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Summary

Bio::Structure::Entry - Bioperl structure Object, describes the whole entry

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Structure::StructureI

Synopsis

  #add synopsis here

Description

This object stores a whole Bio::Structure entry. It can consist of one or
more models (Bio::Structure::Model), which in turn consist of one or more
chains (Bio::Structure::Chain). A chain is composed of residues
(Bio::Structure::Residue) and a residue consists of atoms (Bio::Structure::Atom)
If no specific model or chain is chosen, the first one is choosen.

Methods

Methods description

 Title   : _child
 Usage   : This is an internal function only. It is used to have one 
 	place that keeps track of which object has which other object 
	as child. Thus allowing the underlying modules (Atom, Residue,...)
	to have no knowledge about all this (and thus removing the possibility
	to have no knowledge about all this (and thus removing the possibility
	of reference cycles).
	This method hides the details of manipulating references to an anonymous
	hash.
 Function: To get/set an object's child(ren) 
 Returns : a reference to an array of child(ren) if it exist, undef otherwise. 
 Args    :

 Title   : _create_default_chain
 Usage   : 
 Function: Creates a default Chain for this Model. Typical situation
 	in an X-ray structure where there is only one chain
 Returns : 
 Args    :

 Title   : _create_default_model
 Usage   : 
 Function: Creates a default Model for this Entry. Typical situation
 	in an X-ray structure where there is only one model
 Returns : 
 Args    :

 Title   : _parent
 Usage   : This is an internal function only. It is used to have one 
 	place that keeps track of which object has which other object 
	as parent. Thus allowing the underlying modules (Atom, Residue,...)
	to have no knowledge about all this (and thus removing the possibility
	of reference cycles).
	This method hides the details of manipulating references to an anonymous
	hash.
 Function: To get/set an objects parent 
 Returns : a reference to the parent if it exist, undef otherwise. In the 
 	current implementation each node should have a parent (except Entry).
 Args    :

 Title   : _remove_from_graph
 Usage   : This is an internal function only. It is used to remove from
 	the parent/child graph. We only remove the links from object to
	his parent. Not the ones from object to its children.
 Function: To remove an object from the parent/child graph
 Returns : 
 Args    : the object to be orphaned

 Title   : _remove_models
 Usage   : 
 Function: Removes the models attached to an Entry. Tells the models they
 	don't belong to this Entry any more
 Returns : 
 Args    :

 Title   : add_atom
 Usage   : @atoms  = $structure->add_atom($residue,$atom);
 Function: Adds a (or a list of) Atom objects to a Bio::Structure::Residue.
 Returns : list of Bio::Structure::Atom objects
 Args    : a residue and an atom

 Title   : add_chain
 Usage   : @chains  = $structure->add_chain($add_chain);
 Function: Adds a (or a list of) Chain objects to a Bio::Structure::Entry.
 Returns : 
 Args    :

 Title   : add_model
 Usage   : $structure->add_model($model);
 Function: Adds a (or a list of) Model objects to a Bio::Structure::Entry.
 Returns : 
 Args    : One Model or a reference to an array of Model objects

 Title   : add_residue
 Usage   : @residues  = $structure->add_residue($residue);
 Function: Adds a (or a list of) Residue objects to a Bio::Structure::Entry.
 Returns : list of Bio::Structure::Residue objects
 Args    : One Residue or a reference to an array of Residue objects

 Title   : annotation
 Usage   : $obj->annotation($seq_obj)
 Function:
 Example :
 Returns : value of annotation
 Args    : newvalue (optional)

 Title   : chain
 Usage   : @chains  = $structure->chain($chain);
 Function: Connects a (or a list of) Chain objects to a Bio::Structure::Entry.
 Returns : list of Bio::Structure::Residue objects
 Args    : One Residue or a reference to an array of Residue objects

 Title   : conect
 Usage   : $structure->conect($source);
 Function: get/set method for conect
 Returns : a list of serial numbers for atoms connected to source
 	(together with $entry->get_atom_by_serial($model, $serial) this should be OK for now)
 Args    : the serial number for the source atom

 Title   : get_all_conect_source
 Usage   : @sources = $structure->get_all_conect_source;
 Function: get all the sources for the conect records
 Returns : a list of serial numbers for atoms connected to source
 	(together with $entry->get_atom_by_serial($model, $serial) this should be OK for now)
 Args    : 
 Description : This is a bit of a kludge, but it's the best for now. Conect info might need
 	to go in a sepearte object

 Title   : get_atom_by_serial
 Usage   : $structure->get_atom_by_serial($module, $serial);
 Function: get the Atom for a  for get_atom_by_serial
 Returns : the Atom object with this serial number in the model
 Args    : Model on which to work, serial number for atom
 	(if only a number is supplied, the first model is chosen)

 Title   : get_atoms
 Usage   : $structure->get_atoms($residue);
 Function: general get method for atoms attached to a Residue
 Returns : a list of atoms attached to this residue
 Args    : a residue

 Title   : get_chains
 Usage   : $entry->get_chains($model);
 Function: general get method for chains attached to a Model
 Returns : a list of chains attached to this model
 Args    : a Model

 Title   : get_models
 Usage   : $structure->get_models($structure);
 Function: general get method for models attached to an Entry
 Returns : a list of models attached to this entry
 Args    : an Entry

 Title   : get_residues
 Usage   : $structure->get_residues($chain);
 Function: general get method for residues attached to a Chain
 Returns : a list of residues attached to this chain
 Args    : a chain

 Title   : id
 Usage   : $entry->id("identity");
 Function: Gets/sets the ID 
 Returns : 
 Args    :

 Title   : master
 Usage   : $structure->master($source);
 Function: get/set method for master
 Returns : the master line
 Args    : the master line for this entry

 Title   : model
 Function: Connects a (or a list of) Model objects to a Bio::Structure::Entry.
 	To add a Model (and keep the existing ones) use add_model()
 	It returns a list of Model objects.
 Returns : list of Bio::Structure::Model objects
 Args    : One Model or a reference to an array of Model objects

 Title   : new()
 Usage   : $struc = Bio::Structure::Entry->new( 
                                           -id  => 'structure_id',
                                           );

 Function: Returns a new Bio::Structure::Entry object from basic 
	constructors. Probably most called from Bio::Structure::IO.
 Returns : a new Bio::Structure::Model object

 Title   : parent
 Usage   : $structure->parent($residue);
 Function: returns the parent of the argument
 Returns : the parent of the argument
 Args    : a Bio::Structure object

 Title   : residue
 Usage   : @residues  = $structure->residue($residue);
 Function: Connects a (or a list of) Residue objects to a Bio::Structure::Entry.
 Returns : list of Bio::Structure::Residue objects
 Args    : One Residue or a reference to an array of Residue objects

 Title   : seqres
 Usage   : $seqobj = $structure->seqres("A");
 Function: gets a sequence object containing the sequence from the SEQRES record.
 	    if a chain-ID is given , the sequence for this chain is given, if none
	    is provided the first chain is choosen
 Returns : a Bio::PrimarySeq
 Args    : the chain-ID of the chain you want the sequence from

Methods code

sub DESTROY {

	my $self = shift;

	#print STDERR "DESTROY on $self being called\n";

##	for my $pc (keys %{ $self->{'p_c'} } ) {
##		next unless ( defined ${ $self->{'p_c'} }{$pc} );
##		delete ${$self->{'p_c'}}{$pc};
##	}
##	for my $cp (keys %{ $self->{'c_p'} } ) {
##		next unless ( defined ${ $self->{'c_p'} }{$cp} );
##		delete ${$self->{'c_p'}}{$cp};
##	}
	%{ $self->{'p_c'} } = ();
	%{ $self->{'c_p'} } = ();
}

# copied from Bio::Seq.pm
#

}

sub _child {

	my ($self, $key, $value) = @_;
	
	if ( (!defined $key) || (ref($key) !~ /^Bio::/) ) {
		$self->throw("First argument to _child needs to be a reference to a Bio:: object\n");
	}
	if ( (defined $value) && (ref($value) !~ /^Bio::/) ) {
		$self->throw("Second argument to _child needs to be a reference to a Bio:: object\n");
	}
	# no checking here for consistency of key and value, needs to happen in caller
	
	if (defined $value) {
		if ( !exists(${$self->{'p_c'}}{$key}) || ref(${$self->{'p_c'}}{$key}) !~ /^ARRAY/ ) {
			${$self->{'p_c'}}{$key} = [];
		}
		push @{ ${$self->{'p_c'}}{$key} }, $value;
	}
	return  ${$self->{'p_c'}}{$key};

