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bio::structure::atom

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)