print argument

[bellaguin]

Hello, thank you for making this tool! When I run calculate_rmsd FILE_A FILE_B --print, the resulting output contains XYZ coordinates, but with atomic numbers in the place of element symbols. Is there a reason for doing this, as it seems non-standard for XYZ files?

[rafaelpap]

Line 2056 of calculate_rmsd.py is:
get_coordinates_xyz, is_gzip=settings.format_is_gzip, return_atoms_as_int=True
if you change True to False the atomic symbol is printed.
I cannot comment on the rationale of being True by default.

[charnley]

I agree, for printing, it should default to symbols. The reason for using int internally, is because it is easier/faster to navigate numpy arrays with integers.

[charnley]

@bellaguin , you feedback is correct. Using integers is non-standard (but allowed). Newest version is change to use symbols on --print.