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.
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
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
[1] http://www.ddbst.com/published-parameters-unifac.html
[2] Joback, K. G., & Reid, R. C. (1987). ESTIMATION OF PURE-COMPONENT PROPERTIES FROM GROUP-CONTRIBUTIONS. Chemical Engineering Communications, 57(1–6), 233–243. https://doi.org/10.1080/00986448708960487
[3] Joback, K. G. (1989). Designing molecules possessing desired physical property values [Thesis (Ph. D.), Massachusetts Institute of Technology]. https://dspace.mit.edu/handle/1721.1/14191
[4] Bondi, A. (1966). Estimation of Heat Capacity of Liquids. Industrial & Engineering Chemistry Fundamentals, 5(4), 442–449. https://doi.org/10.1021/i160020a001
[5] Rowlinson, J. S., & Swinton, F. (2013). Liquids and liquid mixtures: Butterworths monographs in chemistry. Butterworth-Heinemann