Generate data for missing species

Executing this notebook requires an active internet connection, as it queries the NCI/CADD Chemical Identifier Resolver web service, to help in suggesting and selecting names for the species

In [1]:
import cirpy # pip install this if you don't have it.

import sys
import os
import re
import numpy
import csv
import cPickle as pickle
import pandas as pd
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))

# 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 cantera import ck2cti 
import rmgpy
import rmgpy.molecule, rmgpy.species, rmgpy.data, rmgpy.data.rmg, rmgpy.thermo.thermoengine
In [2]:
model_name = 'heptane'
In [3]:
csv_filename = 'new-species-{}.csv'.format(model_name)
if not os.path.exists(csv_filename):
    with open(csv_filename,'w') as f:
        f.write('SMILES, Name\n')
smiles_names = pd.read_csv(csv_filename, index_col=0)
In [4]:
smiles_names
Out[4]:
Name
SMILES
CC(=O)C=O NaN
CCCCCC(C)=O NaN
C#CCO NaN
CCCCCCC=O NaN
C=C=CCC NaN
C=C=CC NaN
CCCC(=O)CCC NaN
C=CCCC(C)=O NaN
C=C=CO NaN
CC(C)O NaN
C=CCC(C)=O NaN
C=CCC(=O)CC NaN
CCCCC(=O)CC NaN
O=COC=O NaN
In [5]:
species_list = []
for smiles in smiles_names.index:
    m = rmgpy.molecule.Molecule(SMILES=smiles)
    species = rmgpy.species.Species(molecule=[m])
    species.generateResonanceIsomers()
    species.props['smiles'] = smiles.strip()
    species_list.append(species)
species_list
Out[5]:
[Species(label="", molecule=[Molecule(SMILES="CC(=O)C=O")]),
 Species(label="", molecule=[Molecule(SMILES="CCCCCC(C)=O")]),
 Species(label="", molecule=[Molecule(SMILES="C#CCO")]),
 Species(label="", molecule=[Molecule(SMILES="CCCCCCC=O")]),
 Species(label="", molecule=[Molecule(SMILES="C=C=CCC")]),
 Species(label="", molecule=[Molecule(SMILES="C=C=CC")]),
 Species(label="", molecule=[Molecule(SMILES="CCCC(=O)CCC")]),
 Species(label="", molecule=[Molecule(SMILES="C=CCCC(C)=O")]),
 Species(label="", molecule=[Molecule(SMILES="C=C=CO")]),
 Species(label="", molecule=[Molecule(SMILES="CC(C)O")]),
 Species(label="", molecule=[Molecule(SMILES="C=CCC(C)=O")]),
 Species(label="", molecule=[Molecule(SMILES="C=CCC(=O)CC")]),
 Species(label="", molecule=[Molecule(SMILES="CCCCC(=O)CC")]),
 Species(label="", molecule=[Molecule(SMILES="O=COC=O")])]
In [6]:
rmgDatabase = rmgpy.data.rmg.RMGDatabase()
databasePath = os.path.abspath(os.path.join(os.getenv('RMGpy', '..'), '..', 'RMG-database', 'input'))
print("Loading database from "+databasePath)
rmgDatabase.load(databasePath,
                 kineticsFamilies='default',
                 transportLibraries=['PrimaryTransportLibrary', 'GRI-Mech'],
                 reactionLibraries=[],
                 seedMechanisms=[],
                 thermoLibraries=['primaryThermoLibrary',
                                  'BurkeH2O2',
                                  'thermo_DFT_CCSDTF12_BAC',
                                  'CBS_QB3_1dHR',
                                  'CHO',
                                  'USC-Mech-ii',],
                 solvation=False,
                 )
Loading database from /Users/rwest/Code/RMG-database/input
In [7]:
for s in species_list:
    display(s)
    s.generateTransportData()
    print s.transportData
TransportData(shapeIndex=2, epsilon=(3581.43,'J/mol'), sigma=(5.59226,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=559.41 K, Pc=46.47 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3778.9,'J/mol'), sigma=(6.62378,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=590.26 K, Pc=29.5 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3355.71,'J/mol'), sigma=(5.56877,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=524.15 K, Pc=44.09 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3714.44,'J/mol'), sigma=(6.61211,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=580.19 K, Pc=29.16 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3149.55,'J/mol'), sigma=(5.50528,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=491.95 K, Pc=42.83 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(2996.71,'J/mol'), sigma=(5.18551,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=468.08 K, Pc=48.77 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3778.9,'J/mol'), sigma=(6.62378,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=590.26 K, Pc=29.5 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3641.61,'J/mol'), sigma=(6.10394,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=568.81 K, Pc=36.33 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3437.21,'J/mol'), sigma=(5.57865,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=536.88 K, Pc=44.92 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3366.93,'J/mol'), sigma=(5.85769,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=525.91 K, Pc=38.01 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3499.93,'J/mol'), sigma=(5.78905,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=546.68 K, Pc=40.93 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3641.61,'J/mol'), sigma=(6.10394,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=568.81 K, Pc=36.33 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3778.9,'J/mol'), sigma=(6.62378,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=590.26 K, Pc=29.5 bar (from Joback method)""")
TransportData(shapeIndex=2, epsilon=(3515.87,'J/mol'), sigma=(5.46152,'angstroms'), dipoleMoment=(0,'C*m'), polarizability=(0,'angstroms^3'), rotrelaxcollnum=0, comment="""Epsilon & sigma estimated with Tc=549.17 K, Pc=48.97 bar (from Joback method)""")
In [8]:
# Generate Thermo data
for s in species_list:
    display(s)
    rmgpy.thermo.thermoengine.submit(s)
    print s.thermo
NASA(polynomials=[NASAPolynomial(coeffs=[2.55141,0.0281059,-1.34053e-05,1.41131e-09,3.82981e-13,-34330.4,15.71], Tmin=(100,'K'), Tmax=(1438.66,'K')), NASAPolynomial(coeffs=[8.86728,0.0163469,-7.19389e-06,1.33598e-09,-9.10201e-14,-36748.1,-19.1441], Tmin=(1438.66,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-285.898,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(199.547,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cs-(Cds-Od)HHH) + gauche(Cs(RRRR)) + other(R) + group(Cds-Od(Cds-Od)Cs) + other(R) + group(Cds-Od(Cds-Od)H) + other(R) + group(Od-Cd) + other(R) + group(Od-Cd) + other(R)""")
NASA(polynomials=[NASAPolynomial(coeffs=[0.625471,0.0790041,-4.83873e-05,1.52644e-08,-2.07788e-12,-39517.6,29.8068], Tmin=(100,'K'), Tmax=(1540.57,'K')), NASAPolynomial(coeffs=[10.6942,0.0528615,-2.29334e-05,4.24959e-09,-2.90434e-13,-42619.9,-23.1201], Tmin=(1540.57,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-329.535,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(507.183,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)Cs(CsRR)RR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) + group(Cs-(Cds-Od)CsHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-(Cds-Od)HHH) + gauche(Cs(RRRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Od-Cd) + other(R)""")
NASA(polynomials=[NASAPolynomial(coeffs=[2.79887,0.0225818,-8.01311e-06,-3.43729e-09,2.32957e-12,3315.59,12.9758], Tmin=(100,'K'), Tmax=(1089.7,'K')), NASAPolynomial(coeffs=[7.21412,0.0135296,-5.40154e-06,9.90482e-10,-6.86284e-14,1928.52,-10.6537], Tmin=(1089.7,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(27.181,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(174.604,'J/(mol*K)'), comment="""Thermo library: CHO""")
NASA(polynomials=[NASAPolynomial(coeffs=[0.591069,0.0790396,-4.76913e-05,1.45849e-08,-1.8997e-12,-35776.6,30.5812], Tmin=(100,'K'), Tmax=(1616.88,'K')), NASAPolynomial(coeffs=[11.6691,0.0516337,-2.22663e-05,4.10173e-09,-2.78794e-13,-39358.9,-28.1866], Tmin=(1616.88,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-298.444,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(507.183,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)Cs(CsRR)RR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)Cs(CsRR)RR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) + group(Cs-(Cds-Od)CsHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cds-OdCsH) + other(R) + group(Od-Cd) + other(R)""")
NASA(polynomials=[NASAPolynomial(coeffs=[2.00141,0.0359535,-1.59361e-07,-2.04773e-08,9.05613e-12,14999.4,18.1131], Tmin=(100,'K'), Tmax=(1043.78,'K')), NASAPolynomial(coeffs=[9.31676,0.0253742,-1.00399e-05,1.8545e-09,-1.29899e-13,12521.5,-22.0474], Tmin=(1043.78,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(124.057,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(299.321,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cs-(Cds-Cds)CsHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(CsRRR)) + other(R) + group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Cdd-CdsCds) + other(R)""")
NASA(polynomials=[NASAPolynomial(coeffs=[1.02347,0.0349592,-2.2009e-05,6.94227e-09,-7.87919e-13,18118,19.7507], Tmin=(298,'K'), Tmax=(1000,'K')), NASAPolynomial(coeffs=[17.8156,-0.0042575,1.05118e-05,-4.47384e-09,5.84814e-13,12673.4,-69.8266], Tmin=(1000,'K'), Tmax=(3000,'K'))], Tmin=(298,'K'), Tmax=(3000,'K'), E0=(149.017,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(228.648,'J/(mol*K)'), comment="""Thermo library: USC-Mech-ii""")
NASA(polynomials=[NASAPolynomial(coeffs=[0.322796,0.0877772,-7.61413e-05,4.53164e-08,-1.29005e-11,-39704.4,29.3351], Tmin=(100,'K'), Tmax=(795.421,'K')), NASAPolynomial(coeffs=[5.33267,0.0625846,-2.86353e-05,5.50167e-09,-3.87316e-13,-40501.4,6.31186], Tmin=(795.421,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-331.171,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(507.183,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group(Cs-(Cds-Od)CsHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-(Cds-Od)CsHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Od-Cd) + other(R)""")
NASA(polynomials=[NASAPolynomial(coeffs=[1.27985,0.059765,-3.57353e-05,1.0567e-08,-1.29291e-12,-21308.1,25.7009], Tmin=(100,'K'), Tmax=(1772.11,'K')), NASAPolynomial(coeffs=[12.2674,0.034964,-1.47425e-05,2.66947e-09,-1.78774e-13,-25202.3,-33.5943], Tmin=(1772.11,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-177.972,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(390.78,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cs-(Cds-Od)CsHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-(Cds-Cds)CsHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-(Cds-Od)HHH) + gauche(Cs(RRRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Od-Cd) + other(R)""")
NASA(polynomials=[NASAPolynomial(coeffs=[2.31584,0.0236136,2.0576e-05,-5.73741e-08,2.79867e-11,-3061.59,12.125], Tmin=(100,'K'), Tmax=(901.947,'K')), NASAPolynomial(coeffs=[16.2977,-0.00239905,3.97496e-06,-8.57285e-10,5.72966e-14,-7047.86,-62.0027], Tmin=(901.947,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-26.0646,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(178.761,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cds-CdsOsH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Cdd-CdsCds) + other(R) + group(Os-(Cds-Cd)H) + gauche(Os(RR)) + other(R)""")
NASA(polynomials=[NASAPolynomial(coeffs=[2.40117,0.0252652,1.95923e-05,-4.14255e-08,1.70583e-11,-34733.8,15.4269], Tmin=(100,'K'), Tmax=(983.861,'K')), NASAPolynomial(coeffs=[9.94823,0.0185857,-6.8205e-06,1.26981e-09,-9.17915e-14,-37380.7,-26.7646], Tmin=(983.861,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-289.345,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(270.22,'J/(mol*K)'), comment="""Thermo library: CHO""")
NASA(polynomials=[NASAPolynomial(coeffs=[1.8439,0.0371821,7.58181e-06,-2.84844e-08,1.0818e-11,-17715.3,21.0088], Tmin=(100,'K'), Tmax=(1132.82,'K')), NASAPolynomial(coeffs=[10.9324,0.0291217,-1.35655e-05,2.68708e-09,-1.93818e-13,-21316.4,-30.7772], Tmin=(1132.82,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-148.01,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(320.107,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cs-(Cds-Od)(Cds-Cds)HH) + gauche(Cs(RRRR)) + other(R) + group(Cs-(Cds-Od)HHH) + gauche(Cs(RRRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Od-Cd) + other(R)""")
NASA(polynomials=[NASAPolynomial(coeffs=[0.999159,0.0597035,-3.08502e-05,5.3016e-09,7.75288e-14,-20745.2,25.4029], Tmin=(100,'K'), Tmax=(1600.22,'K')), NASAPolynomial(coeffs=[16.9248,0.0309005,-1.41674e-05,2.64921e-09,-1.79533e-13,-27251.2,-63.319], Tmin=(1600.22,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-173.426,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(390.78,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cs-(Cds-Od)CsHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-(Cds-Od)(Cds-Cds)HH) + gauche(Cs(RRRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(CsRRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Od-Cd) + other(R)""")
NASA(polynomials=[NASAPolynomial(coeffs=[0.322796,0.0877772,-7.61413e-05,4.53164e-08,-1.29005e-11,-39704.4,30.0283], Tmin=(100,'K'), Tmax=(795.421,'K')), NASAPolynomial(coeffs=[5.33267,0.0625846,-2.86353e-05,5.50167e-09,-3.87316e-13,-40501.4,7.005], Tmin=(795.421,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-331.171,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(507.183,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) + group(Cs-(Cds-Od)CsHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-(Cds-Od)CsHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(CsRRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Od-Cd) + other(R)""")
NASA(polynomials=[NASAPolynomial(coeffs=[2.83835,0.0223426,-1.38972e-05,3.49308e-09,-2.44519e-13,-58250,16.6203], Tmin=(100,'K'), Tmax=(1522.34,'K')), NASAPolynomial(coeffs=[9.19078,0.00916701,-4.37895e-06,8.41812e-10,-5.82474e-14,-60591.5,-18.0341], Tmin=(1522.34,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'), E0=(-484.688,'kJ/mol'), Cp0=(33.2579,'J/(mol*K)'), CpInf=(149.66,'J/(mol*K)'), comment="""Thermo group additivity estimation: group(Cds-OdOsH) + other(R) + group(Cds-OdOsH) + other(R) + group(Os-(Cds-Od)(Cds-Od)) + gauche(Os(RR)) + other(R) + group(Od-Cd) + other(R) + group(Od-Cd) + other(R)""")
In [9]:
for s in species_list:
    display(s)
    smiles = s.props['smiles']
    names = cirpy.resolve(smiles, 'names')
    iupac = cirpy.resolve(smiles, 'iupac_name')
    
