`chemparseplot.parse.eon.neb`¶

Module Contents¶

`_validate_data_atoms_match`	Checks if data points count matches structure count.
`load_or_compute_data`	Retrieves data from a parquet cache or triggers a computation callback.
`load_structures_and_calculate_additional_rmsd`	Loads the main trajectory and calculates RMSD for additional comparison structures.
`_process_single_path_step`	Helper to process a single .dat/.con pair into a DataFrame row.
`aggregate_neb_landscape_data`	Aggregates data from multiple NEB steps for landscape visualization.
`load_augmenting_neb_data`	Loads external NEB paths (dat+con) to augment the landscape fit. Forces projection onto the MAIN path’s R/P coordinates.
`compute_profile_rmsd`	Computes RMSD for a 1D profile.
`estimate_rbf_smoothing`	Estimates a smoothing parameter for RBF interpolation.

chemparseplot.parse.eon.neb._validate_data_atoms_match(z_data, atoms, dat_file_name)¶: Checks if data points count matches structure count.

chemparseplot.parse.eon.neb.load_or_compute_data(cache_file: pathlib.Path | None, *, force_recompute: bool, validation_check: collections.abc.Callable[[polars.DataFrame], None], computation_callback: collections.abc.Callable[[], polars.DataFrame], context_name: str) → polars.DataFrame¶: Retrieves data from a parquet cache or triggers a computation callback.

Added in version 0.1.0.

chemparseplot.parse.eon.neb.load_structures_and_calculate_additional_rmsd(con_file: pathlib.Path, additional_con: list[tuple[pathlib.Path, str]], ira_kmax: float, sp_file: pathlib.Path | None = None)¶: Loads the main trajectory and calculates RMSD for additional comparison structures.

Added in version 0.1.0.

chemparseplot.parse.eon.neb._process_single_path_step(dat_file, con_file, y_data_column, ira_instance, ira_kmax, step_idx, ref_atoms=None, prod_atoms=None)¶: Helper to process a single .dat/.con pair into a DataFrame row.

chemparseplot.parse.eon.neb.aggregate_neb_landscape_data(all_dat_paths: list[pathlib.Path], all_con_paths: list[pathlib.Path], y_data_column: int, ira_instance, *, cache_file: pathlib.Path | None = None, force_recompute: bool = False, ira_kmax: float = 1.8, augment_dat: str | None = None, augment_con: str | None = None, ref_atoms: ase.Atoms | None = None, prod_atoms: ase.Atoms | None = None) → polars.DataFrame¶: Aggregates data from multiple NEB steps for landscape visualization.

Added in version 0.1.0.

chemparseplot.parse.eon.neb.load_augmenting_neb_data(dat_pattern: str, con_pattern: str, ref_atoms: ase.Atoms, prod_atoms: ase.Atoms, y_data_column: int, ira_kmax: float) → polars.DataFrame¶: Loads external NEB paths (dat+con) to augment the landscape fit. Forces projection onto the MAIN path’s R/P coordinates.

Added in version 0.1.0.

chemparseplot.parse.eon.neb.compute_profile_rmsd(atoms_list: list[ase.Atoms], *, cache_file: pathlib.Path | None, force_recompute: bool, ira_kmax: float) → polars.DataFrame¶: Computes RMSD for a 1D profile.

Added in version 0.1.0.

chemparseplot.parse.eon.neb.estimate_rbf_smoothing(df: polars.DataFrame) → float¶

Estimates a smoothing parameter for RBF interpolation.

Added in version 0.1.0.

Calculates the median Euclidean distance between sequential points in the path and uses that value as the smoothing factor.