Convert project from python 2 to 3

Question

""" I'm trying to convert a script to python 3 but I get this error

NameError: name 'prot_file' is not defined

yes I have used 2to3 but need some help in the way of the script use lines of a file to create a name a new one and then create that files

I want overcome the error

NameError: name 'prot_file' is not defined and know why is happening I cannot define the prot_file, surf_file and phi_file

Create moved input file

Works for only 1 pqr file so far (not multiple molecules) and only 1 molecular surface.

  fm = open(config_file_moved, 'w')
  for line_full in file(config_file):
    line = line_full.split()
    if line[0]=='FILE':
        if line[2]=='dielectric_interface':
            prot_file = line[1]
            prot_file_moved = prot_file + name
            new_line = line[0] + '\t' + prot_file_moved + '\t' + line[2] + '\n'
            fm.write(new_line)
        if line[2]=='neumann_surface' or line[2]=='dirichlet_surface':
            surf_file = line[1]
            phi_file = line[3]
            fm.write(line_full)
    elif line[0]=='FIELD' and int(line[5])>0:
        pqr_file_aux = line[7]
        pqr_file = pqr_file_aux[:-4]
        pqr_file_moved = pqr_file + name + '.pqr'
        new_line = line[0] + '\t'
        for i in range(1,len(line)):
            if i==7:
                new_line += pqr_file_moved + '\t'
            else:
                new_line += line[i] + '\t'
        fm.write(new_line+'\n')

    else:
        fm.write(line_full)

fm.close()

print 'Protein file: ' + prot_file
print 'Sensor  file: ' + surf_file
print 'Phi     file: ' + phi_file + '\n'

Answer 1

You are currently defining prot_file here:

for line_full in file(config_file):
    line = line_full.split()
    if line[0]=='FILE':
        if line[2]=='dielectric_interface':
            prot_file = line[1]

Now, in some languages, putting the declaration this many levels of indentation inwards would be a problem. Not so in python (2 or 3) - prot_file will now be available outside the for loop, and should be usable where you're using it, right?

...Unless you don't ever take that branch of if statements. Because this is python, the prot_file name only ever gets defined if that particular line is run. If you were to go the entire for loop without the conditions line[0]=='FILE' and line[2]=='dielectric_interference' ever being true, then prot_file would never be defined and inserted into the local namespace. In that case, trying to use prot_file later (as you are in your print statement) would yield the error you're seeing, because it was never actually defined.

The only real good solution to this is to just put a dummy definition (e.g. prot_file = "") at some point that the code will ALWAYS execute - such as the right before the for loop.

It's also worth noting that you could have the same trouble with surf_file and phi_file for the same reason.