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I have an XYZ file in the following format:

X[m] Y[m] DensA_1050c[m] DensB_1200c[m] DensC_1250c[m]
627841.54 231758.7 12.77 12.98 13.17
627841.54 231758.7 12.77 12.98 13.17
627841.54 231758.7 12.77 12.98 13.17
627841.54 231758.7 12.77 12.98 13.17

I am looking for a way to read in the XYZ file in python and then re-write the XYZ file into 3 separate XYZ files like such:

DensA_1050c[m]

X[m] Y[m] Z[m]
627841.54 231758.7 12.77
627841.54 231758.7 12.77
627841.54 231758.7 12.77
627841.54 231758.7 12.77

DensB_1200c[m]

X[m] Y[m] Z[m]
627841.54 231758.7 12.98
627841.54 231758.7 12.98
627841.54 231758.7 12.98
627841.54 231758.7 12.98

DensC_1250c[m]

X[m] Y[m] Z[m]
627841.54 231758.7 13.17
627841.54 231758.7 13.17
627841.54 231758.7 13.17
627841.54 231758.7 13.17

I've tried the following code to read in the XYZ file which works, but I don't know how to parse it to be like the above examples.

import numpy as np

file_location = 'C:/Users/Public/AllData.xyz'
xyz_file = np.genfromtxt(fname=file_location, skip_header=2, dtype='unicode')

print(xyz_file)

The result from the above code is:

['627201.81' '233336.97' '12.94' '13.27' '13.41']
martineau
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hi_ho_2
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    Since there's no formal standard for the XYZ format, you should add a short sample of the contents of the file you have to your question. – martineau Jan 26 '22 at 20:05

1 Answers1

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The following code is very closely tailored to your problem. The row headers which are used for the output file names are hard-coded and mapped to the corresponding column index.

import numpy as np

file_location = 'AllData.xyz'
xyz_file = np.genfromtxt(fname=file_location, skip_header=2, dtype='unicode')

mappings = { 'DensA_1050c.xyz': 2, 'DensB_1200c.xyz' : 3, 'DensC_1250c.xyz' : 4 }

for mapping in mappings:
    with open(mapping, 'w') as output_file:
        for record in xyz_file:
            output_file.write(record[0])
            output_file.write('\t')
            output_file.write(record[1])
            output_file.write('\t')
            output_file.write(record[mappings[mapping]])
            output_file.write('\n')

DensA_1050c.xyz

627841.54   231758.7    12.77
627841.54   231758.7    12.77
627841.54   231758.7    12.77
627841.54   231758.7    12.77

DensB_1200c.xyz

627841.54   231758.7    12.98
627841.54   231758.7    12.98
627841.54   231758.7    12.98
627841.54   231758.7    12.98

DensC_1250c.xyz

627841.54   231758.7    13.17
627841.54   231758.7    13.17
627841.54   231758.7    13.17
627841.54   231758.7    13.17
Gerald Mayr
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