    s.props['names'] = names
    s.props['iupac'] = iupac
    round_trip_smiles = cirpy.resolve(iupac, 'smiles')
    m = rmgpy.molecule.Molecule(SMILES=round_trip_smiles)
    assert s.isIsomorphic(m)
    print iupac
    print names
    
2-Oxopropanal
['2-Oxopropanal', '2-Ketopropionaldehyde', '78-98-8', '.alpha.-Ketopropionaldehyde', '1-Ketopropionaldehyde', 'Acetylformyl', 'Glyoxal, methyl', 'NSC79019', 'Propanal, 2-oxo-', 'Propanedione', 'Propanolone', 'Propionaldehyde, 2-keto', 'Propionaldehyde, 2-oxo-', 'Pyroracemic aldehyde', 'WLN: VHV1', '2-Ketopropionaldehyde', '2-Oxopropanal', 'C00546', '67028_FLUKA', 'Methylglyoxal solution', '2-oxo-propanal', 'METHYL-GLYOXAL', 'acetylformaldehyde', 'methylglyoxal', 'oxopropanal', 'pyruvaldehyde', 'pyruvic aldehyde', '2-Oxopropionaldehyde', '4-01-00-03631 (Beilstein Handbook Reference)', 'Acetalformaldehyde', 'BRN 0906750', 'CCRIS 1741', 'EINECS 201-164-8', 'FEMA No. 2969', 'METHYL GLYOXAL', 'NSC 337790', 'NSC 626580', 'NSC 79019', 'alpha-Ketopropionaldehyde', 'alpha-Ketopropionic aldehyde', 'Propanal, 2-oxo- (9CI)', 'Pyruvaldehyde (8CI)', '1,2-propanedione', 'CH3COCHO', 'CHEBI:17158', 'Pyruvaldehyde solution', 'W296902_ALDRICH', 'AIDS-132495', 'AIDS132495', 'NSC626580', 'LS-139762', 'ZINC01532681', 'PVL', 'M0252_SIGMA']
Heptan-2-one
['Heptan-2-one', '29299-43-2', '110-43-0', 'Methyl-n-pentyl ketone', '537683_SIAL', '68592_FLUKA', '2-Heptanone (natural)', '4-01-00-03318 (Beilstein Handbook Reference)', 'AI3-01230', 'Amyl-methyl-cetone [French]', 'BRN 1699063', 'EINECS 203-767-1', 'FEMA No. 2544', 'FEMA Number 2544', 'HSDB 1122', 'Ketone C-7', 'Methyl-amyl-cetone [French]', 'Methyl-n-amylketone', 'NSC 7313', 'UN1110', 'n-Amyl methyl ketone [UN1110]  [Flammable liquid]', 'Amyl methyl ketone', 'Amyl-methyl-cetone', 'Butylacetone', 'Ketone, methyl pentyl', 'Methyl amyl ketone', 'Methyl n-pentyl ketone', 'Methyl pentyl ketone', 'Methyl-amyl-cetone', 'NSC7313', 'Pentyl methyl ketone', 'WLN: 5V1', 'n-Amyl methyl ketone', 'n-Pentyl methyl ketone', '123366_ALDRICH', 'InChI=1/C7H14O/c1-3-4-5-6-7(2)8/h3-6H2,1-2H', 'LMFA12000004', 'CHEBI:5672', '2-Heptanone', 'C08380', 'Heptan-2-one', 'Methyl n-amyl ketone', '02476_FLUKA', 'Heptanone', 'W254401_ALDRICH', 'ZINC01531087']
Prop-2-yn-1-ol
['Prop-2-yn-1-ol', '107-19-7', '4-01-00-02214 (Beilstein Handbook Reference)', 'AI3-24359', 'Acetylene carbinol', 'Acetylenylcarbinol', 'Agrisynth PA', 'BRN 0506003', 'CCRIS 6781', 'EINECS 203-471-2', 'HSDB 6054', 'NA1986', 'NSC 8804', 'Propargyl alcohol [NA1986]  [Flammable liquid]', 'Propiolic alcohol', 'RCRA waste no. P102', 'RCRA waste number P102', '81820_FLUKA', 'InChI=1/C3H4O/c1-2-3-4/h1,4H,3H', 'NCGC00091559-01', '1-Hydroxy-2-propyne', '1-Propyn-3-ol', '1-Propyn-3-yl alcohol', '2-Propyn-1-ol', '2-Propynol', '2-Propynyl alcohol', '3-Hydroxy-1-propyne', '3-Propynol', 'C05986', 'Ethynylcarbinol', 'NA 1986', 'Prop-2-in-1-ol', 'Prop-2-yn-1-ol', 'Prop-2-yne-1-ol', 'Propargyl alcohol', 'Propynyl alcohol', 'Ethynyl carbinol', 'Methanol, ethynyl-', 'NSC8804', 'WLN: Q2UU1', 'P50803_ALDRICH', 'CHEBI:28905']
Heptanal
['Heptanal', 'Enanthaldehyde', '111-71-7', 'H2120_SIAL', 'Enanthal', 'Enanthaldehyde', 'Enanthic aldehyde', 'Enanthole', 'Heptaldehyde', 'Heptanal', 'Heptanaldehyde', 'Heptyl aldehyde', 'NSC2190', 'Oenanthal', 'Oenanthaldehyde', 'Oenanthic aldehyde', 'Oenanthol', 'WLN: VH6', 'n-Heptaldehyde', 'n-Heptanal', 'n-Heptylaldehyde', 'LMFA06000001', 'NCGC00091807-01', '75170_FLUKA', 'InChI=1/C7H14O/c1-2-3-4-5-6-7-8/h7H,2-6H2,1H', '1-Heptanal', 'W254002_ALDRICH', 'W254010_ALDRICH', '4-01-00-03314 (Beilstein Handbook Reference)', 'AI3-02066', 'Aldehyde C-7', 'BRN 1560236', 'CCRIS 6041', 'EINECS 203-898-4', 'FEMA No. 2540', 'FEMA Number 2541', 'HSDB 6026', 'Heptanal (natural)', 'Heptylaldehyde', 'NSC 2190', 'UN3056', 'n-Heptaldehyde [UN3056]  [Flammable liquid]', 'C14390', 'nchembio882-comp3']
Penta-1,2-diene
['Penta-1,2-diene', '591-95-7', '1,2-PENTADIENE', 'EINECS 209-737-4', 'Penta-1,2-diene', 'InChI=1/C5H8/c1-3-5-4-2/h5H,1,4H2,2H', 'Ethylallene']
buta-1,2-diene
['buta-1,2-diene', '590-19-2', '1,2-Butadien', 'Buta-1,2-dien', 'CH2=C=CH-CH3', '18853_FLUKA', '1,2-BUTADIENE', '1-Methylallene', 'Allene, methyl-', 'EINECS 209-674-2', 'HSDB 5705', 'Methylallene', 'InChI=1/C4H6/c1-3-4-2/h4H,1H2,2H', 'buta-1,2-diene', 'CHEBI:39480', '18855_FLUKA']
Heptan-4-one
['Heptan-4-one', '123-19-3', 'W254606_ALDRICH', 'InChI=1/C7H14O/c1-3-5-7(8)6-4-2/h3-6H2,1-2H', '4-Heptanone', 'Butyrone', 'Di-n-propyl ketone', 'Dipropyl ketone', 'Heptan-4-one', 'NSC8692', 'Propyl ketone', 'WLN: 3V3', '101745_ALDRICH', '46204_RIEDEL', 'ZINC01648177', '4-01-00-03323 (Beilstein Handbook Reference)', '4-Heptanone (natural)', 'AI3-15181', 'BRN 1699049', 'DI(N-PROPYL) KETONE', 'Dipropyl ketone [UN2710]  [Flammable liquid]', 'EINECS 204-608-9', 'FEMA No. 2546', 'NSC 8692', 'UN2710']
