write_oxdna_files has a filename_no_extension argument. However, this is passed to _get_filename_same_name_as_running_python_script, which assumes that any non-None filename already has an extension. Thus, if filename_no_extension is set, no extensions are added, and the top file overwrites the dat file.
write_oxdna_fileshas afilename_no_extensionargument. However, this is passed to_get_filename_same_name_as_running_python_script, which assumes that any non-None filename already has an extension. Thus, iffilename_no_extensionis set, no extensions are added, and the top file overwrites the dat file.