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::Structure::Residue
Inherit
Bio::Root::Root
Synopsis
  #add synopsis here
Description
This object stores a Bio::Structure::Atom
Methods
newDescriptionCode
xDescriptionCode
yDescriptionCode
zDescriptionCode
xyzDescriptionCode
residueDescriptionCode
icodeDescriptionCode
serialDescriptionCode
occupancyDescriptionCode
tempfactorDescriptionCode
segIDDescriptionCode
pdb_atomnameDescriptionCode
elementDescriptionCode
chargeDescriptionCode
sigxDescriptionCode
sigyDescriptionCode
sigzDescriptionCode
sigoccDescriptionCode
sigtempDescriptionCode
anisoDescriptionCode
u11
No description
Code
u22
No description
Code
u33
No description
Code
u12
No description
Code
u13
No description
Code
u23
No description
Code
sigu11
No description
Code
sigu22
No description
Code
sigu33
No description
Code
sigu12
No description
Code
sigu13
No description
Code
sigu23
No description
Code
idDescriptionCode
DESTROY
No description
Code
_remove_residueDescriptionCode
_grandparentDescriptionCode
Methods description
new()code    nextTop
 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
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
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
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 :
residue()codeprevnextTop
 Title   : residue
Usage :
Function: No code here, all parent/child stuff via Entry
Returns :
Args :
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
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
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
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
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
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
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
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
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
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
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
id()codeprevnextTop
 Title   : id
Usage : $atom->id("CZ2")
Function: Gets/sets the ID for this atom
Returns : the ID
Args : the ID
_remove_residue()codeprevnextTop
 Title   : _remove_residue
Usage :
Function: Removes the Residue this Atom is atttached to.
Returns :
Args :
_grandparent()codeprevnextTop
 Title   : _grandparent
Usage :
Function: get/set a symbolic reference to our grandparent
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
    my ($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 $self;
}
xdescriptionprevnextTop
sub x {
	my ($self,$value) = @_;
	if( defined $value) {
		# do we want to check if $value contains really a number ?
$self->{'x'} = $value; } return $self->{'x'};
}
ydescriptionprevnextTop
sub y {
	my ($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 $self->{'z'};
}
xyzdescriptionprevnextTop
sub xyz {
	my ($self) = @_;

	return ($self->x, $self->y, $self->z);
}
residuedescriptionprevnextTop
sub residue {
	my($self, $value) = @_;

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

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

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

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

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

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

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

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

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

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

	if (defined $value) {
		$self->{'sigtemp'} = $value;
	}
	return $self->{'sigtemp'};
}
anisodescriptionprevnextTop
sub aniso {
	my($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 
}
u11descriptionprevnextTop
sub u11 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
u22descriptionprevnextTop
sub u22 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
u33descriptionprevnextTop
sub u33 {
	my ($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,$value);
}
u23descriptionprevnextTop
sub u23 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
sigu11descriptionprevnextTop
sub sigu11 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
sigu22descriptionprevnextTop
sub sigu22 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
sigu33descriptionprevnextTop
sub sigu33 {
	my ($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,$value);
}
sigu23descriptionprevnextTop
sub sigu23 {
	my ($self, $name, $value) = @_;
	$self->aniso($name,$value);
}
iddescriptionprevnextTop
sub id {
        my ($self, $value) = @_;;
        if (defined $value) {
	        $self->{'id'} = $value;
        }
        return $self->{'id'};
}
DESTROYdescriptionprevnextTop
sub DESTROY {
	my $self =  shift;
	
	# dummy, nothing needs to be done here
} #
# from here on only private methods
#
}
_remove_residuedescriptionprevnextTop
sub _remove_residue {
	my ($self) = shift;

	$self->throw("no code here at the moment\n");
}
_grandparentdescriptionprevnextTop
sub _grandparent {
	my($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;
}
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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 the web:
  https://redmine.open-bio.org/projects/bioperl/
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 _