Index

_

__all__ (in module chemparseplot) (in module chemparseplot.api) (in module chemparseplot.parse) (in module chemparseplot.parse.eon) (in module chemparseplot.parse.eon.con_io) (in module chemparseplot.parse.eon.frame_series) (in module chemparseplot.parse.grammar) (in module chemparseplot.parse.orca) (in module chemparseplot.parse.orca.neb) (in module chemparseplot.parse.trajectory) (in module chemparseplot.plot) (in module chemparseplot.units) __getattr__() (in module chemparseplot) (in module chemparseplot.parse) (in module chemparseplot.parse.eon) (in module chemparseplot.parse.grammar) (in module chemparseplot.parse.orca) (in module chemparseplot.plot) (in module chemparseplot.units) __getitem__() (chemparseplot.parse.types.ArrayGroup method) (chemparseplot.parse.types.DataclassMapping method) (chemparseplot.parse.types.ParserAttrs method) __iter__() (chemparseplot.parse.types.ArrayGroup method) (chemparseplot.parse.types.DataclassMapping method) (chemparseplot.parse.types.ParserAttrs method) __len__() (chemparseplot.parse.types.ArrayGroup method) (chemparseplot.parse.types.DataclassMapping method) (chemparseplot.parse.types.ParserAttrs method) __new__() (chemparseplot.parse.eon.saddle_search.EONSaddleStatus method) __post_init__() (chemparseplot.parse.types.OrcaNebResult method) __repr__() (chemparseplot.plot.structs.TwoDimPlot method) _alpha_blit_rgba() (in module chemparseplot.plot.neb) _ALPHABET_SIZE (in module chemparseplot.parse.plumed) _annotate_orca_barrier() (in module chemparseplot.plot.neb) _apply_perspective_tilt() (in module chemparseplot.plot.neb) _augment_minima_points() (in module chemparseplot.plot.neb) _augment_with_gradients() (in module chemparseplot.plot.neb) _calculate_fes_1d() (in module chemparseplot.parse.plumed) _calculate_fes_2d() (in module chemparseplot.parse.plumed) _calculate_rmsd() (in module chemparseplot.parse.orca.neb.opi_parser) _CART_BLOCK_GRAMMAR_SRC (in module chemparseplot.parse.grammar.orca_text) _CART_BLOCK_RE (in module chemparseplot.parse.grammar.orca_text) _cart_g() (in module chemparseplot.parse.grammar.orca_text) _cart_grammar (in module chemparseplot.parse.grammar.orca_text) _cartesian_rmsd() (in module chemparseplot.parse.eon.stitch) _check_xyzrender() (in module chemparseplot.plot.neb) _CLAMP_PRESETS (in module chemparseplot.plot.chemgp) _COLUMN_CASTERS (in module chemparseplot.parse.eon._trajectory_common) _compute_synthetic_gradients() (in module chemparseplot.parse.orca.neb.opi_parser) _crop_transparent_rgba() (in module chemparseplot.plot.neb) _cumulative_rmsd() (in module chemparseplot.parse.eon.stitch) _DOUBLET_MULT (in module chemparseplot.parse.eon.gprd) _ENERGY_FACTORS (in module chemparseplot.plot.structs) _energy_g() (in module chemparseplot.parse.grammar.orca_text) _energy_grammar (in module chemparseplot.parse.grammar.orca_text) _ENERGY_LINE_GRAMMAR_SRC (in module chemparseplot.parse.grammar.orca_text) _ENERGY_LINE_RE (in module chemparseplot.parse.grammar.orca_text) _ENERGY_PINT_NAME (in module chemparseplot.units) _ENERGY_TO_EV (in module chemparseplot.units) _ensure_registry() (in module chemparseplot.units) _ensure_ruhi_cmap() (in module chemparseplot.plot.chemgp) _EXPECTED_COORD_COLS (in module chemparseplot.util)

