Bio::Structure::Atom - Bioperl structure Object, describes an Atom #add synopsis here This object stores a Bio::Structure::Atom

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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email kris.boulez@algonomics.com 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 :