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

[Jordan Willis]

Ok, I will give it a try. updating chain.id = “something” should work in place. I just tested. We need to make sure those conditional statements are working while setting the id.


> On Nov 26, 2015, at 2:59 AM, Claudia Millán Nebot <cmncri at ibmb.csic.es> wrote:
> 
> 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 <mailto: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 <mailto: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 <http://res1.id/>
>>         id2=res2.id <http://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 <http://residue.id/>
>>                if id_res in residues_to_remove:
>>                    chain.detach_child(id_res)
>>                else:
>>                    chain.id <http://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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> 
> <frag27A_0_0_trimmed.pdb><frag27A_0_0.pdb>

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