_extract_initial_energy() (in module chemparseplot.parse.eon.saddle_search) _extract_saddle_info() (in module chemparseplot.parse.eon.saddle_search) _extract_total_time() (in module chemparseplot.parse.eon.saddle_search) _find_log_file() (in module chemparseplot.parse.eon.saddle_search) _flatten() (in module chemparseplot.parse.grammar.orca_text) (in module chemparseplot.parse.grammar.xyz) _frame_with_energy() (in module chemparseplot.parse.eon.stitch) _geometry_to_atoms() (in module chemparseplot.parse.orca.neb.opi_parser) _get_energy() (in module chemparseplot.parse.trajectory.neb) _get_forces() (in module chemparseplot.parse.trajectory.neb) _get_methods() (in module chemparseplot.parse.eon.saddle_search) _get_opi_output() (in module chemparseplot.parse.orca.neb.opi_parser) _grammar_cache (in module chemparseplot.parse.grammar.xyz) _grammar_mod (in module chemparseplot.parse.grammar._deps) _has_opi() (in module chemparseplot.parse.orca.neb.opi_parser) _import_xyzrender() (in module chemparseplot.plot.neb) _INSTALL_HINT (in module chemparseplot.parse.grammar._deps) (in module chemparseplot.parse.orca._opi) _JOST_THEME (in module chemparseplot.plot.chemgp) _LABELS (in module chemparseplot.plot.optimization) _load_mode_dat() (in module chemparseplot.parse.eon.dimer_trajectory) _looks_like_path() (in module chemparseplot.api) _make_visitor() (in module chemparseplot.parse.grammar.xyz) _METHOD_PALETTE (in module chemparseplot.plot.chemgp) _MIN_BIN_SIZE (in module chemparseplot.parse.plumed) _MIN_COLS_1D (in module chemparseplot.parse.plumed) _MIN_COLS_2D (in module chemparseplot.parse.plumed) _N_ATOMS_RE (in module chemparseplot.parse.grammar.orca_text) _nodes_mod (in module chemparseplot.parse.grammar._deps) _normalize_orca_neb_plot_payload() (in module chemparseplot.plot.neb) _opi_output_cls (in module chemparseplot.parse.orca._opi) _opi_probe (in module chemparseplot.parse.orca._opi) _OpiGeometry (class in chemparseplot.parse.orca.neb.opi_parser) _OpiNebImage (class in chemparseplot.parse.orca.neb.opi_parser) _orca_saddle_index() (in module chemparseplot.plot.neb) _OrcaNebPlotPayload (class in chemparseplot.plot.neb) _parse_orca_neb_opi() (in module chemparseplot.parse.orca.neb.opi_parser) _parse_rotation_angles() (in module chemparseplot.plot.neb) _path_to_atoms_list() (in module chemparseplot.parse.trajectory.hdf5) _path_to_profile_dat() (in module chemparseplot.parse.trajectory.hdf5) _plot_orca_profile_keypoints() (in module chemparseplot.plot.neb) _probe (in module chemparseplot.parse.grammar._deps) _process_single_path_step() (in module chemparseplot.parse.eon.neb) _Q (in module chemparseplot.units) _read_metadata_group() (in module chemparseplot.parse.trajectory.hdf5) _read_opi_neb_image() (in module chemparseplot.parse.orca.neb.opi_parser) _read_path_group() (in module chemparseplot.parse.trajectory.hdf5) _read_results_dat() (in module chemparseplot.parse.eon.saddle_search) _readcon() (in module chemparseplot.parse.eon.con_io) _reconstruct_atoms() (in module chemparseplot.parse.trajectory.hdf5) _render_atoms() (in module chemparseplot.plot.neb) _render_ovito() (in module chemparseplot.plot.neb) _render_solvis() (in module chemparseplot.plot.neb) _render_xyzrender() (in module chemparseplot.plot.neb) _require_fallback() (in module chemparseplot.parse.orca.neb.opi_parser) _resize_rgba_image() (in module chemparseplot.plot.neb) _save_orca_figure() (in module chemparseplot.plot.neb) _setup() (in module chemparseplot.plot.chemgp) _STROKE (in module chemparseplot.plot.chemgp) _ureg (in module chemparseplot.units) _validate_data_atoms_match() (in module chemparseplot.parse.eon.neb) _XYZ_GRAMMAR_SRC (in module chemparseplot.parse.grammar.xyz)

A

a_start (chemparseplot.parse.projection.ProjectionBasis attribute) add_data() (chemparseplot.plot.structs.TwoDimPlot method) add_exact_gp() (chemparseplot.parse.chemgp_jsonl.RFFQualityData method) add_record() (chemparseplot.parse.chemgp_jsonl.OptimizerTrace method) add_rff() (chemparseplot.parse.chemgp_jsonl.RFFQualityData method) add_title() (chemparseplot.plot.structs.BasePlotter method) additional_structures (chemparseplot.parse.eon.neb.NebOverlayBundle attribute) aggregate_neb_landscape_data() (in module chemparseplot.parse.eon.neb) annotate_endpoint() (in module chemparseplot.plot.optimization) append() (chemparseplot.parse.chemgp_jsonl.TrainingPointSet method) apply_axis_theme() (in module chemparseplot.plot.theme) ArrayGroup (class in chemparseplot.parse.types)

as_energy_quantity() (in module chemparseplot.units) atomic_numbers (chemparseplot.parse.orca.neb.opi_parser._OpiGeometry attribute) atoms (chemparseplot.parse.eon.neb.NebOverlayStructure attribute) (chemparseplot.parse.grammar.xyz.XyzFrame attribute) (chemparseplot.plot.structs.StructurePlacement attribute) atoms_list (chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData attribute) (chemparseplot.parse.eon.min_trajectory.MinTrajectoryData attribute) (chemparseplot.parse.eon.neb.NebOverlayBundle attribute) atoms_list_from_frames() (in module chemparseplot.parse.eon.frame_series) auto_thin (chemparseplot.plot.neb.SurfaceFitConfig attribute) axis_label() (in module chemparseplot.plot.structs) AxisUnits (class in chemparseplot.plot.structs)

B

b_start (chemparseplot.parse.projection.ProjectionBasis attribute) Backend (in module chemparseplot.parse.orca.neb.opi_parser) BAD_HIGH_BARRIER (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_HIGH_ENERGY (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_MAX_CONCAVE_ITERATIONS (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_MAX_ITERATIONS (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_MD_TRAJECTORY_TOO_SHORT (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_MINIMA (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_NO_BARRIER (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_NO_CONVEX (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute)

BAD_NO_NEGATIVE_MODE_AT_SADDLE (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_NOT_CONNECTED (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) BAD_PREFACTOR (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) barrier (chemparseplot.parse.eon.stitch.StitchedSegment attribute) barrier_forward (chemparseplot.parse.types.OrcaNebResult attribute) (chemparseplot.plot.neb._OrcaNebPlotPayload attribute) barrier_reverse (chemparseplot.parse.types.OrcaNebResult attribute) BasePlotter (class in chemparseplot.plot.structs) BATLOW_THEME (in module chemparseplot.plot.theme) boundary_indices (chemparseplot.parse.eon.stitch.StitchSummary attribute) build_cmap() (in module chemparseplot.plot.theme)

