Bio::Structure
Atom
Summary
Bio::Structure::Atom - Bioperl structure Object, describes an Atom
Package variables
No package variables defined.
Included modules
base qw ( Bio::Root::Root )
Synopsis
Description
This object stores a Bio::Structure::Atom
Methods
Methods description
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 |
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 |
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 |
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 |
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 : |
Title : residue
Usage :
Function: No code here, all parent/child stuff via Entry
Returns :
Args : |
Title : icode
Usage : $icode = $atom->icode($icode)
Function: Sets/gets the icode
Returns : Returns the icode for this atom
Args : reference to an Atom |
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 |
Title : occupancy
Usage : $occupancy = $atom->occupancy($occupancy)
Function: Sets/gets the occupancy
Returns : Returns the occupancy for this atom
Args : reference to an Atom |
Title : tempfactor
Usage : $tempfactor = $atom->tempfactor($tempfactor)
Function: Sets/gets the tempfactor
Returns : Returns the tempfactor for this atom
Args : reference to an Atom |
Title : segID
Usage : $segID = $atom->segID($segID)
Function: Sets/gets the segID
Returns : Returns the segID for this atom
Args : reference to an Atom |
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 |
Title : element
Usage : $element = $atom->element($element)
Function: Sets/gets the element
Returns : Returns the element for this atom
Args : reference to an Atom |
Title : charge
Usage : $charge = $atom->charge($charge)
Function: Sets/gets the charge
Returns : Returns the charge for this atom
Args : reference to an Atom |
Title : sigx
Usage : $sigx = $atom->sigx($sigx)
Function: Sets/gets the sigx
Returns : Returns the sigx for this atom
Args : reference to an Atom |
Title : sigy
Usage : $sigy = $atom->sigy($sigy)
Function: Sets/gets the sigy
Returns : Returns the sigy for this atom
Args : reference to an Atom |
Title : sigz
Usage : $sigz = $atom->sigz($sigz)
Function: Sets/gets the sigz
Returns : Returns the sigz for this atom
Args : reference to an Atom |
Title : sigocc
Usage : $sigocc = $atom->sigocc($sigocc)
Function: Sets/gets the sigocc
Returns : Returns the sigocc for this atom
Args : reference to an Atom |
Title : sigtemp
Usage : $sigtemp = $atom->sigtemp($sigtemp)
Function: Sets/gets the sigtemp
Returns : Returns the sigtemp for this atom
Args : reference to an Atom |
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 |
Title : id
Usage : $atom->id("CZ2")
Function: Gets/sets the ID for this atom
Returns : the ID
Args : the ID |
Title : _remove_residue
Usage :
Function: Removes the Residue this Atom is atttached to.
Returns :
Args : |
Title : _grandparent
Usage :
Function: get/set a symbolic reference to our grandparent
Returns :
Args : |
Methods code
sub new
{ my ($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 $self;} | sub x
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'x'} = $value;
}
return $self->{'x'};} | sub y
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'y'} = $value;
}
return $self->{'y'};} | sub z
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'z'} = $value;
}
return $self->{'z'};} | sub xyz
{ my ($self) = @_;
return ($self->x, $self->y, $self->z); } | sub residue
{ my($self, $value) = @_;
$self->throw("all parent/child stuff via Entry\n");} | sub icode
{ my($self, $value) = @_;
if (defined $value) {
$self->{'icode'} = $value;
}
return $self->{'icode'};} | sub serial
{ my($self, $value) = @_;
if (defined $value) {
$self->{'serial'} = $value;
}
return $self->{'serial'};} | sub occupancy
{ my($self, $value) = @_;
if (defined $value) {
$self->{'occupancy'} = $value;
}
return $self->{'occupancy'};} | sub tempfactor
{ my($self, $value) = @_;
if (defined $value) {
$self->{'tempfactor'} = $value;
}
return $self->{'tempfactor'};} | sub segID
{ my($self, $value) = @_;
if (defined $value) {
$self->{'segID'} = $value;
}
return $self->{'segID'};} | sub pdb_atomname
{ my($self, $value) = @_;
if (defined $value) {
$self->{'pdb_atomname'} = $value;
}
return $self->{'pdb_atomname'};} | sub element
{ my($self, $value) = @_;
if (defined $value) {
$self->{'element'} = $value;
}
return $self->{'element'};} | sub charge
{ my($self, $value) = @_;
if (defined $value) {
$self->{'charge'} = $value;
}
return $self->{'charge'};} | sub sigx
{ my($self, $value) = @_;
if (defined $value) {
$self->{'sigx'} = $value;
}
return $self->{'sigx'};} | sub sigy
{ my($self, $value) = @_;
if (defined $value) {
$self->{'sigy'} = $value;
}
return $self->{'sigy'};} | sub sigz
{ my($self, $value) = @_;
if (defined $value) {
$self->{'sigz'} = $value;
}
return $self->{'sigz'};} | sub sigocc
{ my($self, $value) = @_;
if (defined $value) {
$self->{'sigocc'} = $value;
}
return $self->{'sigocc'};} | sub sigtemp
{ my($self, $value) = @_;
if (defined $value) {
$self->{'sigtemp'} = $value;
}
return $self->{'sigtemp'};} | sub aniso
{ my($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};} | 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,$value); } | sub id
{ my ($self, $value) = @_;;
if (defined $value) {
$self->{'id'} = $value;
}
return $self->{'id'};} | sub DESTROY
{ my $self = shift;
} | sub _remove_residue
{ my ($self) = shift;
$self->throw("no code here at the moment\n");} | sub _grandparent
{ my($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'};} | 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
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
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:
http://bugzilla.open-bio.org/
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _