Raw content of Bio::Structure::Atom
<![CDATA[# $Id: Atom.pm,v 1.8 2002/10/22 07:38:44 lapp Exp $
#
# bioperl module for Bio::Structure::Atom
#
# Cared for by Kris Boulez <kris.boulez@algonomics.com>
#
# Copyright Kris Boulez
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Structure::Atom - Bioperl structure Object, describes an Atom
=head1 SYNOPSIS
#add synopsis here
=head1 DESCRIPTION
This object stores a Bio::Structure::Atom
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Kris Boulez
Email kris.boulez@algonomics.com
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Structure::Atom;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::Structure::Residue;
@ISA = qw(Bio::Root::Root);
=head2 new()
Title : new()
Usage : $struc = Bio::Structure::Atom->new(
-id => 'human_id',
);
Function: Returns a new Bio::Structure::Atom object from basic
constructors. Probably most called from Bio::Structure::IO.
Returns : a new Bio::Structure::Atom object
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my($id, $x, $y, $z) =
$self->_rearrange([qw(
ID
X
Y
Z
)],
@args);
$id && $self->id($id);
$x && $self->x($x);
$y && $self->y($y);
$z && $self->z($z);
return $self;
}
=head2 x()
Title : x
Usage : $x = $atom->x($x);
Function: Set/gets the X coordinate for an Atom
Returns : The value for the X coordinate of the Atom (This is just a number,
it is expected to be in Angstrom, but no garantees)
Args : The X coordinate as a number
=cut
sub x {
my ($self,$value) = @_;
if( defined $value) {
# do we want to check if $value contains really a number ?
$self->{'x'} = $value;
}
return $self->{'x'};
}
=head2 y()
Title : y
Usage : $y = $atom->y($y);
Function: Set/gets the Y coordinate for an Atom
Returns : The value for the Y coordinate of the Atom (This is just a number,
it is eypected to be in Angstrom, but no garantees)
Args : The Y coordinate as a number
=cut
sub y {
my ($self,$value) = @_;
if( defined $value) {
# do we want to check if $value contains really a number ?
$self->{'y'} = $value;
}
return $self->{'y'};
}
=head2 z()
Title : z
Usage : $z = $atom->z($z);
Function: Set/gets the Z coordinate for an Atom
Returns : The value for the Z coordinate of the Atom (This is just a number,
it is ezpected to be in Angstrom, but no garantees)
Args : The Z coordinate as a number
=cut
sub z {
my ($self,$value) = @_;
if( defined $value) {
# do we want to check if $value contains really a number ?
$self->{'z'} = $value;
}
return $self->{'z'};
}
=head2 xyz()
Title : xyz
Usage : ($x,$y,$z) = $atom->xyz;
Function: Gets the XYZ coordinates for an Atom
Returns : A list with the value for the XYZ coordinate of the Atom
Args :
=cut
sub xyz {
my ($self) = @_;
return ($self->x, $self->y, $self->z);
}
=head2 residue()
Title : residue
Usage :
Function: No code here, all parent/child stuff via Entry
Returns :
Args :
=cut
sub residue {
my($self, $value) = @_;
$self->throw("all parent/child stuff via Entry\n");
}
=head2 icode()
Title : icode
Usage : $icode = $atom->icode($icode)
Function: Sets/gets the icode
Returns : Returns the icode for this atom
Args : reference to an Atom
=cut
sub icode {
my($self, $value) = @_;
if (defined $value) {
$self->{'icode'} = $value;
}
return $self->{'icode'};
}
=head2 serial()
Title : serial
Usage : $serial = $atom->serial($serial)
Function: Sets/gets the serial number
Returns : Returns the serial number for this atom
Args : reference to an Atom
=cut
sub serial {
my($self, $value) = @_;
if (defined $value) {
$self->{'serial'} = $value;
}
return $self->{'serial'};
}
=head2 occupancy()
Title : occupancy
Usage : $occupancy = $atom->occupancy($occupancy)
Function: Sets/gets the occupancy
Returns : Returns the occupancy for this atom
Args : reference to an Atom
=cut
sub occupancy {
my($self, $value) = @_;
if (defined $value) {
$self->{'occupancy'} = $value;
}
return $self->{'occupancy'};
}
=head2 tempfactor()
Title : tempfactor
Usage : $tempfactor = $atom->tempfactor($tempfactor)
Function: Sets/gets the tempfactor
Returns : Returns the tempfactor for this atom
Args : reference to an Atom
=cut
sub tempfactor {
my($self, $value) = @_;
if (defined $value) {
$self->{'tempfactor'} = $value;
}
return $self->{'tempfactor'};
}
=head2 segID()
Title : segID
Usage : $segID = $atom->segID($segID)
Function: Sets/gets the segID
Returns : Returns the segID for this atom
Args : reference to an Atom
=cut
sub segID {
my($self, $value) = @_;
if (defined $value) {
$self->{'segID'} = $value;
}
return $self->{'segID'};
}
=head2 pdb_atomname()
Title : pdb_atomname
Usage : $pdb_atomname = $atom->pdb_atomname($pdb_atomname)
Function: Sets/gets the pdb_atomname (atomname used in the PDB file)
Returns : Returns the pdb_atomname for this atom
Args : reference to an Atom
=cut
sub pdb_atomname {
my($self, $value) = @_;
if (defined $value) {
$self->{'pdb_atomname'} = $value;
}
return $self->{'pdb_atomname'};
}
=head2 element()
Title : element
Usage : $element = $atom->element($element)
Function: Sets/gets the element
Returns : Returns the element for this atom
Args : reference to an Atom
=cut
sub element {
my($self, $value) = @_;
if (defined $value) {
$self->{'element'} = $value;
}
return $self->{'element'};
}
=head2 charge()
Title : charge
Usage : $charge = $atom->charge($charge)
Function: Sets/gets the charge
Returns : Returns the charge for this atom
Args : reference to an Atom
=cut
sub charge {
my($self, $value) = @_;
if (defined $value) {
$self->{'charge'} = $value;
}
return $self->{'charge'};
}
=head2 sigx()
Title : sigx
Usage : $sigx = $atom->sigx($sigx)
Function: Sets/gets the sigx
Returns : Returns the sigx for this atom
Args : reference to an Atom
=cut
sub sigx {
my($self, $value) = @_;
if (defined $value) {
$self->{'sigx'} = $value;
}
return $self->{'sigx'};
}
=head2 sigy()
Title : sigy
Usage : $sigy = $atom->sigy($sigy)
Function: Sets/gets the sigy
Returns : Returns the sigy for this atom
Args : reference to an Atom
=cut
sub sigy {
my($self, $value) = @_;
if (defined $value) {
$self->{'sigy'} = $value;
}
return $self->{'sigy'};
}
=head2 sigz()
Title : sigz
Usage : $sigz = $atom->sigz($sigz)
Function: Sets/gets the sigz
Returns : Returns the sigz for this atom
Args : reference to an Atom
=cut
sub sigz {
my($self, $value) = @_;
if (defined $value) {
$self->{'sigz'} = $value;
}
return $self->{'sigz'};
}
=head2 sigocc()
Title : sigocc
Usage : $sigocc = $atom->sigocc($sigocc)
Function: Sets/gets the sigocc
Returns : Returns the sigocc for this atom
Args : reference to an Atom
=cut
sub sigocc {
my($self, $value) = @_;
if (defined $value) {
$self->{'sigocc'} = $value;
}
return $self->{'sigocc'};
}
=head2 sigtemp()
Title : sigtemp
Usage : $sigtemp = $atom->sigtemp($sigtemp)
Function: Sets/gets the sigtemp
Returns : Returns the sigtemp for this atom
Args : reference to an Atom
=cut
sub sigtemp {
my($self, $value) = @_;
if (defined $value) {
$self->{'sigtemp'} = $value;
}
return $self->{'sigtemp'};
}
=head2 aniso()
Title : aniso
Usage : $u12 = $atom->aniso("u12", $u12)
Function: Sets/gets the anisotropic temperature factors
Returns : Returns the requested factor for this atom
Args : reference to an Atom, name of the factor, value for the factor
=cut
sub aniso {
my($self, $name, $value) = @_;
if ( !defined $name) {
$self->throw("You need to supply a name of the anisotropic temp factor you want to get");
}
if (defined $value) {
$self->{$name} = $value;
}
return $self->{$name};
}
# placeholders
sub u11 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub u22 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub u33 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub u12 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub u13 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub u23 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub sigu11 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub sigu22 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub sigu33 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub sigu12 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub sigu13 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
sub sigu23 {
my ($self, $name, $value) = @_;
$self->aniso($name,$value);
}
=head2 id()
Title : id
Usage : $atom->id("CZ2")
Function: Gets/sets the ID for this atom
Returns : the ID
Args : the ID
=cut
sub id {
my ($self, $value) = @_;;
if (defined $value) {
$self->{'id'} = $value;
}
return $self->{'id'};
}
sub DESTROY {
my $self = shift;
# dummy, nothing needs to be done here
}
#
# from here on only private methods
#
=head2 _remove_residue()
Title : _remove_residue
Usage :
Function: Removes the Residue this Atom is atttached to.
Returns :
Args :
=cut
sub _remove_residue {
my ($self) = shift;
$self->throw("no code here at the moment\n");
}
=head2 _grandparent()
Title : _grandparent
Usage :
Function: get/set a symbolic reference to our grandparent
Returns :
Args :
=cut
sub _grandparent {
my($self,$symref) = @_;
if (ref($symref)) {
$self->throw("Thou shall only pass strings in here, no references $symref\n");
}
if (defined $symref) {
$self->{'grandparent'} = $symref;
}
return $self->{'grandparent'};
}
1;
]]>