Class: ViennaRna::Package::EnergyGrid2d

Inherits:
Base
  • Object
show all
Includes:
Enumerable
Defined in:
lib/vienna_rna/package/energy_grid_2d.rb

Direct Known Subclasses

Fftbor2d, Rna2dfold

Defined Under Namespace

Modules: EnergyGrid2dWrapper Classes: Row2d

Instance Attribute Summary

Attributes inherited from Base

#data, #flags, #response, #runtime

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from Base

bootstrap, #debugger, #initialize, #serialize

Methods included from Global::ChainExtensions

included

Methods included from Global::RunExtensions

included

Constructor Details

This class inherits a constructor from ViennaRna::Package::Base

Class Method Details

.aligned_distributions(*energy_grids) ⇒ Object 



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# File 'lib/vienna_rna/package/energy_grid_2d.rb', line 40

def self.aligned_distributions(*energy_grids)
  point_set = set_of_points(*energy_grids)

  energy_grids.map do |grid|
    (grid.distribution + (point_set - grid.map(&:position)).map { |i, j| Row2d.new(i, j, 0, Float::INFINITY) }).sort
  end
end

.inherited(subclass) ⇒ Object 



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# File 'lib/vienna_rna/package/energy_grid_2d.rb', line 6

def self.inherited(subclass)
  subclass.class_eval { prepend EnergyGrid2dWrapper }
end

.set_of_points(*energy_grids) ⇒ Object 



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# File 'lib/vienna_rna/package/energy_grid_2d.rb', line 48

def self.set_of_points(*energy_grids)
  energy_grids.inject([]) { |list, grid| list + grid.map(&:position) }.uniq.sort
end

Instance Method Details

#each(&block) ⇒ Object 



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# File 'lib/vienna_rna/package/energy_grid_2d.rb', line 52

def each(&block)
  distribution.each(&block)
end

#inspect ⇒ Object 



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# File 'lib/vienna_rna/package/energy_grid_2d.rb', line 76

def inspect
  "#<#{self.class.name} on #{data.inspect}>"
end

#quick_plot(num_colors: 8) ⇒ Object 



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# File 'lib/vienna_rna/package/energy_grid_2d.rb', line 56

def quick_plot(num_colors: 8)
  Graphing::R.matrix_heatmap(
    distribution.map(&:i), 
    distribution.map(&:j), 
    distribution.map { |row| Math.log(row.p) },
    title:      "#{self.class.name} Matrix Heatmap",
    x_label:    "Distance from structure 2",
    y_label:    "Distance from structure 1",
    num_colors: num_colors
  )
end

#to_csv(energy_term: :p) ⇒ Object 



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# File 'lib/vienna_rna/package/energy_grid_2d.rb', line 68

def to_csv(energy_term: :p)
  map { |row| row.to_csv(energy_term: energy_term) }.join(?\n) + ?\n
end

#to_csv!(filename, energy_term: :p) ⇒ Object 



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# File 'lib/vienna_rna/package/energy_grid_2d.rb', line 72

def to_csv!(filename, energy_term: :p)
  File.open(filename, ?w) { |file| file.write(to_csv(energy_term: energy_term)) }
end