hex-5-en-2-one
['hex-5-en-2-one', '109-49-9', '5-Hexen-2-one', '5-Hexene-2-one', 'Allylacetone', 'NSC6973', 'ALLYL ACETONE', 'InChI=1/C6H10O/c1-3-4-5-6(2)7/h3H,1,4-5H2,2H', 'EINECS 203-675-1', 'AI3-21995', 'NSC 6973', 'ZINC01867148', 'H13001_ALDRICH', 'SBB009089', '1-Hexen-5-one']
propa-1,2-dien-1-ol
propa-1,2-dien-1-ol
Propan-2-ol
['Propan-2-ol', '8013-70-5', '67-63-0', '5131-95-3', 'Isopropyl alcohol (USP)', 'InChI=1/C3H8O/c1-3(2)4/h3-4H,1-2H', '40301_RIEDEL', '34959_RIEDEL', 'CHEBI:17824', 'Isopropylalkohol', '1-Hydroxy-1-methylethyl', 'Ethyl, 1-hydroxy-1-methyl-', 'LS-1565', '2-Propanol', 'C01845', 'Isopropanol', 'Propan-2-ol', '2-Propanol : Water 31:69 with 0.1% buffer', '2-Propanol solution', '92438_FLUKA', 'N-Term LC Solvent System B', '109827_ALDRICH', '34965_RIEDEL', '2-PROPANOL, ISOPROPANOL', 'IOH', '650447_ALDRICH', '437522_SIAL', 'I9782_SIGMA', '278475_ALDRICH', '33539_RIEDEL', '563935_ALDRICH', 'Alcool isopropylique', '673773_ALDRICH', '40279_RIEDEL', '190764_SIAL', 'Alcohol, rubbing', 'Alcool isopropilico', 'IPA', 'Iso-propylalkohol', 'Isopropenol', 'NSC135801', 'WLN: QY1&1', 'i-Propylalkohol', '40314_RIEDEL', '442369_SUPELCO', '24137_RIEDEL', 'ST5214369', 'sec-propanol', 'Secondary alcohol', '34895_RIEDEL', 'I9516_SIGMA', 'Rubbing alcohol', '1-Methylethanol', '1-Methylethyl alcohol', '2-Hydroxypropane', '2-Propyl alcohol', '4-01-00-01461 (Beilstein Handbook Reference)', 'AI3-01636', 'Alcojel', 'Alcolo', 'Alcool isopropilico [Italian]', 'Alcool isopropylique [French]', 'Alcosolve', 'Alcosolve 2', 'Alkolave', 'Arquad DMCB', 'Avantin', '534021_ALDRICH', 'BRN 0635639', 'CCRIS 2308', 'Caswell No. 507', 'Combi-schutz', 'Dimethylcarbinol', 'EINECS 200-661-7', 'EPA Pesticide Chemical Code 047601', 'FEMA No. 2929', 'FEMA Number 2929', 'HSDB 116', 'Hartosol', 'Imsol A', 'Iso-propyl alcohol', 'Iso-propylalkohol [German]', 'Isohol', 'Isopropanol or isopropyl alcohol [UN1219]  [Flammable liquid]', 'Isopropyl alcohol', 'Isopropyl alcohol (manufacture strong-acid process)', 'Isopropyl alcohol (manufacturing-strong acid process only)', 'Isopropyl alcohol (only persons who manufacture by the strong acid process are subject, supplier notification not required)', 'Isopropyl alcohol [USAN]', 'Isopropyl alcohol, rubbing', 'Lavacol', 'Lutosol', 'NSC 135801', 'Petrohol', 'Propol', 'Spectrar', 'Sterisol hand disinfectant', 'Takineocol', 'UN1219', 'Visco 1152', 'i-Propanol [German]', 'i-Propyl alcohol', 'i-Propylalkohol [German]', 'n-Propan-2-ol', 'sec-Propyl alcohol', '59304_FLUKA', '439207_ALDRICH', '59309_FLUKA', '675431_ALDRICH', 'i-propanol', '40219_RIEDEL', '154970_SIAL', '34863_SIAL', 'Isopropryl alcohol', 'c0519', 'W292907_ALDRICH', 'CHEBI:35681', 'secondary alcohols', 'ZINC00901159', '91237_FLUKA', 'AIDS-186244', 'AIDS186244', 'NCGC00090917-01', 'Avantine', "R-CHOH-R'", '40343_RIEDEL', 'I9030_SIGMA', '443425_SIAL', 'D00137', 'Isopro', 'Isopro (TN)', 'Isopropanol (JP15)']
pent-4-en-2-one
['pent-4-en-2-one', '13891-87-7', 'Allyl methyl ketone', '4-Penten-2-one']
hex-5-en-3-one
['hex-5-en-3-one', '24253-30-3', '5-Hexen-3-one']
Heptan-3-one
['Heptan-3-one', '106-35-4', 'Heptan-3-one', 'N-Butyl ethyl ketone', 'NSC8448', 'WLN: 4V2', '03220_FLUKA', '3-Heptanone solution', 'InChI=1/C7H14O/c1-3-5-6-7(8)4-2/h3-6H2,1-2H', '46203_RIEDEL', '4-01-00-03321 (Beilstein Handbook Reference)', 'AI3-19684', 'Aethylbutylketon [German]', 'BRN 0506161', 'EINECS 203-388-1', 'Eptan-3-one [Italian]', 'Ethyl butyl ketone 3-Heptanone', 'Ethyl-n-butyl ketone', 'Ethylbutylcetone [French]', 'Ethylbutylketon [Dutch]', 'Etilbutilchetone [Italian]', 'FEMA No. 2545', 'HSDB 1816', 'Heptan-3-on [Dutch, German]', 'NSC 8448', '02477_FLUKA', 'ZINC01586745', 'H6511_SIGMA', 'W254509_ALDRICH', '551325_ALDRICH', '3-HEPTANONE', 'Aethylbutylketon', 'Butyl ethyl ketone', 'Eptan-3-one', 'Ethyl butyl ketone', 'Ethyl n-butyl ketone', 'Ethylbutylcetone', 'Ethylbutylketon', 'Etilbutilchetone', 'Heptan-3-on']
formyl formate
['formyl formate', 'formic acid formyl ester', 'methanoyl methanoate', '1558-67-4', 'CHEBI:36657', 'formic acid anhydride', 'formic anhydride']
In [13]:
# If you have a gigantic spreadsheet of imported model data, 
# search it to see if these species have been seen before:
spreadsheet_path = os.path.expanduser('~/Code/RMG-models/modelComparer/output.xls')
if not os.path.exists(spreadsheet_path):
    print "You don't have the spreadsheet, so not checking."
else:
    df = pd.read_excel(spreadsheet_path, sheetname='names', skiprows=4)
    print "Looking for {} names of {} species in {} models".format(df[df.columns[3:]].count().sum(), *df.shape)
    for s in species_list:
        display(s)
        smiles = s.molecule[0].toSMILES()
        formula = s.molecule[0].getFormula()
        print smiles, formula

