Raw content of Bio::Structure::Atom # $Id: Atom.pm,v 1.8 2002/10/22 07:38:44 lapp Exp $ # # bioperl module for Bio::Structure::Atom # # Cared for by Kris Boulez <kris.boulez@algonomics.com> # # Copyright Kris Boulez # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Structure::Atom - Bioperl structure Object, describes an Atom =head1 SYNOPSIS #add synopsis here =head1 DESCRIPTION This object stores a Bio::Structure::Atom =head1 FEEDBACK =head2 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://bio.perl.org/MailList.html - About the mailing lists =head2 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/ =head1 AUTHOR - Kris Boulez Email kris.boulez@algonomics.com =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Structure::Atom; use vars qw(@ISA); use strict; use Bio::Root::Root; use Bio::Structure::Residue; @ISA = qw(Bio::Root::Root); =head2 new() Title : new() Usage : $struc = Bio::Structure::Atom->new( -id => 'human_id', ); Function: Returns a new Bio::Structure::Atom object from basic constructors. Probably most called from Bio::Structure::IO. Returns : a new Bio::Structure::Atom object =cut sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my($id, $x, $y, $z) = $self->_rearrange([qw( ID X Y Z )], @args); $id && $self->id($id); $x && $self->x($x); $y && $self->y($y); $z && $self->z($z); return $self; } =head2 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 =cut sub x { my ($self,$value) = @_; if( defined $value) { # do we want to check if $value contains really a number ? $self->{'x'} = $value; } return $self->{'x'}; } =head2 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 =cut sub y { my ($self,$value) = @_; if( defined $value) { # do we want to check if $value contains really a number ? $self->{'y'} = $value; } return $self->{'y'}; } =head2 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 =cut sub z { my ($self,$value) = @_; if( defined $value) { # do we want to check if $value contains really a number ? $self->{'z'} = $value; } return $self->{'z'}; } =head2 xyz() Title : xyz Usage : ($x,$y,$z) = $atom->xyz; Function: Gets the XYZ coordinates for an Atom Returns : A list with the value for the XYZ coordinate of the Atom Args : =cut sub xyz { my ($self) = @_; return ($self->x, $self->y, $self->z); } =head2 residue() Title : residue Usage : Function: No code here, all parent/child stuff via Entry Returns : Args : =cut sub residue { my($self, $value) = @_; $self->throw("all parent/child stuff via Entry\n"); } =head2 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 =cut sub icode { my($self, $value) = @_; if (defined $value) { $self->{'icode'} = $value; } return $self->{'icode'}; } =head2 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 =cut sub serial { my($self, $value) = @_; if (defined $value) { $self->{'serial'} = $value; } return $self->{'serial'}; } =head2 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 =cut sub occupancy { my($self, $value) = @_; if (defined $value) { $self->{'occupancy'} = $value; } return $self->{'occupancy'}; } =head2 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 =cut sub tempfactor { my($self, $value) = @_; if (defined $value) { $self->{'tempfactor'} = $value; } return $self->{'tempfactor'}; } =head2 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 =cut sub segID { my($self, $value) = @_; if (defined $value) { $self->{'segID'} = $value; } return $self->{'segID'}; } =head2 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 =cut sub pdb_atomname { my($self, $value) = @_; if (defined $value) { $self->{'pdb_atomname'} = $value; } return $self->{'pdb_atomname'}; } =head2 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 =cut sub element { my($self, $value) = @_; if (defined $value) { $self->{'element'} = $value; } return $self->{'element'}; } =head2 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 =cut sub charge { my($self, $value) = @_; if (defined $value) { $self->{'charge'} = $value; } return $self->{'charge'}; } =head2 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 =cut sub sigx { my($self, $value) = @_; if (defined $value) { $self->{'sigx'} = $value; } return $self->{'sigx'}; } =head2 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 =cut sub sigy { my($self, $value) = @_; if (defined $value) { $self->{'sigy'} = $value; } return $self->{'sigy'}; } =head2 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 =cut sub sigz { my($self, $value) = @_; if (defined $value) { $self->{'sigz'} = $value; } return $self->{'sigz'}; } =head2 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 =cut sub sigocc { my($self, $value) = @_; if (defined $value) { $self->{'sigocc'} = $value; } return $self->{'sigocc'}; } =head2 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 =cut sub sigtemp { my($self, $value) = @_; if (defined $value) { $self->{'sigtemp'} = $value; } return $self->{'sigtemp'}; } =head2 aniso() Title : aniso Usage : $u12 = $atom->aniso("u12", $u12) Function: Sets/gets the anisotropic temperature factors Returns : Returns the requested factor for this atom Args : reference to an Atom, name of the factor, value for the factor =cut sub aniso { my($self, $name, $value) = @_; if ( !defined $name) { $self->throw("You need to supply a name of the anisotropic temp factor you want to get"); } if (defined $value) { $self->{$name} = $value; } return $self->{$name}; } # placeholders sub u11 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub u22 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub u33 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub u12 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub u13 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub u23 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu11 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu22 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu33 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu12 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu13 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } sub sigu23 { my ($self, $name, $value) = @_; $self->aniso($name,$value); } =head2 id() Title : id Usage : $atom->id("CZ2") Function: Gets/sets the ID for this atom Returns : the ID Args : the ID =cut sub id { my ($self, $value) = @_;; if (defined $value) { $self->{'id'} = $value; } return $self->{'id'}; } sub DESTROY { my $self = shift; # dummy, nothing needs to be done here } # # from here on only private methods # =head2 _remove_residue() Title : _remove_residue Usage : Function: Removes the Residue this Atom is atttached to. Returns : Args : =cut sub _remove_residue { my ($self) = shift; $self->throw("no code here at the moment\n"); } =head2 _grandparent() Title : _grandparent Usage : Function: get/set a symbolic reference to our grandparent Returns : Args : =cut sub _grandparent { my($self,$symref) = @_; if (ref($symref)) { $self->throw("Thou shall only pass strings in here, no references $symref\n"); } if (defined $symref) { $self->{'grandparent'} = $symref; } return $self->{'grandparent'}; } 1;