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    :