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Chemistry"],"sub_categories":[],"readme":"# PROPKA 3\n\n![Tests](https://github.com/jensengroup/propka/workflows/Tests/badge.svg)\n[![codecov](https://codecov.io/gh/jensengroup/propka/branch/master/graph/badge.svg)](https://codecov.io/gh/jensengroup/propka)\n[![PyPI version](https://badge.fury.io/py/propka.svg)](https://badge.fury.io/py/propka)\n[![RTD status](https://readthedocs.org/projects/propka/badge/)](https://propka.readthedocs.io/)\n\nPROPKA predicts the pKa values of ionizable groups in proteins\n(version 3.0) and protein-ligand complexes (version 3.1 and later)\nbased on the 3D structure.\n\nFor proteins without ligands, both version should produce the same result.\n\nThe method is described in the following papers, which you should cite\nin publications:\n\n* 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)\n\n* 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)\n\n## PROPKA versions\n\nThe code in this repository is named _PROPKA 3_ and it is based on the original PROPKA 3.1 release (described in the papers above). It has undergone various changes, which is reflected in the version numbering. For instance, version 3.2 contains a number of API changes and code refactoring that introduce incompatibilities between the original 3.1 release and the more recent versions. In the future, we will increase the minor version number to indicate further changes to the code base (e.g., release 3.4 or 3.5). The major release number is not expected to change unless major changes to the underlying algorithms are implemented.\n\n## Requirements\n\nPROPKA 3 requires Python 3.8 or higher.  Additional requirements are specified in the `requirements.txt` file and automatically satisfied when installing with [pip](https://pip.pypa.io).\n\n## Installation\n\nPROPKA can be installed on your own computer (as described below) or run from a [web interface](http://server.poissonboltzmann.org) (please [register](http://eepurl.com/by4eQr) first).\n\n### PIP-based installation\n\nThe easiest way to install PROPKA is via the [PyPI archive](https://pypi.org/project/PROPKA/) with the command\n\n    pip install propka\n\nThis installation will install the `propka` Python module and the `propka3` executable script.\nAs always, a virtual environment (e.g., via [virtualenv](https://pypi.org/project/virtualenv/)) is recommended when installing packages.\n\n### Source-based installation\n\nThe source code can be installed by cloning the repository or unpacking from a source code archive and running\n\n    pip install .\n\nin the source directory.\nFor the purposes of testing or development, you may prefer to install PROPKA as an editable module via PIP by running\n\n    pip install -e .\n\nin the source directory.\n\n## Getting started\n\nPROPKA can be used either as a module or via the installed script; i.e., either\n\n    propka3\n\nor\n\n    python -m propka\n\nworks for invoking PROPKA.\n\nA brief list of available options can be obtained by running PROPKA with no options:\n\n    propka3\n\nA longer list of options and descriptions is available using the `--help` option:\n\n    propka3 --help\n\nMost users run PROPKA by invoking the program with a PDB file as its argument; e.g.,\n\n    propka3 1hpx.pdb\n\n## Testing (for developers)\n\nPlease see [`tests/README.md`](tests/README.md) for testing instructions.\nPlease run these tests after making changes to the code and _before_ pushing commits.\n\n## Additional documentation\n\nAdditional documentation can be found at https://propka.readthedocs.io/.\n\n## References / Citations\n\nPlease cite these references in publications:\n\n* 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.\n\n* 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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjensengroup%2Fpropka","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjensengroup%2Fpropka","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjensengroup%2Fpropka/lists"}