dimorphite-dl 1.3.2

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Dimorphite-DL

What is it?

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.

Citation

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.

Licensing

Dimorphite-DL is released under the Apache 2.0 license. See LICENCE.txt for details.

Installation

Edit This edit is made by Sulstice for distribution and installation.

pip install dimorphite_dl

QuickStart

Edit 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-]']

Caveats

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.

Authors and Contacts

See the CONTRIBUTORS.md file for a full list of contributors. Please contact Jacob Durrant ([e-mail]) with any questions.