diff variant_effect_predictor/Bio/Structure/Atom.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Structure/Atom.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,613 @@
+# $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 <[e-mail]>
+#
+# 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.
+
+  [e-mail]             - 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Kris Boulez
+
+Email [e-mail]
+
+=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;