make_it_a_gro.py

#!/usr/bin/python
#import pyiast
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import math
import fileinput
import os.path
import scipy
import csv

from scipy import signal
#from string import lower
""" The goal is to make sepatrate maps of the gme an kno pores of the INDEXC structures in order to be presented in a different color
We read Structre*dat files  (which have been made by invoking the pandasfromXYZ.sh script) and set the center positions of gme and kno cavities"""
   
"""read the splitted isotherm files and collect them in a single file which contains a common set molar concentration steps and the uptakes in cc/g, on each ZIF for the given concentrations. We use an interpolator for the concentration range [01], Datas are not smooth"""

color_key = {'all':'b', 'kno':'r', 'gme':'g'}


def main():

    file_to_read="cone_to_gro.dat"

    structure=pd.read_csv(file_to_read, sep=' ')
    structure.head()
    print(structure)
    data=structure.values
    file_to_gromacs="my_cone.gro"
    OUT=open(file_to_gromacs,'w')
    OUT.write("Generated by Anastasios Gotzias all carbon structure\n "+str(len(data))+"\n")
    for index, line in enumerate(data):
       outline="%5i%-5s%5s%5i%8.3f%8.3f%8.3f" %(1,"CNT",line[0],index,float(line[1]/10.0),float(line[2]/10.0)\
                                     ,float(line[3]/10.0))
       OUT.write(outline+"\n")
    outline="  10   10   10\n"
    OUT.write(outline+"\n")

    exit(0)
if __name__ == "__main__":
    main()