        for testsmiles in df[df.Formula==formula].Species:
            m = rmgpy.molecule.Molecule(SMILES=str(testsmiles))
            if s.isIsomorphic(m):
                print testsmiles
                d = df[df.Species==testsmiles]
                print Counter(d.values[0,2:])
                break
        else:
            print "didn't find in table"
Looking for 8251 names of 418 species in 76 models
CC(=O)C=O C3H4O2
didn't find in table
CCCCCC(C)=O C7H14O
didn't find in table
C#CCO C3H4O
didn't find in table
CCCCCCC=O C7H14O
didn't find in table
C=C=CCC C5H8
didn't find in table
C=C=CC C4H6
C=C=CC
Counter({nan: 35, u'C4H612': 25, u'c4h612': 5, u'C4H6-12': 4, u'CC*C*C': 1, u'iiC4H6': 1, u'C4H6': 1, u'CH2CCHCH3': 1, u'C*C*CC': 1})
CCCC(=O)CCC C7H14O
didn't find in table
C=CCCC(C)=O C6H10O
didn't find in table
C=C=CO C3H4O
didn't find in table
CC(C)O C3H8O
didn't find in table
C=CCC(C)=O C5H8O
didn't find in table
C=CCC(=O)CC C6H10O
didn't find in table
CCCCC(=O)CC C7H14O
didn't find in table
O=COC=O C2H2O3
didn't find in table
In [14]:
# Report possible suggested names, for you to choose from
possibles = {}
for s in species_list:
    possibles[s.props['smiles']] = s.props['names']
possibles
Out[14]:
{'C#CCO': ['Prop-2-yn-1-ol',
  '107-19-7',
  '4-01-00-02214 (Beilstein Handbook Reference)',
  'AI3-24359',
  'Acetylene carbinol',
  'Acetylenylcarbinol',
  'Agrisynth PA',
  'BRN 0506003',
  'CCRIS 6781',
  'EINECS 203-471-2',
  'HSDB 6054',
  'NA1986',
  'NSC 8804',
  'Propargyl alcohol [NA1986]  [Flammable liquid]',
  'Propiolic alcohol',
  'RCRA waste no. P102',
  'RCRA waste number P102',
  '81820_FLUKA',
  'InChI=1/C3H4O/c1-2-3-4/h1,4H,3H',
  'NCGC00091559-01',
  '1-Hydroxy-2-propyne',
  '1-Propyn-3-ol',
  '1-Propyn-3-yl alcohol',
  '2-Propyn-1-ol',
  '2-Propynol',
  '2-Propynyl alcohol',
  '3-Hydroxy-1-propyne',
  '3-Propynol',
  'C05986',
  'Ethynylcarbinol',
  'NA 1986',
  'Prop-2-in-1-ol',
  'Prop-2-yn-1-ol',
  'Prop-2-yne-1-ol',
  'Propargyl alcohol',
  'Propynyl alcohol',
  'Ethynyl carbinol',
  'Methanol, ethynyl-',
  'NSC8804',
  'WLN: Q2UU1',
  'P50803_ALDRICH',
  'CHEBI:28905'],
 'C=C=CC': ['buta-1,2-diene',
  '590-19-2',
  '1,2-Butadien',
  'Buta-1,2-dien',
  'CH2=C=CH-CH3',
  '18853_FLUKA',
  '1,2-BUTADIENE',
  '1-Methylallene',
  'Allene, methyl-',
  'EINECS 209-674-2',
  'HSDB 5705',
  'Methylallene',
  'InChI=1/C4H6/c1-3-4-2/h4H,1H2,2H',
  'buta-1,2-diene',
  'CHEBI:39480',
  '18855_FLUKA'],
 'C=C=CCC': ['Penta-1,2-diene',
  '591-95-7',
  '1,2-PENTADIENE',
  'EINECS 209-737-4',
  'Penta-1,2-diene',
  'InChI=1/C5H8/c1-3-5-4-2/h5H,1,4H2,2H',
  'Ethylallene'],
 'C=C=CO': 'propa-1,2-dien-1-ol',
 'C=CCC(=O)CC': ['hex-5-en-3-one', '24253-30-3', '5-Hexen-3-one'],
 'C=CCC(C)=O': ['pent-4-en-2-one',
  '13891-87-7',
  'Allyl methyl ketone',
  '4-Penten-2-one'],
 'C=CCCC(C)=O': ['hex-5-en-2-one',
  '109-49-9',
  '5-Hexen-2-one',
  '5-Hexene-2-one',
  'Allylacetone',
  'NSC6973',
  'ALLYL ACETONE',
  'InChI=1/C6H10O/c1-3-4-5-6(2)7/h3H,1,4-5H2,2H',
  'EINECS 203-675-1',
  'AI3-21995',
  'NSC 6973',
  'ZINC01867148',
  'H13001_ALDRICH',
  'SBB009089',
  '1-Hexen-5-one'],
 'CC(=O)C=O': ['2-Oxopropanal',
  '2-Ketopropionaldehyde',
  '78-98-8',
  '.alpha.-Ketopropionaldehyde',
  '1-Ketopropionaldehyde',
  'Acetylformyl',
  'Glyoxal, methyl',
  'NSC79019',
  'Propanal, 2-oxo-',
  'Propanedione',
  'Propanolone',
  'Propionaldehyde, 2-keto',
  'Propionaldehyde, 2-oxo-',
  'Pyroracemic aldehyde',
  'WLN: VHV1',
  '2-Ketopropionaldehyde',
  '2-Oxopropanal',
  'C00546',
  '67028_FLUKA',
  'Methylglyoxal solution',
  '2-oxo-propanal',
  'METHYL-GLYOXAL',
  'acetylformaldehyde',
  'methylglyoxal',
  'oxopropanal',
  'pyruvaldehyde',
  'pyruvic aldehyde',
  '2-Oxopropionaldehyde',
  '4-01-00-03631 (Beilstein Handbook Reference)',
  'Acetalformaldehyde',
  'BRN 0906750',
  'CCRIS 1741',
  'EINECS 201-164-8',
  'FEMA No. 2969',
  'METHYL GLYOXAL',
  'NSC 337790',
  'NSC 626580',
  'NSC 79019',
  'alpha-Ketopropionaldehyde',
  'alpha-Ketopropionic aldehyde',
  'Propanal, 2-oxo- (9CI)',
  'Pyruvaldehyde (8CI)',
  '1,2-propanedione',
  'CH3COCHO',
  'CHEBI:17158',
  'Pyruvaldehyde solution',
  'W296902_ALDRICH',
  'AIDS-132495',
  'AIDS132495',
  'NSC626580',
  'LS-139762',
  'ZINC01532681',
  'PVL',
  'M0252_SIGMA'],
 'CC(C)O': ['Propan-2-ol',
  '8013-70-5',
  '67-63-0',
  '5131-95-3',
  'Isopropyl alcohol (USP)',
  'InChI=1/C3H8O/c1-3(2)4/h3-4H,1-2H',
  '40301_RIEDEL',
  '34959_RIEDEL',
  'CHEBI:17824',
  'Isopropylalkohol',
  '1-Hydroxy-1-methylethyl',
  'Ethyl, 1-hydroxy-1-methyl-',
  'LS-1565',
  '2-Propanol',
  'C01845',
  'Isopropanol',
  'Propan-2-ol',
  '2-Propanol : Water 31:69 with 0.1% buffer',
  '2-Propanol solution',
  '92438_FLUKA',
  'N-Term LC Solvent System B',
  '109827_ALDRICH',
  '34965_RIEDEL',
  '2-PROPANOL, ISOPROPANOL',
  'IOH',
  '650447_ALDRICH',
  '437522_SIAL',
  'I9782_SIGMA',
  '278475_ALDRICH',
  '33539_RIEDEL',
  '563935_ALDRICH',
  'Alcool isopropylique',
  '673773_ALDRICH',
  '40279_RIEDEL',
  '190764_SIAL',
  'Alcohol, rubbing',
  'Alcool isopropilico',
  'IPA',
  'Iso-propylalkohol',
  'Isopropenol',
  'NSC135801',
  'WLN: QY1&1',
  'i-Propylalkohol',
  '40314_RIEDEL',
  '442369_SUPELCO',
  '24137_RIEDEL',
  'ST5214369',
  'sec-propanol',
  'Secondary alcohol',
  '34895_RIEDEL',
  'I9516_SIGMA',
  'Rubbing alcohol',
  '1-Methylethanol',
  '1-Methylethyl alcohol',
  '2-Hydroxypropane',
  '2-Propyl alcohol',
  '4-01-00-01461 (Beilstein Handbook Reference)',
  'AI3-01636',
  'Alcojel',
  'Alcolo',
  'Alcool isopropilico [Italian]',
  'Alcool isopropylique [French]',
  'Alcosolve',
  'Alcosolve 2',
  'Alkolave',
  'Arquad DMCB',
  'Avantin',
  '534021_ALDRICH',
  'BRN 0635639',
  'CCRIS 2308',
  'Caswell No. 507',
  'Combi-schutz',
  'Dimethylcarbinol',
  'EINECS 200-661-7',
  'EPA Pesticide Chemical Code 047601',
  'FEMA No. 2929',
  'FEMA Number 2929',
  'HSDB 116',
  'Hartosol',
  'Imsol A',
  'Iso-propyl alcohol',
  'Iso-propylalkohol [German]',
  'Isohol',