}

sub _create_default_chain {

	my ($self) = shift;

	my $chain = Bio::Structure::Chain->new(-id => "default");
	return $chain;

}

sub _create_default_model {

	my ($self) = shift;

	my $model = Bio::Structure::Model->new(-id => "default");
	return $model;

}

sub _parent {

    no strict "refs";
    my ($self, $key, $value) = @_;

    if ( (!defined $key) || (ref($key) !~ /^Bio::/) ) {
	$self->throw("First argument to _parent needs to be a reference to a Bio:: object ($key)\n");
    }
    if ( (defined $value) && (ref($value) !~ /^Bio::/) ) {
	$self->throw("Second argument to _parent needs to be a reference to a Bio:: object\n");
    }
    # no checking here for consistency of key and value, needs to happen in caller

    if (defined $value) {
	# is this value already in, shout
	if (defined ( $self->{'c_p'}->{$key}) && 
	    exists ( $self->{'c_p'}->{$key})
	    ) {
	    $self->throw("_parent: $key already has a parent ${$self->{'c_p'}}{$key}\n");
    }
    ${$self->{'c_p'}}{$key} = $value;
	}
	return ${$self->{'c_p'}}{$key};

}

sub _print_stats_pc {

	# print stats about the parent/child hashes
	my ($self) =@_;
	my $pc = scalar keys %{$self->{'p_c'}};
	my $cp = scalar keys %{$self->{'c_p'}};
	my $now_time = Time::HiRes::time();
	$self->debug("pc stats: P_C $pc C_P $cp $now_time\n");
}


1;

}

sub _remove_from_graph {

	my ($self, $object) = @_;
	
	if ( !defined($object) && ref($object) !~ /^Bio::/) {
		$self->throw("_remove_from_graph needs a Bio object as argument");
	}
	if ( $self->_parent($object) ) {
		my $dad = $self->_parent($object);
		# if we have a parent, remove me as being a child
		for my $k (0 .. $#{$self->_child($dad)}) {
			if ($object eq ${$self->{'p_c'}{$dad}}[$k]) {
				splice(@{$self->{'p_c'}{$dad}}, $k,1);
			}
		}
		delete( $self->{'c_p'}{$object});
	}

}

sub _remove_models {

	my ($self) = shift;

	;

}

sub add_atom {

	my($self,$residue,$atom) = @_;

	if (ref($residue) !~ /^Bio::Structure::Residue/) {
		$self->throw("add_atom: first argument needs to be a Residue object\n");
	}
	if (defined $atom) {
		if (ref($atom) eq "ARRAY") {
    			# if the user passed in a reference to an array
			for my $a ( @{$atom} ) {
				if( ! $a->isa('Bio::Structure::Atom') ) {
					$self->throw("$a is not an Atom\n");
				}
				if ( $self->_parent($a) ) {
					$self->throw("$a already belongs to a parent\n");
				}
				$self->_parent($a, $residue);
				$self->_child($residue, $a);
				# stringify
				#my $str_ref = "$self";
				#$r->_grandparent($str_ref);
			}
		}
		#elsif ( $atom->isa('Bio::Structure::Atom') ) { 
		elsif ( ref($atom) =~ /^Bio::Structure::Atom/ ) { 
			if ( $self->_parent($atom) ) {
				$self->throw("$atom already belongs to a parent\n");
			}
			$self->_parent($atom, $residue);
			$self->_child($residue, $atom);
			# stringify
			#my $str_ref = "$self";
			#$atom->_grandparent($str_ref);
		}
	}
	my $array_ref = $self->_child($residue);
	return $array_ref ? @{$array_ref} : ();

