Describe the bug
When parsing the atom tables it parses the fragments instead of the actual molecular coordinates. Changing the line
start = stop = found[0] + 2
to
start = stop = found[-1] + 2
parses the last fragment, which should correspond to the input geometry. However, there is no guarantee that the indexes on the table correspond to the actual indexes in the input coordinates.
from exatomic import adf
ed = adf.Output('Frags_NiCO4.txt')
ed.parse_atom()
ed.atom
With the original code this will give the first fragment calculation which is for CO.
By changing the code to what I outlined above there also comes the issue with the symbols, as will be shown in the screenshots, which then leads to issues with the Z column.
Expected behavior
Parses the right coordinates and the indexes are guaranteed to be correct.
Screenshots
This is the original behavior where the molecule is Ni(CO)4
This is the behavior when making the simple patch solution as outlined above
Desktop (please complete the following information):
OS: WSL-Ubuntu
Opera
Additional context
This is related to what needs to be done for issue #159
Describe the bug When parsing the atom tables it parses the fragments instead of the actual molecular coordinates. Changing the line
to
parses the last fragment, which should correspond to the input geometry. However, there is no guarantee that the indexes on the table correspond to the actual indexes in the input coordinates.
To Reproduce Can use this file Frags_NiCO4.txt
With the original code this will give the first fragment calculation which is for CO.
By changing the code to what I outlined above there also comes the issue with the symbols, as will be shown in the screenshots, which then leads to issues with the Z column.
Expected behavior Parses the right coordinates and the indexes are guaranteed to be correct.
Screenshots This is the original behavior where the molecule is Ni(CO)4
This is the behavior when making the simple patch solution as outlined above
Desktop (please complete the following information):
Additional context This is related to what needs to be done for issue #159