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#
# = bio/db/pdb/model.rb - model 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::Model
#
# Please refer Bio::PDB::Model.
#
module Bio
require 'bio/db/pdb' unless const_defined?(:PDB)
class PDB
# Bio::PDB::Model is a class to store a model.
#
# The object would contain some chains (Bio::PDB::Chain objects).
class Model
include Utils
include AtomFinder
include ResidueFinder
include ChainFinder
include HetatmFinder
include HeterogenFinder
include Enumerable
include Comparable
# Creates a new Model object
def initialize(serial = nil, structure = nil)
@serial = serial
@structure = structure
@chains = []
@chains_hash = {}
@solvents = Chain.new('', self)
end
# chains in this model
attr_reader :chains
# (OBSOLETE) solvents (water, HOH) in this model
attr_reader :solvents
# serial number of this model. (Integer or nil)
attr_accessor :serial
# for backward compatibility
alias model_serial serial
# (reserved for future extension)
attr_reader :structure
# Adds a chain to this model
def addChain(chain)
raise "Expecting a Bio::PDB::Chain" unless chain.is_a? Bio::PDB::Chain
@chains.push(chain)
if @chains_hash[chain.chain_id] then
$stderr.puts "Warning: chain_id #{chain.chain_id.inspect} is already used" if $VERBOSE
else
@chains_hash[chain.chain_id] = chain
end
self
end
# rehash chains hash
def rehash
begin
chains_bak = @chains
chains_hash_bak = @chains_hash
@chains = []
@chains_hash = {}
chains_bak.each do |chain|
self.addChain(chain)
end
rescue RuntimeError
@chains = chains_bak
@chains_hash = chains_hash_bak
raise
end
self
end
# (OBSOLETE) Adds a solvent molecule to this model
def addSolvent(solvent)
raise "Expecting a Bio::PDB::Residue" unless solvent.is_a? Bio::PDB::Residue
@solvents.addResidue(solvent)
end
# (OBSOLETE) not recommended to use this method
def removeSolvent
@solvents = nil
end
# Iterates over each chain
def each(&x) #:yields: chain
@chains.each(&x)
end
# Alias to override ChainFinder#each_chain
alias each_chain each
# Operator aimed to sort models based on serial number
def <=>(other)
return @serial <=> other.model_serial
end
# Keyed access to chains
def [](key)
#chain = @chains.find{ |chain| key == chain.id }
@chains_hash[key]
end
# stringifies to chains
def to_s
string = ""
if model_serial
string = "MODEL #{model_serial}\n" #Should use proper formatting
end
@chains.each{ |chain| string << chain.to_s }
#if solvent
# string << @solvent.to_s
#end
if model_serial
string << "ENDMDL\n"
end
return string
end
# returns a string containing human-readable representation
# of this object.
def inspect
"#<#{self.class.to_s} serial=#{serial.inspect} chains.size=#{chains.size}>"
end
end #class Model
end #class PDB
end #module Bio
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