[Biopython] Best way to change the chain identifiers of a set of residues

[Claudia Millán Nebot]

Hi Jordan, the removal of the residues is working, is the renaming of the
chains that is causing trouble. I attach an example of input/output
produced by the function.



2015-11-26 9:09 GMT+00:00 Jordan Willis <jwillis0720 at gmail.com>:

> Also, the detach_child method should work in place, so I’m not sure why
> this is not working. Can you give an example PDB?
>
> Jordan
>
> On Nov 25, 2015, at 12:16 PM, Claudia Millán Nebot <cmncri at ibmb.csic.es>
> wrote:
>
> Dear all,
>
> I am writing a function that examines a structure, and if there are
> discontinuous regions that are smaller than a certain size, they will be
> removed from the structure. Then, I would like to write the structure as a
> pdb in which the chain identifiers are different for each discontinuous
> fragment. For that purpose, I want to change the chain id of certain
> residues. ¿What will be the best way to do it? Because right now it is not
> working, of course, because I am iterating over something that I am trying
> to change at the same time. Maybe I am missing something very obvious or
> straightforward, but I do not see what will be the best way to do it...
> ¿Maybe creating and empty chain and using the set_parent method?
>
> The current code looks like this:
> def trimByContinuityLimit(pdb_file,min_size):
>     parser=PDBParser()
>     structure=parser.get_structure(pdb_file[:-4],pdb_file)
>     residues=Selection.unfold_entities(structure,'R')
>
> list_id="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz1234567890"
>     dictio_chainid={}
>     residues_to_remove=[]
>     current_listres=[]
>     index=0
>     for i in range(len(residues)-1):
>         res1=residues[i]
>         res2=residues[i+1]
>         id1=res1.id
>         id2=res2.id
>         check=Bioinformatics.checkContinuity(res1,res2)
>         #print 'check',check
>         #print 'list_id[index]',list_id[index]
>         if check==True:
>             #print "These two residues are consecutive",res1,res2
>             if id1 not in current_listres:
>                 current_listres.append(id1)
>             dictio_chainid[id1]=list_id[index]
>             if id2 not in current_listres:
>                 current_listres.append(id2)
>             dictio_chainid[id2]=list_id[index]
>             #print 'list_id[index]',list_id[index]
>             #print 'id1,dictio_chainid[id1]',dictio_chainid[id1],id1
>             #print 'id2,dictio_chainid[id2]',dictio_chainid[id2],id2
>         elif check==False:
>             #print "These two residues are not consecutive",res1,res2
>             if id1 not in current_listres:
>                current_listres.append(id1)
>                dictio_chainid[id1]=list_id[index]
>             if len(current_listres)<min_size:
>                residues_to_remove.extend(current_listres)
>             if i==len(residues)-2 and min_size>1: # If we reach this
> point, then the last residue is not continuous so it is single :
>                residues_to_remove.append(id2)
>             else:
>                current_listres=[]
>                current_listres.append(id2)
>                index=index+1
>                dictio_chainid[id2]=list_id[index]
>     # Remove the residues and write the pdb
>     for model in structure:
>        for chain in model:
>            for residue in chain:
>                id_res=residue.id
>                if id_res in residues_to_remove:
>                    chain.detach_child(id_res)
>                else:
>                    chain.id=dictio_chainid[id_res]
>     io=PDBIO()
>     io.set_structure(structure)
>     io.save(pdb_file[:-4]+'_trimmed.pdb',write_end=False)
>
> Thanks in advance :)
>
> Claudia
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20151126/f4260eb8/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: frag27A_0_0_trimmed.pdb
Type: chemical/x-pdb
Size: 137785 bytes
Desc: not available
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20151126/f4260eb8/attachment-0002.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: frag27A_0_0.pdb
Type: chemical/x-pdb
Size: 142568 bytes
Desc: not available
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20151126/f4260eb8/attachment-0003.bin>