Class: Bio::PDB::Chain

Inherits:
Object show all
Includes:
AtomFinder, HetatmFinder, HeterogenFinder, ResidueFinder, Utils, Comparable, Enumerable
Defined in:
lib/bio/db/pdb/chain.rb

Overview

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).

Constant Summary

Constants included from Utils

Utils::ElementMass

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from HeterogenFinder

#find_heterogen

Methods included from HetatmFinder

#each_hetatm, #find_hetatm, #hetatms

Methods included from ResidueFinder

#find_residue

Methods included from AtomFinder

#atoms, #each_atom, #find_atom

Methods included from Utils

acos, calculatePlane, #centreOfGravity, convert_to_xyz, dihedral_angle, distance, #finder, #geometricCentre, rad2deg, to_xyz

Constructor Details

#initialize(id = nil, model = nil) ⇒ Chain

Creates a new chain object.


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# File 'lib/bio/db/pdb/chain.rb', line 39

def initialize(id = nil, model = nil)
  
  @chain_id  = id
  
  @model    = model
  
  @residues   = []
  @residues_hash = {}
  @heterogens = []
  @heterogens_hash = {}
end

Instance Attribute Details

#chain_idObject Also known as: id

Identifier of this chain


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# File 'lib/bio/db/pdb/chain.rb', line 52

def chain_id
  @chain_id
end

#heterogensObject (readonly)

heterogens in this chain


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# File 'lib/bio/db/pdb/chain.rb', line 63

def heterogens
  @heterogens
end

#modelObject (readonly)

the model to which this chain belongs.


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# File 'lib/bio/db/pdb/chain.rb', line 57

def model
  @model
end

#residuesObject (readonly)

residues in this chain


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# File 'lib/bio/db/pdb/chain.rb', line 60

def residues
  @residues
end

Instance Method Details

#<=>(other) ⇒ Object

Operator aimed to sort based on chain id


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# File 'lib/bio/db/pdb/chain.rb', line 165

def <=>(other)
  return @chain_id <=> other.chain_id
end

#[](key) ⇒ Object

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.


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# File 'lib/bio/db/pdb/chain.rb', line 76

def [](key)
  get_residue_by_id(key)
end

#aaseqObject Also known as: atom_seq

gets an amino acid sequence of this chain from ATOM records


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# File 'lib/bio/db/pdb/chain.rb', line 181

def aaseq
  unless defined? @aaseq
    string = ""
    last_residue_num = nil
    @residues.each do |residue|
      if last_residue_num and 
          (x = (residue.resSeq.to_i - last_residue_num).abs) > 1 then
        x.times { string << 'X' }
      end
      tlc = residue.resName.capitalize
      olc = (begin
               Bio::AminoAcid.three2one(tlc)
             rescue ArgumentError
               nil
             end || 'X')
      string << olc
    end
    @aaseq = Bio::Sequence::AA.new(string)
  end
  @aaseq
end

#addLigand(ligand) ⇒ Object

Add a heterogen (ligand) to this chain


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# File 'lib/bio/db/pdb/chain.rb', line 99

def addLigand(ligand)
  raise "Expecting a Bio::PDB::Residue" unless ligand.is_a? Bio::PDB::Residue
  @heterogens.push(ligand)
  if @heterogens_hash[ligand.residue_id] then
    $stderr.puts "Warning: heterogen_id (residue_id) #{ligand.residue_id.inspect} is already used" if $VERBOSE
  else
    @heterogens_hash[ligand.residue_id] = ligand
  end
  self
end

#addResidue(residue) ⇒ Object

Add a residue to this chain


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# File 'lib/bio/db/pdb/chain.rb', line 87

def addResidue(residue)
  raise "Expecting a Bio::PDB::Residue" unless residue.is_a? Bio::PDB::Residue
  @residues.push(residue)
  if @residues_hash[residue.residue_id] then
    $stderr.puts "Warning: residue_id #{residue.residue_id.inspect} is already used" if $VERBOSE
  else
    @residues_hash[residue.residue_id] = residue
  end
  self
end

#each(&x) ⇒ Object Also known as: each_residue

Iterates over each residue


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# File 'lib/bio/db/pdb/chain.rb', line 153

def each(&x) #:yields: residue
  @residues.each(&x)
end

#each_heterogen(&x) ⇒ Object

Iterates over each hetero-compound


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# File 'lib/bio/db/pdb/chain.rb', line 160

def each_heterogen(&x) #:yields: heterogen
  @heterogens.each(&x)
end

#get_heterogen_by_id(key) ⇒ Object

get the heterogen (ligand) by id


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# File 'lib/bio/db/pdb/chain.rb', line 81

def get_heterogen_by_id(key)
  #@heterogens.find { |r| r.residue_id == key }
  @heterogens_hash[key]
end

#get_residue_by_id(key) ⇒ Object

get the residue by id


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# File 'lib/bio/db/pdb/chain.rb', line 66

def get_residue_by_id(key)
  #@residues.find { |r| r.residue_id == key }
  @residues_hash[key]
end

#inspectObject

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


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# File 'lib/bio/db/pdb/chain.rb', line 176

def inspect
  "#<#{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}>"
end

#rehashObject

rehash residues hash and heterogens hash


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# File 'lib/bio/db/pdb/chain.rb', line 147

def rehash
  rehash_residues
  rehash_heterogens
end

#rehash_heterogensObject

rehash heterogens hash


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# File 'lib/bio/db/pdb/chain.rb', line 129

def rehash_heterogens
  begin
    heterogens_bak = @heterogens
    heterogens_hash_bak = @heterogens_hash
    @heterogens = []
    @heterogens_hash = {}
    heterogens_bak.each do |heterogen|
      self.addLigand(heterogen)
    end
  rescue RuntimeError
    @heterogens = heterogens_bak
    @heterogens_hash = heterogens_hash_bak
    raise
  end
  self
end

#rehash_residuesObject

rehash residues hash


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# File 'lib/bio/db/pdb/chain.rb', line 111

def rehash_residues
  begin
    residues_bak = @residues
    residues_hash_bak = @residues_hash
    @residues = []
    @residues_hash = {}
    residues_bak.each do |residue|
      self.addResidue(residue)
    end
  rescue RuntimeError
    @residues = residues_bak
    @residues_hash = residues_hash_bak
    raise
  end
  self
end

#to_sObject

Stringifies each residue


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# File 'lib/bio/db/pdb/chain.rb', line 170

def to_s
  @residues.join('') + "TER\n" + @heterogens.join('')
end