  'Isopropanol or isopropyl alcohol [UN1219]  [Flammable liquid]',
  'Isopropyl alcohol',
  'Isopropyl alcohol (manufacture strong-acid process)',
  'Isopropyl alcohol (manufacturing-strong acid process only)',
  'Isopropyl alcohol (only persons who manufacture by the strong acid process are subject, supplier notification not required)',
  'Isopropyl alcohol [USAN]',
  'Isopropyl alcohol, rubbing',
  'Lavacol',
  'Lutosol',
  'NSC 135801',
  'Petrohol',
  'Propol',
  'Spectrar',
  'Sterisol hand disinfectant',
  'Takineocol',
  'UN1219',
  'Visco 1152',
  'i-Propanol [German]',
  'i-Propyl alcohol',
  'i-Propylalkohol [German]',
  'n-Propan-2-ol',
  'sec-Propyl alcohol',
  '59304_FLUKA',
  '439207_ALDRICH',
  '59309_FLUKA',
  '675431_ALDRICH',
  'i-propanol',
  '40219_RIEDEL',
  '154970_SIAL',
  '34863_SIAL',
  'Isopropryl alcohol',
  'c0519',
  'W292907_ALDRICH',
  'CHEBI:35681',
  'secondary alcohols',
  'ZINC00901159',
  '91237_FLUKA',
  'AIDS-186244',
  'AIDS186244',
  'NCGC00090917-01',
  'Avantine',
  "R-CHOH-R'",
  '40343_RIEDEL',
  'I9030_SIGMA',
  '443425_SIAL',
  'D00137',
  'Isopro',
  'Isopro (TN)',
  'Isopropanol (JP15)'],
 'CCCC(=O)CCC': ['Heptan-4-one',
  '123-19-3',
  'W254606_ALDRICH',
  'InChI=1/C7H14O/c1-3-5-7(8)6-4-2/h3-6H2,1-2H',
  '4-Heptanone',
  'Butyrone',
  'Di-n-propyl ketone',
  'Dipropyl ketone',
  'Heptan-4-one',
  'NSC8692',
  'Propyl ketone',
  'WLN: 3V3',
  '101745_ALDRICH',
  '46204_RIEDEL',
  'ZINC01648177',
  '4-01-00-03323 (Beilstein Handbook Reference)',
  '4-Heptanone (natural)',
  'AI3-15181',
  'BRN 1699049',
  'DI(N-PROPYL) KETONE',
  'Dipropyl ketone [UN2710]  [Flammable liquid]',
  'EINECS 204-608-9',
  'FEMA No. 2546',
  'NSC 8692',
  'UN2710'],
 'CCCCC(=O)CC': ['Heptan-3-one',
  '106-35-4',
  'Heptan-3-one',
  'N-Butyl ethyl ketone',
  'NSC8448',
  'WLN: 4V2',
  '03220_FLUKA',
  '3-Heptanone solution',
  'InChI=1/C7H14O/c1-3-5-6-7(8)4-2/h3-6H2,1-2H',
  '46203_RIEDEL',
  '4-01-00-03321 (Beilstein Handbook Reference)',
  'AI3-19684',
  'Aethylbutylketon [German]',
  'BRN 0506161',
  'EINECS 203-388-1',
  'Eptan-3-one [Italian]',
  'Ethyl butyl ketone 3-Heptanone',
  'Ethyl-n-butyl ketone',
  'Ethylbutylcetone [French]',
  'Ethylbutylketon [Dutch]',
  'Etilbutilchetone [Italian]',
  'FEMA No. 2545',
  'HSDB 1816',
  'Heptan-3-on [Dutch, German]',
  'NSC 8448',
  '02477_FLUKA',
  'ZINC01586745',
  'H6511_SIGMA',
  'W254509_ALDRICH',
  '551325_ALDRICH',
  '3-HEPTANONE',
  'Aethylbutylketon',
  'Butyl ethyl ketone',
  'Eptan-3-one',
  'Ethyl butyl ketone',
  'Ethyl n-butyl ketone',
  'Ethylbutylcetone',
  'Ethylbutylketon',
  'Etilbutilchetone',
  'Heptan-3-on'],
 'CCCCCC(C)=O': ['Heptan-2-one',
  '29299-43-2',
  '110-43-0',
  'Methyl-n-pentyl ketone',
  '537683_SIAL',
  '68592_FLUKA',
  '2-Heptanone (natural)',
  '4-01-00-03318 (Beilstein Handbook Reference)',
  'AI3-01230',
  'Amyl-methyl-cetone [French]',
  'BRN 1699063',
  'EINECS 203-767-1',
  'FEMA No. 2544',
  'FEMA Number 2544',
  'HSDB 1122',
  'Ketone C-7',
  'Methyl-amyl-cetone [French]',
  'Methyl-n-amylketone',
  'NSC 7313',
  'UN1110',
  'n-Amyl methyl ketone [UN1110]  [Flammable liquid]',
  'Amyl methyl ketone',
  'Amyl-methyl-cetone',
  'Butylacetone',
  'Ketone, methyl pentyl',
  'Methyl amyl ketone',
  'Methyl n-pentyl ketone',
  'Methyl pentyl ketone',
  'Methyl-amyl-cetone',
  'NSC7313',
  'Pentyl methyl ketone',
  'WLN: 5V1',
  'n-Amyl methyl ketone',
  'n-Pentyl methyl ketone',
  '123366_ALDRICH',
  'InChI=1/C7H14O/c1-3-4-5-6-7(2)8/h3-6H2,1-2H',
  'LMFA12000004',
  'CHEBI:5672',
  '2-Heptanone',
  'C08380',
  'Heptan-2-one',
  'Methyl n-amyl ketone',
  '02476_FLUKA',
  'Heptanone',
  'W254401_ALDRICH',
  'ZINC01531087'],
 'CCCCCCC=O': ['Heptanal',
  'Enanthaldehyde',
  '111-71-7',
  'H2120_SIAL',
  'Enanthal',
  'Enanthaldehyde',
  'Enanthic aldehyde',
  'Enanthole',
  'Heptaldehyde',
  'Heptanal',
  'Heptanaldehyde',
  'Heptyl aldehyde',
  'NSC2190',
  'Oenanthal',
  'Oenanthaldehyde',
  'Oenanthic aldehyde',
  'Oenanthol',
  'WLN: VH6',
  'n-Heptaldehyde',
  'n-Heptanal',
  'n-Heptylaldehyde',
  'LMFA06000001',
  'NCGC00091807-01',
  '75170_FLUKA',
  'InChI=1/C7H14O/c1-2-3-4-5-6-7-8/h7H,2-6H2,1H',
  '1-Heptanal',
  'W254002_ALDRICH',
  'W254010_ALDRICH',
  '4-01-00-03314 (Beilstein Handbook Reference)',
  'AI3-02066',
  'Aldehyde C-7',
  'BRN 1560236',
  'CCRIS 6041',
  'EINECS 203-898-4',
  'FEMA No. 2540',
  'FEMA Number 2541',
  'HSDB 6026',
  'Heptanal (natural)',
  'Heptylaldehyde',
  'NSC 2190',
  'UN3056',
  'n-Heptaldehyde [UN3056]  [Flammable liquid]',
  'C14390',
  'nchembio882-comp3'],
 'O=COC=O': ['formyl formate',
  'formic acid formyl ester',
  'methanoyl methanoate',
  '1558-67-4',
  'CHEBI:36657',
  'formic acid anhydride',
  'formic anhydride']}
In [15]:
# Choose and specify some names for each.
# Unforutnately they can't start with a digit, ruling out many IUPAC names
preferred = {
 'C#CCO': 'prop2yn1ol',
 'C=C=CC': 'C4H612', # buta12diene
 'C=C=CCC': 'penta12diene', # Penta-1,2-diene
 'C=C=CO': 'propadienol', # propa-1,2-dien-1-ol
 'C=CCC(=O)CC': 'hex5en3one',
 'C=CCC(C)=O': 'pent4en2one',
 'C=CCCC(C)=O': 'hex5en2one',
 'CC(=O)C=O': 'oxopropanal',
 'CC(C)O': 'propan2ol',
 'CCCC(=O)CCC': 'heptan4one',
 'CCCCC(=O)CC': 'heptan3one',
 'CCCCCC(C)=O': 'heptan2one',
 'CCCCCCC=O': 'heptanal',
 'O=COC=O': 'formicanhydride',
}
In [19]:
# Check if the chosen names can be correctly resolved using NCI/CADD Chemical Identifier Resolver
for s in species_list:
    display(s)
    smiles = s.molecule[0].toSMILES()
    name = preferred[smiles]
    s.label = name
    round_trip_smiles = cirpy.resolve(name, 'smiles')
    print name
    if round_trip_smiles is None:
        print "WARNING: Cannot interpret above name using NCI/CADD Chemical Identifier Resolver:"
        continue
    m = rmgpy.molecule.Molecule(SMILES=round_trip_smiles)
    if not s.isIsomorphic(m):
        print "WARNING: Cannot resolve above name correctly using NCI/CADD Chemical Identifier Resolver:"
    
