Index

A

add_contacts_constraints() (in module ensemblify.modelling.constraints) add_intrachain_constraints() (in module ensemblify.modelling.constraints) analyze_trajectory() (in module ensemblify.analysis.trajectory) apply() (ensemblify.generation.ensemble_utils.movers.SetRandomDihedralsMover method) (ensemblify.generation.ensemble_utils.samplers.MonteCarloSampler method) apply_basic_idealize() (in module ensemblify.modelling.fusion) apply_constraints() (in module ensemblify.modelling.constraints)

apply_faspr_single() (in module ensemblify.modelling.pdb_processing) apply_pae_constraints() (in module ensemblify.modelling.constraints) apply_pulchra_single() (in module ensemblify.modelling.pdb_processing) apply_restore_single() (in module ensemblify.modelling.pdb_processing) apply_rewrite_single() (in module ensemblify.modelling.pdb_processing) attempt_read_calculated_data() (in module ensemblify.reweighting.data) attempt_read_reweighting_data() (in module ensemblify.reweighting.data) average_saxs_profiles() (in module ensemblify.reweighting.data)

B

bme() (in module ensemblify.reweighting.data)

bme_ensemble_reweighting() (in module ensemblify.reweighting.data)

C

calc_chi2_fit() (in module ensemblify.conversion.conversion_utils) calc_cm_dist() (in module ensemblify.analysis.data) calc_dmax() (in module ensemblify.analysis.data) calc_eed() (in module ensemblify.analysis.data) calc_rg() (in module ensemblify.analysis.data) calc_saxs_data() (in module ensemblify.conversion.conversion_utils) calculate_analysis_data() (in module ensemblify.analysis.data) calculate_contact_matrix() (in module ensemblify.analysis.data) calculate_contact_matrix_frame() (in module ensemblify.analysis.data) calculate_distance_matrix() (in module ensemblify.analysis.data) calculate_distance_matrix_frame() (in module ensemblify.analysis.data) calculate_metrics_data() (in module ensemblify.analysis.data) calculate_ramachandran_data() (in module ensemblify.analysis.data) calculate_ss_assignment() (in module ensemblify.analysis.data) calculate_ss_frequency() (in module ensemblify.analysis.data) check_clashes() (in module ensemblify.generation.ensemble_utils.processing_outputs) check_is_pdb() (in module ensemblify.modelling.fusion)

check_report_pdb_clashes() (in module ensemblify.clash_checking) check_steric_clashes() (in module ensemblify.clash_checking) cif_to_pdb() (in module ensemblify.utils.pdb_manipulation) cleanup_pdbs() (in module ensemblify.utils.pdb_manipulation) correct_exp_saxs_error() (in module ensemblify.reweighting.data) create_analysis_figures() (in module ensemblify.analysis.figures) create_contact_map_fig() (in module ensemblify.analysis.figures) create_distance_matrix_fig() (in module ensemblify.analysis.figures) create_effective_frames_fit_fig() (in module ensemblify.reweighting.figures) create_fusion_pose() (in module ensemblify.modelling.fusion) create_metrics_fig() (in module ensemblify.analysis.figures) create_metrics_traces() (in module ensemblify.analysis.figures) create_ramachandran_figure() (in module ensemblify.analysis.figures) create_reweighting_metrics_fig() (in module ensemblify.reweighting.figures) create_rw_saxs_fits_fig() (in module ensemblify.reweighting.figures) create_single_metrics_fig_directly() (in module ensemblify.analysis.figures) create_ss_frequency_figure() (in module ensemblify.analysis.figures)

D

databases (ensemblify.generation.ensemble_utils.movers.SetRandomDihedralsMover attribute) (ensemblify.generation.ensemble_utils.samplers.MonteCarloSampler attribute) DEFAULT_TRACE_COLOR_PALETTE (in module ensemblify.analysis.colors)

derive_constraint_targets() (in module ensemblify.generation.ensemble_utils.functions) df_from_pdb() (in module ensemblify.utils.pdb_manipulation) df_to_pdb() (in module ensemblify.utils.pdb_manipulation)

E

ensemble2traj() (in module ensemblify.conversion.ensemble2trajectory) ensemblify module ensemblify.analysis module ensemblify.analysis.colors module ensemblify.analysis.data module ensemblify.analysis.figures module ensemblify.analysis.trajectory module ensemblify.clash_checking module ensemblify.config module ensemblify.conversion module ensemblify.conversion.conversion_utils module ensemblify.conversion.ensemble2trajectory module ensemblify.conversion.trajectory2saxs module ensemblify.generation module ensemblify.generation.ensemble module ensemblify.generation.ensemble_utils module ensemblify.generation.ensemble_utils.functions module ensemblify.generation.ensemble_utils.movers module ensemblify.generation.ensemble_utils.movers_utils module

ensemblify.generation.ensemble_utils.processing_inputs module ensemblify.generation.ensemble_utils.processing_outputs module ensemblify.generation.ensemble_utils.samplers module ensemblify.generation.ensemble_utils.sampling module ensemblify.generation.ensemble_utils.sampling_utils module ensemblify.modelling module ensemblify.modelling.constraints module ensemblify.modelling.fusion module ensemblify.modelling.objects module ensemblify.modelling.pdb_processing module ensemblify.reweighting module ensemblify.reweighting.data module ensemblify.reweighting.ensemble module ensemblify.reweighting.figures module ensemblify.utils module ensemblify.utils.misc module ensemblify.utils.pdb_manipulation module extract_pdb_info() (in module ensemblify.utils.pdb_manipulation) extract_plddt_regions() (in module ensemblify.generation.ensemble_utils.processing_inputs)

