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

[João Rodrigues]

Also, instead of unfold_entities, use structure.get_residues() that returns
a list (copy) of the residues that you can safely iterate and use
detach_children() on. Again, on my phone, so it might not be entirely
true...

A qui, 26/11/2015, 18:36, João Rodrigues <j.p.g.l.m.rodrigues at gmail.com>
escreveu:

> Hi Claudia, you can use the build_peptides() function from the
> Bio.PDB.Polypeptides module. This should give you directly the fragments of
> the structure, based on a distance criterion. For the chain, you have to
> create new chains.
>
> I'm on my phone so I can't verify it, but I'd first create a new empty
> structure (and model), get the fragments of the parsed structure, and then
> based on the fragment length add then to the new structure with a
> sequential chain ID. I think this is the optimal way.
>
> What Jordan suggested works wonders if you want to filter a given
> structure. If you want just to remove small fragments, you could just tag
> these residues with a negative bfactor for example and then use this to
> filter with Select() and PDBIO().
>
> Cheers,
>
> João
>
> A qui, 26/11/2015, 14:44, Claudia Millán Nebot <cmncri at ibmb.csic.es>
> escreveu:
>
>> 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
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