}

sub add_chain {

	my($self, $model, $chain) = @_;

	if (ref($model) !~ /^Bio::Structure::Model/) {
		$self->throw("add_chain: first argument needs to be a Model object ($model)\n");
	}
	if (defined $chain) {
		if (ref($chain) eq "ARRAY") {
    			# if the user passed in a reference to an array
			for my $c ( @{$chain} ) {
				if( ! $c->isa('Bio::Structure::Chain') ) {
					$self->throw("$c is not a Chain\n");
				}
				if ( $self->_parent($c) ) {
					$self->throw("$c already assigned to a parent\n");
				}
				$self->_parent($c, $model);
				$self->_child($model, $c);
				# stringify $self ref
				#my $str_ref = "$self";
				#$c->_grandparent($str_ref);
			}
		}
		elsif ( $chain->isa('Bio::Structure::Chain') ) { 
			if ( $self->_parent($chain) ) { # already assigned to parent
				$self->throw("$chain already assigned to a parent\n");
			}
			$self->_parent($chain,$model);
			$self->_child($model, $chain);
			# stringify $self ref
			#my $str_ref = "$self";
			#$chain->_grandparent($str_ref);
		}
		else {
			$self->throw("Supplied a $chain to add_chain, we want a Chain or list of Chains\n");
		}
	}
	my $array_ref = $self->_child($model);
	return $array_ref ? @{$array_ref} : ();

}

sub add_model {

	my($self,$entry,$model) = @_;

	# if only one argument and it's a model, change evrything one place
	# this is for people calling $entry->add_model($model);
	if ( !defined $model && ref($entry) =~ /^Bio::Structure::Model/) {
		$model = $entry;
		$entry = $self;
	}
	# $self and $entry are the same here, but it's used for uniformicity
	if ( !defined($entry) || ref($entry) !~ /^Bio::Structure::Entry/) {
		$self->throw("first argument to add_model needs to be a Bio::Structure::Entry object\n");
	}
	if (defined $model) {
		if (ref($model) eq "ARRAY") {
    			# if the user passed in a reference to an array
			for my $m ( @{$model} ) {
				if( ! $m->isa('Bio::Structure::Model') ) {
					$self->throw("$m is not a Model\n");
				}
				if ( $self->_parent($m) ) {
					$self->throw("$m already assigned to a parent\n");
				}
				push @{$self->{'model'}}, $m;
				# create a stringified version of our ref
				# not used untill we get symbolic ref working
				#my $str_ref = "$self";
				#$m->_grandparent($str_ref);
			}
		}
		elsif ( $model->isa('Bio::Structure::Model') ) { 
			if ( $self->_parent($model) ) { # already assigned to a parent
				$self->throw("$model already assigned\n");
			}
			push @{$self->{'model'}}, $model;
			# create a stringified version of our ref
			#my $str_ref = "$self";
			#$model->_grandparent($str_ref);
		}
		else {
			$self->throw("Supplied a $model to add_model, we want a Model or list of Models\n");
		}
	}

	my $array_ref = $self->{'model'};
	return $array_ref ? @{$array_ref} : ();

}

sub add_residue {

	my($self,$chain,$residue) = @_;

	if (ref($chain) !~ /^Bio::Structure::Chain/) {
		$self->throw("add_residue: first argument needs to be a Chain object\n");
	}
	if (defined $residue) {
		if (ref($residue) eq "ARRAY") {
    			# if the user passed in a reference to an array
			for my $r ( @{$residue} ) {
				if( ! $r->isa('Bio::Structure::Residue') ) {
					$self->throw("$r is not a Residue\n");
				}
				if ( $self->_parent($r) ) {
					$self->throw("$r already belongs to a parent\n");
				}
				$self->_parent($r, $chain);
				$self->_child($chain, $r);
				# stringify
				my $str_ref = "$self";
				$r->_grandparent($str_ref);
			}
		}
		elsif ( $residue->isa('Bio::Structure::Residue') ) { 
			if ( $self->_parent($residue) ) {
				$self->throw("$residue already belongs to a parent\n");
			}
			$self->_parent($residue, $chain);
			$self->_child($chain, $residue);
			# stringify
			my $str_ref = "$self";
			$residue->_grandparent($str_ref);
		}
		else {
			$self->throw("Supplied a $residue to add_residue, we want a Residue or list of Residues\n");
		}
	}
	my $array_ref = $self->_child($chain);
	return $array_ref ? @{$array_ref} : ();

}

sub annotation {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'annotation'} = $value;
    }
    return $obj->{'annotation'};