oxopropanal
heptan2one
prop2yn1ol
heptanal
penta12diene
WARNING: Cannot interpret above name using NCI/CADD Chemical Identifier Resolver:
C4H612
WARNING: Cannot interpret above name using NCI/CADD Chemical Identifier Resolver:
heptan4one
hex5en2one
propadienol
propan2ol
pent4en2one
hex5en3one
heptan3one
formicanhydride
In [20]:
for s in species_list:
    smiles = s.props['smiles']
    name = s.label
    smiles_names.loc[smiles] = name
smiles_names.to_csv(csv_filename)
smiles_names
Out[20]:
Name
SMILES
CC(=O)C=O oxopropanal
CCCCCC(C)=O heptan2one
C#CCO prop2yn1ol
CCCCCCC=O heptanal
C=C=CCC penta12diene
C=C=CC C4H612
CCCC(=O)CCC heptan4one
C=CCCC(C)=O hex5en2one
C=C=CO propadienol
CC(C)O propan2ol
C=CCC(C)=O pent4en2one
C=CCC(=O)CC hex5en3one
CCCCC(=O)CC heptan3one
O=COC=O formicanhydride
In [21]:
thermo_filename = 'new-species-{}-thermo.txt'.format(model_name)
rmgpy.chemkin.saveChemkinFile(thermo_filename, species=species_list, reactions=[])
In [22]:
print(open(thermo_filename).read())
ELEMENTS
	H
	D /2.014/
	T /3.016/
	C
	CI /13.003/
	O
	OI /18.000/
	N
	Ne
	Ar
	He
	Si
	S
	Cl
END

