Index A | B | C | D | E | F | G | H | L | M | N | O | P | R | S | T | U | V | W A A3D_loader (class in mlcg_tk.input_generator.raw_data_loader) accumulate_statistics() (mlcg_tk.input_generator.prior_fit.histogram.HistogramsNL method) (mlcg_tk.input_generator.prior_gen.PriorBuilder method) add_decoy() (in module mlcg_tk.scripts.add_decoys) add_noise_decoy_molecule() (in module mlcg_tk.scripts.add_decoys) add_terminal_embeddings() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) Angles (class in mlcg_tk.input_generator.prior_gen) apply_cg_mapping() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) B batch_matmul() (in module mlcg_tk.input_generator.utils) batch_size (mlcg_tk.input_generator.raw_dataset.CGDataBatch attribute) BBA_loader (class in mlcg_tk.input_generator.raw_data_loader) bmax (mlcg_tk.input_generator.prior_fit.histogram.HistogramsNL attribute) (mlcg_tk.input_generator.prior_gen.Angles attribute) (mlcg_tk.input_generator.prior_gen.Bonds attribute) (mlcg_tk.input_generator.prior_gen.Dihedrals attribute) (mlcg_tk.input_generator.prior_gen.NonBonded attribute) bmin (mlcg_tk.input_generator.prior_fit.histogram.HistogramsNL attribute) (mlcg_tk.input_generator.prior_gen.Angles attribute) (mlcg_tk.input_generator.prior_gen.Bonds attribute) (mlcg_tk.input_generator.prior_gen.Dihedrals attribute) (mlcg_tk.input_generator.prior_gen.NonBonded attribute) Bonds (class in mlcg_tk.input_generator.prior_gen) build_neighborlists() (in module mlcg_tk.scripts.gen_input_data) build_nl() (mlcg_tk.input_generator.prior_gen.Angles method) (mlcg_tk.input_generator.prior_gen.Bonds method) (mlcg_tk.input_generator.prior_gen.NonBonded method) (mlcg_tk.input_generator.prior_gen.PriorBuilder method) C CA_pseudo_dihedral (class in mlcg_tk.input_generator.prior_nls) CATH_ext_loader (class in mlcg_tk.input_generator.raw_data_loader) CATH_loader (class in mlcg_tk.input_generator.raw_data_loader) cg_coords (mlcg_tk.input_generator.raw_dataset.CGDataBatch attribute) cg_embeds (mlcg_tk.input_generator.raw_dataset.CGDataBatch attribute) cg_forces (mlcg_tk.input_generator.raw_dataset.CGDataBatch attribute) cg_matmul() (in module mlcg_tk.input_generator.utils) cg_prior_nls (mlcg_tk.input_generator.raw_dataset.CGDataBatch attribute) CGDataBatch (class in mlcg_tk.input_generator.raw_dataset) CGEmbeddingMap (class in mlcg_tk.input_generator.embedding_maps) CGEmbeddingMapCA (class in mlcg_tk.input_generator.embedding_maps) CGEmbeddingMapFiveBead (class in mlcg_tk.input_generator.embedding_maps) check_graph_distance() (in module mlcg_tk.input_generator.prior_nls) chunker() (in module mlcg_tk.input_generator.utils) Cln_loader (class in mlcg_tk.input_generator.raw_data_loader) combine_datasets() (in module mlcg_tk.scripts.package_training_data) compute_aic() (in module mlcg_tk.input_generator.prior_fit.utils) compute_hist() (in module mlcg_tk.input_generator.prior_fit.histogram) compute_hist_old() (in module mlcg_tk.input_generator.prior_fit.histogram) compute_hist_with_keys() (in module mlcg_tk.input_generator.prior_fit.histogram) compute_hist_with_rep() (in module mlcg_tk.input_generator.prior_fit.histogram) compute_nl_unique_keys() (in module mlcg_tk.input_generator.prior_fit.utils) compute_statistics() (in module mlcg_tk.scripts.fit_priors) concat_forces (mlcg_tk.input_generator.raw_dataset.CGDataBatch attribute) cutoff (mlcg_tk.input_generator.prior_gen.NonBonded attribute) D dataset (mlcg_tk.input_generator.raw_dataset.RawDataset attribute) (mlcg_tk.input_generator.raw_dataset.SimInput attribute) dataset_name (mlcg_tk.input_generator.raw_dataset.RawDataset attribute) (mlcg_tk.input_generator.raw_dataset.SimInput attribute) DatasetLoader (class in mlcg_tk.input_generator.raw_data_loader) ddx2_restricted_quartic_angle_numpy() (in module mlcg_tk.input_generator.prior_fit.restricted_bending) dihedral() (in module mlcg_tk.input_generator.prior_fit.dihedral) dihedral_wrapper_fit_func() (in module mlcg_tk.input_generator.prior_fit.dihedral) Dihedrals (class in mlcg_tk.input_generator.prior_gen) DIMER_ext_loader (class in mlcg_tk.input_generator.raw_data_loader) DIMER_loader (class in mlcg_tk.input_generator.raw_data_loader) dx_restricted_quartic_angle_numpy() (in module mlcg_tk.input_generator.prior_fit.restricted_bending) E embedding_ca() (in module mlcg_tk.input_generator.embedding_maps) embedding_fivebead() (in module mlcg_tk.input_generator.embedding_maps) F filter_cis_frames() (in module mlcg_tk.input_generator.utils) find_extrema_in_range() (in module mlcg_tk.input_generator.prior_fit.restricted_bending) find_minmax() (in module mlcg_tk.input_generator.prior_fit.restricted_bending) fit_dihedral_from_potential_estimates() (in module mlcg_tk.input_generator.prior_fit.dihedral) fit_harmonic_from_potential_estimates() (in module mlcg_tk.input_generator.prior_fit.harmonic) fit_polynomial_from_potential_estimates() (in module mlcg_tk.input_generator.prior_fit.polynomial) fit_potentials() (in module mlcg_tk.input_generator.prior_fit.fit_potentials) fit_priors() (in module mlcg_tk.scripts.fit_priors) fit_rb_from_potential_estimates() (in module mlcg_tk.input_generator.prior_fit.restricted_bending) fit_repulsion_from_potential_estimates() (in module mlcg_tk.input_generator.prior_fit.repulsion) fit_repulsion_from_values() (in module mlcg_tk.input_generator.prior_fit.repulsion) G Gamma1 (class in mlcg_tk.input_generator.prior_nls) Gamma2 (class in mlcg_tk.input_generator.prior_nls) get_dihedral_groups() (in module mlcg_tk.input_generator.utils) get_edges_and_orders() (in module mlcg_tk.input_generator.utils) get_fit_kwargs() (mlcg_tk.input_generator.prior_nls.CA_pseudo_dihedral method) (mlcg_tk.input_generator.prior_nls.Gamma1 method) (mlcg_tk.input_generator.prior_nls.Gamma2 method) (mlcg_tk.input_generator.prior_nls.Non_Bonded method) (mlcg_tk.input_generator.prior_nls.Omega method) (mlcg_tk.input_generator.prior_nls.Phi method) (mlcg_tk.input_generator.prior_nls.Psi method) (mlcg_tk.input_generator.prior_nls.StandardAngles method) (mlcg_tk.input_generator.prior_nls.StandardBonds method) get_nonzero_keys() (in module mlcg_tk.prior_tools.utils) get_output_tag() (in module mlcg_tk.input_generator.utils) get_prior_domain() (in module mlcg_tk.prior_tools.utils) get_prior_model() (mlcg_tk.input_generator.prior_gen.Angles method) (mlcg_tk.input_generator.prior_gen.Bonds method) (mlcg_tk.input_generator.prior_gen.Dihedrals method) (mlcg_tk.input_generator.prior_gen.NonBonded method) get_prior_nls() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) get_strides() (in module mlcg_tk.input_generator.raw_dataset) get_terminal_atoms() (in module mlcg_tk.input_generator.utils) get_traj_groups() (mlcg_tk.input_generator.raw_data_loader.HDF5_loader static method) get_traj_top() (mlcg_tk.input_generator.raw_data_loader.A3D_loader method) (mlcg_tk.input_generator.raw_data_loader.BBA_loader