9ebc76bcdc
- set VERSION to 3.1.0 (introduce a patch level 0 so that it becomes easier to publish packages with small fixes, eg for installation) - got rid of ancient ez_install: just use pip - updated README and INSTALL - updated classifiers in setup.py (license: LGPL v2.1 and other meta data); updated URL to point to http://propka.org because unlike http://propka.ki.ku.dk it is not completely dead and has a link to the pdb2pqr propka server as well as the GitHub page
71 lines
2.6 KiB
Markdown
71 lines
2.6 KiB
Markdown
# PROPKA 3.1
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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 3.1)
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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.
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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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See [propka.ki.ku.dk](http://propka.ki.ku.dk/) for the PROPKA web server,
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using the [tutorial](http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial).
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## Installation
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Clone repository or unpack the tar ball and install with
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[setuptools](http://pythonhosted.org/setuptools/index.html) (note: if
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you don't have setuptools installed you will need an internet
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connection so that the installation procedure can download the
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required files):
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cd propka-3.1
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python setup.py install --user
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This will install the `propka31` script in your executable directory,
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as configured for setuptools, for instance `~/.local/bin`. You can
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change the bin directory with the `--install-scripts` option. For
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example, in order to install in my `bin` directory in my home
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directory:
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python setup.py install --user --install-scripts ~/bin
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## Requirements
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* Python 2.7 or higher or Python 3.1 or higher
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## Getting started
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1. Clone the code from GitHub
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2. `python setup.py install --user`
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2. Run `propka31` with a .pdb file (see Examples)
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## Examples
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Calculate using pdb file
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propka31 1hpx.pdb
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## Testing (for developers)
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Please run `Tests/runtest.py/` after changes 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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