Bio::Structure Atom
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Summary
Bio::Structure::Atom - Bioperl structure Object, describes an Atom
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Structure::Residue
Inherit
Bio::Root::Root
Synopsis
  #add synopsis here
Description
This object stores a Bio::Structure::Atom
Methods
DESTROY
No description
Code
_grandparentDescriptionCode
_remove_residueDescriptionCode
anisoDescriptionCode
chargeDescriptionCode
elementDescriptionCode
icodeDescriptionCode
idDescriptionCode
newDescriptionCode
occupancyDescriptionCode
pdb_atomnameDescriptionCode
residueDescriptionCode
segIDDescriptionCode
serialDescriptionCode
sigoccDescriptionCode
sigtempDescriptionCode
sigu11
No description
Code
sigu12
No description
Code
sigu13
No description
Code
sigu22
No description
Code
sigu23
No description
Code
sigu33
No description
Code
sigxDescriptionCode
sigyDescriptionCode
sigzDescriptionCode
tempfactorDescriptionCode
u11
No description
Code
u12
No description
Code
u13
No description
Code
u22
No description
Code
u23
No description
Code
u33
No description
Code
xDescriptionCode
xyzDescriptionCode
yDescriptionCode
zDescriptionCode
Methods description
_grandparent()code    nextTop
 Title   : _grandparent
Usage :
Function: get/set a symbolic reference to our grandparent
Returns :
Args :
_remove_residue()codeprevnextTop
 Title   : _remove_residue
Usage :
Function: Removes the Residue this Atom is atttached to.
Returns :
Args :
aniso()codeprevnextTop
 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
charge()codeprevnextTop
 Title   : charge
Usage : $charge = $atom->charge($charge)
Function: Sets/gets the charge
Returns : Returns the charge for this atom
Args : reference to an Atom
element()codeprevnextTop
 Title   : element
Usage : $element = $atom->element($element)
Function: Sets/gets the element
Returns : Returns the element for this atom
Args : reference to an Atom
icode()codeprevnextTop
 Title   : icode
Usage : $icode = $atom->icode($icode)
Function: Sets/gets the icode
Returns : Returns the icode for this atom
Args : reference to an Atom
id()codeprevnextTop
 Title   : id
Usage : $atom->id("CZ2")
Function: Gets/sets the ID for this atom
Returns : the ID
Args : the ID
new()codeprevnextTop
 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
occupancy()codeprevnextTop
 Title   : occupancy
Usage : $occupancy = $atom->occupancy($occupancy)
Function: Sets/gets the occupancy
Returns : Returns the occupancy for this atom
Args : reference to an Atom
pdb_atomname()codeprevnextTop
 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
residue()codeprevnextTop
 Title   : residue
Usage :
Function: No code here, all parent/child stuff via Entry
Returns :
Args :
segID()codeprevnextTop
 Title   : segID
Usage : $segID = $atom->segID($segID)
Function: Sets/gets the segID
Returns : Returns the segID for this atom
Args : reference to an Atom
serial()codeprevnextTop
 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
sigocc()codeprevnextTop
 Title   : sigocc
Usage : $sigocc = $atom->sigocc($sigocc)
Function: Sets/gets the sigocc
Returns : Returns the sigocc for this atom
Args : reference to an Atom
sigtemp()codeprevnextTop
 Title   : sigtemp
Usage : $sigtemp = $atom->sigtemp($sigtemp)
Function: Sets/gets the sigtemp
Returns : Returns the sigtemp for this atom
Args : reference to an Atom
sigx()codeprevnextTop
 Title   : sigx
Usage : $sigx = $atom->sigx($sigx)
Function: Sets/gets the sigx
Returns : Returns the sigx for this atom
Args : reference to an Atom
sigy()codeprevnextTop
 Title   : sigy
Usage : $sigy = $atom->sigy($sigy)
Function: Sets/gets the sigy
Returns : Returns the sigy for this atom
Args : reference to an Atom
sigz()codeprevnextTop
 Title   : sigz
Usage : $sigz = $atom->sigz($sigz)
Function: Sets/gets the sigz
Returns : Returns the sigz for this atom
Args : reference to an Atom
tempfactor()codeprevnextTop
 Title   : tempfactor
Usage : $tempfactor = $atom->tempfactor($tempfactor)
Function: Sets/gets the tempfactor
Returns : Returns the tempfactor for this atom
Args : reference to an Atom
x()codeprevnextTop
 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
xyz()codeprevnextTop
 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 :
y()codeprevnextTop
 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
z()codeprevnextTop
 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
Methods code
DESTROYdescriptionprevnextTop
sub DESTROY {
	my $self =  shift;
	
