Method: Bio::PDB#initialize

Defined in:

lib/bio/db/pdb/pdb.rb

#initialize(str) ⇒ PDB

Creates a new Bio::PDB object from given str.

# File 'lib/bio/db/pdb/pdb.rb', line 1444

def initialize(str)
  #Aha! Our entry into the world of PDB parsing, we initialise a PDB
  #object with the whole PDB file as a string
  #each PDB has an array of the lines of the original file
  #a bit memory-tastic! A hash of records and an array of models
  #also has an id

  @data = str.split(/[\r\n]+/)
  @hash = {}
  @models = []
  @id = nil

  #Flag to say whether the current line is part of a continuation
  cont = false

  #Empty current model
  cModel    = Model.new
  cChain    = nil #Chain.new
  cResidue  = nil #Residue.new
  cLigand   = nil #Heterogen.new
  c_atom    = nil

  #Goes through each line and replace that line with a PDB::Record
  @data.collect! do |line|
    #Go to next if the previous line was contiunation able, and
    #add_continuation returns true. Line is added by add_continuation
    next if cont and cont = cont.add_continuation(line)

    #Make the new record
    f = Record.get_record_class(line).new.initialize_from_string(line)
    #p f
    #Set cont
    cont = f if f.continue?
    #Set the hash to point to this record either by adding to an
    #array, or on it's own
    key = f.record_name
    if a = @hash[key] then
      a << f
    else
      @hash[key] = [ f ]
    end

    # Do something for ATOM and HETATM
    if key == 'ATOM' or key == 'HETATM' then
      if cChain and f.chainID == cChain.id
        chain = cChain
      else
        if chain = cModel[f.chainID]
          cChain = chain unless cChain
        else
          # If we don't have chain, add a new chain
          newChain = Chain.new(f.chainID, cModel)
          cModel.addChain(newChain)
          cChain = newChain
          chain = newChain
        end
        # chain might be changed, clearing cResidue and cLigand
        cResidue = nil
        cLigand = nil
      end
    end

    case key
    when 'ATOM'
      c_atom = f
      residueID = Residue.get_residue_id_from_atom(f)

      if cResidue and residueID == cResidue.id
        residue = cResidue
      else
        if residue = chain.get_residue_by_id(residueID)
          cResidue = residue unless cResidue
        else
          # add a new residue
          newResidue = Residue.new(f.resName, f.resSeq, f.iCode, chain)
          chain.addResidue(newResidue)
          cResidue = newResidue
          residue = newResidue
        end
      end
      
      f.residue = residue
      residue.addAtom(f)

    when 'HETATM'
      c_atom = f
      residueID = Heterogen.get_residue_id_from_atom(f)

      if cLigand and residueID == cLigand.id
        ligand = cLigand
      else
        if ligand = chain.get_heterogen_by_id(residueID)
          cLigand = ligand unless cLigand
        else
          # add a new heterogen
          newLigand = Heterogen.new(f.resName, f.resSeq, f.iCode, chain)
          chain.addLigand(newLigand)
          cLigand = newLigand
          ligand = newLigand
          #Each model has a special solvent chain. (for compatibility)
          if f.resName == 'HOH'
            cModel.addSolvent(newLigand)
          end
        end
      end

      f.residue = ligand
      ligand.addAtom(f)

    when 'MODEL'
      c_atom = nil
      cChain = nil
      cResidue = nil
      cLigand = nil
      if cModel.model_serial or cModel.chains.size > 0 then
        self.addModel(cModel)
      end
      cModel = Model.new(f.serial)

    when 'TER'
      if c_atom
        c_atom.ter = f
      else
        #$stderr.puts "Warning: stray TER?"
      end
    when 'SIGATM'
      if c_atom
        #$stderr.puts "Warning: duplicated SIGATM?" if c_atom.sigatm
        c_atom.sigatm = f
      else
        #$stderr.puts "Warning: stray SIGATM?"
      end
    when 'ANISOU'
      if c_atom
        #$stderr.puts "Warning: duplicated ANISOU?" if c_atom.anisou
        c_atom.anisou = f
      else
        #$stderr.puts "Warning: stray ANISOU?"
      end
    when 'SIGUIJ'
      if c_atom and c_atom.anisou
        #$stderr.puts "Warning: duplicated SIGUIJ?" if c_atom.anisou.siguij
        c_atom.anisou.siguij = f
      else
        #$stderr.puts "Warning: stray SIGUIJ?"
      end

    else
      c_atom = nil

    end
    f
  end #each
  #At the end we need to add the final model
  self.addModel(cModel)
  @data.compact!
end