Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.
This version is a class object that is representative of dimorhitedl.
If you use Dimorphite-DL in your research, please cite:
Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An open-source program for enumerating the ionization states of drug-like small molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.
Dimorphite-DL is released under the Apache 2.0 license. See LICENCE.txt for details.
Edit This edit is made by Sulstice for distribution and installation.
pip install dimorphite_dlEdit This edit is made by Sulstice for distribution and installation.
from dimorphite_dl import DimorphiteDL
dimorphite_dl = DimorphiteDL(
min_ph=4.5,
max_ph=8.0,
max_variants=128,
label_states=False,
pka_precision=1.0
)
print(dimorphite_dl.protonate('CC(=O)O'))
>>>
['CC(=O)[O-]']
Dimorphite-DL deprotonates indoles and pyrroles around pH 14.5. But these substructures can also be protonated around pH -3.5. Dimorphite does not perform the protonation.
See the CONTRIBUTORS.md file for a full list of contributors. Please contact
Jacob Durrant (durrantj@pitt.edu) with any questions.