Python programming on Pythonanywhere

[jbowers9]

Hi all;
I've already posted to P_Anywhere's site but... I'm trying to run a script that needs a data file piped to it. Now P_ Anywhere gives you a resident directory and mine contains the program and the data file. Sooo...
bonds.py ethane.xyz maybe? Nah. Doesn't like that. But! I did get it to run before but can't remember how. Is someone familiar enough w/PythonAnywhere to show me the error of my ways?
1) The script does work, 2) The files are resident, 3) The piping syntax and/or what console I'm in may be the problem

 

[phyzguy]

Can you post the Python code that is reading the data file? It's best if you enclose it with the code tags like the following:

print("Hello world")

 

[jbowers9]

Mentor note: Added code tags to preserve Python formatting, and altered some comment delimiters,
that were being misinterpreted as LaTex markers.

print("
# # IO FUNCTIONS # #

# read file data into a 2-d array
def get_file_string_array(file_name):
    try:
        file = open(file_name, "r")
    except IOError:
        print('Error: file (%s) not found!\n' % (file_name))
        sys.exit()
    lines = file.readlines()
    file.close()
    array = []
    for line in lines:
        array.append(line.split())
    return array")

Remainder of program follows. It's not mine, but as I've said it does work. I got it to work a few weeks ago.

import sys, math

# # CONSTANTS # #

# threshold beyond average of covalent radiii to determine bond cutoff
bond_thresh = 1.2

# covalent (or ionic) radii by atomic element (Angstroms) from
# "Inorganic Chemistry" 3rd ed, Housecroft, Appendix 6, pgs 1013-1014
cov_rads = {  'H' : 0.37, 'C' : 0.77, 'O' : 0.73, 'N' : 0.75, 'F' : 0.71,
  'P' : 1.10, 'S' : 1.03, 'Cl': 0.99, 'Br': 1.14, 'I' : 1.33, 'He': 0.30,
  'Ne': 0.84, 'Ar': 1.00, 'Li': 1.02, 'Be': 0.27, 'B' : 0.88, 'Na': 1.02,
  'Mg': 0.72, 'Al': 1.30, 'Si': 1.18, 'K' : 1.38, 'Ca': 1.00, 'Sc': 0.75,
  'Ti': 0.86, 'V' : 0.79, 'Cr': 0.73, 'Mn': 0.67, 'Fe': 0.61, 'Co': 0.64,
  'Ni': 0.55, 'Cu': 0.46, 'Zn': 0.60, 'Ga': 1.22, 'Ge': 1.22, 'As': 1.22,
  'Se': 1.17, 'Kr': 1.03, 'X' : 0.00}

# # IO FUNCTIONS # #

# read file data into a 2-d array
def get_file_string_array(file_name):
    try:
        file = open(file_name, "r")
    except IOError:
        print('Error: file (%s) not found!\n' % (file_name))
        sys.exit()
    lines = file.readlines()
    file.close()
    array = []
    for line in lines:
        array.append(line.split())
    return array

# read in geometry from xyz file
def get_geom(xyz_file_name):
    xyz_array = get_file_string_array(xyz_file_name)
    n_atoms = int(xyz_array[0][0])
    at_types = ['' for i in range(n_atoms)]
    coords = [[0.0 for j in range(3)] for i in range(n_atoms)]
    for i in range(n_atoms):
        at_types[ i] = xyz_array[i+2][0]
        for j in range(3):
            coords[ i][j] = float(xyz_array[i+2][j+1])
    geom = [at_types, coords]
    return geom

# input syntax and usage warnings
def get_inputs():
    if (not len(sys.argv) == 2):
        print('Usage: bonds.py XYZ_FILE\n')
        print('  XYZ_FILE: coordinates of target molecule\n')
        sys.exit()
    else:
        xyz_file_name = sys.argv[1]
        return xyz_file_name

# print geometry to screen
def print_geom(geom, comment):
    at_types, coords = geom[0:2]
    n_atoms = len(at_types)
    print('%i\n%s\n' % (n_atoms, comment), end='')
    for i in range(n_atoms):
        print('%-2s' % (at_types[ i]), end='')
        for j in range(3):
            print(' %12.6f' % (coords[ i][j]), end='')
        print('\n', end='')
    print('\n', end='')

# print bond graph to screen
def print_bond_graph(geom, bond_graph, comment):
    at_types = geom[0]
    n_atoms = len(at_types)
    print('%s\n' % (comment), end='')
    for i in range(n_atoms):
        print(' %4i %-2s -' % (i+1, at_types[I]), end='')
        for j in range(len(bond_graph[ i])):
            print(' %i' % (bond_graph[ i ][j] + 1), end='')
        print('\n', end='')
    print('\n', end='')

