ugropy is a Python library to obtain subgroups from different thermodynamic
group contribution models using both the name or the SMILES representation of a
molecule. If the name is given, the library uses the
PubChemPy library to obtain the SMILES
representation from PubChem. In both cases, ugropy uses the
RDKit library to search the functional groups
in the molecule.
ugropy is in an early development stage, leaving issues of examples of
molecules that ugropy fails solving the subgroups of a model is very helpful.
ugropy is tested for Python 3.10, 3.11 and 3.12 on Linux, Windows and Mac
OS.
You can try ugropy from its Binder. Open the binder.ipynb file to explore the basic features.
- Classic liquid-vapor UNIFAC
- Predictive Soave-Redlich-Kwong (PSRK)
- Joback
ugropy allows you to convert the obtained functional groups or estimated
properties to the input format required by the following thermodynamic
libraries:
You can check the full tutorial here.
Get groups from the molecule's name:
from ugropy import Groups
hexane = Groups("hexane")
print(hexane.unifac.subgroups)
print(hexane.psrk.subgroups)
print(hexane.joback.subgroups){'CH3': 2, 'CH2': 4}
{'CH3': 2, 'CH2': 4}
{'-CH3': 2, '-CH2-': 4}
Get groups from molecule's SMILES:
propanol = Groups("CCCO", "smiles")
print(propanol.unifac.subgroups)
print(propanol.psrk.subgroups)
print(propanol.joback.subgroups){'CH3': 1, 'CH2': 2, 'OH': 1}
{'CH3': 1, 'CH2': 2, 'OH': 1}
{'-CH3': 1, '-CH2-': 2, '-OH (alcohol)': 1}
Estimate properties with the Joback model!
limonene = Groups("limonene")
print(limonene.joback.subgroups)
print(f"{limonene.joback.critical_temperature} K")
print(f"{limonene.joback.vapor_pressure(176 + 273.15)} bar"){'-CH3': 2, '=CH2': 1, '=C<': 1, 'ring-CH2-': 3, 'ring>CH-': 1, 'ring=CH-': 1, 'ring=C<': 1}
657.4486692170663 K
1.0254019428522743 bar
Visualize your results! (The next code creates the ugropy logo)
from IPython.display import SVG
mol = Groups("CCCC1=C(COC(C)(C)COC(=O)OCC)C=C(CC2=CC=CC=C2)C=C1", "smiles")
svg = mol.unifac.draw(
title="ugropy",
width=800,
height=450,
title_font_size=50,
legend_font_size=14
)
SVG(svg)Write down the Clapeyron.jl .csv input files.
from ugropy import writers
names = ["limonene", "adrenaline", "Trinitrotoluene"]
grps = [Groups(n) for n in names]
# Write the csv files into a database directory
writers.to_clapeyron(
molecules_names=names,
unifac_groups=[g.unifac.subgroups for g in grps],
psrk_groups=[g.psrk.subgroups for g in grps],
joback_objects=[g.joback for g in grps],
path="database"
)Obtain the Caleb Bell's Thermo subgroups
from ugropy import unifac
names = ["hexane", "2-butanone"]
grps = [Groups(n) for n in names]
[writers.to_thermo(g.unifac.subgroups, unifac) for g in grps][{1: 2, 2: 4}, {1: 1, 2: 1, 18: 1}]
pip install ugropy