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Man Pages


Manual Reference Pages  -  BIO::STRUCTURE::ATOM (3)

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NAME

Bio::Structure::Atom - Bioperl structure Object, describes an Atom

CONTENTS

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://github.com/bioperl/bioperl-live/issues



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    :



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