule=[Molecule(SMILES="CC[CH]O")]),
 'c3h6oh-2': Species(label="c3h6oh-2", molecule=[Molecule(SMILES="C[CH]CO")]),
 'c3h6ooh1-2': Species(label="c3h6ooh1-2", molecule=[Molecule(SMILES="C[CH]COO")]),
 'c3h6ooh1-2o2': Species(label="c3h6ooh1-2o2", molecule=[Molecule(SMILES="CC(COO)O[O]")]),
 'c3h6ooh1-3': Species(label="c3h6ooh1-3", molecule=[Molecule(SMILES="[CH2]CCOO")]),
 'c3h6ooh1-3o2': Species(label="c3h6ooh1-3o2", molecule=[Molecule(SMILES="[O]OCCCOO")]),
 'c3h6ooh2-1': Species(label="c3h6ooh2-1", molecule=[Molecule(SMILES="[CH2]C(C)OO")]),
 'c3h6ooh2-1o2': Species(label="c3h6ooh2-1o2", molecule=[Molecule(SMILES="CC(CO[O])OO")]),
 'c3h6ooh2-2': Species(label="c3h6ooh2-2", molecule=[Molecule(SMILES="C[C](C)OO")]),
 'c3h8': Species(label="c3h8", molecule=[Molecule(SMILES="CCC")]),
 'c3ket12': Species(label="c3ket12", molecule=[Molecule(SMILES="CC(C=O)OO")]),
 'c3ket13': Species(label="c3ket13", molecule=[Molecule(SMILES="O=CCCOO")]),
 'c3ket21': Species(label="c3ket21", molecule=[Molecule(SMILES="CC(=O)COO")]),
 'c4h10': Species(label="c4h10", molecule=[Molecule(SMILES="CCCC")]),
 'c4h2': Species(label="c4h2", molecule=[Molecule(SMILES="C#CC#C")]),
 'c4h3-i': Species(label="c4h3-i", molecule=[Molecule(SMILES="C#C[C]=C"), Molecule(SMILES="[CH]=C=C=C")]),
 'c4h3-n': Species(label="c4h3-n", molecule=[Molecule(SMILES="[CH]=CC#C")]),
 'c4h4': Species(label="c4h4", molecule=[Molecule(SMILES="C#CC=C")]),
 'c4h4o': Species(label="c4h4o", molecule=[Molecule(SMILES="C1C=COC=1")]),
 'c4h5-2': Species(label="c4h5-2", molecule=[Molecule(SMILES="C=C=[C]C"), Molecule(SMILES="[CH2]C#CC")]),
 'c4h5-i': Species(label="c4h5-i", molecule=[Molecule(SMILES="C=[C]C=C"), Molecule(SMILES="[CH2]C=C=C")]),
 'c4h5-n': Species(label="c4h5-n", molecule=[Molecule(SMILES="[CH]=CC=C")]),
 'c4h5oh-13': Species(label="c4h5oh-13", molecule=[Molecule(SMILES="C=CC=CO")]),
 'c4h6': Species(label="c4h6", molecule=[Molecule(SMILES="C=CC=C")]),
 'c4h6-2': Species(label="c4h6-2", molecule=[Molecule(SMILES="CC#CC")]),
 'c4h612': Species(label="c4h612", molecule=[Molecule(SMILES="C=C=CC")]),
 'c4h6o23': Species(label="c4h6o23", molecule=[Molecule(SMILES="C1=COCC1")]),
 'c4h6o25': Species(label="c4h6o25", molecule=[Molecule(SMILES="C1=CCOC1")]),
 'c4h6oh1-13': Species(label="c4h6oh1-13", molecule=[Molecule(SMILES="CC=C[CH]O"), Molecule(SMILES="C[CH]C=CO")]),
 'c4h6oh1-32': Species(label="c4h6oh1-32", molecule=[Molecule(SMILES="C=C(O)[CH]C"), Molecule(SMILES="[CH2]C(O)=CC")]),
 'c4h71-1': Species(label="c4h71-1", molecule=[Molecule(SMILES="[CH]=CCC")]),
 'c4h71-2': Species(label="c4h71-2", molecule=[Molecule(SMILES="C=[C]CC")]),
 'c4h71-3': Species(label="c4h71-3", molecule=[Molecule(SMILES="C=C[CH]C"), Molecule(SMILES="[CH2]C=CC")]),
 'c4h71-4': Species(label="c4h71-4", molecule=[Molecule(SMILES="[CH2]CC=C")]),
 'c4h72-2': Species(label="c4h72-2", molecule=[Molecule(SMILES="C[C]=CC")]),
 'c4h7o': Species(label="c4h7o", molecule=[Molecule(SMILES="C=CC(C)[O]")]),
 'c4h7oh-1ooh-2': Species(label="c4h7oh-1ooh-2", molecule=[Molecule(SMILES="CC[CH]C(O)OO")]),
 'c4h7oh-1ooh-2o2': Species(label="c4h7oh-1ooh-2o2", molecule=[Molecule(SMILES="CCC(O[O])C(O)OO")]),
 'c4h7oh-1ooh-3': Species(label="c4h7oh-1ooh-3", molecule=[Molecule(SMILES="C[CH]CC(O)OO")]),
 'c4h7oh-1ooh-3o2': Species(label="c4h7oh-1ooh-3o2", molecule=[Molecule(SMILES="CC(CC(O)OO)O[O]")]),
 'c4h7oh-1ooh-4': Species(label="c4h7oh-1ooh-4", molecule=[Molecule(SMILES="[CH2]CCC(O)OO")]),
 'c4h7oh-1ooh-4o2': Species(label="c4h7oh-1ooh-4o2", molecule=[Molecule(SMILES="[O]OCCCC(O)OO")]),
 'c4h7oh-2ooh-1': Species(label="c4h7oh-2ooh-1", molecule=[Molecule(SMILES="CCC([CH]O)OO")]),
 'c4h7oh-2ooh-1o2': Species(label="c4h7oh-2ooh-1o2", molecule=[Molecule(SMILES="CCC(OO)C(O)O[O]")]),
 'c4h7oh-2ooh-3': Species(label="c4h7oh-2ooh-3", molecule=[Molecule(SMILES="C[CH]C(CO)OO")]),
 'c4h7oh-2ooh-3o2': Species(label="c4h7oh-2ooh-3o2", molecule=[Molecule(SMILES="CC(O[O])C(CO)OO")]),
 'c4h7oh-2ooh-4': Species(label="c4h7oh-2ooh-4", molecule=[Molecule(SMILES="[CH2]CC(CO)OO")]),
 'c4h7oh-2ooh-4o2': Species(label="c4h7oh-2ooh-4o2", molecule=[Molecule(SMILES="[O]OCCC(CO)OO")]),
 'c4h7oh-3ooh-1': Species(label="c4h7oh-3ooh-1", molecule=[Molecule(SMILES="CC(C[CH]O)OO")]),
 'c4h7oh-3ooh-1o2': Species(label="c4h7oh-3ooh-1o2", molecule=[Molecule(SMILES="CC(CC(O)O[O])OO")]),
 'c4h7oh-3ooh-2': Species(label="c4h7oh-3ooh-2", molecule=[Molecule(SMILES="CC([CH]CO)OO")]),
 'c4h7oh-3ooh-2o2': Species(label="c4h7oh-3ooh-2o2", molecule=[Molecule(SMILES="CC(OO)C(CO)O[O]")]),
 'c4h7oh-3ooh-4': Species(label="c4h7oh-3ooh-4", molecule=[Molecule(SMILES="[CH2]C(CCO)OO")]),
 'c4h7oh-3ooh-4o2': Species(label="c4h7oh-3ooh-4o2", molecule=[Molecule(SMILES="[O]OCC(CCO)OO")]),
 'c4h7oh-4ooh-1': Species(label="c4h7oh-4ooh-1", molecule=[Molecule(SMILES="O[CH]CCCOO")]),
 'c4h7oh-4ooh-1o2': Species(label="c4h7oh-4ooh-1o2", molecule=[Molecule(SMILES="[O]OC(O)CCCOO")]),
 'c4h7oh-4ooh-2': Species(label="c4h7oh-4ooh-2", molecule=[Molecule(SMILES="OC[CH]CCOO")]),
 'c4h7oh-4ooh-2o2': Species(label="c4h7oh-4ooh-2o2", molecule=[Molecule(SMILES="[O]OC(CO)CCOO")]),
 'c4h7oh-4ooh-3': Species(label="c4h7oh-4ooh-3", molecule=[Molecule(SMILES="OCC[CH]COO")]),
 'c4h7oh-4ooh-3o2': Species(label="c4h7oh-4ooh-3o2", molecule=[Molecule(SMILES="[O]OC(CCO)COO")]),
 'c4h7oh1-1': Species(label="c4h7oh1-1", molecule=[Molecule(SMILES="CCC=CO")]),
 'c4h7oh1-2': Species(label="c4h7oh1-2", molecule=[Molecule(SMILES="C=C(O)CC")]),
 'c4h7oh1-3': Species(label="c4h7oh1-3", molecule=[Molecule(SMILES="C=CC(C)O")]),
 'c4h7oh1-4': Species(label="c4h7oh1-4", molecule=[Molecule(SMILES="C=CCCO")]),
 'c4h7oh2-1': Species(label="c4h7oh2-1", molecule=[Molecule(SMILES="CC=CCO")]),
 'c4h7oh2-2': Species(label="c4h7oh2-2", molecule=[Molecule(SMILES="CC=C(C)O")]),
 'c4h7oho1-2': Species(label="c4h7oho1-2", molecule=[Molecule(SMILES="CC1CC(O)O1")]),
 'c4h7oho1-3': Species(label="c4h7oho1-3", molecule=[Molecule(SMILES="CC1CC(O)O1")]),
 'c4h7oho1-4': Species(label="c4h7oho1-4", molecule=[Molecule(SMILES="OC1CCCO1")]),
 'c4h7oho2-3': Species(label="c4h7oho2-3", molecule=[Molecule(SMILES="CC1OC1CO")]),
 'c4h7oho2-4': Species(label="c4h7oho2-4", molecule=[Molecule(SMILES="OCC1CCO1")]),
 'c4h7oho3-4': Species(label="c4h7oho3-4", molecule=[Molecule(SMILES="OCCC1CO1")]),
 'c4h8-1': Species(label="c4h8-1", molecule=[Molecule(SMILES="C=CCC")]),
 'c4h8-2': Species(label="c4h8-2", molecule=[Molecule(SMILES="CC=CC")]),
 'c4h8o1-2': Species(label="c4h8o1-2", molecule=[Molecule(SMILES="CCC1CO1")]),
 'c4h8o1-3': Species(label="c4h8o1-3", molecule=[Molecule(SMILES="CC1CCO1")]),
 'c4h8o1-4': Species(label="c4h8o1-4", molecule=[Molecule(SMILES="C1CCOC1")]),
 'c4h8o2-3': Species(label="c4h8o2-3", molecule=[Molecule(SMILES="CC1OC1C")]),
 'c4h8oh-1': Species(label="c4h8oh-1", molecule=[Molecule(SMILES="CCC[CH]O")]),
 'c4h8oh-1o': Species(label="c4h8oh-1o", molecule=[Molecule(SMILES="CCCC([O])O")]),
 'c4h8oh-1o2': Species(label="c4h8oh-1o2", molecule=[Molecule(SMILES="CCCC(O)O[O]")]),
 'c4h8oh-1o2h': Species(label="c4h8oh-1o2h", molecule=[Molecule(SMILES="CCCC(O)OO")]),
 'c4h8oh-2': Species(label="c4h8oh-2", molecule=[Molecule(SMILES="CC[CH]CO")]),
 'c4h8oh-2o': Species(label="c4h8oh-2o", molecule=[Molecule(SMILES="CCC([O])CO")]),
 'c4h8oh-2o2': Species(label="c4h8oh-2o2", molecule=[Molecule(SMILES="CCC(CO)O[O]")]),
 'c4h8oh-2o2h': Species(label="c4h8oh-2o2h", molecule=[Molecule(SMILES="CCC(CO)OO")]),
 'c4h8oh-3': Species(label="c4h8oh-3", molecule=[Molecule(SMILES="C[CH]CCO")]),
 'c4h8oh-3o': Species(label="c4h8oh-3o", molecule=[Molecule(SMILES="CC([O])CCO")]),
 'c4h8oh-3o2': Species(label="c4h8oh-3o2", molecule=[Molecule(SMILES="CC(CCO)O[O]")]),
 'c4h8oh-3o2h': Species(label="c4h8oh-3o2h", molecule=[Molecule(SMILES="CC(CCO)OO")]),
 'c4h8oh-4': Species(label="c4h8oh-4", molecule=[Molecule(SMILES="[CH2]CCCO")]),
 'c4h8oh-4o': Species(label="c4h8oh-4o", molecule=[Molecule(SMILES="[O]CCCCO")]),
 'c4h8oh-4o2': Species(label="c4h8oh-4o2", molecule=[Molecule(SMILES="[O]OCCCCO")]),
 'c4h8oh-4o2h': Species(label="c4h8oh-4o2h", molecule=[Molecule(SMILES="OCCCCOO")]),
 'c4h8ooh1-1': Species(label="c4h8ooh1-1", molecule=[Molecule(SMILES="CCC[CH]OO")]),
 'c4h8ooh1-2': Species(label="c4h8ooh1-2", molecule=[Molecule(SMILES="CC[CH]COO")]),
 'c4h8ooh1-2o2': Species(label="c4h8ooh1-2o2", molecule=[Molecule(SMILES="CCC(COO)O[O]")]),
 'c4h8ooh1-3': Species(label="c4h8ooh1-3", molecule=[Molecule(SMILES="C[CH]CCOO")]),
 'c4h8ooh1-3o2': Species(label="c4h8ooh1-3o2", molecule=[Molecule(SMILES="CC(CCOO)O[O]")]),
 'c4h8ooh1-4': Species(label="c4h8ooh1-4", molecule=[Molecule(SMILES="[CH2]CCCOO")]),
 'c4h8ooh1-4o2': Species(label="c4h8ooh1-4o2", molecule=[Molecule(SMILES="[O]OCCCCOO")]),
 'c4h8ooh2-1': Species(label="c4h8ooh2-1", molecule=[Molecule(SMILES="[CH2]C(CC)OO")]),
 'c4h8ooh2-1o2': Species(label="c4h8ooh2-1o2", molecule=[Molecule(SMILES="CCC(CO[O])OO")]),
 'c4h8ooh2-2': Species(label="c4h8ooh2-2", molecule=[Molecule(SMILES="CC[C](C)OO")]),
 'c4h8ooh2-3': Species(label="c4h8ooh2-3", molecule=[Molecule(SMILES="C[CH]C(C)OO")]),
 'c4h8ooh2-3o2': Species(label="c4h8ooh2-3o2", molecule=[Molecule(SMILES="CC(O[O])C(C)OO")]),
 'c4h8ooh2-4': Species(label="c4h8ooh2-4", molecule=[Molecule(SMILES="[CH2]CC(C)OO")]),
 'c4h8ooh2-4o2': Species(label="c4h8ooh2-4o2", molecule=[Molecule(SMILES="CC(CCO[O])OO")]),
 'c4ohket1-2': Species(label="c4ohket1-2", molecule=[Molecule(SMILES="CCC(OO)C(=O)O")]),
 'c4ohket1-3': Species(label="c4ohket1-3", molecule=[Molecule(SMILES="CC(CC(=O)O)OO")]),
 'c4ohket1-4': Species(label="c4ohket1-4", molecule=[Molecule(SMILES="O=C(O)CCCOO")]),
 'c4ohket2-1': Species(label="c4ohket2-1", molecule=[Molecule(SMILES="CCC(=O)C(O)OO")]),
 'c4ohket2-3': Species(label="c4ohket2-3", molecule=[Molecule(SMILES="CC(OO)C(=O)CO")]),
 'c4ohket2-4': Species(label="c4ohket2-4", molecule=[Molecule(SMILES="O=C(CO)CCOO")]),
 'c4ohket3-1': Species(label="c4ohket3-1", molecule=[Molecule(SMILES="CC(=O)CC(O)OO")]),
 'c4ohket3-2': Species(label="c4ohket3-2", molecule=[Molecule(SMILES="CC(=O)C(CO)OO")]),
 'c4ohket3-4': Species(label="c4ohket3-4", molecule=[Molecule(SMILES="O=C(CCO)COO")]),
 'c4ohket4-1': Species(label="c4ohket4-1", molecule=[Molecule(SMILES="O=CCCC(O)OO")]),
 'c4ohket4-2': Species(label="c4ohket4-2", molecule=[Molecule(SMILES="O=CCC(CO)OO")]),
 'c4ohket4-3': Species(label="c4ohket4-3", molecule=[Molecule(SMILES="O=CC(CCO)OO")]),
 'cc3h4': Species(label="cc3h4", molecule=[Molecule(SMILES="C1=CC1")]),
 'cc4h8o': Species(label="cc4h8o", molecule=[Molecule(SMILES="CC1COC1")]),
 'ch': Species(label="ch", molecule=[Molecule(SMILES="[CH]")]),
 'ch*': Species(label="ch*", molecule=[Molecule(SMILES="[CH]")]),
 'ch2': Species(label="ch2", molecule=[Molecule(SMILES="[CH2]")]),
 'ch2(s)': Species(label="ch2(s)", molecule=[Molecule(SMILES="[CH2]")]),
 'ch2cch2oh': Species(label="ch2cch2oh", molecule=[Molecule(SMILES="C=[C]CO")]),
 'ch2ch2cho': Species(label="ch2ch2cho", molecule=[Molecule(SMILES="[CH2]CC=O")]),
 'ch2ch2coch3': Species(label="ch2ch2coch3", molecule=[Molecule(SMILES="[CH2]CC(C)=O")]),
 'ch2chchcho': Species(label="ch2chchcho", molecule=[Molecule(SMILES="[CH2]C=CC=O"), Molecule(SMILES="C=C[CH]C=O"), Molecule(SMILES="C=CC=C[O]")]),
 'ch2cho': Species(label="ch2cho", molecule=[Molecule(SMILES="C=C[O]"), Molecule(SMILES="[CH2]C=O")]),
 'ch2choohcoch3': Species(label="ch2choohcoch3", molecule=[Molecule(SMILES="[CH2]C(OO)C(C)=O")]),
 'ch2co': Species(label="ch2co", molecule=[Molecule(SMILES="C=C=O")]),
 'ch2o': Species(label="ch2o", molecule=[Molecule(SMILES="C=O")]),
 'ch2o2h': Species(label="ch2o2h", molecule=[Molecule(SMILES="[CH2]OO")]),
 'ch2och2o2h': Species(label="ch2och2o2h", molecule=[Molecule(SMILES="[CH2]OCOO")]),
 'ch2ocho': Species(label="ch2ocho", molecule=[Molecule(SMILES="[CH2]OC=O")]),
 'ch2oh': Species(label="ch2oh", molecule=[Molecule(SMILES="[CH2]O")]),
 'ch3': Species(label="ch3", molecule=[Molecule(SMILES="[CH3]")]),
 'ch3chchcho': Species(label="ch3chchcho", molecule=[Molecule(SMILES="CC=CC=O")]),
 'ch3chchco': Species(label="ch3chchco", molecule=[Molecule(SMILES="CC=C[C]=O"), Molecule(SMILES="C[CH]C=C=O")]),
 'ch3chchoh': Species(label="ch3chchoh", molecule=[Molecule(SMILES="CC=CO")]),
 'ch3chco': Species(label="ch3chco", molecule=[Molecule(SMILES="CC=C=O")]),
 'ch3chcoch3': Species(label="ch3chcoch3", molecule=[Molecule(SMILES="CC=C(C)[O]"), Molecule(SMILES="C[CH]C(C)=O")]),
 'ch3cho': Species(label="ch3cho", molecule=[Molecule(SMILES="CC=O")]),
 'ch3choococh3': Species(label="ch3choococh3", molecule=[Molecule(SMILES="CC(=O)C(C)O[O]")]),
 'ch3co': Species(label="ch3co", molecule=[Molecule(SMILES="C[C]=O")]),
 'ch3co2': Species(label="ch3co2", molecule=[Molecule(SMILES="CC([O])=O"), Molecule(SMILES="CC([O])=O")]),
 'ch3co3': Species(label="ch3co3", molecule=[Molecule(SMILES="CC(=O)O[O]")]),
 'ch3co3h': Species(label="ch3co3h", molecule=[Molecule(SMILES="CC(=O)OO")]),
 'ch3coch2': Species(label="ch3coch2", molecule=[Molecule(SMILES="[CH2]C(C)=O"), Molecule(SMILES="C=C(C)[O]")]),
 'ch3coch2o2': Species(label="ch3coch2o2", molecule=[Molecule(SMILES="CC(=O)CO[O]")]),
 'ch3coch3': Species(label="ch3coch3", molecule=[Molecule(SMILES="CC(C)=O")]),
 'ch3o': Species(label="ch3o", molecule=[Molecule(SMILES="C[O]")]),
 'ch3o2': Species(label="ch3o2", molecule=[Molecule(SMILES="CO[O]")]),
 'ch3o2h': Species(label="ch3o2h", molecule=[Molecule(SMILES="COO")]),
 'ch3och2': Species(label="ch3och2", molecule=[Molecule(SMILES="[CH2]OC")]),
 'ch3och2o': Species(label="ch3och2o", molecule=[Molecule(SMILES="COC[O]")]),
 'ch3och2o2': Species(label="ch3och2o2", molecule=[Molecule(SMILES="COCO[O]")]),
 'ch3och2o2h': Species(label="ch3och2o2h", molecule=[Molecule(SMILES="COCOO")]),
 'ch3och3': Species(label="ch3och3", molecule=[Molecule(SMILES="COC")]),
 'ch3ocho': Species(label="ch3ocho", molecule=[Molecule(SMILES="COC=O")]),
 'ch3oco': Species(label="ch3oco", molecule=[Molecule(SMILES="CO[C]=O")]),
 'ch3oh': Species(label="ch3oh", molecule=[Molecule(SMILES="CO")]),
 'ch4': Species(label="ch4", molecule=[Molecule(SMILES="C")]),
 'co': Species(label="co", molecule=[Molecule(SMILES="[C-]#[O+]")]),
 'co2': Species(label="co2", molecule=[Molecule(SMILES="O=C=O")]),
 'h': Species(label="h", molecule=[Molecule(SMILES="[H]")]),
 'h2': Species(label="h2", molecule=[Molecule(SMILES="[H][H]")]),
 'h2c4o': Species(label="h2c4o", molecule=[Molecule(SMILES="C=C=C=C=O")]),
 'h2cc': Species(label="h2cc", molecule=[Molecule(SMILES="[C]=C")]),
 'h2o': Species(label="h2o", molecule=[Molecule(SMILES="O")]),
 'h2o2': Species(label="h2o2", molecule=[Molecule(SMILES="OO")]),
 'hcco': Species(label="hcco", molecule=[Molecule(SMILES="C#C[O]"), Molecule(SMILES="[CH]=C=O")]),
 'hccoh': Species(label="hccoh", molecule=[Molecule(SMILES="C#CO")]),
 'hco': Species(label="hco", molecule=[Molecule(SMILES="[CH]=O")]),
 'hcoh': Species(label="hcoh", molecule=[Molecule(SMILES="[CH]O")]),
 'ho2': Species(label="ho2", molecule=[Molecule(SMILES="[O]O")]),
 'ho2ch2co': Species(label="ho2ch2co", molecule=[Molecule(SMILES="O=[C]COO")]),
 'ho2ch2ocho': Species(label="ho2ch2ocho", molecule=[Molecule(SMILES="O=COCOO")]),
 'ho2cho': Species(label="ho2cho", molecule=[Molecule(SMILES="O=COO")]),
 'hoc2h4cho': Species(label="hoc2h4cho", molecule=[Molecule(SMILES="O=CCCO")]),
 'hoc2h4co': Species(label="hoc2h4co", molecule=[Molecule(SMILES="O=[C]CCO")]),
 'hoc3h6o2': Species(label="hoc3h6o2", molecule=[Molecule(SMILES="[O]OCCCO")]),
 'hoch2cho': Species(label="hoch2cho", molecule=[Molecule(SMILES="O=CCO")]),
 'hoch2co': Species(label="hoch2co", molecule=[Molecule(SMILES="O=[C]CO")]),
 'hoch2o': Species(label="hoch2o", molecule=[Molecule(SMILES="[O]CO")]),
 'hoch2o2': Species(label="hoch2o2", molecule=[Molecule(SMILES="[O]OCO")]),
 'hoch2o2h': Species(label="hoch2o2h", molecule=[Molecule(SMILES="OCOO")]),
 'hoch2oco': Species(label="hoch2oco", molecule=[Molecule(SMILES="O=[C]OCO")]),
 'hocho': Species(label="hocho", molecule=[Molecule(SMILES="O=CO")]),
 'ic3h5ch2oh': Species(label="ic3h5ch2oh", molecule=[Molecule(SMILES="C=C(C)CO")]),
 'ic3h5cho': Species(label="ic3h5cho", molecule=[Molecule(SMILES="C=C(C)C=O")]),
 'ic3h5co': Species(label="ic3h5co", molecule=[Molecule(SMILES="C=C(C)[C]=O"), Molecule(SMILES="[CH2]C(C)=C=O")]),
 'ic3h5o2hcho': Species(label="ic3h5o2hcho", molecule=[Molecule(SMILES="[CH2]C(C)(C=O)OO")]),