C

calculate() (chemparseplot.parse.eon.gprd.HDF5Calculator method) (chemparseplot.parse.eon.gprd.HDF5CalculatorDimerMidpoint method) calculate_fes_from_hills() (in module chemparseplot.parse.plumed) calculate_landscape_coords() (in module chemparseplot.parse.neb_utils) chemparseplot module chemparseplot.api module chemparseplot.parse module chemparseplot.parse.chemgp_hdf5 module chemparseplot.parse.chemgp_jsonl module chemparseplot.parse.converter module chemparseplot.parse.eon module chemparseplot.parse.eon._trajectory_common module chemparseplot.parse.eon.con_io module chemparseplot.parse.eon.dimer_trajectory module chemparseplot.parse.eon.frame_series module chemparseplot.parse.eon.gprd module chemparseplot.parse.eon.min_trajectory module chemparseplot.parse.eon.minimization module chemparseplot.parse.eon.neb module chemparseplot.parse.eon.saddle_search module chemparseplot.parse.eon.stitch module chemparseplot.parse.file_ module chemparseplot.parse.grammar module chemparseplot.parse.grammar._deps module chemparseplot.parse.grammar.orca_text module chemparseplot.parse.grammar.xyz module chemparseplot.parse.neb_utils module chemparseplot.parse.orca module chemparseplot.parse.orca._opi module chemparseplot.parse.orca.geomscan module chemparseplot.parse.orca.neb module chemparseplot.parse.orca.neb.interp module chemparseplot.parse.orca.neb.opi_parser module

chemparseplot.parse.patterns module chemparseplot.parse.plumed module chemparseplot.parse.projection module chemparseplot.parse.trajectory module chemparseplot.parse.trajectory.hdf5 module chemparseplot.parse.trajectory.neb module chemparseplot.parse.types module chemparseplot.plot module chemparseplot.plot.chemgp module chemparseplot.plot.geomscan module chemparseplot.plot.neb module chemparseplot.plot.optimization module chemparseplot.plot.plumed module chemparseplot.plot.structs module chemparseplot.plot.theme module chemparseplot.units module chemparseplot.util module cmap_landscape (chemparseplot.plot.theme.PlotTheme attribute) cmap_profile (chemparseplot.plot.theme.PlotTheme attribute) coerce_metadata_value() (in module chemparseplot.parse.eon._trajectory_common) comment (chemparseplot.parse.grammar.xyz.XyzFrame attribute) ComparisonData (class in chemparseplot.parse.chemgp_jsonl) ComparisonRecord (class in chemparseplot.parse.chemgp_jsonl) compute_cumulative_distance() (in module chemparseplot.parse.trajectory.neb) compute_profile_rmsd() (in module chemparseplot.parse.eon.neb) compute_projection_basis() (in module chemparseplot.parse.projection) compute_synthetic_gradients() (in module chemparseplot.parse.neb_utils) compute_tangent_force() (in module chemparseplot.parse.trajectory.neb) CON_SUFFIXES (in module chemparseplot.parse.eon.con_io) converged (chemparseplot.parse.types.OrcaNebResult attribute) convergence (chemparseplot.parse.types.TrajectoryNebResult attribute) convert_energy() (in module chemparseplot.plot.structs) convert_energy_curvature() (in module chemparseplot.plot.structs) convert_energy_magnitude() (in module chemparseplot.units) convert_neb_values() (in module chemparseplot.plot.neb) coordinates (chemparseplot.parse.orca.neb.opi_parser._OpiGeometry attribute) coordinates() (chemparseplot.parse.grammar.xyz.XyzFrame method) counts (chemparseplot.parse.grammar.xyz.XyzFrame property) create_full_traj_from_hdf5() (in module chemparseplot.parse.eon.gprd) create_geom_traj_from_hdf5() (in module chemparseplot.parse.eon.gprd) create_landscape_axes() (in module chemparseplot.plot.optimization) create_landscape_dataframe() (in module chemparseplot.parse.neb_utils) create_multicol_pattern() (in module chemparseplot.parse.patterns) create_nwchem_trajectory() (in module chemparseplot.parse.eon.gprd)

D

d_rff (chemparseplot.parse.chemgp_jsonl.RFFApproxRecord attribute) d_rff_values (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) dat_df (chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData attribute) (chemparseplot.parse.eon.min_trajectory.MinTrajectoryData attribute) data (chemparseplot.parse.types.ArrayGroup attribute) (chemparseplot.parse.types.ParserAttrs attribute) DataclassMapping (class in chemparseplot.parse.types) default_neb_ylabel() (in module chemparseplot.plot.neb)

default_strip_zoom() (in module chemparseplot.plot.optimization) detect_clamp() (in module chemparseplot.plot.chemgp) DIGIT (in module chemparseplot.parse.patterns) dimension (chemparseplot.parse.types.PlumedFesResult attribute) DIMER_METADATA_COLUMNS (in module chemparseplot.parse.eon.dimer_trajectory) dimer_trajectory_from_frames() (in module chemparseplot.parse.eon.frame_series) DimerTrajectoryData (class in chemparseplot.parse.eon.dimer_trajectory) distance (chemparseplot.plot.structs.AxisUnits attribute) (chemparseplot.plot.structs.EnergyPath attribute)

