Bio::Structure::Atom(3pm)

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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    :