convert_native_nebscape_run_setup_to_soda

soda_analyzer.convert_native_nebscape_run_setup_to_soda(native_root, output_root, *, setup_source=None, slab_file=None, reaction_smiles_file=None, parameters_file=None, output_structure_file='pos.xyz', output_reaction_file=None, config_filename='config.ini', overwrite=False, strict=True, print_report=True, text_output=True)

Convert a supported native NEBScape run setup skeleton to SODA files.

Parameters:

  • native_root (str or pathlib.Path) – Directory containing the corresponding native workflow input or output files.

  • output_root (str or pathlib.Path) – Destination directory for the converted SODA run setup.

  • setup_source (str or pathlib.Path, optional) – Native setup Python file or source text; None uses discovery in the native directory. Default: None.

  • slab_file (str or pathlib.Path, optional) – Native slab structure path; None uses the path found in the setup. Default: None.

  • reaction_smiles_file (str or pathlib.Path, optional) – Native reaction SMILES file; None uses the path found in the setup. Default: None.

  • parameters_file (str or pathlib.Path, optional) – Native JSON/YAML settings file; None uses discovery in the native directory. Default: None.

  • output_structure_file (str, optional) – Converted slab filename relative to the output directory. Default: 'pos.xyz'.

  • output_reaction_file (str, optional) – Copied reaction filename; None retains the native filename. Default: None.

  • config_filename (str, optional) – SODA configuration filename relative to the run directory. Default: 'config.ini'.

  • overwrite (bool, optional) – Allow replacement of existing destination files. Default: False.

  • strict (bool, optional) – Reject unsupported or inconsistent input rather than accepting a partial conversion. Default: True.

  • print_report (bool, optional) – Print the formatted report in addition to returning its dictionary. Default: True.

  • text_output (bool, optional) – Use a human-readable report when true, or JSON when false. Default: True.

Returns:

dict – Contains written_files, converted calculator and parameters, CLI options, ready_to_run, and diagnostics.

Notes

The converter flips native/SODA XYZ fixed tags, copies the reaction list, writes a SODA config.ini, optionally maps JSON/YAML parameter files, and reports unsupported native Python setup patterns. It does not execute native NEBScape source.