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Consolidate documentation.

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Addresses https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442016279.
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Nathan Baker
2020-06-18 08:19:22 -07:00
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INSTALL
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## Installation
Clone repository or unpack the tar ball and install with
[pip](https://pip.pypa.io):
pip install <source directory>
This will install the `propka32` script in your executable
directory. The `propka` Python module will also become available for import
and can be invoked in lieu of the `propka32` script via:
python -m propka

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README.md
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@@ -4,7 +4,7 @@ PROPKA predicts the pKa values of ionizable groups in proteins
(version 3.0) and protein-ligand complexes (version 3.2 and later) (version 3.0) and protein-ligand complexes (version 3.2 and later)
based on the 3D structure. based on the 3D structure.
For proteins without ligands both version should produce the same result. For proteins without ligands, both version should produce the same result.
The method is described in the following papers, which you should cite The method is described in the following papers, which you should cite
in publications: in publications:
@@ -13,45 +13,66 @@ in publications:
* 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) * 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)
## Requirements
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).
## Installation ## Installation
Clone repository or unpack the tar ball and install with ### PIP-based installation
[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 download the
required files):
cd <source directory> The easiest way to install PROPKA is via the [PyPI archive](https://pypi.org/project/PROPKA/) with the command
python setup.py install --user
This will install the `propka32` script in your executable directory, pip install propka
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 the `bin` directory in the home
directory:
python setup.py install --user --install-scripts ~/bin As always, a virtual environment (e.g., via [virtualenv](https://pypi.org/project/virtualenv/)) is recommended when installing packages.
For the purposes of testing or development, you may prefer to install PROPKA as For the purposes of testing or development, you may prefer to install PROPKA as
an editable module via PIP by running an editable module via PIP by running
```
pip install -e . pip install -e .
```
from within a virtual environment (e.g., via [virtualenv](https://pypi.org/project/virtualenv/)).
## Requirements ### Source-based installation
* Python 3.5 or higher The source code can be installed by cloning the repository or unpacking from a source code archive and running
pip install .
in the source directory.
Installation is also possible with
[setuptools](http://pythonhosted.org/setuptools/index.html) which offers additional customization options; e.g.
python setup.py install --user
will install the `propka32` script in your executable directory,
as configured for setuptools, for instance `~/.local/bin` while
python setup.py install --user --install-scripts ~/bin
will install the script in the `bin` subdirectory of your home directory.
## Getting started ## Getting started
1. Clone the code from GitHub PROPKA can be used either as a module or via the installed script; i.e., either
2. `python setup.py install --user`
2. Run `propka32` with a .pdb file (see Examples)
## Examples propka32
Calculate using pdb file or
python -m propka
works for invoking PROPKA.
A brief list of available options can be obtained by running PROPKA with no options:
propka32
A longer list of options and descriptions is available using the `--help` option:
propka32 --help
Most users run PROPKA by invoking the program with a PDB file as its argument; e.g.,
propka32 1hpx.pdb propka32 1hpx.pdb
@@ -67,6 +88,3 @@ Please cite these references in publications:
* 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. * 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. 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. * 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.