Index

A

aggregate_properties (pyfracval.schemas.Metadata attribute) AggregateProperties (class in pyfracval.schemas) all_coords (pyfracval.pca_subclusters.Subclusterer attribute)

all_radii (pyfracval.pca_subclusters.Subclusterer attribute) apply_retry_rotation_mode() (in module pyfracval.experimental.retry_modes) attempt_index (pyfracval.event_log.MergeEvent attribute)

B

batch_calculate_positions_pca() (in module pyfracval.pca_kernels) (in module pyfracval.utils) batch_check_overlaps_cca() (in module pyfracval.cca_kernels) (in module pyfracval.utils) batch_check_overlaps_pca() (in module pyfracval.pca_kernels) (in module pyfracval.utils)

batch_rotate_cluster_cca() (in module pyfracval.cca_kernels) (in module pyfracval.utils) bounding_volume_precheck() (in module pyfracval.experimental.pair_prefilters) build_feasibility_graph() (in module pyfracval.cca.matching)

C

calculate_cluster_properties() (in module pyfracval.fractal) (in module pyfracval.utils) calculate_mass() (in module pyfracval.fractal) (in module pyfracval.utils) calculate_max_overlap_cca() (in module pyfracval.overlap) (in module pyfracval.utils) calculate_max_overlap_cca_auto() (in module pyfracval.overlap) (in module pyfracval.utils) calculate_max_overlap_cca_fast() (in module pyfracval.overlap) (in module pyfracval.utils) calculate_max_overlap_cca_parallel() (in module pyfracval.overlap) (in module pyfracval.utils) calculate_max_overlap_pca() (in module pyfracval.overlap) (in module pyfracval.utils) calculate_max_overlap_pca_auto() (in module pyfracval.overlap) (in module pyfracval.utils) calculate_max_overlap_pca_fast() (in module pyfracval.overlap) (in module pyfracval.utils) calculate_max_overlap_pca_parallel() (in module pyfracval.overlap) (in module pyfracval.utils) calculate_rg() (in module pyfracval.fractal) (in module pyfracval.utils) candidates_tried (pyfracval.event_log.MergeEvent attribute)

cca_sticking_v1_kernel() (in module pyfracval.cca_kernels) CCAggregator (class in pyfracval.cca) (class in pyfracval.cca.aggregator) (class in pyfracval.cca_agg) cluster_leaf_fraction() (in module pyfracval.cca.matching) cluster_pair_leaf_class() (in module pyfracval.cca.matching) cluster_surface_reach() (in module pyfracval.cca.pairing) ClusterEntry (class in pyfracval) (class in pyfracval.schemas) cm (pyfracval.pca_agg.PCAggregator attribute) compute_aggregate_quality() (in module pyfracval.quality) compute_empirical_rg() (in module pyfracval.fractal) (in module pyfracval.utils) compute_empirical_rg_polydisperse() (in module pyfracval.fractal) compute_fft_correlation() (in module pyfracval.experimental.fft_docking) compute_forces() (in module pyfracval.experimental.soft_relaxation) compute_gap_scale() (in module pyfracval) (in module pyfracval.gap_scaling) compute_overlap_census() (in module pyfracval.overlap_statistics) compute_pair_correlation_dimensions() (in module pyfracval.fractal) (in module pyfracval.utils) coords (pyfracval.pca_agg.PCAggregator attribute) cross3() (in module pyfracval.geometry)

D

densify_aggregate() (in module pyfracval.densify)

density_correlation() (in module pyfracval.correlation) Df (pyfracval.schemas.SimulationParameters attribute)

E

EnvironmentConfig (class in pyfracval.environments) estimate_success_probability() (in module pyfracval.feasibility)

EventLog (class in pyfracval.event_log) ext_case (pyfracval.schemas.SimulationParameters attribute) extract_top_k_peaks() (in module pyfracval.experimental.fft_docking)

F

fft_dock_sticking() (in module pyfracval.experimental.fft_docking) filter_catalog() (in module pyfracval) (in module pyfracval.catalog)

find_touching_pairs() (in module pyfracval.app) fit_correlation_slope() (in module pyfracval.correlation) from_file() (pyfracval.schemas.Metadata class method)

G

gamma_calculation() (in module pyfracval.fractal) (in module pyfracval.utils) gamma_pc (pyfracval.event_log.MergeEvent attribute) gamma_real (pyfracval.event_log.MergeEvent attribute) generate_aggregates_parallel() (in module pyfracval.batch_runner)

generate_aggregates_sequential() (in module pyfracval.batch_runner) generation_info (pyfracval.schemas.Metadata attribute) GenerationInfo (class in pyfracval.schemas) get_client() (in module pyfracval.dask_runner) get_env_config() (in module pyfracval.environments) get_results() (pyfracval.pca_subclusters.Subclusterer method)

