Bio::Structure::Atom.3pm

Langue: en

Autres versions - même langue

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

Sommaire

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: 
   http://bugzilla.open-bio.org/

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    :