F

format_alphafold_report() (in module ensemblify.generation.ensemble_utils.processing_inputs) format_mobidb_report() (in module ensemblify.generation.ensemble_utils.processing_inputs)

format_ted_report() (in module ensemblify.generation.ensemble_utils.processing_inputs) fuse_structures() (in module ensemblify.modelling.fusion)

G

generate_ensemble() (in module ensemblify.generation.ensemble) get_alphafold_data() (in module ensemblify.generation.ensemble_utils.processing_inputs) get_alphafold_plddt() (in module ensemblify.generation.ensemble_utils.processing_inputs) get_array_extremum() (in module ensemblify.utils.misc) get_mobidb_data() (in module ensemblify.generation.ensemble_utils.processing_inputs)

get_name() (ensemblify.generation.ensemble_utils.movers.SetRandomDihedralsMover method) get_protein_info() (in module ensemblify.generation.ensemble_utils.processing_inputs) get_ss_bounds() (in module ensemblify.generation.ensemble_utils.movers_utils) get_targets_from_plddt() (in module ensemblify.generation.ensemble_utils.functions) get_ted_data() (in module ensemblify.generation.ensemble_utils.processing_inputs) GLOBAL_CONFIG (in module ensemblify.config)

J

join_pdbs() (in module ensemblify.conversion.conversion_utils)

K

kde() (in module ensemblify.utils.misc)

L

log_file (ensemblify.generation.ensemble_utils.movers.SetRandomDihedralsMover attribute) (ensemblify.generation.ensemble_utils.samplers.MonteCarloSampler attribute)

M

make_atom_pair_constraint() (in module ensemblify.modelling.constraints) module ensemblify ensemblify.analysis ensemblify.analysis.colors ensemblify.analysis.data ensemblify.analysis.figures ensemblify.analysis.trajectory ensemblify.clash_checking ensemblify.config ensemblify.conversion ensemblify.conversion.conversion_utils ensemblify.conversion.ensemble2trajectory ensemblify.conversion.trajectory2saxs ensemblify.generation ensemblify.generation.ensemble ensemblify.generation.ensemble_utils ensemblify.generation.ensemble_utils.functions ensemblify.generation.ensemble_utils.movers ensemblify.generation.ensemble_utils.movers_utils ensemblify.generation.ensemble_utils.processing_inputs ensemblify.generation.ensemble_utils.processing_outputs ensemblify.generation.ensemble_utils.samplers ensemblify.generation.ensemble_utils.sampling ensemblify.generation.ensemble_utils.sampling_utils ensemblify.modelling ensemblify.modelling.constraints ensemblify.modelling.fusion ensemblify.modelling.objects ensemblify.modelling.pdb_processing ensemblify.reweighting ensemblify.reweighting.data ensemblify.reweighting.ensemble ensemblify.reweighting.figures ensemblify.utils ensemblify.utils.misc ensemblify.utils.pdb_manipulation

MonteCarloSampler (class in ensemblify.generation.ensemble_utils.samplers) move_topology_pdb() (in module ensemblify.conversion.conversion_utils) mover (ensemblify.generation.ensemble_utils.samplers.MonteCarloSampler attribute)

O

optimize_database() (in module ensemblify.generation.ensemble_utils.movers_utils)

P

pack_sidechains() (in module ensemblify.modelling.fusion) params (ensemblify.generation.ensemble_utils.samplers.MonteCarloSampler attribute) PARULA_COLORSCALE (in module ensemblify.analysis.colors) process_exp_saxs_data() (in module ensemblify.reweighting.data)

process_input_pdb() (in module ensemblify.generation.ensemble_utils.processing_inputs) process_pdb() (in module ensemblify.generation.ensemble_utils.processing_outputs) process_pdb_structure() (in module ensemblify.modelling.pdb_processing) process_pulchra_output() (in module ensemblify.clash_checking)

R

read_database() (in module ensemblify.generation.ensemble_utils.movers_utils) read_input_parameters() (in module ensemblify.generation.ensemble_utils.processing_inputs) register_input_clashes() (in module ensemblify.generation.ensemble_utils.processing_inputs)

reweight_ensemble() (in module ensemblify.reweighting.ensemble) round_to_nearest_multiple() (in module ensemblify.utils.misc) run_sampling() (in module ensemblify.generation.ensemble_utils.sampling)

S

sample_pdb() (in module ensemblify.generation.ensemble_utils.sampling_utils) scorefxn (ensemblify.generation.ensemble_utils.samplers.MonteCarloSampler attribute) SetRandomDihedralsMover (class in ensemblify.generation.ensemble_utils.movers) setup_databases() (in module ensemblify.generation.ensemble_utils.movers_utils) setup_ensemble_gen_params() (in module ensemblify.generation.ensemble_utils.processing_inputs) setup_fold_tree() (in module ensemblify.generation.ensemble_utils.functions) setup_minmover() (in module ensemblify.modelling.objects)

setup_mover() (in module ensemblify.generation.ensemble_utils.movers) setup_pose() (in module ensemblify.modelling.objects) setup_samplers() (in module ensemblify.generation.ensemble_utils.samplers) setup_sampling_initial_pose() (in module ensemblify.generation.ensemble_utils.sampling_utils) setup_sampling_logging() (in module ensemblify.generation.ensemble_utils.sampling_utils) setup_sampling_parameters() (in module ensemblify.generation.ensemble_utils.sampling_utils) show_config() (in module ensemblify.config) suggest_targets() (in module ensemblify.generation.ensemble_utils.processing_inputs)

T

traj2saxs() (in module ensemblify.conversion.trajectory2saxs)

trim_database() (in module ensemblify.generation.ensemble_utils.movers_utils)

U

update_config() (in module ensemblify.config)

V

variance (ensemblify.generation.ensemble_utils.movers.SetRandomDihedralsMover attribute)