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Function read_coordinates() in extract_coords_into_inp_xyz.py fails #42

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wverastegui opened this issue Oct 14, 2024 · 0 comments · Fixed by #43
Closed

Function read_coordinates() in extract_coords_into_inp_xyz.py fails #42

wverastegui opened this issue Oct 14, 2024 · 0 comments · Fixed by #43
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@wverastegui
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wverastegui commented Oct 14, 2024

It fails when using the following input file:
scores_lower_than_200_mol_per_class_name_smiles.zip

It works with the older version - written below:

def read_coordinates(n_atoms, gamess_output, line_number):
    start, end = compute_start_end_indices(n_atoms, line_number, 4)
    data = []
    for i in range(start, end):
    data.append(gamess_output[i].split())
    atomic_number = []
    element_symbol = []
    x_coord = []
    y_coord = []
    z_coord = []
    for line in data:
        element_symbol.append(line[0])
        atomic_number.append(line[1])
        x_coord.append(line[2])
        y_coord.append(line[3])
        z_coord.append(line[4])
    return element_symbol,x_coord,y_coord,z_coord
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