[BioPython] suggestions for Bio.PDB

[Catherine Letondal]

Hi,

On Apr 17, 2005, at 3:39 PM, thamelry at binf.ku.dk wrote:

> Hi,
>
>> Would it be possible for the get_structure() method in PDBParser to
>> accept a filehandle
>
> You're not the first to suggest this - it's already in
> the CVS version, also for generating PDB output with PDBIO.

Ok, thanks.

>> Another suggestion: it could be useful to keep a record of the read
>> structure, just in case the user would like to benefit from biopython
>> PDB modules, but also do some custom analysis.
>
> I don't think this would be very useful, it's easy enough to just read 
> in
> the file separately.

Ok (the student who made the suggestion had a lot of files to read, 
that's why - but if you implement the filehandle parameter, it's fine)


> BTW, I'm soon going to start to implement a parser for the new
> PDB XML format. Any suggestions, comments, etc. regarding this
> are welcome.

A suggestion (not related to XML) from one of the teachers of our 
course: a method returning embedded elements at any level would be 
useful. For instance, a get_residues() method enabling to directly 
iterate on residues whatever the chain would be very convenient :

p = PDBParser()
s = p.get_structure('...')

for residue in s.get_residues():
	...

Similarly:
for atom in s.get_atoms():
	...

I'm aware it's easy to implement with a simple function - at the same 
time it might be useful enough to have it available directly in the 
Structure class?

Thanks in advance,

--
Catherine Letondal -- Institut Pasteur -- Informatics in Biology Course
www.pasteur.fr/formation/infobio/infobio-en.html