7a25ec6598
Changed script name to propka3 based on https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442326049 Updated additional information in setup.py
91 lines
3.4 KiB
Markdown
91 lines
3.4 KiB
Markdown
# PROPKA 3.2
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PROPKA predicts the pKa values of ionizable groups in proteins
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(version 3.0) and protein-ligand complexes (version 3.2 and later)
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based on the 3D structure.
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For proteins without ligands, both version should produce the same result.
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The method is described in the following papers, which you should cite
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in publications:
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* Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295. doi:[10.1021/ct200133y](https://doi.org/10.1021/ct200133y)
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* Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537. doi:[10.1021/ct100578z](https://doi.org/10.1021/ct100578z)
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## Requirements
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PROPKA 3.2 requires Python 3.5 or higher. Additional requirements are specified in the `requirements.txt` file and automatically satisfied when installing with [pip](https://pip.pypa.io).
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## Installation
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### PIP-based installation
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The easiest way to install PROPKA is via the [PyPI archive](https://pypi.org/project/PROPKA/) with the command
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pip install propka
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As always, a virtual environment (e.g., via [virtualenv](https://pypi.org/project/virtualenv/)) is recommended when installing packages.
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For the purposes of testing or development, you may prefer to install PROPKA as
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an editable module via PIP by running
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pip install -e .
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### Source-based installation
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The source code can be installed by cloning the repository or unpacking from a source code archive and running
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pip install .
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in the source directory.
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Installation is also possible with
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[setuptools](http://pythonhosted.org/setuptools/index.html) which offers additional customization options; e.g.
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python setup.py install --user
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will install the `propka3` script in your executable directory,
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as configured for setuptools, for instance `~/.local/bin` while
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python setup.py install --user --install-scripts ~/bin
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will install the script in the `bin` subdirectory of your home directory.
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## Getting started
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PROPKA can be used either as a module or via the installed script; i.e., either
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propka3
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or
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python -m propka
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works for invoking PROPKA.
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A brief list of available options can be obtained by running PROPKA with no options:
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propka3
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A longer list of options and descriptions is available using the `--help` option:
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propka3 --help
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Most users run PROPKA by invoking the program with a PDB file as its argument; e.g.,
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propka3 1hpx.pdb
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## Testing (for developers)
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Please see [`tests/README.md`](tests/README.md) for testing instructions.
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Please run these tests after making changes to the code and _before_ pushing commits.
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## References / Citations
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Please cite these references in publications:
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* Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
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* Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.
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