PyProt is a Python package for working with protein structure files. It comes with a collection of ready-to-use scripts for the most common file operations and protein analyses.

[download pyprot.zip] [link to pyprot on GitHub]

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## ReadMe Contents

• Scripts and command line tools
• Tutorials
• API documentation
• Installation

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Scripts and command line tools

PyProt provides ready-to-use command line scripts that are using the underlying pyprot objects to work with PDB and MOL2 files.
The scripts are located in the subdirectory ./scripts and can be used after pyprot was successfully installed.

List of command line tools

• Working with PDB files

  • Center of Mass
  • Grab atoms within a radius
  • Root-mean-square deviation (RMSD)
  • PDB to FASTA converter
  • PDB atom and residue renumbering
  • B-factor statistics
  • PDB downloader
  • Separating ATOM and HETATM sections
  • Extracting Ligands from PDB files

• Working with MOL2 files

  • Transfer charges
  • Split multi-MOL2 files
  • MOL2 functional group filter
  • MOL2 intermolecular functional group screening

API documentation

Please find the API documentation at http://rasbt.github.io/pyprot/.

Tutorials

In progress ...

Installation

PyProt was build and tested in Python 3.

The pyprot package can be installed via

pip install pyprot

Alternatively, you can download pyprot directly from GitHub (pyprot-master.zip), unzip the archive, and install it via

python setup.py install

After successful installation, the pyprot API is ready to use.

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If you are also interested in using the available scripts and tools you have two options:

a) If you downloaded pyprot from GitHub, you can use the scripts from the pyprot/scripts/ subdirectory.

b) If you installed pyprot via pip, you can download the the scripts bundle separately (pyprot-scripts.zip).

For more details, please see the separate Installation Documentation.