E

e (chemparseplot.parse.chemgp_jsonl.TrainingPointSet attribute) edgecolor (chemparseplot.plot.theme.PlotTheme attribute) eigenvalue_axis_label() (in module chemparseplot.plot.structs) end (chemparseplot.parse.eon.stitch.StitchedSegment attribute) energies (chemparseplot.parse.chemgp_jsonl.OptimizerTrace attribute) (chemparseplot.parse.types.OrcaNebResult attribute) (chemparseplot.parse.types.TrajectoryNebPath attribute) (chemparseplot.plot.neb._OrcaNebPlotPayload attribute) energies_from_frames() (in module chemparseplot.parse.eon.frame_series) energies_hartree (chemparseplot.parse.grammar.orca_text.OrcaTextSummary attribute) energy (chemparseplot.parse.chemgp_jsonl.ComparisonRecord attribute) (chemparseplot.parse.chemgp_jsonl.StationaryPoint attribute) (chemparseplot.plot.structs.AxisUnits attribute) (chemparseplot.plot.structs.EnergyPath attribute) energy_axis_label() (in module chemparseplot.plot.structs) energy_ev (chemparseplot.parse.orca.neb.opi_parser._OpiNebImage attribute) energy_mae (chemparseplot.parse.chemgp_jsonl.RFFExactRecord attribute) energy_mae_vs_gp (chemparseplot.parse.chemgp_jsonl.RFFApproxRecord attribute) (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute)

energy_mae_vs_true (chemparseplot.parse.chemgp_jsonl.RFFApproxRecord attribute) (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) energy_quantity() (in module chemparseplot.units) ENERGY_UNITS (in module chemparseplot.units) EnergyPath (class in chemparseplot.plot.structs) enforce_strip_clearance() (in module chemparseplot.plot.optimization) ensure_trace() (chemparseplot.parse.chemgp_jsonl.ComparisonData method) EonSaddleResults (class in chemparseplot.parse.eon.saddle_search) EONSaddleStatus (class in chemparseplot.parse.eon.saddle_search) estimate_rbf_smoothing() (in module chemparseplot.parse.eon.neb) exact_energy_mae (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) exact_gradient_mae (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) extract_cartesian_angstrom_blocks() (in module chemparseplot.parse.grammar.orca_text) extract_energy_data() (in module chemparseplot.parse.orca.geomscan) extract_final_energies_hartree() (in module chemparseplot.parse.grammar.orca_text) extract_interp_points() (in module chemparseplot.parse.orca.neb.interp) extract_n_atoms() (in module chemparseplot.parse.grammar.orca_text) extract_orca_geomscan_energy() (in module chemparseplot.api) extract_profile_data() (in module chemparseplot.parse.trajectory.neb) extract_saddle_gprd() (in module chemparseplot.parse.eon.saddle_search)

F

f_para (chemparseplot.parse.types.TrajectoryNebPath attribute) facecolor (chemparseplot.plot.theme.PlotTheme attribute) FAILED_PREFACTOR (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) fes (chemparseplot.parse.types.PlumedFesResult attribute) fes_result (chemparseplot.parse.types.PlumedMinimaResult attribute) final_atoms (chemparseplot.parse.eon.min_trajectory.MinTrajectoryData attribute) final_energy (chemparseplot.parse.grammar.orca_text.OrcaTextSummary property) final_energy_hartree (chemparseplot.parse.grammar.orca_text.OrcaTextSummary property) find_fes_minima() (in module chemparseplot.parse.plumed) find_file_paths() (in module chemparseplot.parse.file_) font_family (chemparseplot.plot.theme.PlotTheme attribute) font_size (chemparseplot.plot.theme.PlotTheme attribute)

force (chemparseplot.parse.chemgp_jsonl.ComparisonRecord attribute) forces (chemparseplot.parse.chemgp_jsonl.OptimizerTrace attribute) (chemparseplot.parse.types.OrcaNebResult attribute) frame_rows_to_table() (in module chemparseplot.parse.eon._trajectory_common) frame_with_energy() (in module chemparseplot.parse.eon.con_io) from_mapping() (chemparseplot.parse.chemgp_jsonl.ComparisonRecord class method) (chemparseplot.parse.chemgp_jsonl.GPGridRecord class method) (chemparseplot.parse.chemgp_jsonl.RFFApproxRecord class method) (chemparseplot.parse.chemgp_jsonl.RFFExactRecord class method) (chemparseplot.parse.types.OrcaNebResult class method) (chemparseplot.plot.neb.SurfaceFitConfig class method) from_records() (chemparseplot.parse.chemgp_jsonl.GPQualityGrid class method) from_value() (chemparseplot.parse.eon.saddle_search.EONSaddleStatus class method)

G

geometry (chemparseplot.parse.orca.neb.opi_parser._OpiNebImage attribute) get_atoms_from_hdf5() (in module chemparseplot.parse.eon.gprd) get_grammar_class() (in module chemparseplot.parse.grammar._deps) get_node_visitor_class() (in module chemparseplot.parse.grammar._deps) get_opi_output_class() (in module chemparseplot.parse.orca._opi) get_theme() (in module chemparseplot.plot.theme) GOOD (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) gp_e (chemparseplot.parse.chemgp_jsonl.GPGridRecord attribute) (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) gp_var (chemparseplot.parse.chemgp_jsonl.GPGridRecord attribute) (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) GPGridRecord (class in chemparseplot.parse.chemgp_jsonl) GPQualityData (class in chemparseplot.parse.chemgp_jsonl) GPQualityGrid (class in chemparseplot.parse.chemgp_jsonl)

grad_p (chemparseplot.parse.types.OrcaNebResult attribute) (chemparseplot.plot.neb._OrcaNebPlotPayload attribute) grad_r (chemparseplot.parse.types.OrcaNebResult attribute) (chemparseplot.plot.neb._OrcaNebPlotPayload attribute) gradient (chemparseplot.parse.orca.neb.opi_parser._OpiNebImage attribute) gradient_mae (chemparseplot.parse.chemgp_jsonl.RFFExactRecord attribute) gradient_mae_vs_gp (chemparseplot.parse.chemgp_jsonl.RFFApproxRecord attribute) (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) gradient_mae_vs_true (chemparseplot.parse.chemgp_jsonl.RFFApproxRecord attribute) (chemparseplot.parse.chemgp_jsonl.RFFQualityData attribute) gradients (chemparseplot.parse.types.TrajectoryNebPath attribute) grammar_available() (in module chemparseplot.api) (in module chemparseplot.parse.grammar._deps) gridcolor (chemparseplot.plot.theme.PlotTheme attribute) grids (chemparseplot.parse.chemgp_jsonl.GPQualityData attribute)

