rmgpy.rmg.model.Species

class rmgpy.rmg.model.Species(index=-1, label='', thermo=None, conformer=None, molecule=None, transportData=None, molecularWeight=None, energyTransferModel=None, reactive=True, props=None, creationIteration=0)
aug_inchi

aug_inchi: str

calculateCp0(self) → double

Return the value of the heat capacity at zero temperature in J/mol*K.

calculateCpInf(self) → double

Return the value of the heat capacity at infinite temperature in J/mol*K.

conformer

conformer: rmgpy.statmech.conformer.Conformer

copy(self, bool deep=False) → Species

Create a copy of the current species. If the kw argument ‘deep’ is True, then a deep copy will be made of the Molecule objects in self.molecule.

For other complex attributes, a deep copy will always be made.

energyTransferModel

energyTransferModel: object

fromAdjacencyList(self, adjlist)

Load the structure of a species as a Molecule object from the given adjacency list adjlist and store it as the first entry of a list in the molecule attribute. Does not generate resonance isomers of the loaded molecule.

fromSMILES(self, smiles)

Load the structure of a species as a Molecule object from the given SMILES string smiles and store it as the first entry of a list in the molecule attribute. Does not generate resonance isomers of the loaded molecule.

generateEnergyTransferModel(self)

Generate the collisional energy transfer model parameters for the species. This “algorithm” is very much in need of improvement.

generateResonanceIsomers(self, bool keepIsomorphic=True)

Generate all of the resonance isomers of this species. The isomers are stored as a list in the molecule attribute. If the length of molecule is already greater than one, it is assumed that all of the resonance isomers have already been generated.

generateStatMech(self)

Generate molecular degree of freedom data for the species. You must have already provided a thermodynamics model using e.g. generateThermoData().

generateTransportData(self)

Generate the transportData parameters for the species.

generate_aug_inchi(self)
getAugmentedInChI(self)
getDensityOfStates(self, ndarray Elist) → ndarray

Return the density of states \(\rho(E) \ dE\) at the specified energies Elist in J/mol above the ground state.

getEnthalpy(self, double T) → double

Return the enthalpy in J/mol for the species at the specified temperature T in K.

getEntropy(self, double T) → double

Return the entropy in J/mol*K for the species at the specified temperature T in K.

getFreeEnergy(self, double T) → double

Return the Gibbs free energy in J/mol for the species at the specified temperature T in K.

getHeatCapacity(self, double T) → double

Return the heat capacity in J/mol*K for the species at the specified temperature T in K.

getMolecularWeight(self)
getPartitionFunction(self, double T) → double

Return the partition function for the species at the specified temperature T in K.

getResonanceHybrid(self)

Returns a molecule object with bond orders that are the average of all the resonance structures.

getSumOfStates(self, ndarray Elist) → ndarray

Return the sum of states \(N(E)\) at the specified energies Elist in J/mol.

getSymmetryNumber(self)

Get the symmetry number for the species, which is the highest symmetry number amongst its resonance isomers and the resonance hybrid. This function is currently used for website purposes and testing only as it requires additional calculateSymmetryNumber calls.

getThermoData(self)

Returns a thermoData object of the current Species object.

If the thermo object already exists, it is either of the (Wilhoit, ThermoData) type, or it is a Future.

If the type of the thermo attribute is Wilhoit, or ThermoData, then it is converted into a NASA format.

If it is a Future, then a blocking call is made to retrieve the NASA object. If the thermo object did not exist yet, the thermo object is generated.

getTransportData(self)

Returns the transport data associated with this species, and calculates it if it is not yet available.

hasStatMech(self) → bool

Return True if the species has statistical mechanical parameters, or False otherwise.

hasThermo(self) → bool

Return True if the species has thermodynamic parameters, or False otherwise.

index

index: ‘int’

isIdentical(self, other) → bool

Return True if at least one molecule of the species is identical to other, which can be either a Molecule object or a Species object.

isIsomorphic(self, other) → bool

Return True if the species is isomorphic to other, which can be either a Molecule object or a Species object.

label

label: str

molecularWeight

Species.getMolecularWeight(self)

molecule

molecule: list

props

props: dict

reactive

reactive: ‘bool’

setMolecularWeight(self, value)
symmetryNumber

symmetryNumber: ‘short’

thermo

thermo: object

toAdjacencyList(self)

Return a string containing each of the molecules’ adjacency lists.

toCantera(self, useChemkinIdentifier=False)

Converts the RMG Species object to a Cantera Species object with the appropriate thermo data.

If useChemkinIdentifier is set to False, the species label is used instead. Be sure that species’ labels are unique when setting it False.

toChemkin(self)

Return the chemkin-formatted string for this species.

transportData

transportData: object