[Biopython] Merging different pdbs into a single object structure and writing it
Claudia Millán Nebot
cmncri at ibmb.csic.es
Wed Jun 25 15:48:21 UTC 2014
Hi :) I'm newbie to BioPython and I am trying to do the following:
I have a set of different pdbs that I want to merge together into a single
file. I would like to take into consideration that there could be issues
with the naming, so, after reading a few other posts in this same list, I
came up with the following code:
list_parsers=[]
list_of_structures=[]
for index in range(len(list_of_filenames)):
parser=PDBParser()
list_parsers.append(parser)
structure=parser.get_structure(list_of_filenames[index][:-4],list_of_filenames[index])
list_of_structures.append(structure)
i_chain = 65
for structure in list_of_structures:
for chain in structure:
chain.id = chr(i_chain)
i_chain += 1
io=PDBIO()
for structure in list_of_structures:
io.set_structure(structure)
io.save(clust_fold+key[:-4]+"_fused.pda")
This is not working, as I guess i'm just changing the structure set each
time I do io.set_structure, and writing the last one. And as there is not
such a thing as the append_structure() method I have just tried a silly
thing. So my question would be which is the best way to get the pdbs
merged? Should I save as independent unfold entities and then write them by
using a Select class?
Thanks in advance and regards,
Claudia Millán (cmncri at ibmb.csic.es)
Crystallographic Methods Group
http://chango.ibmb.csic.es
Institut de Biologia Molecular de Barcelona (IBMB-CSIC)
Barcelona, Spain
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20140625/724219ba/attachment.html>
More information about the Biopython
mailing list