H

HAS_OPI (in module chemparseplot.parse.orca.neb.opi_parser) HDF5Calculator (class in chemparseplot.parse.eon.gprd) HDF5CalculatorDimerMidpoint (class in chemparseplot.parse.eon.gprd) highest_energy (chemparseplot.parse.eon.stitch.StitchSummary attribute)

highest_index (chemparseplot.parse.eon.stitch.StitchSummary attribute) highlight_color (chemparseplot.plot.theme.PlotTheme attribute) hills (chemparseplot.parse.types.PlumedFesResult attribute) history_to_landscape_df() (in module chemparseplot.parse.trajectory.hdf5) history_to_profile_dats() (in module chemparseplot.parse.trajectory.hdf5)

I

id (chemparseplot.parse.chemgp_jsonl.StationaryPoint attribute) images (chemparseplot.parse.types.TrajectoryNebPath attribute) implemented_properties (chemparseplot.parse.eon.gprd.HDF5Calculator attribute) (chemparseplot.parse.eon.gprd.HDF5CalculatorDimerMidpoint attribute) INIT (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) initial_atoms (chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData attribute) (chemparseplot.parse.eon.min_trajectory.MinTrajectoryData attribute)

INSET_IMAGE_ZOOM_SCALE (in module chemparseplot.plot.neb) InsetImagePos (class in chemparseplot.plot.neb) INTERP_PAT (in module chemparseplot.parse.orca.neb.interp) inverse_sd_to_ab() (in module chemparseplot.parse.projection) is_con_path() (in module chemparseplot.parse.eon.con_io) iter_steps (chemparseplot.parse.eon.saddle_search.EonSaddleResults attribute) ix (chemparseplot.parse.chemgp_jsonl.GPGridRecord attribute) iy (chemparseplot.parse.chemgp_jsonl.GPGridRecord attribute)

K

kind (chemparseplot.parse.chemgp_jsonl.StationaryPoint attribute)

L

label (chemparseplot.parse.eon.neb.NebOverlayStructure attribute) (chemparseplot.parse.eon.stitch.StitchedSegment attribute) (chemparseplot.plot.structs.EnergyPath attribute) (chemparseplot.plot.structs.StructurePlacement attribute) (chemparseplot.plot.structs.XYData attribute) landscape_half_span() (in module chemparseplot.plot.neb) landscape_projection_basis() (in module chemparseplot.plot.neb) last_geometry (chemparseplot.parse.grammar.orca_text.OrcaTextSummary attribute) load_augmenting_neb_data() (in module chemparseplot.parse.eon.neb) load_dimer_trajectory() (in module chemparseplot.parse.eon.dimer_trajectory) load_min_trajectory() (in module chemparseplot.parse.eon.min_trajectory) load_movie_and_table() (in module chemparseplot.parse.eon._trajectory_common) load_neb_history() (in module chemparseplot.parse.trajectory.hdf5) load_neb_result() (in module chemparseplot.parse.trajectory.hdf5) load_optional_payload() (in module chemparseplot.parse.eon._trajectory_common) load_or_compute_data() (in module chemparseplot.parse.eon.neb) load_structures_and_calculate_additional_rmsd() (in module chemparseplot.parse.eon.neb)

load_trajectory() (in module chemparseplot.parse.trajectory.neb) log (in module chemparseplot.parse.eon._trajectory_common) (in module chemparseplot.parse.eon.dimer_trajectory) (in module chemparseplot.parse.eon.gprd) (in module chemparseplot.parse.eon.min_trajectory) (in module chemparseplot.parse.eon.neb) (in module chemparseplot.parse.eon.saddle_search) (in module chemparseplot.parse.eon.stitch) (in module chemparseplot.parse.file_) (in module chemparseplot.parse.neb_utils) (in module chemparseplot.parse.trajectory.hdf5) (in module chemparseplot.parse.trajectory.neb) (in module chemparseplot.plot.chemgp) (in module chemparseplot.plot.neb) (in module chemparseplot.plot.optimization) (in module chemparseplot.plot.theme) (in module chemparseplot.util)

M

m (chemparseplot.plot.structs.UnitConverted property) main() (in module chemparseplot.util) mark_saddle_point() (in module chemparseplot.plot.neb) max_force (chemparseplot.parse.chemgp_jsonl.ComparisonRecord attribute) max_surface_points (chemparseplot.plot.neb.SurfaceFitConfig attribute) meta (chemparseplot.parse.chemgp_jsonl.GPQualityData attribute) metadata (chemparseplot.parse.types.TrajectoryNebResult attribute) metadata_value() (in module chemparseplot.parse.eon._trajectory_common) method (chemparseplot.parse.chemgp_jsonl.ComparisonRecord attribute) (chemparseplot.parse.chemgp_jsonl.OptimizerTrace attribute) min_e_result() (in module chemparseplot.parse.eon.minimization) MIN_METADATA_COLUMNS (in module chemparseplot.parse.eon.min_trajectory) MIN_PATH_LENGTH (in module chemparseplot.plot.neb) min_trajectory_from_frames() (in module chemparseplot.parse.eon.frame_series) minima (chemparseplot.parse.types.PlumedMinimaResult attribute) MinTrajectoryData (class in chemparseplot.parse.eon.min_trajectory) mode_vector (chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData attribute) module chemparseplot chemparseplot.api chemparseplot.parse chemparseplot.parse.chemgp_hdf5 chemparseplot.parse.chemgp_jsonl chemparseplot.parse.converter chemparseplot.parse.eon chemparseplot.parse.eon._trajectory_common chemparseplot.parse.eon.con_io chemparseplot.parse.eon.dimer_trajectory chemparseplot.parse.eon.frame_series chemparseplot.parse.eon.gprd chemparseplot.parse.eon.min_trajectory chemparseplot.parse.eon.minimization chemparseplot.parse.eon.neb chemparseplot.parse.eon.saddle_search chemparseplot.parse.eon.stitch chemparseplot.parse.file_ chemparseplot.parse.grammar chemparseplot.parse.grammar._deps chemparseplot.parse.grammar.orca_text chemparseplot.parse.grammar.xyz chemparseplot.parse.neb_utils chemparseplot.parse.orca chemparseplot.parse.orca._opi chemparseplot.parse.orca.geomscan chemparseplot.parse.orca.neb chemparseplot.parse.orca.neb.interp chemparseplot.parse.orca.neb.opi_parser chemparseplot.parse.patterns chemparseplot.parse.plumed chemparseplot.parse.projection chemparseplot.parse.trajectory chemparseplot.parse.trajectory.hdf5 chemparseplot.parse.trajectory.neb chemparseplot.parse.types chemparseplot.plot chemparseplot.plot.chemgp chemparseplot.plot.geomscan chemparseplot.plot.neb chemparseplot.plot.optimization chemparseplot.plot.plumed chemparseplot.plot.structs chemparseplot.plot.theme chemparseplot.units chemparseplot.util

