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
