def example_human_readable_params(): """ The human readable parameters are the labels of the inputs in the original web page See example_original_parameters (below) - It doesn't differentiate upper and lowercase - Any extraneous space is ignored """ params = { 'number of protein atoms': 50, # Example of case insensitivity and removal of spare spaces 'constraints in the PROTEIN ': 'bonds to hydrogens only', } print '-' * 20 print 'Example with 50 protein atoms, bonds to hydrogen only\n' print 'Temperatures only\n', get_temperatures(params), '\n' _print_temperatures_table(get_temperatures_energies(params))
def example_original_params(): """ The original web form parameters are the following Exchange probability: Pdes, Lower temperature limit: Tlow, Number of water molecules: Nw, Number of protein atoms: Np, Hydrogens in protein: Hff, Values: 0 (All H), 1 (Polar H), Simulation type: Alg, Values: 0 (NPT), 1 (NVT), Tolerance: Tol, Upper temperature limit: Thigh, Constraints in water: WC, Values: 0 (Fully flexible), 2 (Flexible Angle), 3 (Rigid) Constraints in the protein: PC, Values: 0 (Fully flexible), 1 (Bonds to hydrogens only), 2 (All bonds) Virtual sites in protein: Vs, Values: 0 (None), 1( Virtual hydrogen) """ # Use original variables interface params = {'Np': 20} # Set number of protein atoms print '-' * 20 print 'Example with Np=20 (number of protein atoms)\n' print 'Temperatures only\n', get_temperatures(params), '\n' _print_temperatures_table(get_temperatures_energies(params))
print "---------------------------------------------------------" print "COMMAND: python get_temperatures.py Np Pdes Tlow Thigh > temperatures.dat" print "---------------------------------------------------------" print "where: \n" print "Exchange probability: Pdes," print "Lower temperature limit: Tlow," print "Number of water molecules: Nw," print "Number of protein atoms: Np," print "Hydrogens in protein: Hff, Values: 0 (All H), 1 (Polar H)," print "Simulation type: Alg, Values: 0 (NPT), 1 (NVT)," print "Tolerance: Tol," print "Upper temperature limit: Thigh," print "Constraints in water: WC, Values: 0 (Fully flexible), 2 (Flexible Angle), 3 (Rigid)" print "Constraints in the protein: PC, Values: 0 (Fully flexible), 1 (Bonds to hydrogens only), 2 (All bonds)" print "Virtual sites in protein: Vs, Values: 0 (None), 1(Virtual hydrogen)" print "---------------------------------------------------------" quit() params = { 'Np': sys.argv[1], 'Pdes': sys.argv[2], 'Tlow': sys.argv[3], 'Thigh': sys.argv[4], 'Hff': 0, 'WC': 3, 'Alg': 0, 'PC': 0 } print "\n".join([str(x) for x in get_temperatures(params)]) # python teste.py 200 > temperatures.dat