 'ic3h5oh': Species(label="ic3h5oh", molecule=[Molecule(SMILES="C=C(C)O")]),
 'ic3h6cho': Species(label="ic3h6cho", molecule=[Molecule(SMILES="[CH2]C(C)C=O")]),
 'ic3h6choh': Species(label="ic3h6choh", molecule=[Molecule(SMILES="CC(C)=CO")]),
 'ic3h6co': Species(label="ic3h6co", molecule=[Molecule(SMILES="CC(C)=C=O")]),
 'ic3h6oh': Species(label="ic3h6oh", molecule=[Molecule(SMILES="[CH2]C(C)O")]),
 'ic3h7': Species(label="ic3h7", molecule=[Molecule(SMILES="C[CH]C")]),
 'ic3h7cho': Species(label="ic3h7cho", molecule=[Molecule(SMILES="CC(C)C=O")]),
 'ic3h7co': Species(label="ic3h7co", molecule=[Molecule(SMILES="CC(C)[C]=O")]),
 'ic3h7o': Species(label="ic3h7o", molecule=[Molecule(SMILES="CC(C)[O]")]),
 'ic3h7o2': Species(label="ic3h7o2", molecule=[Molecule(SMILES="CC(C)O[O]")]),
 'ic3h7o2h': Species(label="ic3h7o2h", molecule=[Molecule(SMILES="CC(C)OO")]),
 'ic4h10': Species(label="ic4h10", molecule=[Molecule(SMILES="CC(C)C")]),
 'ic4h6oh': Species(label="ic4h6oh", molecule=[Molecule(SMILES="[CH2]C(=C)CO"), Molecule(SMILES="[CH2]C(=C)CO")]),
 'ic4h7': Species(label="ic4h7", molecule=[Molecule(SMILES="[CH2]C(=C)C"), Molecule(SMILES="[CH2]C(=C)C")]),
 'ic4h7o': Species(label="ic4h7o", molecule=[Molecule(SMILES="C=C(C)C[O]")]),
 'ic4h7oh': Species(label="ic4h7oh", molecule=[Molecule(SMILES="C=C(C)CO")]),
 'ic4h7oh-1ooh-2': Species(label="ic4h7oh-1ooh-2", molecule=[Molecule(SMILES="C[C](C)C(O)OO")]),
 'ic4h7oh-1ooh-2o2': Species(label="ic4h7oh-1ooh-2o2", molecule=[Molecule(SMILES="CC(C)(O[O])C(O)OO")]),
 'ic4h7oh-1ooh-3': Species(label="ic4h7oh-1ooh-3", molecule=[Molecule(SMILES="[CH2]C(C)C(O)OO")]),
 'ic4h7oh-1ooh-3o2': Species(label="ic4h7oh-1ooh-3o2", molecule=[Molecule(SMILES="CC(CO[O])C(O)OO")]),
 'ic4h7oh-2ooh-1': Species(label="ic4h7oh-2ooh-1", molecule=[Molecule(SMILES="CC(C)([CH]O)OO")]),
 'ic4h7oh-2ooh-1o2': Species(label="ic4h7oh-2ooh-1o2", molecule=[Molecule(SMILES="CC(C)(OO)C(O)O[O]")]),
 'ic4h7oh-2ooh-3': Species(label="ic4h7oh-2ooh-3", molecule=[Molecule(SMILES="[CH2]C(C)(CO)OO")]),
 'ic4h7oh-2ooh-3o2': Species(label="ic4h7oh-2ooh-3o2", molecule=[Molecule(SMILES="CC(CO)(CO[O])OO")]),
 'ic4h7oh-3ooh-1': Species(label="ic4h7oh-3ooh-1", molecule=[Molecule(SMILES="CC([CH]O)COO")]),
 'ic4h7oh-3ooh-1o2': Species(label="ic4h7oh-3ooh-1o2", molecule=[Molecule(SMILES="CC(COO)C(O)O[O]")]),
 'ic4h7oh-3ooh-2': Species(label="ic4h7oh-3ooh-2", molecule=[Molecule(SMILES="C[C](CO)COO")]),
 'ic4h7oh-3ooh-2o2': Species(label="ic4h7oh-3ooh-2o2", molecule=[Molecule(SMILES="CC(CO)(COO)O[O]")]),
 'ic4h7oh-3ooh-3': Species(label="ic4h7oh-3ooh-3", molecule=[Molecule(SMILES="[CH2]C(CO)COO")]),
 'ic4h7oh-3ooh-3o2': Species(label="ic4h7oh-3ooh-3o2", molecule=[Molecule(SMILES="[O]OCC(CO)COO")]),
 'ic4h7oho1-2': Species(label="ic4h7oho1-2", molecule=[Molecule(SMILES="CC1(C)OC1O")]),
 'ic4h7oho1-3': Species(label="ic4h7oho1-3", molecule=[Molecule(SMILES="CC1COC1O")]),
 'ic4h7oho2-3': Species(label="ic4h7oho2-3", molecule=[Molecule(SMILES="CC1(CO)CO1")]),
 'ic4h7oho3-3': Species(label="ic4h7oho3-3", molecule=[Molecule(SMILES="OCC1COC1")]),
 'ic4h7ooh': Species(label="ic4h7ooh", molecule=[Molecule(SMILES="C=C(C)COO")]),
 'ic4h8': Species(label="ic4h8", molecule=[Molecule(SMILES="C=C(C)C")]),
 'ic4h8o': Species(label="ic4h8o", molecule=[Molecule(SMILES="[CH2]C(C)C[O]")]),
 'ic4h8o2h-i': Species(label="ic4h8o2h-i", molecule=[Molecule(SMILES="[CH2]C(C)COO")]),
 'ic4h8o2h-t': Species(label="ic4h8o2h-t", molecule=[Molecule(SMILES="C[C](C)COO")]),
 'ic4h8oh': Species(label="ic4h8oh", molecule=[Molecule(SMILES="C[C](C)CO")]),
 'ic4h8oh-1': Species(label="ic4h8oh-1", molecule=[Molecule(SMILES="CC(C)[CH]O")]),
 'ic4h8oh-1o': Species(label="ic4h8oh-1o", molecule=[Molecule(SMILES="CC(C)C([O])O")]),
 'ic4h8oh-1o2': Species(label="ic4h8oh-1o2", molecule=[Molecule(SMILES="CC(C)C(O)O[O]")]),
 'ic4h8oh-1o2h': Species(label="ic4h8oh-1o2h", molecule=[Molecule(SMILES="CC(C)C(O)OO")]),
 'ic4h8oh-2': Species(label="ic4h8oh-2", molecule=[Molecule(SMILES="C[C](C)CO")]),
 'ic4h8oh-2o': Species(label="ic4h8oh-2o", molecule=[Molecule(SMILES="CC(C)([O])CO")]),
 'ic4h8oh-2o2': Species(label="ic4h8oh-2o2", molecule=[Molecule(SMILES="CC(C)(CO)O[O]")]),
 'ic4h8oh-2o2h': Species(label="ic4h8oh-2o2h", molecule=[Molecule(SMILES="CC(C)(CO)OO")]),
 'ic4h8oh-3': Species(label="ic4h8oh-3", molecule=[Molecule(SMILES="[CH2]C(C)CO")]),
 'ic4h8oh-3o': Species(label="ic4h8oh-3o", molecule=[Molecule(SMILES="CC(C[O])CO")]),
 'ic4h8oh-3o2': Species(label="ic4h8oh-3o2", molecule=[Molecule(SMILES="CC(CO)CO[O]")]),
 'ic4h8oh-3o2h': Species(label="ic4h8oh-3o2h", molecule=[Molecule(SMILES="CC(CO)COO")]),
 'ic4h8ooh-io2': Species(label="ic4h8ooh-io2", molecule=[Molecule(SMILES="CC(CO[O])COO")]),
 'ic4h8ooh-to2': Species(label="ic4h8ooh-to2", molecule=[Molecule(SMILES="CC(C)(COO)O[O]")]),
 'ic4h9': Species(label="ic4h9", molecule=[Molecule(SMILES="[CH2]C(C)C")]),
 'ic4h9o': Species(label="ic4h9o", molecule=[Molecule(SMILES="CC(C)C[O]")]),
 'ic4h9o2': Species(label="ic4h9o2", molecule=[Molecule(SMILES="CC(C)CO[O]")]),
 'ic4h9o2h': Species(label="ic4h9o2h", molecule=[Molecule(SMILES="CC(C)COO")]),
 'ic4h9oh': Species(label="ic4h9oh", molecule=[Molecule(SMILES="CC(C)CO")]),
 'ic4ketii': Species(label="ic4ketii", molecule=[Molecule(SMILES="CC(C=O)COO")]),
 'ic4ketit': Species(label="ic4ketit", molecule=[Molecule(SMILES="CC(C)(C=O)OO")]),