	# dummy, nothing needs to be done here
} #
# from here on only private methods
#
}
_grandparentdescriptionprevnextTop
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;
}
_remove_residuedescriptionprevnextTop
sub _remove_residue {
	my ($self) = shift;

	$self->throw("no code here at the moment\n");
}
anisodescriptionprevnextTop
sub aniso {
	my($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 
}
chargedescriptionprevnextTop
sub charge {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'charge'} = $value;
	}
	return $self->{'charge'};
}
elementdescriptionprevnextTop
sub element {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'element'} = $value;
	}
	return $self->{'element'};
}
icodedescriptionprevnextTop
sub icode {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'icode'} = $value;
	}
	return $self->{'icode'};
}
iddescriptionprevnextTop
sub id {
        my ($self, $value) = @_;;
        if (defined $value) {
	        $self->{'id'} = $value;
        }
        return $self->{'id'};
}
newdescriptionprevnextTop
sub new {
    my ($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 $self;
}
occupancydescriptionprevnextTop
sub occupancy {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'occupancy'} = $value;
	}
	return $self->{'occupancy'};
}
pdb_atomnamedescriptionprevnextTop
sub pdb_atomname {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'pdb_atomname'} = $value;
	}
	return $self->{'pdb_atomname'};
}
residuedescriptionprevnextTop
sub residue {
	my($self, $value) = @_;

	$self->throw("all parent/child stuff via Entry\n");
}
segIDdescriptionprevnextTop
sub segID {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'segID'} = $value;
	}
	return $self->{'segID'};
}
serialdescriptionprevnextTop
sub serial {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'serial'} = $value;
	}
	return $self->{'serial'};
}
sigoccdescriptionprevnextTop
sub sigocc {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'sigocc'} = $value;
	}
	return $self->{'sigocc'};
}
sigtempdescriptionprevnextTop
sub sigtemp {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'sigtemp'} = $value;
	}
	return $self->{'sigtemp'};
}
sigu11descriptionprevnextTop
sub sigu11 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
sigu12descriptionprevnextTop
sub sigu12 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
sigu13descriptionprevnextTop
sub sigu13 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
sigu22descriptionprevnextTop
sub sigu22 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
sigu23descriptionprevnextTop
sub sigu23 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
sigu33descriptionprevnextTop
sub sigu33 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
sigxdescriptionprevnextTop
sub sigx {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'sigx'} = $value;
	}
	return $self->{'sigx'};
}
sigydescriptionprevnextTop
sub sigy {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'sigy'} = $value;
	}
	return $self->{'sigy'};
}
sigzdescriptionprevnextTop
sub sigz {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'sigz'} = $value;
	}
	return $self->{'sigz'};
}
tempfactordescriptionprevnextTop
sub tempfactor {
	my($self, $value) = @_;

	if (defined $value) {
		$self->{'tempfactor'} = $value;
	}
	return $self->{'tempfactor'};
}
u11descriptionprevnextTop
sub u11 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
u12descriptionprevnextTop
sub u12 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
u13descriptionprevnextTop
sub u13 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
u22descriptionprevnextTop
sub u22 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
u23descriptionprevnextTop
sub u23 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
u33descriptionprevnextTop
sub u33 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
xdescriptionprevnextTop
sub x {
	my ($self,$value) = @_;
	if( defined $value) {
		# do we want to check if $value contains really a number ?
$self->{'x'} = $value; } return $self->{'x'};
}
xyzdescriptionprevnextTop
sub xyz {
	my ($self) = @_;

	return ($self->x, $self->y, $self->z);
}
ydescriptionprevnextTop
sub y {
	my ($self,$value) = @_;
	if( defined $value) {
		# do we want to check if $value contains really a number ?
$self->{'y'} = $value; } return $self->{'y'};
}
zdescriptionprevnextTop
sub z {
	my ($self,$value) = @_;
	if( defined $value) {
		# do we want to check if $value contains really a number ?
$self->{'z'} = $value; } return $self->{'z'};
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Reporting BugsTop
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/
AUTHOR - Kris BoulezTop
Email kris.boulez@algonomics.com
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _