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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. The
PDBFinder II includes information from multiple sequence alignments and
quality checks, making it ideally suited for structure analysis and
prediction.
Go to the official
PDBFinder/PDBFinderII site at the CMBI.
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