SPECIES
    oxopropanal         ! oxopropanal
    heptan2one          ! heptan2one
    prop2yn1ol          ! prop2yn1ol
    heptanal            ! heptanal
    penta12diene        ! penta12diene
    C4H612              ! C4H612
    heptan4one          ! heptan4one
    hex5en2one          ! hex5en2one
    propadienol         ! propadienol
    propan2ol           ! propan2ol
    pent4en2one         ! pent4en2one
    hex5en3one          ! hex5en3one
    heptan3one          ! heptan3one
    formicanhydride     ! formicanhydride
END



THERM ALL
    300.000  1000.000  5000.000

! Thermo group additivity estimation: group(Cs-(Cds-Od)HHH) + gauche(Cs(RRRR)) + other(R) + group(Cds-Od(Cds-Od)Cs) + other(R) + group(Cds-Od(Cds-Od)H)
! + other(R) + group(Od-Cd) + other(R) + group(Od-Cd) + other(R)
oxopropanal             H   4C   3O   2     G   100.000  5000.000 1438.66      1
 8.86727975E+00 1.63469496E-02-7.19389455E-06 1.33598378E-09-9.10200847E-14    2
-3.67480596E+04-1.91441494E+01 2.55141215E+00 2.81058934E-02-1.34053418E-05    3
 1.41131089E-09 3.82981498E-13-3.43304075E+04 1.57100003E+01                   4

! Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)Cs(CsRR)RR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) +
! other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) + group(Cs-(Cds-Od)CsHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) +
! gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-(Cds-Od)HHH) + gauche(Cs(RRRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Od-Cd) + other(R)
heptan2one              H  14C   7O   1     G   100.000  5000.000 1540.57      1
 1.06941671E+01 5.28615154E-02-2.29333732E-05 4.24958615E-09-2.90433823E-13    2
-4.26199059E+04-2.31201481E+01 6.25470758E-01 7.90040789E-02-4.83872753E-05    3
 1.52644225E-08-2.07788010E-12-3.95175737E+04 2.98067873E+01                   4

! Thermo library: CHO
prop2yn1ol              H   4C   3O   1     G   100.000  5000.000 1089.70      1
 7.21412170E+00 1.35296418E-02-5.40153999E-06 9.90482256E-10-6.86284031E-14    2
 1.92852358E+03-1.06537059E+01 2.79887153E+00 2.25818469E-02-8.01311052E-06    3
-3.43729334E-09 2.32956902E-12 3.31559388E+03 1.29758109E+01                   4

! Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)Cs(CsRR)RR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)Cs(CsRR)RR)) +
! other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) + group(Cs-(Cds-Od)CsHH) +
! gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cds-OdCsH) + other(R) + group(Od-Cd) + other(R)
heptanal                H  14C   7O   1     G   100.000  5000.000 1616.88      1
 1.16690651E+01 5.16336636E-02-2.22663252E-05 4.10172828E-09-2.78794424E-13    2
-3.93589239E+04-2.81866106E+01 5.91069173E-01 7.90396272E-02-4.76912819E-05    3
 1.45849036E-08-1.89969638E-12-3.57765798E+04 3.05812321E+01                   4

! Thermo group additivity estimation: group(Cs-(Cds-Cds)CsHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(CsRRR)) + other(R) + group
! (Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Cdd-CdsCds) + other(R)
penta12diene            H   8C   5          G   100.000  5000.000 1043.78      1
 9.31676115E+00 2.53742392E-02-1.00399325E-05 1.85449737E-09-1.29898839E-13    2
 1.25214683E+04-2.20473944E+01 2.00141332E+00 3.59534977E-02-1.59360575E-07    3
-2.04773271E-08 9.05613207E-12 1.49994272E+04 1.81131417E+01                   4

! Thermo library: USC-Mech-ii
C4H612                  H   6C   4          G   298.000  3000.000 1000.00      1
 1.78156000E+01-4.25750000E-03 1.05118000E-05-4.47384000E-09 5.84814000E-13    2
 1.26734000E+04-6.98266000E+01 1.02347000E+00 3.49592000E-02-2.20090000E-05    3
 6.94227000E-09-7.87919000E-13 1.81180000E+04 1.97507000E+01                   4

! Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group(Cs
! -(Cds-Od)CsHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-(Cds-Od)CsHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) +
! gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Od-Cd) + other(R)
heptan4one              H  14C   7O   1     G   100.000  5000.000  795.42      1
 5.33267287E+00 6.25846114E-02-2.86352679E-05 5.50167210E-09-3.87316350E-13    2
-4.05014204E+04 6.31185615E+00 3.22796397E-01 8.77771786E-02-7.61413375E-05    3
 4.53163546E-08-1.29005248E-11-3.97043960E+04 2.93351371E+01                   4

