Save Dataframe with fixed-width columns

Question

I need to edit input from a program that works with fixed-width columns. I managed to load it properly and worked out what I needed, but I don't know how to save the edited file to keep the same width of columns.

import pandas as pd

file = pd.read_fwf('file.inp', 
                  colspecs = [(0, 6), (6, 11), (11, 16), (16, 20), (20, 22), 
                              (22, 26), (26, 38), (38, 46), (46, 54), (54, 61),
                              (61, 68), (68, 90)])

The problem is that the number of spaces between the columns or the length of the strings of data vary, so I can't simply add fixed number of white spaces between the columns.

The file to edit looks like this:

ATOM    873  N   ALA A  59      41.629  23.754-163.394  1.00 12.93           N
ATOM   5089  NH1 ARG A 315      21.344 -13.371 187.612  1.00 66.09           N1+
ATOM   7839 H5''   A B   3      31.406  -4.882-165.817  1.00 16.98           H 
HETATM 7766 H161 G3A B   1      42.941   1.714-165.146  1.00 14.70           H  

It is a mixture of numbers, strings, special characters and columns glued together.

Answer 1

As I commented, I could not find a write_fdf method in pandas. However, I think you can achieve what you want with tabulate . I am basing the following code on this post and I have not run it:

import pandas as pd
from tabulate import tabulate


df = pd.read_fwf('file.inp', 
                  colspecs = [(0, 6), (6, 11), (11, 16), (16, 20), (20, 22), 
                              (22, 26), (26, 38), (38, 46), (46, 54), (54, 61),
                              (61, 68), (68, 90)])


with open("...", "w") as f:
    f.write(
        tabulate(
            [list(row) for row in df.values],
            tablefmt="plain"
        )
    )

Note again that I have not run this and is only to demo how to use tabulate:

• I have not passed headers parameter which you can use if you need to
• I used format "plain" to avoid any table-like decorations

More on tabulate here

UPDATE : I realize the output needs to align to specific columns so the following seems to get close enough (minor specs editing might be needed):

import pandas as pd
import sys


# Mock data
lst = [
    ["ATOM", 873, "N", "ALA", "A", 59, 41.629, 23.754, -163.394, 1.00, 12.93, "N"],
    ["ATOM", 5089, "NH1", "ARG", "A", 315, 21.344, -13.371, 187.612, 1.00 ,66.09, "N1+"],
    ["ATOM", 7839, "H5''", "A", "B", 3, 31.406, -4.882, -165.817, 1.00, 16.98, "H" ],
    ["HETATM", 7766, "H161", "G3A", "B", 1, 42.941, 1.714, -165.146, 1.00, 14.70, "H"],
]

# NOTE the spaces at the end, only when needed
colspecs = [
    "{: <6} ", # left, width=6
    "{: >4} ", # right, width=4
    "{: >4} ",
    "{: >3} ",
    "{: >1} ",
    "{: >3} ",
    "{: >11} ",
    "{: >7}",
    "{: >8} ",
    "{: >5} ",
    "{: <15} ",
    "{: <3}",
]


def write_fdf(fpath, pd, specs):
    """
    Write a Pandas dataframe in fixed width column format with the given
    column specs

    Args:
        fpath: File path
        ps: Dataframe
        specs: A list of python formats
    """
    with open(fpath, "w") as f:
        for _, row in df.iterrows():
            for idx, value in enumerate(row):
                sys.stdout.write(specs[idx].format(value))
                f.write(specs[idx].format(value))

            f.write("\n")
            print("")


df = pd.DataFrame(lst)
write_fdf("/tmp/out.dat", pd, colspecs)

Output:

$ python ~/tmp/test.py
ATOM    873    N ALA A  59      41.629  23.754-163.394   1.0 12.93           N
ATOM   5089  NH1 ARG A 315      21.344 -13.371 187.612   1.0 66.09           N1+
ATOM   7839 H5''   A B   3      31.406  -4.882-165.817   1.0 16.98           H
HETATM 7766 H161 G3A B   1      42.941   1.714-165.146   1.0 14.7            H


$ cat /tmp/out.dat
ATOM    873    N ALA A  59      41.629  23.754-163.394   1.0 12.93           N
ATOM   5089  NH1 ARG A 315      21.344 -13.371 187.612   1.0 66.09           N1+
ATOM   7839 H5''   A B   3      31.406  -4.882-165.817   1.0 16.98           H
HETATM 7766 H161 G3A B   1      42.941   1.714-165.146   1.0 14.7            H

However, I see one exceptions in the formatting which seem to break the rules: row=0, col=2: "N" seems to be centered in your example