}


#
# from here on only private methods
#

}

sub chain {

	my ($self, $chain) = @_;

	if ( ! $self->model ) {
		$self->_create_default_model;
	}
	my @models = $self->model;
	my $first_model = $models[0];

	if ( defined $chain) {
	
		if( (ref($chain) eq "ARRAY") ||
		      ($chain->isa('Bio::Structure::Chain')) ) {
			# remove existing ones, tell they've become orphan
			my @obj = $self->get_chains($first_model);
			if (@obj) {
				for my $c (@obj) {
					$self->_remove_from_graph($c);
				}
			}
			# add the new ones
			$self->add_chain($first_model,$chain);
		}
		else {
			$self->throw("Supplied a $chain to chain, we want a Bio::Structure::Chain or a list of these\n");
		}
	}
	$self->get_chains($first_model);

}

sub conect {

	my ($self, $source, $serial, $type) = @_;
	
	if ( !defined $source ) {
		$self->throw("You need to supply at least a source to conect");
	}
	if ( defined $serial && defined $type ) {
		if ( !exists(${$self->{'conect'}}{$source}) || ref(${$self->{'conect'}}{$source} !~ /^ARRAY/ ) ) {
			${$self->{'conect'}}{$source} = [];
		}
		# we also need to store type, a conect object might be better 
		my $c = $serial . "_" . $type;
		push @{ ${$self->{'conect'}}{$source} }, $c;
	}
	return @{ ${$self->{'conect'}}{$source} };

}

sub get_all_conect_source {

	my ($self) = shift;
	my (@sources);

	for my $source (sort {$a<=>$b} keys %{$self->{'conect'}}) {
		push @sources, $source;
	}
	return @sources;

}

sub get_atom_by_serial {

	my ($self, $model, $serial) = @_;

	if ($model =~ /^\d+$/ && !defined $serial) { # only serial given
		$serial = $model;
		my @m = $self->get_models($self);
		$model = $m[0];
	}
	if ( !defined $model || ref($model) !~ /^Bio::Structure::Model/ ) {
		$self->throw("Could not find (first) model\n");
	}
	if ( !defined $serial || ($serial !~ /^\d+$/) ) {
		$self->throw("The serial number you provided looks fishy ($serial)\n");
	}
	for my $chain ($self->get_chains($model) ) {
		for my $residue ($self->get_residues($chain) ) {
			for my $atom ($self->get_atoms($residue) ) {
				# this could get expensive, do we cache ???
				next unless ($atom->serial == $serial);
				return $atom;
			}
		}
	}

}

sub get_atoms {

	my ($self, $residue) = @_;

	if ( !defined $residue) {
		$self->throw("get_atoms needs a Residue as argument");
	}
	# pass through to add_atom
	$self->add_atom($residue);

}

sub get_chains {

	my ($self, $model) = @_;

	if (! defined $model) {
		$model = ($self->get_models)[0];
	}
	# pass through to add_chain
	$self->add_chain($model);

}

sub get_models {

	my ($self, $entry) = @_;

	# self and entry can be the same
	if ( !defined $entry) {
		$entry = $self;
	}
	# pass through to add_model
	$self->add_model($entry);

}

sub get_residues {

	my ($self, $chain) = @_;

	if ( !defined $chain) {
		$self->throw("get_residues needs a Chain as argument");
	}
	# pass through to add_residue
	$self->add_residue($chain);

}

sub id {

	my ($self, $value) = @_;
	if (defined $value) {
		$self->{'id'} = $value;
	}
	return $self->{'id'};

}

sub master {

	my ($self, $value) = @_;
	if (defined $value) {
		$self->{'master'} = $value;
	}
	return $self->{'master'};

}

sub model {

	my ($self, $model) = @_;
	
	if( defined $model) {
		if( (ref($model) eq "ARRAY") ||
		      ($model->isa('Bio::Structure::Model')) ) {
			# remove existing ones, tell they've become orphan
			my @obj = $self->model;
			if (@obj) {
				for my $m (@obj) {
					$self->_remove_from_graph($m);
					$self->{'model'} = [];
				}
			}
			# add the new ones
			$self->add_model($self,$model);
		}
		else {
			$self->throw("Supplied a $model to model, we want a Bio::Structure::Model or a list of these\n");
		}
   	}
	# give back list of models via general get method
	$self->get_models($self);

