Bio::Structure::Atom(3pm) User Contributed Perl Documentation Bio::Structure::Atom(3pm)
NAME
Bio::Structure::Atom - Bioperl structure Object, describes an Atom
SYNOPSIS
#add synopsis here
DESCRIPTION
This object stores a Bio::Structure::Atom
FEEDBACK
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
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 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 the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Kris Boulez
Email kris.boulez@algonomics.com
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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
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 :
residue()
Title : residue
Usage :
Function: No code here, all parent/child stuff via Entry
Returns :
Args :
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
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
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
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
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
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
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
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
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
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
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
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
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
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
id()
Title : id
Usage : $atom->id("CZ2")
Function: Gets/sets the ID for this atom
Returns : the ID
Args : the ID
_remove_residue()
Title : _remove_residue
Usage :
Function: Removes the Residue this Atom is atttached to.
Returns :
Args :
_grandparent()
Title : _grandparent
Usage :
Function: get/set a symbolic reference to our grandparent
Returns :
Args :
perl v5.14.2 2012-03-02 Bio::Structure::Atom(3pm)