Class: Chem::PdbDic

Inherits:
Object
  • Object
show all
Defined in:
lib/chem/db/pdb_dic.rb

Defined Under Namespace

Classes: PdbDicAtom, PdbDicBond, PdbDicMolecule

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(file, &block) ⇒ PdbDic

Returns a new instance of PdbDic.



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# File 'lib/chem/db/pdb_dic.rb', line 59

def initialize file, &block
  @mols = {}
  parse(file, &block)
end

Instance Attribute Details

#mols ⇒ Object (readonly)

Returns the value of attribute mols.



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# File 'lib/chem/db/pdb_dic.rb', line 58

def mols
  @mols
end

Class Method Details

.each(file, &block) ⇒ Object 



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# File 'lib/chem/db/pdb_dic.rb', line 108

def PdbDic.each file, &block
  PdbDic.new(file, &block)
end

.open(file, &block) ⇒ Object 



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# File 'lib/chem/db/pdb_dic.rb', line 111

def PdbDic.open(file, &block)
  PdbDic.new(file, &block)
end

Instance Method Details

#parse(file, &block) ⇒ Object 



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# File 'lib/chem/db/pdb_dic.rb', line 64

def parse file, &block
  i = 0
  @input = File.open(file, 'r')
  res = nil
  while !@input.eof?
    line = @input.readline
    case line
    when /^RESIDUE/
      mol = PdbDicMolecule.new
      res = line.split[1]
      @mols[res] = mol
#           if line.split[1] == 'ACY'
#             puts 'Found ACY'
#             exit
#           end
#          puts "'%s'" % line[0..5]
    when /^CONECT/
      atom = mol.atoms[line[11..15].strip] ||= PdbDicAtom.new(line[11..15].strip)
      line[20..-1].chop.split.each do |atom_id|
        if ! mol.atoms[atom_id]
          atom2 = PdbDicAtom.new(atom_id)
          mol.atoms[atom_id] = atom2
          bond = PdbDicBond.new
          bond.b = atom
          bond.e = atom2
          bond.v = 1
          mol.bonds.push(bond)
        end
      end
    when "\n"
      mol.bonds.each do |bond|
        bond.b.neighbor.push(bond.e) if ! bond.b.neighbor.include?(bond.e)
        bond.e.neighbor.push(bond.b) if ! bond.e.neighbor.include?(bond.b)
      end
#          i += 1
      if block
        yield res, mol
      end
      return if i >= 100
    else
#          puts line
    end
  end
end