}

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my($id, $model, $chain, $residue ) =
        $self->_rearrange([qw(
			      ID
			      MODEL
			      CHAIN
			      RESIDUE
                              )],
                          @args);

    # where to store parent->child relations (1 -> 1..n)
    #  value to this hash will be an array ref
    #  by using Tie::RefHash we can store references in this hash
    $self->{'p_c'} = ();
    tie %{ $self->{'p_c'} } , "Tie::RefHash";
    
    # where to store child->parent relations (1 -> 1)
    $self->{'c_p'} = ();
    tie %{ $self->{'c_p'} } , "Tie::RefHash";

    $id      && $self->id($id);

    $self->{'model'} = [];
    $model   && $self->model($model);


    if($chain) {
	if ( ! defined($self->model) ) { # no model yet, create default one
		$self->_create_default_model;
	}
	for my $m ($self->model) { # add this chain on all models
		$m->chain($chain);
    	}
    }

    $residue  && $self->residue($residue);

    # taken from Bio::Seq (or should we just inherit Bio::Seq and override some methods)
    my $ann = Bio::Annotation::Collection->new;
    $self->annotation($ann);

    return $self;

}

sub parent {

	my ($self, $obj) = @_;
	
	if ( !defined $obj) {
		$self->throw("parent: you need to supply an argument to get the parent from\n");
	}

	# for now we pass on to _parent, untill we get the symbolic ref thing working.
	$self->_parent($obj);

}

sub residue {

	my ($self, $residue) = @_;

	if ( ! $self->model ) {
		my $m = $self->_create_default_model;
		$self->add_model($self,$m);
	}
	my @models = $self->model;
	my $first_model = $models[0];
	
	if ( ! $self->get_chains($first_model) ) {
		my $c = $self->_create_default_chain;
		$self->add_chain($first_model, $c);
	}
	my @chains = $self->get_chains($first_model);
	my $first_chain = $chains[0];

	if( defined $residue) {
		if( (ref($residue) eq "ARRAY") ||
		      ($residue->isa('Bio::Structure::Residue')) ) {
			# remove existing ones, tell they've become orphan
			my @obj = $self->get_residues($first_chain);
			if (@obj) {
				for my $r (@obj) {
					$self->_remove_from_graph($r);
				}
			}
			# add the new ones
			$self->add_residue($first_chain,$residue);
		}
		else {
			$self->throw("Supplied a $residue to residue, we want a Bio::Structure::Residue or a list of these\n");
		}
   	}
	$self->get_residues($first_chain);

}

sub seqres {

	my ($self, $chainid) = @_;
	my $s_u = "x3 A1 x7 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3";
	my (%seq_ch);
	if ( !defined $chainid) {
		my $m = ($self->get_models($self))[0];
		my $c = ($self->get_chains($m))[0];
		$chainid = $c->id;
	}
	my $seqres = ($self->annotation->get_Annotations("seqres"))[0];
	my $seqres_string = $seqres->as_text;
$self->debug("seqres : $seqres_string\n");
	$seqres_string =~ s/^Value: //;
	# split into lines of 62 long
	my @l = unpack("A62" x (length($seqres_string)/62), $seqres_string);
	for my $line (@l) {
		# get out chain_id and sequence
		# we use a1, as A1 strips all spaces :(
		my ($chid, $seq) = unpack("x3 a1 x7 A51", $line);
		if ($chid eq " ") {
			$chid = "default";
		}
		$seq =~ s/(\w+)/\u\L$1/g;	# ALA -> Ala  (for SeqUtils)
		$seq =~ s/\s//g; 		# strip all spaces
		$seq_ch{$chid} .= $seq;
$self->debug("seqres : $chid $seq_ch{$chid}\n");
	}
	# do we have a seqres for this chainid
	if(! exists $seq_ch{$chainid} ) {
		$self->warn("There is no SEQRES known for chainid\" $chainid\"");
		return undef;
	}

	# this will break for non-protein structures (about 10% for now) XXX KB
	my $pseq = Bio::PrimarySeq->new(-alphabet => 'protein');
	$pseq = Bio::SeqUtils->seq3in($pseq,$seq_ch{$chainid});
	my $id = $self->id . "_" . $chainid;
	$pseq->id($id);
	return $pseq;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
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  bioperl-bugs@bio.perl.org
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Email kris.boulez@algonomics.com

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _