[Biopython-dev] Is Bio.Crystal obsolete?

Peter biopython-dev at maubp.freeserve.co.uk
Mon Jul 16 18:50:49 UTC 2007


I just had a look at the Bio.Crystal module by Katharine Lindner (2002), 
consisting of the single file Bio/Crystal/__init__.py whose preamble states:

 > Hetero, Crystal and Chain exist to represent the NDB Atlas
 > structure.  Atlas is a minimal subset of the PDB format.  Heteo
 > supports a 3 alphameric code. The NDB web interface is located at
 > ...

The old link should probably be updated as it doesn't work, perhaps:
http://ndbserver.rutgers.edu/atlas/index.html

As far as I can see, they now provide their downloads in PDB, CIF and an 
XML file format - and the PDB files look like full thing to me at first 
glance rather than a minimal subset.

There is a unit test, Tests/test_Crystal.py but no example input files.

This module looks obsolete to me - can we mark it as deprecated after 
checking on the main list no one uses it (as done for Bio.Kabat back in 
March 2007)?

Peter




More information about the Biopython-dev mailing list