class Bio::PDB::Chain

Bio::PDB::Chain is a class to store a chain.

The object would contain some residues (Bio::PDB::Residue objects) and some heterogens (Bio::PDB::Heterogen objects).

Attributes

chain_id [RW]

Identifier of this chain

heterogens [R]

heterogens in this chain

id [RW]

Identifier of this chain

model [R]

the model to which this chain belongs.

residues [R]

residues in this chain

Public Class Methods

new (id = nil, model = nil)

Source

   # File lib/bio/db/pdb/chain.rb
40 def initialize(id = nil, model = nil)
41   
42   @chain_id  = id
43   
44   @model    = model
45   
46   @residues   = []
47   @residues_hash = {}
48   @heterogens = []
49   @heterogens_hash = {}
50 end

Creates a new chain object.

Public Instance Methods

<=> (other)

Source

    # File lib/bio/db/pdb/chain.rb
166 def <=>(other)
167   return @chain_id <=> other.chain_id
168 end

Operator aimed to sort based on chain id

[] (key)

Source

   # File lib/bio/db/pdb/chain.rb
77 def [](key)
78   get_residue_by_id(key)
79 end

get the residue by id.

Compatibility Note: Now, you cannot find HETATMS in this method. To add “LIGAND” to the id is no longer available. To get heterogens, you must use get_heterogen_by_id.

aaseq ()

Source

    # File lib/bio/db/pdb/chain.rb
182 def aaseq
183   unless defined? @aaseq
184     string = String.new
185     last_residue_num = nil
186     @residues.each do |residue|
187       if last_residue_num and 
188           (x = (residue.resSeq.to_i - last_residue_num).abs) > 1 then
189         x.times { string << 'X' }
190       end
191       tlc = residue.resName.capitalize
192       olc = (begin
193                Bio::AminoAcid.three2one(tlc)
194              rescue ArgumentError
195                nil
196              end || 'X')
197       string << olc
198     end
199     @aaseq = Bio::Sequence::AA.new(string)
200   end
201   @aaseq
202 end

gets an amino acid sequence of this chain from ATOM records

Also aliased as: atom_seq

addLigand (ligand)

Source

    # File lib/bio/db/pdb/chain.rb
100 def addLigand(ligand)
101   raise "Expecting a Bio::PDB::Residue" unless ligand.is_a? Bio::PDB::Residue
102   @heterogens.push(ligand)
103   if @heterogens_hash[ligand.residue_id] then
104     $stderr.puts "Warning: heterogen_id (residue_id) #{ligand.residue_id.inspect} is already used" if $VERBOSE
105   else
106     @heterogens_hash[ligand.residue_id] = ligand
107   end
108   self
109 end

Add a heterogen (ligand) to this chain

addResidue (residue)

Source

   # File lib/bio/db/pdb/chain.rb
88 def addResidue(residue)
89   raise "Expecting a Bio::PDB::Residue" unless residue.is_a? Bio::PDB::Residue
90   @residues.push(residue)
91   if @residues_hash[residue.residue_id] then
92     $stderr.puts "Warning: residue_id #{residue.residue_id.inspect} is already used" if $VERBOSE
93   else
94     @residues_hash[residue.residue_id] = residue
95   end
96   self
97 end

Add a residue to this chain

atom_seq ()

for backward compatibility

Alias for: aaseq

each () { |residue| ... }

Source

    # File lib/bio/db/pdb/chain.rb
154 def each(&x) #:yields: residue
155   @residues.each(&x)
156 end

Iterates over each residue

Also aliased as: each_residue

each_heterogen () { |heterogen| ... }

Source

    # File lib/bio/db/pdb/chain.rb
161 def each_heterogen(&x) #:yields: heterogen
162   @heterogens.each(&x)
163 end

Iterates over each hetero-compound

each_residue ()

Alias to override ResidueFinder#each_residue

Alias for: each

get_heterogen_by_id (key)

Source

   # File lib/bio/db/pdb/chain.rb
82 def get_heterogen_by_id(key)
83   #@heterogens.find { |r| r.residue_id == key }
84   @heterogens_hash[key]
85 end

get the heterogen (ligand) by id

get_residue_by_id (key)

Source

   # File lib/bio/db/pdb/chain.rb
67 def get_residue_by_id(key)
68   #@residues.find { |r| r.residue_id == key }
69   @residues_hash[key]
70 end

get the residue by id

inspect ()

Source

    # File lib/bio/db/pdb/chain.rb
177 def inspect
178   "#<#{self.class.to_s} id=#{chain_id.inspect} model.serial=#{(model ? model.serial : nil).inspect} residues.size=#{residues.size} heterogens.size=#{heterogens.size} aaseq=#{aaseq.inspect}>"
179 end

returns a string containing human-readable representation of this object.

rehash ()

Source

    # File lib/bio/db/pdb/chain.rb
148 def rehash
149   rehash_residues
150   rehash_heterogens
151 end

rehash residues hash and heterogens hash

rehash_heterogens ()

Source

    # File lib/bio/db/pdb/chain.rb
130 def rehash_heterogens
131   begin
132     heterogens_bak = @heterogens
133     heterogens_hash_bak = @heterogens_hash
134     @heterogens = []
135     @heterogens_hash = {}
136     heterogens_bak.each do |heterogen|
137       self.addLigand(heterogen)
138     end
139   rescue RuntimeError
140     @heterogens = heterogens_bak
141     @heterogens_hash = heterogens_hash_bak
142     raise
143   end
144   self
145 end

rehash heterogens hash

rehash_residues ()

Source

    # File lib/bio/db/pdb/chain.rb
112 def rehash_residues
113   begin
114     residues_bak = @residues
115     residues_hash_bak = @residues_hash
116     @residues = []
117     @residues_hash = {}
118     residues_bak.each do |residue|
119       self.addResidue(residue)
120     end
121   rescue RuntimeError
122     @residues = residues_bak
123     @residues_hash = residues_hash_bak
124     raise
125   end
126   self
127 end

rehash residues hash

to_s ()

Source

    # File lib/bio/db/pdb/chain.rb
171 def to_s
172   @residues.join('') + "TER\n" + @heterogens.join('')
173 end

Stringifies each residue