permute_tri.rb

permute_tri.rb

a = [60, -60]

# 4 refers to number of 60s or -60s in each element of array
a = a.repeated_permutation(6).to_a
puts "The array contains #{a.length} elements."

#creates output file called permute.txt
out_file = File.new("permute_out.txt", "w")


while a.length != 0
	#Removes last element from array and saves it in new array
	individual_struc = a.pop
	
	#Change this line to match your sequence
	line1 = "var = sequence {ACE PHE ALA PHE NHE}"

	#puts "Currently building structure: #{individual_struc.to_s}."
	phi3 = individual_struc.pop
	#puts "phi3 = #{phi3}"
	psi3 = individual_struc.pop
	#puts "psi3 = #{psi3}"
	phi2 = individual_struc.pop
	#puts "phi2 = #{phi2}"
	psi2 = individual_struc.pop
	#puts "psi2 = #{psi2}"
	phi1 = individual_struc.pop
	#puts "phi1 = #{phi1}"
	psi1 = individual_struc.pop
	#puts "psi1 = #{psi1}"

	psi1 = psi1.to_s
	psi2 = psi2.to_s
	psi3 = psi3.to_s
	phi1 = phi1.to_s
	phi2 = phi2.to_s
	phi3 = phi3.to_s

	line2 = 'impose var {2} {{"N" "CA" "C" "N" ' + psi1 + '}}'
	line3 = 'impose var {1} {{"C" "N" "CA" "C" ' + phi1 + '}}'
	line4 = 'impose var {3} {{"N" "CA" "C" "N" ' + psi2 + '}}'
	line5 = 'impose var {2} {{"C" "N" "CA" "C" ' + phi2 + '}}'
  line6 = 'impose var {4} {{"N" "CA" "C" "N" ' + psi3 + '}}'
  line7 = 'impose var {3} {{"C" "N" "CA" "C" ' + phi3 + '}}'
	
	puts line1
	file_slug = "#{psi1}_#{phi1}_#{psi2}_#{phi2}_#{psi3}_#{phi3}"
	#puts file_slug
	
	#change faf to your structure
	line8 = "saveamberparm var faf_#{file_slug}.prmtop faf_#{file_slug}.inpcrd"

	#puts "The array now contains #{a.length} elements."
	out_file.puts(line1)
	out_file.puts(line2)
	out_file.puts(line3)
	out_file.puts(line4)
	out_file.puts(line5)
	out_file.puts(line6)
	out_file.puts(line7)
	out_file.puts(line8)
	
	out_file.puts("\n")
end

out_file.close