/ 
BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Structure::Atom

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    :