I

i_orden (pyfracval.cca.aggregator.CCAggregator attribute) (pyfracval.cca.CCAggregator attribute) (pyfracval.cca_agg.CCAggregator attribute) (pyfracval.pca_subclusters.Subclusterer attribute)

i_t (pyfracval.cca.aggregator.CCAggregator attribute) (pyfracval.cca.CCAggregator attribute) (pyfracval.cca_agg.CCAggregator attribute) initial_mass (pyfracval.pca_agg.PCAggregator attribute) install_wheel_on_workers() (in module pyfracval.dask_runner)

K

kf (pyfracval.schemas.SimulationParameters attribute)

L

leaf_weighted_matching() (in module pyfracval.cca.matching) load_catalog() (in module pyfracval) (in module pyfracval.catalog)

lognormal_pp_radii() (in module pyfracval.particle_generation)

M

m1 (pyfracval.pca_agg.PCAggregator attribute) mass (pyfracval.pca_agg.PCAggregator attribute) max_cardinality_matching() (in module pyfracval.cca.matching) max_feasible_df() (in module pyfracval.feasibility) max_overlap_of_rmin (pyfracval.event_log.MergeEvent attribute) max_overlap_of_rsum (pyfracval.event_log.MergeEvent attribute) max_self_overlap() (in module pyfracval.quality) MergeEvent (class in pyfracval.event_log) Metadata (class in pyfracval.schemas) min_overlap (pyfracval.event_log.MergeEvent attribute) model_config (pyfracval.pca_subclusters.Subclusterer attribute) (pyfracval.schemas.Metadata attribute) (pyfracval.schemas.OverlapCensus attribute) (pyfracval.schemas.SimulationParameters attribute) model_post_init() (pyfracval.pca_subclusters.Subclusterer method) module pyfracval pyfracval.app pyfracval.batch_runner pyfracval.catalog pyfracval.cca pyfracval.cca.aggregator pyfracval.cca.candidates pyfracval.cca.fallbacks pyfracval.cca.matching pyfracval.cca.pairing pyfracval.cca.rescue pyfracval.cca.sticking pyfracval.cca_agg pyfracval.cca_kernels pyfracval.correlation pyfracval.dask_runner pyfracval.densify pyfracval.environments pyfracval.event_log pyfracval.experimental pyfracval.experimental.candidate_policies pyfracval.experimental.fft_docking pyfracval.experimental.gamma_expansion pyfracval.experimental.pair_prefilters pyfracval.experimental.retry_modes pyfracval.experimental.soft_relaxation pyfracval.feasibility pyfracval.fractal pyfracval.gap_scaling pyfracval.geometry pyfracval.main_runner pyfracval.overlap pyfracval.overlap_statistics pyfracval.particle_generation pyfracval.pca_agg pyfracval.pca_kernels pyfracval.pca_subclusters pyfracval.quality pyfracval.schemas pyfracval.utils pyfracval.visualization

N

N (pyfracval.cca.aggregator.CCAggregator attribute) (pyfracval.cca.CCAggregator attribute) (pyfracval.cca_agg.CCAggregator attribute) (pyfracval.pca_agg.PCAggregator attribute) (pyfracval.pca_subclusters.Subclusterer attribute) (pyfracval.schemas.SimulationParameters attribute) n1 (pyfracval.pca_agg.PCAggregator attribute) n_feasible_pairs (pyfracval.event_log.MergeEvent attribute) n_offending_particles (pyfracval.event_log.MergeEvent attribute) n_pairs_overlapping (pyfracval.event_log.MergeEvent attribute)

n_particles_dropped (pyfracval.event_log.MergeEvent attribute) n_subcl_percentage (pyfracval.schemas.SimulationParameters attribute) norm3() (in module pyfracval.geometry) not_able_cca (pyfracval.cca.aggregator.CCAggregator attribute) (pyfracval.cca.CCAggregator attribute) (pyfracval.cca_agg.CCAggregator attribute) not_able_pca (pyfracval.pca_agg.PCAggregator attribute) (pyfracval.pca_subclusters.Subclusterer attribute) number_clusters (pyfracval.pca_subclusters.Subclusterer attribute) number_clusters_processed (pyfracval.pca_subclusters.Subclusterer attribute)

O

out_of_fitted_range() (in module pyfracval.feasibility)

outcome (pyfracval.event_log.MergeEvent attribute) OverlapCensus (class in pyfracval.schemas)