method) (mlcg_tk.input_generator.raw_data_loader.CATH_ext_loader method) (mlcg_tk.input_generator.raw_data_loader.CATH_loader method) (mlcg_tk.input_generator.raw_data_loader.Cln_loader method) (mlcg_tk.input_generator.raw_data_loader.DatasetLoader method) (mlcg_tk.input_generator.raw_data_loader.DIMER_ext_loader method) (mlcg_tk.input_generator.raw_data_loader.DIMER_loader method) (mlcg_tk.input_generator.raw_data_loader.HDF5_loader method) (mlcg_tk.input_generator.raw_data_loader.MHC_loader method) (mlcg_tk.input_generator.raw_data_loader.NTL9_loader method) (mlcg_tk.input_generator.raw_data_loader.OPEP_loader method) (mlcg_tk.input_generator.raw_data_loader.ProteinG_loader method) (mlcg_tk.input_generator.raw_data_loader.SimInput_loader method) (mlcg_tk.input_generator.raw_data_loader.Trpcage_loader method) (mlcg_tk.input_generator.raw_data_loader.Villin_loader method) (mlcg_tk.input_generator.raw_data_loader.WWdomain_loader method) H harmonic() (in module mlcg_tk.input_generator.prior_fit.harmonic) has_delta_forces_output() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) has_saved_cg_output() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) HDF5_loader (class in mlcg_tk.input_generator.raw_data_loader) histograms (mlcg_tk.input_generator.prior_gen.PriorBuilder attribute) HistogramsNL (class in mlcg_tk.input_generator.prior_fit.histogram) L load_all_batches_training_inputs() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) load_cg_force_map() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) load_cg_output() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) load_cg_output_into_batches() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) load_coords_forces() (mlcg_tk.input_generator.raw_data_loader.A3D_loader method) (mlcg_tk.input_generator.raw_data_loader.BBA_loader method) (mlcg_tk.input_generator.raw_data_loader.CATH_ext_loader method) (mlcg_tk.input_generator.raw_data_loader.CATH_loader method) (mlcg_tk.input_generator.raw_data_loader.Cln_loader method) (mlcg_tk.input_generator.raw_data_loader.DatasetLoader method) (mlcg_tk.input_generator.raw_data_loader.DIMER_ext_loader method) (mlcg_tk.input_generator.raw_data_loader.DIMER_loader method) (mlcg_tk.input_generator.raw_data_loader.HDF5_loader method) (mlcg_tk.input_generator.raw_data_loader.MHC_loader method) (mlcg_tk.input_generator.raw_data_loader.NTL9_loader method) (mlcg_tk.input_generator.raw_data_loader.OPEP_loader method) (mlcg_tk.input_generator.raw_data_loader.ProteinG_loader method) (mlcg_tk.input_generator.raw_data_loader.Trpcage_loader method) (mlcg_tk.input_generator.raw_data_loader.Villin_loader method) (mlcg_tk.input_generator.raw_data_loader.WWdomain_loader method) load_training_inputs() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) M map_cg_topology() (in module mlcg_tk.input_generator.utils) merge_statistics() (in module mlcg_tk.scripts.merge_statistics) MHC_loader (class in mlcg_tk.input_generator.raw_data_loader) min_pair (mlcg_tk.input_generator.prior_gen.NonBonded attribute) mlcg_tk.input_generator module mlcg_tk.input_generator.embedding_maps module mlcg_tk.input_generator.prior_fit module mlcg_tk.input_generator.prior_fit.dihedral module mlcg_tk.input_generator.prior_fit.fit_potentials module mlcg_tk.input_generator.prior_fit.harmonic module mlcg_tk.input_generator.prior_fit.histogram module mlcg_tk.input_generator.prior_fit.polynomial module