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Structural Bioinformatics Tools

As long as you are not doing computationally intensive things like molecular modeling or running simulations, Python is a very convenient way of making quick progress in a short time. We are preparing the release of Python interfaces for a number of file formats that are frequently used in structural bioinformatics: PDB, DSSP, HSSP, FSSP and PDBFinder. For the moment, only PDBFinder is available. Also note that you can develop your own Python plugins for YASARA. All Python modules listed here are licensed under the GNU GPL. After downloading a module, look at the header and search for the string "__repr__" to see how it works.


YASARA Macro Interface

In addition to letting YASARA run Python scripts, you can also let Python scripts run YASARA. In this reversed case, your Python script creates a YASARA macro using the Yanaconda macro language and sends it to YASARA.
Download the Python module yasara_macro.py (requires disk.py below)

PDBFinder and PDBFinder II Interface

The PDBFinder is a quick and easy way to retrieve all relevant information from PDB files, including the sequences.
Go to the official PDBFinder site at the CMBI and download the current PDBFinder via FTP.
To parse the PDBFinder, download the Python module pdbfinder_file.py (requires disk.py below)


Disk access tools

This Python module provides convenience functions for handling files and directories that are either missing or too complicated in Python's standard os. module. Required by most other modules listed here. Download the Python module disk.py