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#
# = bio/db/pdb/atom.rb - Coordinate class for PDB
#
# Copyright:: Copyright (C) 2004, 2006
# Alex Gutteridge <alexg@ebi.ac.uk>
# Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
#
# = Bio::PDB::Coordinate
#
# Coordinate class for PDB.
#
# = Compatibility Note
#
# From bioruby 0.7.0, the Bio::PDB::Atom class is no longer available.
# Please use Bio::PDB::Record::ATOM and Bio::PDB::Record::HETATM instead.
#
require 'matrix'
module Bio
require 'bio/db/pdb' unless const_defined?(:PDB)
class PDB
# Bio::PDB::Coordinate is a class to store a 3D coordinate.
# It inherits Vector (in bundled library in Ruby).
#
class Coordinate < Vector
# same as Vector.[x,y,z]
def self.[](x,y,z)
super
end
# same as Vector.elements
def self.elements(array, *a)
raise 'Size of given array must be 3' if array.size != 3
super
end
# x
def x; self[0]; end
# y
def y; self[1]; end
# z
def z; self[2]; end
# x=(n)
def x=(n); self[0]=n; end
# y=(n)
def y=(n); self[1]=n; end
# z=(n)
def z=(n); self[2]=n; end
# Implicit conversion to an array.
#
# Note that this method would be deprecated in the future.
#
#--
# Definition of 'to_ary' means objects of the class is
# implicitly regarded as an array.
#++
def to_ary; self.to_a; end
# returns self.
def xyz; self; end
# distance between <em>object2</em>.
def distance(object2)
Utils::convert_to_xyz(object2)
(self - object2).r
end
end #class Coordinate
end #class PDB
end #class Bio
|
