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Re-packaged with setuptools for standard installation

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* 'python setup.py install' will install
  - a package 'propka' (which contains everything that 'Source' contained
    in the original distribution)
  - an executable script 'propka31' (which is identical to the original
    'propka.py' script but it is automatically generated via the setuptools
    mechanism; it uses propka.run.main().
* 'pip install' will also work
* the README.md file was changed to reflect the alterations
* metadata in the setup.py file was added

NOTE: The licence is still unclear!
This commit is contained in:
Oliver Beckstein
2013-07-25 11:14:44 -07:00
parent 695fbb4fbe
commit b928c18bab
29 changed files with 1348 additions and 577 deletions
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56
README.md
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@@ -1,45 +1,69 @@
# PROPKA 3.1
PROPKA predicts the pKa values of ionizable groups in
proteins (version 3.0) and
protein-ligand complexes (version 3.1)
based in the 3D structure.
PROPKA predicts the pKa values of ionizable groups in proteins
(version 3.0) and protein-ligand complexes (version 3.1)
based on the 3D structure.
For proteins without ligands both version should produce the same result.
The method is described in the following papers, which you should cite
in publications:
* Søndergaard, 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.
* 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.
* Olsson, Mats HM, Chresten R. Søndergaard, 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.
* 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.
See [propka.ki.ku.dk](http://propka.ki.ku.dk/) for the PROPKA web server,
using the [tutorial](http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial).
## Modifications
This release of PROPKA 3.1 was modified by Oliver Beckstein
<oliver.beckstein@asu.edu> from the released version.
* Included patches from
https://github.com/schrodinger/propka-3.1/tree/python27-compat to
make it compatible with Python 2.7
* Packaged for installation with setuptools.
## Installation
No installation needed. Just clone and run.
Clone repository or unpack the tar ball and install with
[setuptools](http://pythonhosted.org/setuptools/index.html) (note: if
you don't have setuptools installed you will need an internet
connection so that the installation procedure can sownload the
required files):
cd propka-3.1
python setup.py install --user
This will install the `propka31` script in your executable directory,
as configured for setuptools, for instance `~/.local/bin`. You can
change the bin directory with the `--install-scripts` option. For
example, in order to install in my `bin` directory in my home
directory:
python setup.py install --user --install-scripts ~/bin
## Requirements
* Python 3.1 or higher
* Python 2.7 or higher or Python 3.1 or higher
## Getting started
1. Clone the code from GitHub
2. Run 'propka.py' with a .pdb file (see Examples)
2. `python setup.py install --user`
2. Run `propka31` with a .pdb file (see Examples)
## Examples
Calculate using pdb file
./propka.py 1hpx.pdb
propka31 1hpx.pdb
If for some reason your setup with python3.1+ is
not located in '/usr/bin/python3', run the script
python3.2 propka.py 1hpx.pdb
## Testing (for developers)
@@ -49,9 +73,9 @@ Please run `Tests/runtest.py/` after changes before pushing commits.
Please cite these references in publications:
* Søndergaard, 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.
* 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.
* Olsson, Mats HM, Chresten R. Søndergaard, 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.
* 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.