N

n_atoms (chemparseplot.parse.grammar.orca_text.OrcaTextSummary attribute) n_frames (chemparseplot.parse.eon.stitch.StitchSummary attribute) n_images (chemparseplot.parse.types.OrcaNebResult attribute) (chemparseplot.plot.neb._OrcaNebPlotPayload attribute) n_train (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) name (chemparseplot.plot.theme.PlotTheme attribute) natoms (chemparseplot.parse.grammar.xyz.XyzFrame attribute) neb_path_arrays() (in module chemparseplot.parse.eon.frame_series)

NebOverlayBundle (class in chemparseplot.parse.eon.neb) NebOverlayStructure (class in chemparseplot.parse.eon.neb) NEGATIVE_BARRIER (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) NONLOCAL_ABORT (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) NONNEGATIVE_ABORT (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) normalize_energy_unit() (in module chemparseplot.units) np_txt() (in module chemparseplot.parse.converter) nx (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) ny (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute)

O

opi_available() (in module chemparseplot.parse.orca._opi) OPTIMIZER_ERROR (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) OptimizerTrace (class in chemparseplot.parse.chemgp_jsonl) oracle_calls (chemparseplot.parse.chemgp_jsonl.ComparisonRecord attribute) (chemparseplot.parse.chemgp_jsonl.OptimizerTrace attribute)

orca_version (chemparseplot.parse.types.OrcaNebResult attribute) OrcaAtomCoord (class in chemparseplot.parse.grammar.orca_text) OrcaNebResult (class in chemparseplot.parse.types) OrcaTextSummary (class in chemparseplot.parse.grammar.orca_text) out_dir (chemparseplot.parse.eon.stitch.StitchSummary attribute) OVERLAY_COLORS (in module chemparseplot.plot.optimization)

P

p (chemparseplot.parse.eon.neb.NebOverlayStructure attribute) parse_climb_con() (in module chemparseplot.parse.eon.dimer_trajectory) parse_climb_dat() (in module chemparseplot.parse.eon.dimer_trajectory) parse_comparison_jsonl() (in module chemparseplot.parse.chemgp_jsonl) parse_eon_saddle() (in module chemparseplot.parse.eon.saddle_search) parse_gp_quality_jsonl() (in module chemparseplot.parse.chemgp_jsonl) parse_min_con() (in module chemparseplot.parse.eon.min_trajectory) parse_min_dat() (in module chemparseplot.parse.eon.min_trajectory) parse_orca_final_energy() (in module chemparseplot.api) parse_orca_neb() (in module chemparseplot.parse.orca.neb.opi_parser) parse_orca_neb_fallback() (in module chemparseplot.parse.orca.neb.opi_parser) parse_orca_text_file() (in module chemparseplot.parse.grammar.orca_text) parse_orca_text_summary() (in module chemparseplot.parse.grammar.orca_text) parse_rff_quality_jsonl() (in module chemparseplot.parse.chemgp_jsonl) parse_target_coords() (in module chemparseplot.util) parse_xyz() (in module chemparseplot.api) parse_xyz_file() (in module chemparseplot.parse.grammar.xyz) parse_xyz_text() (in module chemparseplot.parse.grammar.xyz) ParserAttrs (class in chemparseplot.parse.types) path (chemparseplot.parse.types.TrajectoryNebResult attribute) path_norm (chemparseplot.parse.projection.ProjectionBasis attribute) pcv1 (chemparseplot.parse.types.PlumedFesResult attribute) pcv2 (chemparseplot.parse.types.PlumedFesResult attribute) peak_energy (chemparseplot.parse.eon.stitch.StitchedSegment attribute) per (chemparseplot.parse.types.PlumedFesResult attribute) pes_calls (chemparseplot.parse.eon.saddle_search.EonSaddleResults attribute) plot_convergence_curve() (in module chemparseplot.plot.chemgp) plot_convergence_panel() (in module chemparseplot.plot.optimization) plot_dimer_mode_evolution() (in module chemparseplot.plot.optimization) plot_eigenvalue_path() (in module chemparseplot.plot.neb) plot_energy_path() (in module chemparseplot.plot.neb) plot_energy_paths() (in module chemparseplot.plot.geomscan) plot_energy_profile() (in module chemparseplot.plot.chemgp) plot_fes_1d() (in module chemparseplot.plot.plumed)