! Thermo group additivity estimation: group(Cs-(Cds-Od)CsHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-(Cds-Cds)CsHH) + gauche(Cs(CsRRR)) + other(R) +
! group(Cs-(Cds-Od)HHH) + gauche(Cs(RRRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cds-
! CdsHH) + gauche(CsOsCdSs) + other(R) + group(Od-Cd) + other(R)
hex5en2one              H  10C   6O   1     G   100.000  5000.000 1772.11      1
 1.22673803E+01 3.49639561E-02-1.47424665E-05 2.66946935E-09-1.78773680E-13    2
-2.52023366E+04-3.35942951E+01 1.27985196E+00 5.97649777E-02-3.57352680E-05    3
 1.05669525E-08-1.29290989E-12-2.13081170E+04 2.57009161E+01                   4

! Thermo group additivity estimation: group(Cds-CdsOsH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Cdd-
! CdsCds) + other(R) + group(Os-(Cds-Cd)H) + gauche(Os(RR)) + other(R)
propadienol             H   4C   3O   1     G   100.000  5000.000  901.95      1
 1.62976867E+01-2.39905418E-03 3.97496224E-06-8.57284616E-10 5.72966396E-14    2
-7.04786284E+03-6.20027499E+01 2.31584489E+00 2.36135637E-02 2.05759708E-05    3
-5.73741409E-08 2.79866622E-11-3.06158539E+03 1.21249748E+01                   4

! Thermo library: CHO
propan2ol               H   8C   3O   1     G   100.000  5000.000  983.86      1
 9.94822736E+00 1.85856809E-02-6.82049858E-06 1.26980689E-09-9.17915272E-14    2
-3.73806623E+04-2.67645960E+01 2.40117490E+00 2.52652046E-02 1.95923301E-05    3
-4.14254559E-08 1.70582767E-11-3.47338454E+04 1.54268950E+01                   4

! Thermo group additivity estimation: group(Cs-(Cds-Od)(Cds-Cds)HH) + gauche(Cs(RRRR)) + other(R) + group(Cs-(Cds-Od)HHH) + gauche(Cs(RRRR)) + other(R)
! + group(Cds-OdCsCs) + other(R) + group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group(Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Od-Cd) +
! other(R)
pent4en2one             H   8C   5O   1     G   100.000  5000.000 1132.82      1
 1.09324041E+01 2.91217084E-02-1.35654566E-05 2.68707822E-09-1.93818092E-13    2
-2.13164173E+04-3.07771717E+01 1.84389770E+00 3.71821339E-02 7.58181251E-06    3
-2.84843905E-08 1.08180105E-11-1.77153459E+04 2.10088096E+01                   4

! Thermo group additivity estimation: group(Cs-(Cds-Od)CsHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-(Cds-Od)(Cds-Cds)HH) + gauche(Cs(RRRR)) +
! other(R) + group(Cs-CsHHH) + gauche(Cs(CsRRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Cds-CdsCsH) + gauche(CsOsCdSs) + other(R) + group
! (Cds-CdsHH) + gauche(CsOsCdSs) + other(R) + group(Od-Cd) + other(R)
hex5en3one              H  10C   6O   1     G   100.000  5000.000 1600.22      1
 1.69247517E+01 3.09005374E-02-1.41674016E-05 2.64920602E-09-1.79532917E-13    2
-2.72511503E+04-6.33190213E+01 9.99159418E-01 5.97035176E-02-3.08502457E-05    3
 5.30160471E-09 7.75288271E-14-2.07451617E+04 2.54028529E+01                   4

! Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) + group(Cs-CsCsHH) + gauche(Cs(Cs(CsRR)CsRR)) + other(R) +
! group(Cs-(Cds-Od)CsHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-(Cds-Od)CsHH) + gauche(Cs(CsRRR)) + other(R) + group(Cs-CsHHH) +
! gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(CsRRR)) + other(R) + group(Cds-OdCsCs) + other(R) + group(Od-Cd) + other(R)
heptan3one              H  14C   7O   1     G   100.000  5000.000  795.42      1
 5.33267287E+00 6.25846114E-02-2.86352679E-05 5.50167210E-09-3.87316350E-13    2
-4.05014204E+04 7.00500333E+00 3.22796397E-01 8.77771786E-02-7.61413375E-05    3
 4.53163546E-08-1.29005248E-11-3.97043960E+04 3.00282843E+01                   4

! Thermo group additivity estimation: group(Cds-OdOsH) + other(R) + group(Cds-OdOsH) + other(R) + group(Os-(Cds-Od)(Cds-Od)) + gauche(Os(RR)) + other(R)
! + group(Od-Cd) + other(R) + group(Od-Cd) + other(R)
formicanhydride         H   2C   2O   3     G   100.000  5000.000 1522.34      1
 9.19078336E+00 9.16701111E-03-4.37894780E-06 8.41812304E-10-5.82473977E-14    2
-6.05914952E+04-1.80341419E+01 2.83834887E+00 2.23426474E-02-1.38972026E-05    3
 3.49308202E-09-2.44518803E-13-5.82500111E+04 1.66202650E+01                   4

END



REACTIONS    KCAL/MOLE   MOLES

END


In [23]:
transport_filename = 'new-species-{}-transport.txt'.format(model_name)
rmgpy.chemkin.saveTransportFile(transport_filename,species_list)
In [24]:
print(open(transport_filename).read())
! Species         Shape    LJ-depth  LJ-diam   DiplMom   Polzblty  RotRelaxNum Data     
! Name            Index    epsilon/k_B sigma     mu        alpha     Zrot      Source   
oxopropanal         2     430.747     5.592     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=559.41 K, Pc=46.47 bar (from Joback method)
heptan2one          2     454.497     6.624     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=590.26 K, Pc=29.5 bar (from Joback method)
prop2yn1ol          2     403.598     5.569     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=524.15 K, Pc=44.09 bar (from Joback method)
heptanal            2     446.744     6.612     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=580.19 K, Pc=29.16 bar (from Joback method)
penta12diene        2     378.803     5.505     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=491.95 K, Pc=42.83 bar (from Joback method)
C4H612              2     360.421     5.186     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=468.08 K, Pc=48.77 bar (from Joback method)
heptan4one          2     454.497     6.624     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=590.26 K, Pc=29.5 bar (from Joback method)
hex5en2one          2     437.984     6.104     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=568.81 K, Pc=36.33 bar (from Joback method)
propadienol         2     413.401     5.579     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=536.88 K, Pc=44.92 bar (from Joback method)
propan2ol           2     404.948     5.858     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=525.91 K, Pc=38.01 bar (from Joback method)
pent4en2one         2     420.945     5.789     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=546.68 K, Pc=40.93 bar (from Joback method)
hex5en3one          2     437.984     6.104     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=568.81 K, Pc=36.33 bar (from Joback method)
heptan3one          2     454.497     6.624     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=590.26 K, Pc=29.5 bar (from Joback method)
formicanhydride     2     422.861     5.462     0.000     0.000     0.000    ! Epsilon & sigma estimated with Tc=549.17 K, Pc=48.97 bar (from Joback method)

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# Check that we can convert it into cantera
outdir = 'CanteraFiles'
new_parser = ck2cti.Parser()
surfaces = new_parser.convertMech(inputFile=thermo_filename,
                              thermoFile=None,
                              transportFile=transport_filename,
                                surfaceFile=None,
                              phaseName='gas',
                              outName=os.path.join(outdir,model_name+'.new-species.cti'),
                                  permissive=True)
Wrote CTI mechanism file to 'CanteraFiles/heptane.new-species.cti'.
Mechanism contains 14 species and 0 reactions.
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