P

PcaFailureEvent (class in pyfracval.event_log) PCAggregator (class in pyfracval.pca_agg) plot_particles() (in module pyfracval.visualization) pool_size (pyfracval.event_log.MergeEvent attribute) pyfracval module pyfracval.app module pyfracval.batch_runner module pyfracval.catalog module pyfracval.cca module pyfracval.cca.aggregator module pyfracval.cca.candidates module pyfracval.cca.fallbacks module pyfracval.cca.matching module pyfracval.cca.pairing module pyfracval.cca.rescue module pyfracval.cca.sticking module pyfracval.cca_agg module pyfracval.cca_kernels module pyfracval.correlation module pyfracval.dask_runner module pyfracval.densify module pyfracval.environments module pyfracval.event_log module pyfracval.experimental module

pyfracval.experimental.candidate_policies module pyfracval.experimental.fft_docking module pyfracval.experimental.gamma_expansion module pyfracval.experimental.pair_prefilters module pyfracval.experimental.retry_modes module pyfracval.experimental.soft_relaxation module pyfracval.feasibility module pyfracval.fractal module pyfracval.gap_scaling module pyfracval.geometry module pyfracval.main_runner module pyfracval.overlap module pyfracval.overlap_statistics module pyfracval.particle_generation module pyfracval.pca_agg module pyfracval.pca_kernels module pyfracval.pca_subclusters module pyfracval.quality module pyfracval.schemas module pyfracval.utils module pyfracval.visualization module

R

r_max (pyfracval.pca_agg.PCAggregator attribute) radial_compress() (in module pyfracval.densify) radii (pyfracval.pca_agg.PCAggregator attribute) random_normal_custom() (in module pyfracval.particle_generation) random_point_sc() (in module pyfracval.geometry) (in module pyfracval.utils) record() (pyfracval.event_log.EventLog method) reorder_candidates_by_policy() (in module pyfracval.experimental.candidate_policies) resolve_densities() (in module pyfracval.fractal) resolve_overlaps() (in module pyfracval.densify) retry_sticking_with_drops() (in module pyfracval.cca.rescue) rg1 (pyfracval.pca_agg.PCAggregator attribute) rodrigues_rotation() (in module pyfracval.geometry) (in module pyfracval.utils)

rotations_used (pyfracval.event_log.MergeEvent attribute) round_index (pyfracval.event_log.MergeEvent attribute) rp_g (pyfracval.schemas.SimulationParameters attribute) rp_gstd (pyfracval.schemas.SimulationParameters attribute) run() (pyfracval.pca_agg.PCAggregator method) run_cca() (pyfracval.cca.aggregator.CCAggregator method) (pyfracval.cca.CCAggregator method) (pyfracval.cca_agg.CCAggregator method) run_gamma_expansion() (in module pyfracval.experimental.gamma_expansion) run_simulation() (in module pyfracval.main_runner) run_subclustering() (pyfracval.pca_subclusters.Subclusterer method) RunEvent (class in pyfracval.event_log)

S

sample_so3_rotations() (in module pyfracval.experimental.fft_docking) save_to_file() (pyfracval.schemas.Metadata method) seed (pyfracval.schemas.SimulationParameters attribute) select_drop_candidates() (in module pyfracval.cca.rescue) set_coefficients() (in module pyfracval.feasibility) set_context() (pyfracval.event_log.EventLog method) shuffle_array() (in module pyfracval.utils) simulation_parameters (pyfracval.schemas.Metadata attribute) SimulationParameters (class in pyfracval.schemas)

soft_relaxation() (in module pyfracval.experimental.soft_relaxation) soft_sticking() (in module pyfracval.experimental.soft_relaxation) sort_clusters() (in module pyfracval.utils) sphere_intersection_volume() (in module pyfracval.correlation) spherical_cap_angle() (in module pyfracval.geometry) (in module pyfracval.utils) Subclusterer (class in pyfracval.pca_subclusters) sum_rmax (pyfracval.event_log.MergeEvent attribute) surface_accessible_mask() (in module pyfracval.experimental.pair_prefilters)

T

to_dict() (pyfracval.schemas.Metadata method) to_yaml_header() (pyfracval.schemas.Metadata method)

tol_ov (pyfracval.schemas.SimulationParameters attribute) two_sphere_intersection() (in module pyfracval.geometry) (in module pyfracval.utils)

V

validate_fractal_structure() (in module pyfracval.fractal) (in module pyfracval.utils) validate_placement() (in module pyfracval.experimental.fft_docking)

voronoi_local_density() (in module pyfracval.densify) voronoi_migrate_step() (in module pyfracval.densify) voxelize_cluster() (in module pyfracval.experimental.fft_docking)

W

warn_if_difficult() (in module pyfracval.feasibility)