plot_fes_2d() (in module chemparseplot.plot.plumed) plot_fps_projection() (in module chemparseplot.plot.chemgp) plot_gp_progression() (in module chemparseplot.plot.chemgp) plot_hyperparameter_sensitivity() (in module chemparseplot.plot.chemgp) plot_landscape_path_overlay() (in module chemparseplot.plot.neb) plot_landscape_surface() (in module chemparseplot.plot.neb) plot_mmf_peaks_overlay() (in module chemparseplot.plot.neb) plot_neb_evolution() (in module chemparseplot.plot.neb) plot_nll_landscape() (in module chemparseplot.plot.chemgp) plot_optimization_landscape() (in module chemparseplot.plot.optimization) plot_optimization_profile() (in module chemparseplot.plot.optimization) plot_orca_neb_energy_profile() (in module chemparseplot.plot.neb) plot_orca_neb_landscape() (in module chemparseplot.plot.neb) plot_orca_neb_profile() (in module chemparseplot.plot.neb) plot_phase_points_overlay() (in module chemparseplot.plot.neb) plot_rff_quality() (in module chemparseplot.plot.chemgp) plot_single_ended_convergence() (in module chemparseplot.plot.optimization) plot_single_ended_profile() (in module chemparseplot.plot.optimization) plot_structure_inset() (in module chemparseplot.plot.neb) plot_structure_strip() (in module chemparseplot.plot.neb) plot_surface_contour() (in module chemparseplot.plot.chemgp) plot_trust_region() (in module chemparseplot.plot.chemgp) plot_variance_overlay() (in module chemparseplot.plot.chemgp) PlotTheme (class in chemparseplot.plot.theme) PlumedFesResult (class in chemparseplot.parse.types) PlumedMinimaResult (class in chemparseplot.parse.types) polyorder (chemparseplot.plot.neb.SmoothingParams attribute) POSCON_FILENAME (in module chemparseplot.util) POTENTIAL_FAILED (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) profile_strip_payload() (in module chemparseplot.plot.neb) profile_structure_indices() (in module chemparseplot.plot.neb) project_landscape_path() (in module chemparseplot.plot.optimization) project_to_sd() (in module chemparseplot.parse.projection) ProjectionBasis (class in chemparseplot.parse.projection)

R

r (chemparseplot.parse.eon.neb.NebOverlayStructure attribute) rad (chemparseplot.plot.neb.InsetImagePos attribute) read_con_as_ase() (in module chemparseplot.parse.eon.con_io) read_con_frames() (in module chemparseplot.parse.eon.con_io) read_first_atoms() (in module chemparseplot.parse.eon.con_io) read_first_structure() (in module chemparseplot.parse.eon._trajectory_common) read_h5_grid() (in module chemparseplot.parse.chemgp_hdf5) read_h5_metadata() (in module chemparseplot.parse.chemgp_hdf5) read_h5_path() (in module chemparseplot.parse.chemgp_hdf5) read_h5_points() (in module chemparseplot.parse.chemgp_hdf5) read_h5_table() (in module chemparseplot.parse.chemgp_hdf5) read_optional_first() (in module chemparseplot.parse.eon._trajectory_common) redraw_plot() (chemparseplot.plot.structs.TwoDimPlot method) render_endpoint_strip() (in module chemparseplot.plot.optimization) render_single_ended_landscape() (in module chemparseplot.plot.optimization) render_structure_to_image() (in module chemparseplot.plot.neb) require_dat_file() (in module chemparseplot.parse.eon._trajectory_common)

reset_grammar_cache() (in module chemparseplot.parse.grammar._deps) reset_opi_cache() (in module chemparseplot.parse.orca._opi) resolve_movie_file() (in module chemparseplot.parse.eon._trajectory_common) result_to_atoms_list() (in module chemparseplot.parse.trajectory.hdf5) result_to_profile_dat() (in module chemparseplot.parse.trajectory.hdf5) RFFApproxRecord (class in chemparseplot.parse.chemgp_jsonl) RFFExactRecord (class in chemparseplot.parse.chemgp_jsonl) RFFQualityData (class in chemparseplot.parse.chemgp_jsonl) rmdat() (chemparseplot.plot.structs.TwoDimPlot method) rmsd_p (chemparseplot.parse.types.OrcaNebResult attribute) (chemparseplot.plot.neb._OrcaNebPlotPayload attribute) rmsd_r (chemparseplot.parse.types.OrcaNebResult attribute) (chemparseplot.plot.neb._OrcaNebPlotPayload attribute) rows (chemparseplot.parse.types.PlumedFesResult attribute) RUHI_COLORS (in module chemparseplot.plot.theme) RUHI_THEME (in module chemparseplot.plot.theme) rxn_coord (chemparseplot.parse.types.TrajectoryNebPath attribute)

S

saddle_atoms (chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData attribute) saddle_energy (chemparseplot.parse.eon.saddle_search.EonSaddleResults attribute) saddle_point (chemparseplot.parse.eon.neb.NebOverlayBundle attribute) safe_plot() (in module chemparseplot.plot.chemgp) save_landscape_figure() (in module chemparseplot.plot.optimization) save_plot() (in module chemparseplot.plot.chemgp) (in module chemparseplot.plot.neb) save_standard_figure() (in module chemparseplot.plot.optimization) segments (chemparseplot.parse.eon.stitch.StitchSummary attribute) series_from_frames() (in module chemparseplot.parse.eon.frame_series) set_labels() (chemparseplot.plot.structs.TwoDimPlot method) set_units() (chemparseplot.plot.structs.TwoDimPlot method) setup_global_theme() (in module chemparseplot.plot.theme) setup_publication_theme() (in module chemparseplot.plot.theme) SmoothingParams (class in chemparseplot.plot.neb) source (chemparseplot.parse.types.OrcaNebResult attribute) start (chemparseplot.parse.eon.stitch.StitchedSegment attribute)