 'ic4ohket1-2': Species(label="ic4ohket1-2", molecule=[Molecule(SMILES="CC(C)(OO)C(=O)O")]),
 'ic4ohket1-3': Species(label="ic4ohket1-3", molecule=[Molecule(SMILES="CC(COO)C(=O)O")]),
 'ic4ohket3-1': Species(label="ic4ohket3-1", molecule=[Molecule(SMILES="CC(C=O)C(O)OO")]),
 'ic4ohket3-2': Species(label="ic4ohket3-2", molecule=[Molecule(SMILES="CC(C=O)(CO)OO")]),
 'ic4ohket3-3': Species(label="ic4ohket3-3", molecule=[Molecule(SMILES="O=CC(CO)COO")]),
 'iic4h7q2-i': Species(label="iic4h7q2-i", molecule=[Molecule(SMILES="[CH2]C(COO)COO")]),
 'iic4h7q2-t': Species(label="iic4h7q2-t", molecule=[Molecule(SMILES="C[C](COO)COO")]),
 'n2': Species(label="n2", molecule=[Molecule(SMILES="N#N")]),
 'nc3h7': Species(label="nc3h7", molecule=[Molecule(SMILES="[CH2]CC")]),
 'nc3h7cho': Species(label="nc3h7cho", molecule=[Molecule(SMILES="CCCC=O")]),
 'nc3h7co': Species(label="nc3h7co", molecule=[Molecule(SMILES="CCC[C]=O")]),
 'nc3h7o': Species(label="nc3h7o", molecule=[Molecule(SMILES="CCC[O]")]),
 'nc3h7o2': Species(label="nc3h7o2", molecule=[Molecule(SMILES="CCCO[O]")]),
 'nc3h7o2h': Species(label="nc3h7o2h", molecule=[Molecule(SMILES="CCCOO")]),
 'nc4h9oh': Species(label="nc4h9oh", molecule=[Molecule(SMILES="CCCCO")]),
 'nc4ket12': Species(label="nc4ket12", molecule=[Molecule(SMILES="CCC(C=O)OO")]),
 'nc4ket13': Species(label="nc4ket13", molecule=[Molecule(SMILES="CC(CC=O)OO")]),
 'nc4ket14': Species(label="nc4ket14", molecule=[Molecule(SMILES="O=CCCCOO")]),
 'nc4ket21': Species(label="nc4ket21", molecule=[Molecule(SMILES="CCC(=O)COO")]),
 'nc4ket23': Species(label="nc4ket23", molecule=[Molecule(SMILES="CC(=O)C(C)OO")]),
 'nc4ket24': Species(label="nc4ket24", molecule=[Molecule(SMILES="CC(=O)CCOO")]),
 'o': Species(label="o", molecule=[Molecule(SMILES="[O]")]),
 'o2': Species(label="o2", molecule=[Molecule(SMILES="[O][O]")]),
 'o2c2h4oh': Species(label="o2c2h4oh", molecule=[Molecule(SMILES="[O]OCCO")]),
 'o2c4h8cho': Species(label="o2c4h8cho", molecule=[Molecule(SMILES="CC(C)(C=O)CO[O]")]),
 'o2ch2cho': Species(label="o2ch2cho", molecule=[Molecule(SMILES="[O]OCC=O")]),
 'o2ch2och2o2h': Species(label="o2ch2och2o2h", molecule=[Molecule(SMILES="[O]OCOCOO")]),
 'o2cho': Species(label="o2cho", molecule=[Molecule(SMILES="[O]OC=O")]),
 'o2hc4h8co': Species(label="o2hc4h8co", molecule=[Molecule(SMILES="CC(C)([C]=O)COO")]),
 'och2o2h': Species(label="och2o2h", molecule=[Molecule(SMILES="[O]COO")]),
 'och2ocho': Species(label="och2ocho", molecule=[Molecule(SMILES="[O]COC=O")]),
 'ocho': Species(label="ocho", molecule=[Molecule(SMILES="[O]C=O"), Molecule(SMILES="[O]C=O")]),
 'oh': Species(label="oh", molecule=[Molecule(SMILES="[OH]")]),
 'oh*': Species(label="oh*", molecule=[Molecule(SMILES="[OH]")]),
 'pc2h4oh': Species(label="pc2h4oh", molecule=[Molecule(SMILES="[CH2]CO")]),
 'pc4h9': Species(label="pc4h9", molecule=[Molecule(SMILES="[CH2]CCC")]),
 'pc4h9o': Species(label="pc4h9o", molecule=[Molecule(SMILES="CCCC[O]")]),
 'pc4h9o2': Species(label="pc4h9o2", molecule=[Molecule(SMILES="CCCCO[O]")]),
 'pc4h9o2h': Species(label="pc4h9o2h", molecule=[Molecule(SMILES="CCCCOO")]),
 'sc2h4oh': Species(label="sc2h4oh", molecule=[Molecule(SMILES="C[CH]O")]),
 'sc3h5cho': Species(label="sc3h5cho", molecule=[Molecule(SMILES="CC=CC=O")]),
 'sc3h5co': Species(label="sc3h5co", molecule=[Molecule(SMILES="CC=C[C]=O"), Molecule(SMILES="C[CH]C=C=O")]),
 'sc4h7oh-1ooh-2': Species(label="sc4h7oh-1ooh-2", molecule=[Molecule(SMILES="C[CH]C(C)(O)OO")]),
 'sc4h7oh-1ooh-2o2': Species(label="sc4h7oh-1ooh-2o2", molecule=[Molecule(SMILES="CC(O[O])C(C)(O)OO")]),
 'sc4h7oh-1ooh-3': Species(label="sc4h7oh-1ooh-3", molecule=[Molecule(SMILES="[CH2]CC(C)(O)OO")]),
 'sc4h7oh-1ooh-3o2': Species(label="sc4h7oh-1ooh-3o2", molecule=[Molecule(SMILES="CC(O)(CCO[O])OO")]),
 'sc4h7oh-1ooh-m': Species(label="sc4h7oh-1ooh-m", molecule=[Molecule(SMILES="[CH2]C(O)(CC)OO")]),
 'sc4h7oh-1ooh-mo2': Species(label="sc4h7oh-1ooh-mo2", molecule=[Molecule(SMILES="CCC(O)(CO[O])OO")]),
 'sc4h7oh-2ooh-1': Species(label="sc4h7oh-2ooh-1", molecule=[Molecule(SMILES="C[C](O)C(C)OO")]),
 'sc4h7oh-2ooh-1o2': Species(label="sc4h7oh-2ooh-1o2", molecule=[Molecule(SMILES="CC(OO)C(C)(O)O[O]")]),
 'sc4h7oh-2ooh-3': Species(label="sc4h7oh-2ooh-3", molecule=[Molecule(SMILES="[CH2]C(OO)C(C)O")]),
 'sc4h7oh-2ooh-3o2': Species(label="sc4h7oh-2ooh-3o2", molecule=[Molecule(SMILES="CC(O)C(CO[O])OO")]),
 'sc4h7oh-2ooh-m': Species(label="sc4h7oh-2ooh-m", molecule=[Molecule(SMILES="[CH2]C(O)C(C)OO")]),
 'sc4h7oh-2ooh-mo2': Species(label="sc4h7oh-2ooh-mo2", molecule=[Molecule(SMILES="CC(OO)C(O)CO[O]")]),
 'sc4h7oh-3ooh-1': Species(label="sc4h7oh-3ooh-1", molecule=[Molecule(SMILES="C[C](O)CCOO")]),
 'sc4h7oh-3ooh-1o2': Species(label="sc4h7oh-3ooh-1o2", molecule=[Molecule(SMILES="CC(O)(CCOO)O[O]")]),
 'sc4h7oh-3ooh-2': Species(label="sc4h7oh-3ooh-2", molecule=[Molecule(SMILES="CC(O)[CH]COO")]),
 'sc4h7oh-3ooh-2o2': Species(label="sc4h7oh-3ooh-2o2", molecule=[Molecule(SMILES="CC(O)C(COO)O[O]")]),
 'sc4h7oh-3ooh-m': Species(label="sc4h7oh-3ooh-m", molecule=[Molecule(SMILES="[CH2]C(O)CCOO")]),
 'sc4h7oh-3ooh-mo2': Species(label="sc4h7oh-3ooh-mo2", molecule=[Molecule(SMILES="[O]OCC(O)CCOO")]),
 'sc4h7oh-mooh-1': Species(label="sc4h7oh-mooh-1", molecule=[Molecule(SMILES="CC[C](O)COO")]),
 'sc4h7oh-mooh-1o2': Species(label="sc4h7oh-mooh-1o2", molecule=[Molecule(SMILES="CCC(O)(COO)O[O]")]),
 'sc4h7oh-mooh-2': Species(label="sc4h7oh-mooh-2", molecule=[Molecule(SMILES="C[CH]C(O)COO")]),
