Class: Mddb::Molecule

Inherits:
Object
  • Object
show all
Includes:
Calculations, MongoMapper::Document
Defined in:
lib/mddb/molecule.rb

Instance Method Summary collapse

Methods included from Calculations

included, #list_calculations, #run

Instance Method Details

#calc_rg ⇒ Object 



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# File 'lib/mddb/molecule.rb', line 13

def calc_rg
  sum_ij = 0
  self.atoms.each do |i|
    self.atoms.each do |j|
      sum_ij += (i.position.distance_to j.position)**2
    end
  end

  rg2 = sum_ij / (2*(32**2))
  rg = rg2**0.5

  self.rg = rg/0.529
  self.save
end

#calc_sasa ⇒ Object 



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# File 'lib/mddb/molecule.rb', line 28

def calc_sasa 
  nodes=GsdSphere.new(1000).nodes
  r_oxygen = 1.58
  r_monomer = 1.58
  surface = 0
  origin = Point[0,0,0]
  self.atoms.each do |atom|
    nodes.each do |node|
      pos_tranformation = origin.vector_to atom.position
      
      point = node + pos_tranformation

      v_radius = atom.position.vector_to point

      test_point = atom.position + (v_radius * (r_oxygen + r_monomer))
      other_atoms =  self.atoms - [atom]

      inside = false

      other_atoms.each do |other|
        if (test_point.distance_to other.position) < (r_oxygen + r_monomer)
          inside = true
        end
      end

      surface += 1 if inside == false
    end
  end
  self.sasa = surface.to_f/(self.atoms.count*nodes.count)
  self.save
end

#mass ⇒ Object 



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# File 'lib/mddb/molecule.rb', line 72

def mass
  mass = 0
  self.atoms.each do |a|
    mass += a.mass
  end
  mass
end

#timeline ⇒ Object 



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# File 'lib/mddb/molecule.rb', line 60

def timeline
  self.class.where(:mid => self.mid).all
end

#timestep(n = 0) ⇒ Object 



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# File 'lib/mddb/molecule.rb', line 64

def timestep n=0
  if self.fid + n <= Frame.count and self.fid + n > 0
    self.class.where(:mid => self.mid, :fid => (self.fid+n)).all
  else
    raise "Bad timestep. No frame exists or out of range"
  end
end