stationary (chemparseplot.parse.chemgp_jsonl.GPQualityData attribute) StationaryPoint (class in chemparseplot.parse.chemgp_jsonl) step (chemparseplot.parse.chemgp_jsonl.ComparisonRecord attribute) steps (chemparseplot.parse.chemgp_jsonl.OptimizerTrace attribute) stitch_neb_segments() (in module chemparseplot.parse.eon.stitch) StitchedSegment (class in chemparseplot.parse.eon.stitch) StitchSummary (class in chemparseplot.parse.eon.stitch) STRIP_IMAGE_ZOOM_SCALE (in module chemparseplot.plot.neb) StructurePlacement (class in chemparseplot.plot.structs) suite_pins() (in module chemparseplot.api) summary (chemparseplot.parse.chemgp_jsonl.ComparisonData attribute) surface_fit_indices() (in module chemparseplot.plot.neb) SurfaceFitConfig (class in chemparseplot.plot.neb) symbol (chemparseplot.parse.grammar.orca_text.OrcaAtomCoord attribute) (chemparseplot.parse.grammar.xyz.XyzAtom attribute) symbols (chemparseplot.parse.grammar.xyz.XyzFrame property) system (chemparseplot.parse.grammar.xyz.XyzFrame property)

T

T (in module chemparseplot.parse.eon._trajectory_common) table_from_dimer_metadata() (in module chemparseplot.parse.eon.dimer_trajectory) table_from_min_metadata() (in module chemparseplot.parse.eon.min_trajectory) target_coords_text (in module chemparseplot.util) terminal_only (chemparseplot.parse.eon.saddle_search.EonSaddleResults property) termination_status (chemparseplot.parse.eon.saddle_search.EonSaddleResults attribute) textcolor (chemparseplot.plot.theme.PlotTheme attribute) THEMES (in module chemparseplot.plot.theme) THREE_COL_NUM (in module chemparseplot.parse.patterns) to() (chemparseplot.plot.structs.UnitSeries method) to_magnitude() (in module chemparseplot.plot.structs) traces (chemparseplot.parse.chemgp_jsonl.ComparisonData attribute)

train_e (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) train_x (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) train_y (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) TrainingPointSet (class in chemparseplot.parse.chemgp_jsonl) trajectory_to_landscape_df() (in module chemparseplot.parse.trajectory.neb) trajectory_to_profile_dat() (in module chemparseplot.parse.trajectory.neb) TrajectoryNebPath (class in chemparseplot.parse.types) TrajectoryNebResult (class in chemparseplot.parse.types) true_e (chemparseplot.parse.chemgp_jsonl.GPGridRecord attribute) (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) TWO_COL_NUM (in module chemparseplot.parse.patterns) TwoDimPlot (class in chemparseplot.plot.structs)

U

u_a (chemparseplot.parse.projection.ProjectionBasis attribute) u_b (chemparseplot.parse.projection.ProjectionBasis attribute) UnitConverted (class in chemparseplot.plot.structs)

UnitSeries (class in chemparseplot.plot.structs) UNKNOWN (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute) update_labels() (chemparseplot.plot.structs.TwoDimPlot method)

V

v_a (chemparseplot.parse.projection.ProjectionBasis attribute)

v_b (chemparseplot.parse.projection.ProjectionBasis attribute) validate_hdf5_structure() (in module chemparseplot.parse.chemgp_hdf5)

W

well_energy (chemparseplot.parse.eon.stitch.StitchedSegment attribute) window_length (chemparseplot.plot.neb.SmoothingParams attribute)

write_atoms_as_con() (in module chemparseplot.parse.eon.con_io) write_con_frames() (in module chemparseplot.parse.eon.con_io) write_xyz_text() (in module chemparseplot.parse.grammar.xyz)

X

x (chemparseplot.parse.chemgp_jsonl.GPGridRecord attribute) (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) (chemparseplot.parse.chemgp_jsonl.StationaryPoint attribute) (chemparseplot.parse.chemgp_jsonl.TrainingPointSet attribute) (chemparseplot.parse.grammar.orca_text.OrcaAtomCoord attribute) (chemparseplot.parse.grammar.xyz.XyzAtom attribute) (chemparseplot.parse.types.PlumedFesResult attribute) (chemparseplot.plot.neb.InsetImagePos attribute) (chemparseplot.plot.structs.StructurePlacement attribute) (chemparseplot.plot.structs.XYData attribute)

XYData (class in chemparseplot.plot.structs) xyz_grammar() (in module chemparseplot.parse.grammar.xyz) XyzAtom (class in chemparseplot.parse.grammar.xyz) XyzFrame (class in chemparseplot.parse.grammar.xyz)

Y

y (chemparseplot.parse.chemgp_jsonl.GPGridRecord attribute) (chemparseplot.parse.chemgp_jsonl.GPQualityGrid attribute) (chemparseplot.parse.chemgp_jsonl.StationaryPoint attribute) (chemparseplot.parse.chemgp_jsonl.TrainingPointSet attribute) (chemparseplot.parse.grammar.orca_text.OrcaAtomCoord attribute) (chemparseplot.parse.grammar.xyz.XyzAtom attribute) (chemparseplot.parse.types.PlumedFesResult attribute) (chemparseplot.plot.neb.InsetImagePos attribute) (chemparseplot.plot.structs.StructurePlacement attribute) (chemparseplot.plot.structs.XYData attribute)

Z

z (chemparseplot.parse.grammar.orca_text.OrcaAtomCoord attribute) (chemparseplot.parse.grammar.xyz.XyzAtom attribute)

ZEROMODE_ABORT (chemparseplot.parse.eon.saddle_search.EONSaddleStatus attribute)