 'sc4h7oh-mooh-2o2': Species(label="sc4h7oh-mooh-2o2", molecule=[Molecule(SMILES="CC(O[O])C(O)COO")]),
 'sc4h7oh-mooh-3': Species(label="sc4h7oh-mooh-3", molecule=[Molecule(SMILES="[CH2]CC(O)COO")]),
 'sc4h7oh-mooh-3o2': Species(label="sc4h7oh-mooh-3o2", molecule=[Molecule(SMILES="[O]OCCC(O)COO")]),
 'sc4h7oho1-2': Species(label="sc4h7oho1-2", molecule=[Molecule(SMILES="CC1OC1(C)O")]),
 'sc4h7oho1-3': Species(label="sc4h7oho1-3", molecule=[Molecule(SMILES="CC1OC1(C)O")]),
 'sc4h7oho1-m': Species(label="sc4h7oho1-m", molecule=[Molecule(SMILES="CCC1(O)CO1")]),
 'sc4h7oho2-3': Species(label="sc4h7oho2-3", molecule=[Molecule(SMILES="CC(O)C1CO1")]),
 'sc4h7oho2-m': Species(label="sc4h7oho2-m", molecule=[Molecule(SMILES="CC1OCC1O")]),
 'sc4h7oho3-m': Species(label="sc4h7oho3-m", molecule=[Molecule(SMILES="OC1CCOC1")]),
 'sc4h8oh-1': Species(label="sc4h8oh-1", molecule=[Molecule(SMILES="CC[C](C)O")]),
 'sc4h8oh-1o': Species(label="sc4h8oh-1o", molecule=[Molecule(SMILES="CCC(C)([O])O")]),
 'sc4h8oh-1o2': Species(label="sc4h8oh-1o2", molecule=[Molecule(SMILES="CCC(C)(O)O[O]")]),
 'sc4h8oh-1o2h': Species(label="sc4h8oh-1o2h", molecule=[Molecule(SMILES="CCC(C)(O)OO")]),
 'sc4h8oh-2': Species(label="sc4h8oh-2", molecule=[Molecule(SMILES="C[CH]C(C)O")]),
 'sc4h8oh-2o': Species(label="sc4h8oh-2o", molecule=[Molecule(SMILES="CC([O])C(C)O")]),
 'sc4h8oh-2o2': Species(label="sc4h8oh-2o2", molecule=[Molecule(SMILES="CC(O)C(C)O[O]")]),
 'sc4h8oh-2o2h': Species(label="sc4h8oh-2o2h", molecule=[Molecule(SMILES="CC(O)C(C)OO")]),
 'sc4h8oh-3': Species(label="sc4h8oh-3", molecule=[Molecule(SMILES="[CH2]CC(C)O")]),
 'sc4h8oh-3o': Species(label="sc4h8oh-3o", molecule=[Molecule(SMILES="CC(O)CC[O]")]),
 'sc4h8oh-3o2': Species(label="sc4h8oh-3o2", molecule=[Molecule(SMILES="CC(O)CCO[O]")]),
 'sc4h8oh-3o2h': Species(label="sc4h8oh-3o2h", molecule=[Molecule(SMILES="CC(O)CCOO")]),
 'sc4h8oh-mo': Species(label="sc4h8oh-mo", molecule=[Molecule(SMILES="CCC(O)C[O]")]),
 'sc4h8oh-mo2': Species(label="sc4h8oh-mo2", molecule=[Molecule(SMILES="CCC(O)CO[O]")]),
 'sc4h8oh-mo2h': Species(label="sc4h8oh-mo2h", molecule=[Molecule(SMILES="CCC(O)COO")]),
 'sc4h8ohm': Species(label="sc4h8ohm", molecule=[Molecule(SMILES="[CH2]C(O)CC")]),
 'sc4h9': Species(label="sc4h9", molecule=[Molecule(SMILES="C[CH]CC")]),
 'sc4h9o': Species(label="sc4h9o", molecule=[Molecule(SMILES="CCC(C)[O]")]),
 'sc4h9o2': Species(label="sc4h9o2", molecule=[Molecule(SMILES="CCC(C)O[O]")]),
 'sc4h9o2h': Species(label="sc4h9o2h", molecule=[Molecule(SMILES="CCC(C)OO")]),
 'sc4h9oh': Species(label="sc4h9oh", molecule=[Molecule(SMILES="CCC(C)O")]),
 'sc4ohket2-1': Species(label="sc4ohket2-1", molecule=[Molecule(SMILES="CC(=O)C(C)(O)OO")]),
 'sc4ohket2-3': Species(label="sc4ohket2-3", molecule=[Molecule(SMILES="CC(O)C(=O)COO")]),
 'sc4ohket2-m': Species(label="sc4ohket2-m", molecule=[Molecule(SMILES="CC(=O)C(O)COO")]),
 'sc4ohket3-1': Species(label="sc4ohket3-1", molecule=[Molecule(SMILES="CC(O)C(C=O)OO")]),
 'sc4ohket3-2': Species(label="sc4ohket3-2", molecule=[Molecule(SMILES="CC(O)(CC=O)OO")]),
 'sc4ohket3-m': Species(label="sc4ohket3-m", molecule=[Molecule(SMILES="O=CCC(O)COO")]),
 'sc4ohketm-1': Species(label="sc4ohketm-1", molecule=[Molecule(SMILES="CCC(O)(C=O)OO")]),
 'sc4ohketm-2': Species(label="sc4ohketm-2", molecule=[Molecule(SMILES="CCC(O)(C=O)OO")]),
 'sc4ohketm-3': Species(label="sc4ohketm-3", molecule=[Molecule(SMILES="O=CC(O)CCOO")]),
 'tc3h6cho': Species(label="tc3h6cho", molecule=[Molecule(SMILES="C[C](C)C=O"), Molecule(SMILES="CC(C)=C[O]")]),
 'tc3h6o2cho': Species(label="tc3h6o2cho", molecule=[Molecule(SMILES="CC(C)(C=O)O[O]")]),
 'tc3h6o2hco': Species(label="tc3h6o2hco", molecule=[Molecule(SMILES="CC(C)([C]=O)OO")]),
 'tc3h6ocho': Species(label="tc3h6ocho", molecule=[Molecule(SMILES="CC(C)([O])C=O")]),
 'tc3h6oh': Species(label="tc3h6oh", molecule=[Molecule(SMILES="C[C](C)O")]),
 'tc3h6ohcho': Species(label="tc3h6ohcho", molecule=[Molecule(SMILES="CC(C)(O)C=O")]),
 'tc4h7oh-ooh': Species(label="tc4h7oh-ooh", molecule=[Molecule(SMILES="[CH2]C(C)(O)COO")]),
 'tc4h7oh-ooh-o2': Species(label="tc4h7oh-ooh-o2", molecule=[Molecule(SMILES="CC(O)(CO[O])COO")]),
 'tc4h7oho': Species(label="tc4h7oho", molecule=[Molecule(SMILES="CC1(O)COC1")]),
 'tc4h8cho': Species(label="tc4h8cho", molecule=[Molecule(SMILES="[CH2]C(C)(C)C=O")]),
 'tc4h8o2h-i': Species(label="tc4h8o2h-i", molecule=[Molecule(SMILES="[CH2]C(C)(C)OO")]),
 'tc4h8oh': Species(label="tc4h8oh", molecule=[Molecule(SMILES="[CH2]C(C)(C)O")]),
 'tc4h8oh-o': Species(label="tc4h8oh-o", molecule=[Molecule(SMILES="CC(C)(O)C[O]")]),
 'tc4h8oh-o2': Species(label="tc4h8oh-o2", molecule=[Molecule(SMILES="CC(C)(O)CO[O]")]),
 'tc4h8oh-o2h': Species(label="tc4h8oh-o2h", molecule=[Molecule(SMILES="CC(C)(O)COO")]),
 'tc4h8ooh-io2': Species(label="tc4h8ooh-io2", molecule=[Molecule(SMILES="CC(C)(CO[O])OO")]),
 'tc4h9': Species(label="tc4h9", molecule=[Molecule(SMILES="C[C](C)C")]),
 'tc4h9o': Species(label="tc4h9o", molecule=[Molecule(SMILES="CC(C)(C)[O]")]),
 'tc4h9o2': Species(label="tc4h9o2", molecule=[Molecule(SMILES="CC(C)(C)O[O]")]),
 'tc4h9o2h': Species(label="tc4h9o2h", molecule=[Molecule(SMILES="CC(C)(C)OO")]),
 'tc4h9oh': Species(label="tc4h9oh", molecule=[Molecule(SMILES="CC(C)(C)O")]),
 'tc4ohket': Species(label="tc4ohket", molecule=[Molecule(SMILES="CC(O)(C=O)COO")]),
 'tic4h7q2-i': Species(label="tic4h7q2-i", molecule=[Molecule(SMILES="[CH2]C(C)(COO)OO")])}

