Index

A

add_phenotypes_to_df() (multidms.Model method) (multidms.model.Model method) add_validation_loss() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method)

additive_model() (in module multidms.biophysical) all_mutations (multidms.model_collection.ModelCollection property) (multidms.ModelCollection property)

B

binarymaps (multidms.Data property) (multidms.data.Data property)

bundle_idxs (multidms.Data property) (multidms.data.Data property)

C

color_gradient_hex() (in module multidms.plot) conditional_loss (multidms.Model property) (multidms.model.Model property) conditions (multidms.Data property) (multidms.data.Data property) (multidms.model_collection.ModelCollection property) (multidms.ModelCollection property)

converged (multidms.Model property) (multidms.model.Model property) convergence_trajectory_df (multidms.Model property) (multidms.model.Model property) convergence_trajectory_df() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) convert_subs_wrt_ref_seq() (multidms.Data method) (multidms.data.Data method)

D

Data (class in multidms) (class in multidms.data)

data (multidms.Model property) (multidms.model.Model property) difference_matrix() (in module multidms.utils)

E

explode_params_dict() (in module multidms.utils)

F

fit() (multidms.Model method) (multidms.model.Model method)

fit_models() (in module multidms) (in module multidms.model_collection) fit_one_model() (in module multidms.model_collection)

G

get_condition_params() (multidms.Model method) (multidms.model.Model method) get_conditional_loss_df() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) get_df_loss() (multidms.Model method) (multidms.model.Model method)

get_mutations_df() (multidms.Model method) (multidms.model.Model method) get_variants_df() (multidms.Model method) (multidms.model.Model method)

I

identity_activation() (in module multidms.biophysical)

L

latent_frombinary() (multidms.Model method) (multidms.model.Model method) latent_fromsubs() (multidms.Model method) (multidms.model.Model method)

loss (multidms.Model property) (multidms.model.Model property)

M

Model (class in multidms) (class in multidms.model) model_components (multidms.Model property) (multidms.model.Model property) ModelCollection (class in multidms) (class in multidms.model_collection) ModelCollectionFitError module multidms multidms.biophysical multidms.data multidms.model multidms.model_collection multidms.plot multidms.utils multidms module multidms.biophysical module multidms.data module multidms.model module

multidms.model_collection module multidms.plot module multidms.utils module mut_param_dataset_correlation() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) mut_param_heatmap() (multidms.Model method) (multidms.model.Model method) (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) mut_param_traceplot() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) mutation_site_summary_df() (multidms.Model method) (multidms.model.Model method) mutations (multidms.Data property) (multidms.data.Data property) mutations_df (multidms.Data property) (multidms.data.Data property) mutparser (multidms.Data property) (multidms.data.Data property) my_concat() (in module multidms.utils)

N

name (multidms.Data property) (multidms.data.Data property) (multidms.Model property) (multidms.model.Model property)

nn_global_epistasis() (in module multidms.biophysical) non_identical_mutations (multidms.Data property) (multidms.data.Data property) non_identical_sites (multidms.Data property) (multidms.data.Data property)

P

params (multidms.Model property) (multidms.model.Model property) parse_mut (multidms.Data property) (multidms.data.Data property) parse_muts (multidms.Data property) (multidms.data.Data property) phenotype_frombinary() (multidms.Model method) (multidms.model.Model method) phenotype_fromsubs() (multidms.Model method) (multidms.model.Model method) plot_epistasis() (multidms.Model method) (multidms.model.Model method) plot_func_score_boxplot() (multidms.Data method) (multidms.data.Data method)

plot_param_heatmap() (multidms.Model method) (multidms.model.Model method) plot_param_hist() (multidms.Model method) (multidms.model.Model method) plot_pred_accuracy() (multidms.Model method) (multidms.model.Model method) plot_shifts_by_site() (multidms.Model method) (multidms.model.Model method) plot_times_seen_hist() (multidms.Data method) (multidms.data.Data method) proximal_box_constraints() (in module multidms.biophysical) proximal_objective() (in module multidms.biophysical)

R

reference (multidms.Data property) (multidms.data.Data property) (multidms.model_collection.ModelCollection property) (multidms.ModelCollection property)

reference_index (multidms.Data property) (multidms.data.Data property) reference_sequence_conditions (multidms.Data property) (multidms.data.Data property) rereference() (in module multidms.utils)

S

scaled_training_data (multidms.Data property) (multidms.data.Data property) shared_mutations (multidms.model_collection.ModelCollection property) (multidms.ModelCollection property) shift_sparsity() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) sigmoidal_global_epistasis() (in module multidms.biophysical) single_mut_encodings (multidms.Data property) (multidms.data.Data property) site_map (multidms.Data property) (multidms.data.Data property)

site_map_union (multidms.model_collection.ModelCollection property) (multidms.ModelCollection property) smooth_objective() (in module multidms.biophysical) softplus_activation() (in module multidms.biophysical) softplus_global_epistasis() (in module multidms.biophysical) split_apply_combine_muts() (multidms.model_collection.ModelCollection method) (multidms.ModelCollection method) split_sub() (in module multidms.utils) split_subs() (in module multidms.utils) stack_fit_models() (in module multidms.model_collection) state (multidms.Model property) (multidms.model.Model property)

T

targets (multidms.Data property) (multidms.data.Data property)

training_data (multidms.Data property) (multidms.data.Data property) transform() (in module multidms.utils)

V

variants_df (multidms.Data property) (multidms.data.Data property)

W

wildtype_df (multidms.Model property) (multidms.model.Model property)