# print list of bond lengths to screen
def print_bonds(geom, bonds):
    at_types = geom[0]
    n_bonds = len(bonds)
    print('%i bond(s) found (Angstrom)' % (n_bonds))
    for q in range(n_bonds):
        n1, n2  = bonds[q][0:2]
        r12 = bonds[q][2]
        nstr = '%i-%i' % (n1+1, n2+1)
        tstr = '(%s-%s) ' % (at_types[n1], at_types[n2])
        print(' %-15s  %-13s    %6.4f\n' % (nstr, tstr, r12), end='')
    print('\n', end='')

# # MATH FUNCTIONS # #

# calculate distance between two 3-d cartesian coordinates
def get_r12(coords1, coords2):
    r2 = 0.0
    for p in range(3):
        r2 += (coords2[p] - coords1[p])**2
    r = math.sqrt(r2)
    return r

# # TOPOLOGY FUNCTIONS # #

# build graph of which atoms are covalently bonded
def get_bond_graph(geom):
    at_types, coords = geom[0:2]
    n_atoms = len(at_types)
    bond_graph = [[] for i in range(n_atoms)]
    for i in range(n_atoms):
        covrad1 = cov_rads[at_types[I]]
        for j in range(i+1, n_atoms):
            covrad2 = cov_rads[at_types[j]]
            thresh = bond_thresh * (covrad1 + covrad2)
            r12 = get_r12(coords[I], coords[j])
            if (r12 < thresh):
                bond_graph[I].append(j)
                bond_graph[j].append(i)
    return bond_graph

# determine atoms which are covalently bonded from bond graph
def get_bonds(geom, bond_graph):
    at_types, coords = geom[0:2]
    n_atoms = len(at_types)
    bonds = []
    for i in range(n_atoms):
        for a in range(len(bond_graph[ i])):
            j = bond_graph[I][a]
            if (i < j):
                r12 = get_r12(coords[I], coords[j])
                bonds.append([i, j, r12])
    return bonds

# # MAIN BLOCK # #

# read in geometry, determine bonded topology
xyz_file_name = get_inputs()
geom = get_geom(xyz_file_name)
bond_graph = get_bond_graph(geom)

# calculate bond lengths
bonds = get_bonds(geom, bond_graph)

# print resulting values
print_geom(geom, 'initial geometry')
print_bond_graph(geom, bond_graph, 'bond graph')
print_bonds(geom, bonds)

# end of program

 

[phyzguy]

When you say it "Doesn't like that.", what error does it give? Are you sure the "ethane.xyz" file is in the same directory as "bonds.py"?

 

[jbowers9]

Usage: bonds.py XYZ_FILE XYZ_FILE: coordinates of target molecule Traceback (most recent call last): File "/home/jbowers9/bonds.py", line 138, in <module> xyz_file_name = get_inputs() File "/home/jbowers9/bonds.py", line 52, in get_inputs sys.exit()SystemExit>>> >>> /home/jbowers9/bonds.py /home/jbowers9/ethane.xyz
File "<stdin>", line 1 /home/jbowers9/bonds.py /home/jbowers9/ethane.xyz ^SyntaxError: invalid syntax

/home/jbowers9/bonds.py

/home/jbowers9/ethane.xyz

 

[jbowers9]

bonds.py ethane.xyz
File "<stdin>", line 1
bonds.py ethane.xyz
^
SyntaxError: invalid syntax

 

[phyzguy]

Sorry, I don't know enough about the pythonanywhere environment to understand what the problem is. Maybe someone else does. In a standard environment like unix you would type,

python bonds.py ethane.xyz

It looks like pythonanywhere invokes Python automatically. You might try:

bonds.py

and then after it comes back:

ethane.xyz

 

[Mark44]

Usage: bonds.py XYZ_FILE XYZ_FILE: coordinates of target molecule Traceback (most recent call last): File "/home/jbowers9/bonds.py", line 138, in <module> xyz_file_name = get_inputs() File "/home/jbowers9/bonds.py", line 52, in get_inputs sys.exit()SystemExit>>> >>> /home/jbowers9/bonds.py /home/jbowers9/ethane.xyz
File "<stdin>", line 1 /home/jbowers9/bonds.py /home/jbowers9/ethane.xyz ^SyntaxError: invalid syntax

/home/jbowers9/bonds.py

/home/jbowers9/ethane.xyz

It appears to me that you are trying to pass the name of the input file as a command line argument, but your program isn't set up to operate that way. What you're calling your "main block" has an input statement that expects the user to type in the name of the input file.

To have your program process command-line arguments, you need to import the argparse module, which is described in the Python docs.