speciesList = species_dict.values()

# Generate resonance isomers
for species in speciesList:
    species.generateResonanceIsomers()
    if len(species.molecule)>1:
        print(species.label, species.molecule)

('ch3chchco', [Molecule(SMILES="CC=C[C]=O"), Molecule(SMILES="C[CH]C=C=O")])
('ocho', [Molecule(SMILES="[O]C=O"), Molecule(SMILES="[O]C=O")])
('sc3h5co', [Molecule(SMILES="CC=C[C]=O"), Molecule(SMILES="C[CH]C=C=O")])
('hcco', [Molecule(SMILES="C#C[O]"), Molecule(SMILES="[CH]=C=O")])
('c4h5-2', [Molecule(SMILES="C=C=[C]C"), Molecule(SMILES="[CH2]C#CC")])
('c4h5-i', [Molecule(SMILES="C=[C]C=C"), Molecule(SMILES="[CH2]C=C=C")])
('ic4h7', [Molecule(SMILES="[CH2]C(=C)C"), Molecule(SMILES="[CH2]C(=C)C")])
('c4h3-i', [Molecule(SMILES="C#C[C]=C"), Molecule(SMILES="[CH]=C=C=C")])
('c2h3co', [Molecule(SMILES="C=C[C]=O"), Molecule(SMILES="[CH2]C=C=O")])
('c2h3choch2', [Molecule(SMILES="[CH2]C=CO[CH2]"), Molecule(SMILES="[CH2]O[CH]C=C")])
('ch3co2', [Molecule(SMILES="CC([O])=O"), Molecule(SMILES="CC([O])=O")])
('c4h71-3', [Molecule(SMILES="C=C[CH]C"), Molecule(SMILES="[CH2]C=CC")])
('ic4h6oh', [Molecule(SMILES="[CH2]C(=C)CO"), Molecule(SMILES="[CH2]C(=C)CO")])
('c3h5-a', [Molecule(SMILES="[CH2]C=C"), Molecule(SMILES="[CH2]C=C")])
('ch2cho', [Molecule(SMILES="C=C[O]"), Molecule(SMILES="[CH2]C=O")])
('c2h5coch2', [Molecule(SMILES="[CH2]C(=O)CC"), Molecule(SMILES="C=C([O])CC")])
('c4h6oh1-32', [Molecule(SMILES="C=C(O)[CH]C"), Molecule(SMILES="[CH2]C(O)=CC")])
('c3h6cho-3', [Molecule(SMILES="CC[CH]C=O"), Molecule(SMILES="CCC=C[O]")])
('c3h3', [Molecule(SMILES="C#C[CH2]"), Molecule(SMILES="[CH]=C=C")])
('ch3coch2', [Molecule(SMILES="[CH2]C(C)=O"), Molecule(SMILES="C=C(C)[O]")])
('ch2chchcho', [Molecule(SMILES="[CH2]C=CC=O"), Molecule(SMILES="C=C[CH]C=O"), Molecule(SMILES="C=CC=C[O]")])
('ch3chcoch3', [Molecule(SMILES="CC=C(C)[O]"), Molecule(SMILES="C[CH]C(C)=O")])
('c4h6oh1-13', [Molecule(SMILES="CC=C[CH]O"), Molecule(SMILES="C[CH]C=CO")])
('ic3h5co', [Molecule(SMILES="C=C(C)[C]=O"), Molecule(SMILES="[CH2]C(C)=C=O")])
('tc3h6cho', [Molecule(SMILES="C[C](C)C=O"), Molecule(SMILES="CC(C)=C[O]")])

