The Hard? way

The get_groups function

In some situation you may not require to instantiate all the models supported by ugropy, for that, you can search the model’s groups individually.

from ugropy import joback, psrk, unifac, get_groups

hexane = get_groups(unifac, "hexane")
nicotine = get_groups(psrk, "nicotine")
limonene = get_groups(joback, "limonene")

print(hexane.subgroups)
print(nicotine.subgroups)
print(limonene.subgroups)

{'CH3': 2, 'CH2': 4}
{'CH2': 3, 'CH3N': 1, 'C5H4N': 1, 'CH': 1}
{'-CH3': 2, '=CH2': 1, '=C<': 1, 'ring-CH2-': 3, 'ring>CH-': 1, 'ring=CH-': 1, 'ring=C<': 1}

Also, you can visualize the fragmentation results as in the “easy way” tutorial

from IPython.display import SVG

SVG(hexane.draw())

SVG(nicotine.draw())

SVG(limonene.draw(width=600))

The get_groups function have the signature:

get_groups(
    model=psrk,
    identifier="nicotine",
    identifier_type="name"
);

As in the Groups class you can use “name”, “smiles” or “mol” as identifier type. This can be useful for whatever you are doing and skip the overhead of setting models that you don’t want. The Groups class is pretended to be used when you think: “I want all of this molecule”. The fragmentation_model parameters represents an ugropy fragmentation model.

from ugropy import FragmentationModel

Joback

For context, check the Joback’s article: https://doi.org/10.1080/00986448708960487

The JobackProperties object is instantiated by the Group object, as we saw in the previous tutorial. However, a JobackProperties object can also be instantiated individually:

from ugropy.properties import JobackProperties

joback_carvone = JobackProperties("carvone")

joback_carvone.g_formation

34.800000000000004

As with a Groups object, the signature of a Joback object is as follows similarly, in the Groups class, you can use “name,” “smiles,” or “mol” as the identifier type with the addition that you can provide the Joback’s functional groups as a dictionary directly:

carvone  = JobackProperties(
    identifier="carvone",
    identifier_type="name",
    normal_boiling_point=None
)

hex_g = JobackProperties(identifier={"-CH3": 2, "-CH2-": 4}, identifier_type="groups")

hex_n = JobackProperties(identifier="hexane", identifier_type="name")

print(hex_g.critical_pressure)
print(hex_n.critical_pressure)

31.070992245923176
31.070992245923176

The normal_boiling_temperature parameter, if provided, is used in the Joback properties calculations instead of the Joback-estimated normal boiling temperature. Let’s examine an example from the original Joback’s article:

mol = JobackProperties("p-dichlorobenzene")

print(f"Estimated normal boiling point: {mol.normal_boiling_point} K")
print(f"Critical temperature: {mol.critical_temperature} K")

Estimated normal boiling point: 443.4 K
Critical temperature: 675.1671746814928 K

The critical temperature necessitates the estimation of the normal boiling point. Joback recommends that if the experimental value of the normal boiling point is known, it should be used instead of the estimated value.

mol = JobackProperties("p-dichlorobenzene", normal_boiling_point=447.3)

print(f"Experimental normal boiling point: {mol.exp_nbt} K")
print(f"Estimated normal boiling point: {mol.normal_boiling_point} K")
print(f"Critical temperature: {mol.critical_temperature} K")

Experimental normal boiling point: 447.3 K
Estimated normal boiling point: 443.4 K
Critical temperature: 681.1057222260526 K

The experimental value of the critical temperature for p-dichlorobenzene is 685 K. In this example, the error is not significant, but Joback warns that errors could be more significant in other cases.

Refer to the full documentation of the Joback object for information on units and further explanation.

JobackProperties?

Init signature:
JobackProperties(
    identifier: str,
    identifier_type: str = 'name',
    normal_boiling_point: float = None,
) -> None
Docstring:
Joback [1] group contribution properties estimator.

Parameters
----------
identifier : str or rdkit.Chem.rdchem.Mol
    Identifier of a molecule (name, SMILES, groups, or Chem.rdchem.Mol).
    Example: you can use hexane, CCCCCC, {"-CH3": 2, "-CH2-": 4} for name,
    SMILES and groups respectively.
identifier_type : str, optional
    Use 'name' to search a molecule by name, 'smiles' to provide the
    molecule SMILES representation, 'groups' to provide Joback groups or
    'mol' to provide a rdkit.Chem.rdchem.Mol object, by default "name".
normal_boiling_point : float, optional
    If provided, will be used to estimate critical temperature, acentric
    factor, and vapor pressure instead of the estimated normal boiling
    point, by default None.

Attributes
----------
subgroups : dict
    Joback functional groups of the molecule.
exp_nbt : float
    User provided experimental normal boiling point [K].
critical_temperature : float
    Joback estimated critical temperature [K].
critical_pressure : float
    Joback estimated critical pressure [bar].
critical_volume : float
    Joback estimated critical volume [cm³/mol].
normal_boiling_point : float
    Joback estimated normal boiling point [K].
fusion_temperature : float
    Joback estimated fusion temperature [K].
h_formation : float
    Joback estimated enthalpy of formation ideal gas at 298 K [kJ/mol].
g_formation : float
    Joback estimated Gibbs energy of formation ideal gas at 298 K [K].
heat_capacity_ideal_gas_params : dict
    Joback estimated Reid's ideal gas heat capacity equation parameters
    [J/mol/K].
h_fusion : float
    Joback estimated fusion enthalpy [kJ/mol].
h_vaporization : float
    Joback estimated vaporization enthalpy at the normal boiling point
    [kJ/mol].
sum_na : float
    Joback n_A contribution to liquid viscosity [N/s/m²].
sum_nb : float
    Joback n_B contribution to liquid viscosity [N/s/m²].
molecular_weight : float
    Molecular weight from Joback's subgroups [g/mol].
acentric_factor : float
    Acentric factor from Lee and Kesler's equation [2].
vapor_pressure_params : dict
    Vapor pressure G and k parameters for the Riedel-Plank-Miller [2]
    equation [bar].
File:           ~/code/ugropy/ugropy/properties/joback_properties.py
Type:           type
Subclasses: