VanKrevelenSideBySide.py

'''
Takes a csv as an input and works through the compounds to extract the number of C, H, O, and N
present. It also notes if N is present and marks those points, then calculates the ratios of
H:C, O:C, and N:C and plots them and generates side by side 3D plots to create a stereoscopic
effect. Note graphics should be approximately 6 cm apart so adjustments may need to be made
based on the size screen you are working on.
'''

import os
import sys

import matplotlib.pyplot as plt

from extractNeededElementalData import extract_needed_elemental_data
from processElementalData import process_elemental_data


# Graphs the data provided and labels axes
def plotSideBySide(ratiosList):
    area = 10.0

    fig = plt.figure(figsize=(17, 7))
    fig.suptitle('Van Krevelen Diagram - Side By Side', fontsize=14, fontweight='bold')
    ax = fig.add_subplot(121, projection='3d')

    ax.set_xlabel('O:C Ratio')
    ax.set_ylabel('H:C Ratio')
    ax.set_zlabel('N:C Ratio')

    # Creates a list for plotting purposes where two elements are lists of compounds with N and without respectively
    listByN = [[], []]
    withN = None
    withoutN = None
    for i in range(len(ratiosList[2])):
        if ratiosList[2][i]:
            listByN[0].append([ratiosList[1][i], ratiosList[0][i], ratiosList[3][i], 'r', '^'])
        else:
            listByN[1].append([ratiosList[1][i], ratiosList[0][i], ratiosList[3][i], 'b', 'o'])

    counter = 0
    for i in listByN:
        for j in i:
            if counter == 0:
                withN = ax.scatter(xs=j[0], ys=j[1], zs=j[2], s=15.0, c=j[3], marker=j[4], alpha=.25)
            else:
                withoutN = ax.scatter(xs=j[0], ys=j[1], zs=j[2], s=15.0, c=j[3], marker=j[4], alpha=.25)
        counter += 1

    if withoutN and withN:
        plt.legend((withN, withoutN), ('Does have N', 'Does not have N'), scatterpoints=1, loc='lower left', ncol=1, fontsize=9)

    '''
    Second plot rotated 6 degrees per stereoscopic best practices.
    '''
    ax2 = fig.add_subplot(122, projection='3d')

    ax2.set_xlabel('O:C Ratio')
    ax2.set_ylabel('H:C Ratio')
    ax2.set_zlabel('N:C Ratio')

    withoutN = None
    withN = None

    counter = 0
    for i in listByN:
        for j in i:
            if counter == 0:
                withN = ax2.scatter(xs=j[0], ys=j[1], zs=j[2], s=15.0, c=j[3], marker=j[4], alpha=.25)
            else:
                withoutN = ax2.scatter(xs=j[0], ys=j[1], zs=j[2], s=15.0, c=j[3], marker=j[4], alpha=.25)
        counter += 1

    ax2.azim -= 6

    if withN and withoutN:
        plt.legend((withN, withoutN), ('Does have N', 'Does not have N'), scatterpoints=1, loc='lower left', ncol=1, fontsize=9)


    plt.tight_layout(w_pad=.18)

    '''
    If you would rather not display the file and just want to save it in a specific format, remove the comment from the
    line below (delete the first #) and comment out the next line (add a # to the front of the line of code that says
    plt.show()).
    '''

    # plt.save("filename.pdf") # or whatever file type you need.
    plt.show()

    print("done")

'''
Uncomment this section if you wish to run this script using the BMRB online data base and use the more
flexible commandline options.

usage_mesg = 'VanKrevelenSideBySide.py <txt file(s)>'

# Checks if files are available.
filename_txt = sys.argv[1]
if not os.access(filename_txt, os.R_OK):
    print "%s is not accessible." % filename_txt
    print usage_mesg
    sys.exit(1)

# Checks if the right number of arguments are provided.
if len(sys.argv) == 2:
    filename_txt = sys.argv[1]
    elementalList = extract_needed_elemental_data(filename_txt)
    ratiosList = process_elemental_data(elementalList)
    plotSideBySide(ratiosList)
'''