from collections import namedtuple
Model = namedtuple('Model', ['name','path','species_dict'])

butanol = Model(model_name, model_path, species_dict)

Now read in heptane

model_name = 'heptane'
model_path = 'nheptane-LLNL31'

get_species_dict = KineticsLibrary().getSpecies
species_dict = get_species_dict(os.path.join(model_path, 'RMG-Py-kinetics-library', 'dictionary.txt'))

speciesList = species_dict.values()

# Generate resonance isomers
for species in speciesList:
    species.generateResonanceIsomers()
    if len(species.molecule)>1:
        print(species.label, species.molecule)

('C4H8CHO-4', [Molecule(SMILES="CCC[CH]C=O"), Molecule(SMILES="CCCC=C[O]")])
('C2H5COC2H4S', [Molecule(SMILES="C[CH]C(=O)CC"), Molecule(SMILES="CC=C([O])CC")])
('CH3COCH2', [Molecule(SMILES="[CH2]C(C)=O"), Molecule(SMILES="C=C(C)[O]")])
('IC3H5CO', [Molecule(SMILES="C=C(C)[C]=O"), Molecule(SMILES="[CH2]C(C)=C=O")])
('C6H102OOH5-4', [Molecule(SMILES="CC=C[CH]C(C)OO"), Molecule(SMILES="C[CH]C=CC(C)OO")])
('C2H5COCH2', [Molecule(SMILES="[CH2]C(=O)CC"), Molecule(SMILES="C=C([O])CC")])
('NC3H7COCH2', [Molecule(SMILES="[CH2]C(=O)CCC"), Molecule(SMILES="C=C([O])CCC")])
('C3H6COCH3-3', [Molecule(SMILES="CCC=C(C)[O]"), Molecule(SMILES="CC[CH]C(C)=O")])
('IC4H7', [Molecule(SMILES="[CH2]C(=C)C"), Molecule(SMILES="[CH2]C(=C)C")])
('C5H10CHO-5', [Molecule(SMILES="CCCC[CH]C=O"), Molecule(SMILES="CCCCC=C[O]")])
('HCCO', [Molecule(SMILES="C#C[O]"), Molecule(SMILES="[CH]=C=O")])
('C5H92-4', [Molecule(SMILES="C[CH]C=CC"), Molecule(SMILES="C[CH]C=CC")])
('C4H71-3', [Molecule(SMILES="C=C[CH]C"), Molecule(SMILES="[CH2]C=CC")])
('CH2CHO', [Molecule(SMILES="[CH2]C=O"), Molecule(SMILES="C=C[O]")])
('C6H102OOH6-4', [Molecule(SMILES="CC=C[CH]CCOO"), Molecule(SMILES="C[CH]C=CCCOO")])
('C3H6CHO-3', [Molecule(SMILES="CC[CH]C=O"), Molecule(SMILES="CCC=C[O]")])
('C5H91-3', [Molecule(SMILES="[CH2]C=CCC"), Molecule(SMILES="C=C[CH]CC")])
('OCHO', [Molecule(SMILES="[O]C=O"), Molecule(SMILES="[O]C=O")])
('C6H101OOH5-3', [Molecule(SMILES="[CH2]C=CCC(C)OO"), Molecule(SMILES="C=C[CH]CC(C)OO")])
('C6H101OOH6-3', [Molecule(SMILES="[CH2]C=CCCCOO"), Molecule(SMILES="C=C[CH]CCCOO")])
('C3H6COC2H5-3', [Molecule(SMILES="CC[CH]C(=O)CC"), Molecule(SMILES="CCC=C([O])CC")])
('C3H2', [Molecule(SMILES="[CH]=C=[CH]"), Molecule(SMILES="[CH]C#C"), Molecule(SMILES="[CH]C#C")])
('C3H3', [Molecule(SMILES="C#C[CH2]"), Molecule(SMILES="[CH]=C=C")])
('C4H7CO1-1', [Molecule(SMILES="CCC=C[C]=O"), Molecule(SMILES="CC[CH]C=C=O")])
('C4H8COCH3-4', [Molecule(SMILES="CCCC=C(C)[O]"), Molecule(SMILES="CCC[CH]C(C)=O")])
('IC4H6OH', [Molecule(SMILES="[CH2]C(=C)CO"), Molecule(SMILES="[CH2]C(=C)CO")])
('C3H5-A', [Molecule(SMILES="[CH2]C=C"), Molecule(SMILES="[CH2]C=C")])
('CH3CO2', [Molecule(SMILES="CC([O])=O"), Molecule(SMILES="CC([O])=O")])
('C6H101OOH4-3', [Molecule(SMILES="C=C[CH]C(CC)OO"), Molecule(SMILES="[CH2]C=CC(CC)OO")])
('C6H112-4', [Molecule(SMILES="CC=C[CH]CC"), Molecule(SMILES="C[CH]C=CCC")])
('SC3H5CO', [Molecule(SMILES="CC=C[C]=O"), Molecule(SMILES="C[CH]C=C=O")])
('NC3H7COC2H4S', [Molecule(SMILES="C[CH]C(=O)CCC"), Molecule(SMILES="CC=C([O])CCC")])
('CH3CHCOCH3', [Molecule(SMILES="CC=C(C)[O]"), Molecule(SMILES="C[CH]C(C)=O")])
('SC2H4COC2H3', [Molecule(SMILES="C=CC(=O)[CH]C"), Molecule(SMILES="C=CC([O])=CC")])
('NC4H9COCH2', [Molecule(SMILES="[CH2]C(=O)CCCC"), Molecule(SMILES="C=C([O])CCCC")])
('C7H132-4', [Molecule(SMILES="CC=C[CH]CCC"), Molecule(SMILES="C[CH]C=CCCC")])
('C4H6CHO1-13', [Molecule(SMILES="C[CH]C=CC=O"), Molecule(SMILES="CC=C[CH]C=O"), Molecule(SMILES="CC=CC=C[O]")])
('TC3H6CHO', [Molecule(SMILES="C[C](C)C=O"), Molecule(SMILES="CC(C)=C[O]")])
('C7H131-3', [Molecule(SMILES="[CH2]C=CCCCC"), Molecule(SMILES="C=C[CH]CCCC")])
('C6H103OOH1-2', [Molecule(SMILES="CCC=C[CH]COO"), Molecule(SMILES="CC[CH]C=CCOO")])
('C2H3CHCHO', [Molecule(SMILES="C=C[CH]C=O"), Molecule(SMILES="C=CC=C[O]"), Molecule(SMILES="[CH2]C=CC=O")])
('C7H133-5', [Molecule(SMILES="CC[CH]C=CCC"), Molecule(SMILES="CC[CH]C=CCC")])
('C2H3CO', [Molecule(SMILES="[CH2]C=C=O"), Molecule(SMILES="C=C[C]=O")])
('C4H6CHO1-43', [Molecule(SMILES="C=C[CH]CC=O"), Molecule(SMILES="[CH2]C=CCC=O")])
('C4H6CHO1-44', [Molecule(SMILES="C=CC[CH]C=O"), Molecule(SMILES="C=CCC=C[O]")])
('C6H111-3', [Molecule(SMILES="[CH2]C=CCCC"), Molecule(SMILES="C=C[CH]CCC")])

heptane = Model(model_name, model_path, species_dict)

for but_name, but_species in butanol.species_dict.iteritems():
    for hep_name, hep_species in heptane.species_dict.iteritems():
        if but_species.isIsomorphic(hep_species):
            print but_name
            print hep_name
            print but_species.molecule[0].toSMILES()
            display(but_species)
            print "-"*20

tc4h8ooh-io2
TC4H8OOH-IO2
CC(C)(CO[O])OO

--------------------
ch3o
CH3O
C[O]

--------------------
o2ch2och2o2h
O2CH2OCH2O2H
[O]OCOCOO

--------------------
och2o2h
OCH2O2H
[O]COO

--------------------
ic3h6oh
C3H6OH
[CH2]C(C)O

--------------------
o2
O2
[O][O]

--------------------
c2h4o2h
C2H4O2H
[CH2]COO

--------------------
ch3chchco
SC3H5CO
CC=C[C]=O

--------------------
ocho
OCHO
[O]C=O

--------------------
och2ocho
OCH2OCHO
[O]COC=O