Python: Concate code to a single string

Using the code below, the code from a source file can be concatenated to a single string. This string however can still be printed and formates nicely on a JavaScript console. It returns a string variable `s' and requires two command line arguments.

# Usage:
# > python ~/path/to/script/multiline.py <name_of_ouput_variable>  

    filename = sys.argv[1]
    
    f = open(filename, "r")
    d = f.readlines()
    f.close()
    
    s = "var %s = " % sys.argv[2]
    s = s.strip()
    
    # s += '"' + "".join(d).replace("\n", "") + '";'

    cnt = 0
    n = len(d)

    # '\\n' is explicitly written to the 'source'-file such that
    # the JavaScript console can print the source code including line
    # breaks.
    for line in d:
        # First line.
        if cnt == 0:
            s += "\n" + '  "' + d[cnt].replace("\n", "") + '\\n"\n'
            cnt += 1
        # Inbetween lines.
        elif cnt > 0 and cnt < (n-1):
            s += '+ "' + d[cnt].replace("\n", "") + '\\n"\n'
            cnt += 1
        # Last line.
        else:
            s += '+ "' + d[cnt].replace("\n", "") + '"'

Python 004: My first closure

Depending on the presence of a number of files, a couple of functions had to be called. But depending on the kind of file, a different function was required. However, for each file, the logic to determine if the corresponding function should be called or not is the same. For technical reasons, the respective functions are in different modules (executed through some Ajax).

So it seemed to me I would have to write the logic part specifically for each case, i.e. for each case where a file is available or not.

Something as below:

if file_exists('-ini'):
    function_one()
if not file_exists('-ini'):
    generate_ini_file()
    function_one()
if file_exits('-fin'):
    function_two()
if not file_exists('-fin'):
    generate_fin_file()
    function_two()

and so on. However, I remembered, in Python everything is an object. Even functions. So, why not prepare a function, which takes care of the logic and the execution of the function which I want to apply to each of the corresponding files. But then, where should the applied function come from? Exactly, from a closure. This basically is a function which generates functions at runtime. What kind of arguments does it take? Precicely, the function you actually want to call. Huh? Yes, of course the applied function needs to be defined somewhere, but thats another story, lets assume we have it. It could look something like this:

def translate_com(target):
    """Calling VMD and returning the output directly."""
    vmd_src = 'mol load pdb %s-fix.pdb\n' % (bio_lib.pdb_base_path + target)\
            + 'set HOME ' + bio_lib.vmd_base_path + '\n'\
            + 'molinfo 0 get center\n'\
            + 'env\n'
    comp = Popen([bio_lib.vmd_cmd_path, '-dispdev', 'text', '-eofexit'],
                  stdout=PIPE, stdin=PIPE, stderr=PIPE, shell=False)
    comp.stdin.write(vmd_src)
    vmd_com_result = comp.communicate()[0]

    for line in vmd_com_result.split('\n'):
        if len(line) > 0 and line[0] == '{':
            com_xyz = [float(i) for i in line[1:-1].split()]
    com_xyz = [i*(-1) for i in com_xyz] 
    # Calling the VMD reorientation script.
    reo_src = bio_lib.get_reo_src(com_xyz, target)
    vmdp = Popen([bio_lib.vmd_cmd_path, '-dispdev', 'text', '-eofexit'],
                  stdin=PIPE, stdout=PIPE, stderr=PIPE, shell=False)
    vmdp.stdin.write(reo_src)
    print vmdp.communicate()[0]

It does something, other functions are doing similar things. This is, e.g., the 'function_two' above. So for each of these, there would be a logic block as this:

def check_availability_and_translate(target):
    # Use upload.
    if uploaded:
        # Force overwrite.
        if overwrite:
            translate_com(target)
        # Does not exist.
        if not os.path.exists(bio_lib.pdb_base_path + target + '-reo.pdb'):
            translate_com(target)
    # Download.
    else:
        # Use existing.
        if os.path.exists(bio_lib.pdb_base_path + target + '-reo.pdb'):
            print "Structure available." 
        # Fixed structure not available.
        else:
            reo.translate_com(target)

In the above, there's also a bit of user interaction coming in, but that's not the point. The point is, all this is the same for each of my functions. So, lets generate a function that returns this logic, but takes the 'translate_com' function as an argument and calls it whenever *a* function is called:

def closure(state):
    """
        'state': '-ini', '-fin', '-reo'
    """
    def check_availability_and_apply(target, uploaded, overwrite, func):
        # Use upload.
        if uploaded:
            print "Uploaded"
            # Force overwrite.
            if overwrite:
                print "Overwriting"
                func(target)
            # Does not exist.
            if not os.path.exists(pdb_base_path + target + state):
                print "Not found, fixing."
                func(target)
            # Use existing.
        # Download.
        else:
            # Use existing.
            if os.path.exists(pdb_base_path + target + state):
                print "Structure available."
            # Structure not available.
            else:
                func(target)
    return check_availability_and_apply

The fun is in the last line. As one can see, a function is returned which was built within the closure. So how can I now call (or maybe better "apply") the 'translate_com' function?

closure('-ini.pdb')(target, uploaded, overwrite, translate_com)

And how about another function?

closure('-fix.pdb')(target, uploaded, overwrite, fix_pdb)

This is really cool, because now file checks are in one place and application is in a separate place. So only one place to edit.
I would really like to hear my boss asking me now: "So how many lines of code did you write yesterday?" Then I could answer: "Well, actually like -200."

Python 003: Summing specific items of nested lists

Say we're faced with the challenge of summing the last element of a list of nested lists.
An example might be

a=[[2,4,6],
   [4,2,5],
   [2,5,6]]

where we're interested in the sum of 6+5+6. In Python this can conveniently be done using the reduce/lambda pair of functions:

>>> reduce(lambda x,y: x+y, [i[-1] for i in a])
17
>>>

Python 002: Averaging over values

A common task is to display raw data together with a more informative average value. The figure below shows the energy of a harmonic oscillator together with the average value of the energy at the same time. The values are from a Monte Carlo simulation.

The question is how to generate the list of average values most efficiently. In the present case, I calculated the average over something like nsamples/100 values and plotted a corresponding point. But if I want to let the list of averages be of the same length as the list of raw data points, i naturally will be able to only plot the first points of the raw data. How is this done correctly?

Eav = array([reduce(lambda x,y: x+y, i)/len(i) for i in [E[i:i+segm] for i in range(0, len(E), segm)]] )

I have been pointed out to a solution making use of the numpy.convolve method.

means = convolve(E, ones(100)/100.0, 'same')

This calculates the average throughout the simulation, instead of only at the end. By doing so, the number of calculated averages is the same as the number of samples. The figure below shows the obtained output.

I only plotted the average now, since the raw data overlays the graphs of the average. What I wonder is why the average at the end drops to zero.

Python 002: Version Introspection

When working with Python 2.x and Python 3.x at the same time, its quite probably that the version of the currently running version of Python becomes a question of interest.
One can obtain the version of the running Python instance by issueing

from sys import version_info
if version_info < (3,0):
   print version_info
else:
   print(version_info)

Python 001: Module introspection

Python has great self introspection capabilities.

Sometimes flow of control runs through different modules. If I want to know which module is currently in the scope, here is how I can do this:

#!/usr/bin/env python3

import os.path
def getModuleName():
    print("Current module:".ljust(30), os.path.abspath(__file__))

getModuleName()

Adding the above to the module should make it possible to get the location and name of the module in scope at runtime.