Made util.py work for GLYCAM_06 residue names, fix for XYZ.py and hbonds.py

[GoogleCodeExporter]

Because I intend to use the hydrogen bond analysis for my work with the GLYCAM 
force field I ran into some problems.

This is just a quick fix that makes timesteps available in XYZ files and makes 
the regular expression in "convert_aa_code" accept GLYCAM residue names (e.g. 
4GB, 2eB, YaA, ...).

Furthermore I fixed an error when calling save_table() in hbonds.py.

I haven't tested it thoroughly, because I was just using the hydrogen bond 
analysis.

You can checkout my source at 
http://code.google.com/r/lukasgrossar-mdanalysis-glycam/

I'm thinking about further adjustments to hbonds.py, e.g. being able to switch 
between various DEFAULT_ACCEPTOR and DEFAULT_DONOR values to accommodate 
further force-fields, but I'll work that out some other time.

Original issue reported on code.google.com by lukas.gr...@gmail.com on 30 Jan 2012 at 1:20

[GoogleCodeExporter]

Many thanks. I pulled and merge your changes into a single commit rev 
239140871ed8 

(I also added you to AUTHORS and as a contributor.)

Original comment by orbeckst on 3 Feb 2012 at 6:22

• Changed state: Fixed
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• Removed labels: ****

[GoogleCodeExporter]

This issue was closed by revision 1993fc3a811e.

Original comment by orbeckst on 11 Feb 2012 at 8:27

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