Need help to read gromac file in Python

Question

I have a gromac file to extract specific details from it. File format is follows. Only i need values in each column.

Generated by trjconv : a bunch of waters t=   0.00000
 3000
    1SOL     OW    1   1.5040   2.7580   0.6820
    1SOL    HW1    2   1.4788   2.7853   0.7702
    1SOL    HW2    3   1.4640   2.8230   0.6243
    2SOL     OW    4   1.5210   0.9510   2.2050
    2SOL    HW1    5   1.5960   0.9780   2.1520
    2SOL    HW2    6   1.4460   0.9940   2.1640
 1000SOL     OW 2998   1.5310   1.7952   2.1981
 1000SOL    HW1 2999   1.4560   1.7375   2.1836
 1000SOL    HW2 3000   1.6006   1.7369   2.2286
   3.12736   3.12736   3.12736
Generated by trjconv : a bunch of waters t= 9000.00000
 3000
    1SOL     OW    1   1.1579   0.4255   2.1329
    1SOL    HW1    2   1.0743   0.3793   2.1385
    1SOL    HW2    3   1.1514   0.4772   2.0526
    2SOL     OW    4   2.2976   2.5403   0.1574
    2SOL    HW1    5   2.2161   2.4981   0.1847
    2SOL    HW2    6   2.3118   2.6092   0.2223
 1000SOL     OW 2998   2.5927   1.0233   0.4695   
 1000SOL    HW1 2999   2.5927   0.9869   0.3810
 1000SOL    HW2 3000   2.5365   0.9642   0.5197
  3.10941   3.10941   3.10941

I have tried following codes to read it.

F = open('Data.gro', 'r')
for line in F:
      P = line.split('\t')

I want to extract data as below in to float variables.

My idea was after split the data called as P[3], P[4], P[6] But I failed. When i am reading file i want to skip information after ever 3000 lines. There are information given in three line after every 3000 line. and also I want to skip first two lines as well. The .gro file has specific format.

http://manual.gromacs.org/current/online/gro.html

Out put should be as below. i am going to do some calculations using those values.

First Set

X = [1.5040, 1.4788, 14640,... , 1.6006]
Y = [2.7580, 2.7853,           , 1.7369]
Z = [0.6820, 0.7702,           , 2.2286]

Second Set

X = [1.1579, 1.0743, ,... , 2.5365]
Y = [0.4255, 0.3793, ,... , 0.9642]
Z = [2.1329, 2.1329, ,... , 0.5197]

Please read my question care fully. I need some guidance to write above program. I am new one to python. I have done research but I couldn't find any help to extract those numbers.

Thank you

Answer 1

Finally I was able to written full program to read my gromac file. This might help some one if want to read data from grmomac file and extract specific values from it. This code adjusted to read 10 rows after specific place find. I used this to read 3000 rows. This is working 100% successfully.

F = open('Data.gro', 'r')
A = open('XYZ.txt', 'w')
XO = []
YO = []
ZO = []
XHW1 = []
YHW1 = []
ZHW1 = []
XHW2 = []
YHW2 = []
ZHW2 = []
I = range(1, 10)
with open('Data.gro') as F:
    for line in F:
        if line.split()[0] == '3000':
            A.write('Frame' + '\n')
            for R in I:
                line = next(F)
                P = line.split()
                if P[1] == 'OW':
                    x = float(P[3])
                    y = float(P[4])
                    z = float(P[5])
                    XO.append(x)
                    YO.append(y)
                    ZO.append(z)
                else:
                    if P[1] == 'HW1':
                        x = float(P[3])
                        y = float(P[4])
                        z = float(P[5])
                        XHW1.append(x)
                        YHW1.append(y)
                        ZHW1.append(z)
                    else:
                       if P[1] == 'HW2':
                            x = float(P[3])
                            y = float(P[4])
                            z = float(P[5])
                            XHW2.append(x)
                            YHW2.append(y)
                            ZHW2.append(z)
                       else:
                            pass
                if line.split()[2] == '3000':
                    A.write('Oxygen atoms XYZ coordinates:' + '\n')
                    A.write("%s\n" % (XO))
                    A.write("%s\n" % (YO))
                    A.write("%s\n\n" % (ZO))
                    A.write('Hydrogen 1 atoms XYZ coordinates:' + '\n')
                    A.write("%s\n" % (XHW1))
                    A.write("%s\n" % (YHW1))
                    A.write("%s\n\n" % (ZHW1))
                    A.write('Hydrogen 2 atoms XYZ coordinates:' + '\n')
                    A.write("%s\n" % (XHW2))
                    A.write("%s\n" % (YHW2))
                    A.write("%s\n\n" % (ZHW2))
                    XO = []
                    YO = []
                    ZO = []
                    XHW1 = []
                    YHW1 = []
                    ZHW1 = []
                    XHW2 = []
                    YHW2 = []
                    ZHW2 = []
                    R +=1
                else:
                    pass
        else:
            pass

A.close()

Thanx some people help me to solve specific points. Thanx goes to them also. This is a really nice website. I like this. This help lot to learn things.