The easy way

The Groups class

ugropy is relatively straightforward to use, but let’s explore what it has to offer. Now, let’s start with the easy methods…

We’ll utilize the Groups class to retrieve the subgroups of all the models supported by ugropy.

from ugropy import Groups

carvone = Groups("carvone")

carvone.unifac.subgroups

{'CH3': 2, 'CH2': 1, 'CH': 1, 'CH2=C': 1, 'CH=C': 1, 'CH2CO': 1}

Well, that was easy… ugropy utilizes PubChemPy (link) to access PubChem and retrieve the SMILES representation of the molecule. ugropy then employs the SMILES representation along with the rdkit (link) library to identify the functional groups of the molecules.

The complete signature of the Groups class is as follows:

carvone = Groups(
    identifier="carvone",
    identifier_type="name",
    normal_boiling_temperature=None
)

The identifier_type argument (default: “name”) can be set to “name”, “smiles” or “mol”.

When “name” is set, ugropy will use the identifier argument to search in pubchem for the canonical SMILES of the molecule.

When “smiles” is set, ugropy uses it directly, this also means that the library will not suffer the overhead of searching on pubchem. Try it yourself:

carvone = Groups(
    identifier="CC1=CCC(CC1=O)C(=C)C",
    identifier_type="smiles",
    normal_boiling_temperature=None
)

carvone.unifac.subgroups

{'CH3': 2, 'CH2': 1, 'CH': 1, 'CH2=C': 1, 'CH=C': 1, 'CH2CO': 1}

If you are familiar with the rdkit library, you’ll know that there are numerous ways to define a molecule (e.g., SMILES, SMARTS, PDB file, InChIKey, etc.). ugropy supports the provision of a Mol object from the rdkit library.

from rdkit import Chem

mol_obj = Chem.MolFromInchi("InChI=1S/C10H14O/c1-7(2)9-5-4-8(3)10(11)6-9/h4,9H,1,5-6H2,2-3H3")

carvone = Groups(
    identifier=mol_obj,
    identifier_type="mol",
    normal_boiling_temperature=None
)

carvone.unifac.subgroups

{'CH3': 2, 'CH2': 1, 'CH': 1, 'CH2=C': 1, 'CH=C': 1, 'CH2CO': 1}

The current supported models are the classic liquid-vapor UNIFAC, Predictive Soave-Redlich-Kwong (PSRK) and Joback. You can access the functional groups this way:

carvone = Groups("carvone")

print(carvone.unifac.subgroups)

print(carvone.psrk.subgroups)

print(carvone.joback.subgroups)

{'CH3': 2, 'CH2': 1, 'CH': 1, 'CH2=C': 1, 'CH=C': 1, 'CH2CO': 1}
{'CH3': 2, 'CH2': 1, 'CH': 1, 'CH2=C': 1, 'CH=C': 1, 'CH2CO': 1}
{'-CH3': 2, '=CH2': 1, '=C<': 1, 'ring-CH2-': 2, 'ring>CH-': 1, 'ring=CH-': 1, 'ring=C<': 1, '>C=O (ring)': 1}

You may notice that the joback attribute is a different object. That’s because it’s a JobackProperties object, which contains all the properties that the Joback model can estimate. This will be discussed later in the Joback tutorial. As an example:

carvone.joback.normal_boiling_point

516.47

Finally, if the normal_boiling_temperature parameter is provided, it is used in the Joback properties calculations instead of the Joback-estimated normal boiling temperature (refer to the Joback tutorial).

The full documentation of the Groups class may be accessed in the API documentation. Or you can do…

Groups?

Init signature:
Groups(
    identifier: str,
    identifier_type: str = 'name',
    normal_boiling_temperature: float = None,
) -> None
Docstring:
Group class.

Stores the solved FragmentationModels subgroups of a molecule.

Parameters
----------
identifier : str or rdkit.Chem.rdchem.Mol
    Identifier of a molecule (name, SMILES or Chem.rdchem.Mol). Example:
    hexane or CCCCCC.
identifier_type : str, optional
    Use 'name' to search a molecule by name, 'smiles' to provide the
    molecule SMILES representation or 'mol' to provide a
    rdkit.Chem.rdchem.Mol object, by default "name".
normal_boiling_temperature : float, optional
    If provided, will be used to estimate critical temperature, acentric
    factor, and vapor pressure instead of the estimated normal boiling
    point in the Joback group contribution model, by default None.

Attributes
----------
identifier : str
    Identifier of a molecule. Example: hexane or CCCCCC.
identifier_type : str, optional
    Use 'name' to search a molecule by name or 'smiles' to provide the
    molecule SMILES representation, by default "name".
mol_object : rdkit.Chem.rdchem.Mol
    RDKit Mol object.
molecular_weight : float
    Molecule's molecular weight from rdkit.Chem.Descriptors.MolWt [g/mol].
unifac : Fragmentation
    Classic LV-UNIFAC subgroups.
psrk : Fragmentation
    Predictive Soave-Redlich-Kwong subgroups.
joback : JobackProperties
    JobackProperties object that contains the Joback subgroups and the
    estimated properties of the molecule.
File:           ~/code/ugropy/ugropy/groups.py
Type:           type
Subclasses:

Also, you can visualize the fragmentation result simply doing:

from IPython.display import SVG

svg = carvone.unifac.draw(width=600)

SVG(svg)

You can save the figure by doing:

with open("figure.svg", "w") as f:
    f.write(svg)

Check the full documentation of the draw funcion:

carvone.unifac.draw?

Signature:
carvone.unifac.draw(
    title: str = '',
    width: float = 400,
    height: float = 200,
    title_font_size: float = 12,
    legend_font_size: float = 12,
    font: str = 'Helvetica',
) -> Union[str, List[str]]
Docstring:
Create a svg representation of the fragmentation result.

Parameters
----------
title : str, optional
    Graph title, by default ""
width : int, optional
    Graph width, by default 400
height : int, optional
    Graph height, by default 200
title_font_size : int, optional
    Font size of graph's title, by default 12
legend_font_size : int, optional
    Legend font size, by default 12
font : str, optional
    Text font, by default "Helvetica"

Returns
-------
Union[str, List[str]]
    SVG of the fragmentation solution/s.
File:      ~/code/ugropy/ugropy/core/fragmentation_object.py
Type:      method

WARNING

For the UNIFAC, and PSRK groups the aldehyde group is change to HCO according to the discussion: https://github.com/ClapeyronThermo/Clapeyron.jl/issues/225

This is more consistent with the ether groups and formate group.