mlcg_tk.input_generator.prior_fit.repulsion module mlcg_tk.input_generator.prior_fit.restricted_bending module mlcg_tk.input_generator.prior_fit.utils module mlcg_tk.input_generator.prior_gen module mlcg_tk.input_generator.prior_nls module mlcg_tk.input_generator.raw_data_loader module mlcg_tk.input_generator.raw_dataset module mlcg_tk.input_generator.utils module mlcg_tk.prior_tools module mlcg_tk.prior_tools.utils module mlcg_tk.scripts.add_decoys module mlcg_tk.scripts.fit_priors module mlcg_tk.scripts.gen_input_data module mlcg_tk.scripts.gen_sim_input module mlcg_tk.scripts.merge_statistics module mlcg_tk.scripts.package_training_data module mlcg_tk.scripts.produce_delta_forces module module mlcg_tk.input_generator mlcg_tk.input_generator.embedding_maps mlcg_tk.input_generator.prior_fit mlcg_tk.input_generator.prior_fit.dihedral mlcg_tk.input_generator.prior_fit.fit_potentials mlcg_tk.input_generator.prior_fit.harmonic mlcg_tk.input_generator.prior_fit.histogram mlcg_tk.input_generator.prior_fit.polynomial mlcg_tk.input_generator.prior_fit.repulsion mlcg_tk.input_generator.prior_fit.restricted_bending mlcg_tk.input_generator.prior_fit.utils mlcg_tk.input_generator.prior_gen mlcg_tk.input_generator.prior_nls mlcg_tk.input_generator.raw_data_loader mlcg_tk.input_generator.raw_dataset mlcg_tk.input_generator.utils mlcg_tk.prior_tools mlcg_tk.prior_tools.utils mlcg_tk.scripts.add_decoys mlcg_tk.scripts.fit_priors mlcg_tk.scripts.gen_input_data mlcg_tk.scripts.gen_sim_input mlcg_tk.scripts.merge_statistics mlcg_tk.scripts.package_training_data mlcg_tk.scripts.produce_delta_forces N name (mlcg_tk.input_generator.prior_gen.Angles attribute) (mlcg_tk.input_generator.prior_gen.Bonds attribute) (mlcg_tk.input_generator.prior_gen.Dihedrals attribute) (mlcg_tk.input_generator.prior_gen.NonBonded attribute) (mlcg_tk.input_generator.raw_dataset.SampleCollection attribute) names (mlcg_tk.input_generator.raw_dataset.RawDataset attribute) nbins (mlcg_tk.input_generator.prior_fit.histogram.HistogramsNL attribute) (mlcg_tk.input_generator.prior_gen.Angles attribute) (mlcg_tk.input_generator.prior_gen.Bonds attribute) (mlcg_tk.input_generator.prior_gen.Dihedrals attribute) (mlcg_tk.input_generator.prior_gen.NonBonded attribute) neg_log_likelihood() (in module mlcg_tk.input_generator.prior_fit.utils) nl_builder (mlcg_tk.input_generator.prior_gen.Angles attribute) (mlcg_tk.input_generator.prior_gen.Bonds attribute) (mlcg_tk.input_generator.prior_gen.Dihedrals attribute) (mlcg_tk.input_generator.prior_gen.NonBonded attribute) (mlcg_tk.input_generator.prior_gen.PriorBuilder attribute) nl_names (mlcg_tk.input_generator.prior_nls.CA_pseudo_dihedral attribute), [1] (mlcg_tk.input_generator.prior_nls.Gamma1 attribute), [1] (mlcg_tk.input_generator.prior_nls.Gamma2 attribute), [1] (mlcg_tk.input_generator.prior_nls.Non_Bonded attribute), [1] (mlcg_tk.input_generator.prior_nls.Omega attribute), [1] (mlcg_tk.input_generator.prior_nls.Phi attribute), [1] (mlcg_tk.input_generator.prior_nls.Psi attribute), [1] (mlcg_tk.input_generator.prior_nls.StandardAngles attribute), [1] (mlcg_tk.input_generator.prior_nls.StandardBonds attribute), [1] Non_Bonded (class in mlcg_tk.input_generator.prior_nls) NonBonded (class in mlcg_tk.input_generator.prior_gen) NTL9_loader (class in mlcg_tk.input_generator.raw_data_loader) O Omega (class in mlcg_tk.input_generator.prior_nls) OPEP_loader (class in mlcg_tk.input_generator.raw_data_loader) optimal_offset() (in module mlcg_tk.prior_tools.utils) P package_training_data() (in module mlcg_tk.scripts.package_training_data) pdb_fn (mlcg_tk.input_generator.raw_dataset.SampleCollection attribute) pdb_fns (mlcg_tk.input_generator.raw_dataset.SimInput attribute) percentile (mlcg_tk.input_generator.prior_gen.NonBonded attribute) Phi (class in mlcg_tk.input_generator.prior_nls) plot_histograms() (mlcg_tk.input_generator.prior_fit.histogram.HistogramsNL method) polynomial() (in module mlcg_tk.input_generator.prior_fit.polynomial) polynomial_wrapper_fit_func() (in module mlcg_tk.input_generator.prior_fit.polynomial) prior_cls (mlcg_tk.input_generator.prior_gen.Angles attribute) (mlcg_tk.input_generator.prior_gen.PriorBuilder attribute) prior_evaluator() (in module mlcg_tk.prior_tools.utils) prior_fit_fn (mlcg_tk.input_generator.prior_gen.Angles attribute) (mlcg_tk.input_generator.prior_gen.Bonds attribute) (mlcg_tk.input_generator.prior_gen.Dihedrals attribute) (mlcg_tk.input_generator.prior_gen.NonBonded attribute) (mlcg_tk.input_generator.prior_gen.PriorBuilder attribute) PriorBuilder (class in mlcg_tk.input_generator.prior_gen) process_coords_forces() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) process_raw_dataset() (in module mlcg_tk.scripts.gen_input_data) process_sim_input() (in module mlcg_tk.scripts.gen_sim_input) produce_delta_forces() (in module mlcg_tk.scripts.produce_delta_forces) ProteinG_loader (class in mlcg_tk.input_generator.raw_data_loader) Psi (class in mlcg_tk.input_generator.prior_nls) R RawDataset (class in mlcg_tk.input_generator.raw_dataset) remove_baseline_forces_collated() (in module mlcg_tk.scripts.produce_delta_forces) replace_gly_ca_stats (mlcg_tk.input_generator.prior_nls.Omega attribute) replace_gly_stats() (in module mlcg_tk.input_generator.prior_fit.fit_potentials) repulsion() (in module mlcg_tk.input_generator.prior_fit.repulsion) res_exclusion (mlcg_tk.input_generator.prior_gen.NonBonded attribute) restricted_quartic_angle() (in module mlcg_tk.input_generator.prior_fit.restricted_bending) S SampleCollection (class in mlcg_tk.input_generator.raw_dataset) save_cg_output() (mlcg_tk.input_generator.raw_dataset.SampleCollection method) separate_termini (mlcg_tk.input_generator.prior_gen.Angles attribute) (mlcg_tk.input_generator.prior_gen.Bonds attribute) (mlcg_tk.input_generator.prior_gen.NonBonded attribute) SimInput (class in mlcg_tk.input_generator.raw_dataset) SimInput_loader (class in mlcg_tk.input_generator.raw_data_loader) slice_coord_forces() (in module mlcg_tk.input_generator.utils) split_bulk_termini() (in module mlcg_tk.input_generator.utils) StandardAngles (class in mlcg_tk.input_generator.prior_nls) StandardBonds (class in mlcg_tk.input_generator.prior_nls) stride (mlcg_tk.input_generator.raw_dataset.CGDataBatch attribute) symmetrized_keys_generator() (in module mlcg_tk.prior_tools.utils) T tag (mlcg_tk.input_generator.raw_dataset.RawDataset attribute) (mlcg_tk.input_generator.raw_dataset.SampleCollection attribute) (mlcg_tk.input_generator.raw_dataset.SimInput attribute) Trpcage_loader (class in mlcg_tk.input_generator.raw_data_loader) U update_partition_file() (in module mlcg_tk.scripts.add_decoys) V Villin_loader (class in mlcg_tk.input_generator.raw_data_loader) W with_attrs() (in module mlcg_tk.input_generator.utils) WWdomain_loader (class in mlcg_tk.input_generator.raw_data_loader)