[Bioperl-l] extract and write a pdb chain

[Joan Segura Mora]

Hi again,


To extract a pdb chain in a file, I have had to do it adding atom by
atom to a new structure.

use Bio::Structure::IO;
use strict;

my $structio = Bio::Structure::IO->new(-file => "101m.pdb",'-format' =>
'pdb');
my $struc = $structio->next_structure;
my $new_struct = Bio::Structure::Entry->new( -id  => 'structure_id');

for my $model ($struc->get_models){
	$new_struct->add_model($model);
	for my $chain ($struc->get_chains) {
		$new_struct->add_chain($model,$chain);
		if($chain->id eq "A"){
			foreach my $res ($struc->get_residues($chain)){
				$new_struct->add_residue($chain,$res);
				foreach my $atom  ($struc->get_atoms($res)){
					$new_struct->add_atom($res,$atom);
				}
			}
		}
		last;
	}
	last;
}

my $out = Bio::Structure::IO->new(-file => ">out.pdb",'-format' =>
'pdb');
$out->write_structure($new_struct);

I suppose that there should be a more elegant way to do it.

If someone knows it and can explain it I will be very grateful.

kind regards, 
Joan

On Mon, 2009-12-14 at 10:39 +0000, Joan Segura Mora wrote:
> Hi Brian,
> 
> I am not calling the method add_chain, I am calling the method chain
> 
> http://doc.bioperl.org/releases/bioperl-1.0.1/Bio/Structure/Entry.html#POD6
> 
> and if I don't use as an argument an object of type
> 
> Bio::Structure::Chain
> 
> I get an error like this (-->depends of the argument<--)
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Supplied a -->Bio::Structure::Residue=HASH(0x11be6a0)<-- to chain,
> we want a Bio::Structure::Chain or a list of these
> 
> STACK: Error::throw
> STACK:
> Bio::Root::Root::throw /usr/local/share/perl/5.8.8/Bio/Root/Root.pm:368
> STACK:
> Bio::Structure::Entry::chain /usr/local/share/perl/5.8.8/Bio/Structure/Entry.pm:314
> STACK: read_pdb.pl:11
> -----------------------------------------------------------
> 
> 
> And if I use a Chain object I get the error that I told you.
> 
> I have try this code:
> 
> use Bio::Structure::IO;
> use strict;
> 
> my $structio = Bio::Structure::IO->new(-file => "101m.pdb",'-format' =>
> 'pdb');
> my $struc = $structio->next_structure;
> my $new_entry = Bio::Structure::Entry->new( -id  => 'structure_id');
> my $model = Bio::Structure::Model->new( -id  => '0');
> 
> for my $chain ($struc->get_chains) {
>         if($chain->id eq "A"){
>                 $new_entry->add_chain($model,$chain);
> 
>                 last;
>         }
> }
> $new_entry->add_model($model);
> my $out = Bio::Structure::IO->new(-file => ">out.pdb",'-format' =>
> 'pdb');
> $out->write_structure($new_entry);
> 
> 
> But I get an empty pdb
> 
> HEADER    DEFAULT CLASSIFICATION                  24-JAN-70
> stru              
> REMARK
> 1                                                                      
> TER       1          A
> 0                                                      
> MASTER                                                                          
> END  
> 
> I am trying a lot of combinations, but I can't write a single chain into
> a file. I don't know what I am doing wrong.
> 
> Thanks for helping
> 
> regards,
> Joan
> 
> 
> On Fri, 2009-12-11 at 15:37 -0500, Brian Osborne wrote:
> > Joan,
> > 
> > It looks to me like the first argument to the add_chain() method has  
> > to be a Model object, the second is the Chain itself. See Structure/ 
> > Entry.pm, for example. However if you're seeing some documentation  
> > that says something else then tell us where, it needs to be corrected.
> > 
> > In Bio::Structure an Entry consists of one or Models, each of which  
> > has one or more Chains. This allows you to build macromolecular  
> > complexes (an Entry), which could have more than one defined proteins  
> > or protein complexes (Models).
> > 
> > Brian O.
> > 
> > On Dec 11, 2009, at 11:44 AM, Joan Segura Mora wrote:
> > 
> > > Hello,
> > >
> > > I am trying to do a very easy think but I don't get it. I want to  
> > > write
> > > in a file a chain of a pdb. I have try a lot of thinks but what I  
> > > think
> > > that it should work is the next script:
> > >
> > > use Bio::Structure::IO;
> > > use strict;
> > >
> > > my $structio = Bio::Structure::IO->new(-file => "101m.pdb",'-format'  
> > > =>
> > > 'pdb');
> > > my $struc = $structio->next_structure;
> > >
> > > my $new_entry = Bio::Structure::Entry->new( -id  => 'structure_id');
> > >
> > > for my $chain ($struc->get_chains) {
> > > 	if($chain->id eq "A"){
> > > 		$new_entry->chain($chain);
> > > 		last;
> > > 	}
> > > }
> > >
> > > my $out = Bio::Structure::IO->new(-file => ">out.pdb",'-format' =>
> > > 'pdb');#
> > > $out->write_structure($new_entry);
> > >
> > > it doesn't. I get the next error:
> > >
> > > ------------- EXCEPTION: Bio::Root::Exception -------------
> > > MSG: add_chain: first argument needs to be a Model object ()
> > >
> > > STACK: Error::throw
> > > STACK:
> > > Bio::Root::Root::throw /usr/local/share/perl/5.8.8/Bio/Root/Root.pm: 
> > > 368
> > > STACK:
> > > Bio::Structure::Entry::add_chain /usr/local/share/perl/5.8.8/Bio/ 
> > > Structure/Entry.pm:335
> > > STACK:
> > > Bio::Structure::Entry::get_chains /usr/local/share/perl/5.8.8/Bio/ 
> > > Structure/Entry.pm:391
> > > STACK:
> > > Bio::Structure::Entry::chain /usr/local/share/perl/5.8.8/Bio/ 
> > > Structure/Entry.pm:304
> > > STACK: read_pdb.pl:10
> > > -----------------------------------------------------------
> > >
> > > As far I understand the documentation, the method chain of the object
> > > Bio::Structure::Entry requires an as input an object of type Chain.
> > >
> > > Any solution will be very welcome.
> > >
> > > best regards,
> > > Joan
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
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