Index

A

AggregatedResidues (class in MDSimsEval.rmsf_baseline_models) agonist_baseline (MDSimsEval.rmsf_baseline_models.AggregatedResidues attribute) agonist_residue_baseline (MDSimsEval.rmsf_baseline_models.KSDistance attribute) (MDSimsEval.rmsf_baseline_models.ResidueMajority attribute)

AnalysisActor (class in MDSimsEval.AnalysisActorClass) antagonist_baseline (MDSimsEval.rmsf_baseline_models.AggregatedResidues attribute) antagonist_residue_baseline (MDSimsEval.rmsf_baseline_models.KSDistance attribute) (MDSimsEval.rmsf_baseline_models.ResidueMajority attribute)

B

BaselineClassifier (class in MDSimsEval.rmsf_baseline_models)

bootstrap_dataset() (in module MDSimsEval.rmsf_baseline_models) bootstrapped_residue_analysis() (in module MDSimsEval.rmsf_bootstrapped_analysis)

C

calculate_average_cols_rg() (in module MDSimsEval.rg_sasa_analysis) calculate_average_cols_sasa() (in module MDSimsEval.rg_sasa_analysis) choose_known_ligands() (MDSimsEval.rmsf_baseline_models.MDStoKNN method)

corr_matrix() (in module MDSimsEval.rmsf_analysis) create_bar_plots_avg_stde() (in module MDSimsEval.rmsf_analysis) create_correlation_df() (in module MDSimsEval.rmsf_bootstrapped_analysis) create_pairwise_distances() (MDSimsEval.rmsf_baseline_models.MDStoKNN method)

D

drug_name (MDSimsEval.AnalysisActorClass.AnalysisActor attribute)

F

find_high_k() (in module MDSimsEval.rmsf_analysis) find_rmsf_of_residues() (in module MDSimsEval.rmsf_bootstrapped_analysis) find_top_k() (in module MDSimsEval.rmsf_analysis)

fit() (MDSimsEval.rmsf_baseline_models.AggregatedResidues method) (MDSimsEval.rmsf_baseline_models.KSDistance method) (MDSimsEval.rmsf_baseline_models.MDStoKNN method) (MDSimsEval.rmsf_baseline_models.ResidueMajority method)

G

get_avg_rmsf_per_residue() (in module MDSimsEval.rmsf_analysis)

get_frames_number() (MDSimsEval.AnalysisActorClass.AnalysisActor method)

H

hbonds (MDSimsEval.AnalysisActorClass.AnalysisActor attribute)

I

info() (MDSimsEval.AnalysisActorClass.AnalysisActor method)

initialize_pools() (in module MDSimsEval.rmsf_bootstrapped_analysis)

K

KSDistance (class in MDSimsEval.rmsf_baseline_models)

L

loadings_heatmap() (in module MDSimsEval.pca_analysis)

M

MDSimsEval.AnalysisActorClass module MDSimsEval.pca_analysis module MDSimsEval.rg_sasa_analysis module MDSimsEval.rmsf_analysis module MDSimsEval.rmsf_baseline_models module MDSimsEval.rmsf_bootstrapped_analysis module MDSimsEval.utils.create_analysis_actor_dict module

MDStoKNN (class in MDSimsEval.rmsf_baseline_models) mdtraj (MDSimsEval.AnalysisActorClass.AnalysisActor attribute) method (MDSimsEval.rmsf_baseline_models.AggregatedResidues attribute) (MDSimsEval.rmsf_baseline_models.KSDistance attribute) (MDSimsEval.rmsf_baseline_models.ResidueMajority attribute) minimal_stat_test() (in module MDSimsEval.rmsf_bootstrapped_analysis) module MDSimsEval.AnalysisActorClass MDSimsEval.pca_analysis MDSimsEval.rg_sasa_analysis MDSimsEval.rmsf_analysis MDSimsEval.rmsf_baseline_models MDSimsEval.rmsf_bootstrapped_analysis MDSimsEval.utils.create_analysis_actor_dict

P

pca_res (MDSimsEval.AnalysisActorClass.AnalysisActor attribute) pca_xyz (MDSimsEval.AnalysisActorClass.AnalysisActor attribute) perform_analysis() (MDSimsEval.AnalysisActorClass.AnalysisActor method) plot_hists_summary() (in module MDSimsEval.rmsf_bootstrapped_analysis) populate_variance_showcase_df() (in module MDSimsEval.pca_analysis)

predict() (MDSimsEval.rmsf_baseline_models.AggregatedResidues method) (MDSimsEval.rmsf_baseline_models.KSDistance method) (MDSimsEval.rmsf_baseline_models.MDStoKNN method) (MDSimsEval.rmsf_baseline_models.ResidueMajority method) project_pca_on_2d() (in module MDSimsEval.pca_analysis)

R

replacement_swap() (in module MDSimsEval.rmsf_bootstrapped_analysis) reset_rmsf_calculations() (in module MDSimsEval.rmsf_analysis) ResidueMajority (class in MDSimsEval.rmsf_baseline_models)

rg_res (MDSimsEval.AnalysisActorClass.AnalysisActor attribute) rg_sasa_mean_mean_plot() (in module MDSimsEval.rg_sasa_analysis) rg_sasa_std_std_plot() (in module MDSimsEval.rg_sasa_analysis) rmsf_res (MDSimsEval.AnalysisActorClass.AnalysisActor attribute)

S

salt_bridges_df (MDSimsEval.AnalysisActorClass.AnalysisActor attribute) salt_bridges_over_time (MDSimsEval.AnalysisActorClass.AnalysisActor attribute) sasa_res (MDSimsEval.AnalysisActorClass.AnalysisActor attribute) scree_plot() (in module MDSimsEval.pca_analysis) selected_residues (MDSimsEval.rmsf_baseline_models.AggregatedResidues attribute) (MDSimsEval.rmsf_baseline_models.KSDistance attribute) (MDSimsEval.rmsf_baseline_models.ResidueMajority attribute) sensitivity_calc() (in module MDSimsEval.rmsf_bootstrapped_analysis) sort_residues_by_loadings() (in module MDSimsEval.pca_analysis)

start (MDSimsEval.rmsf_baseline_models.AggregatedResidues attribute) (MDSimsEval.rmsf_baseline_models.KSDistance attribute) (MDSimsEval.rmsf_baseline_models.ResidueMajority attribute) stat_test_residues() (in module MDSimsEval.rmsf_analysis) stop (MDSimsEval.rmsf_baseline_models.AggregatedResidues attribute) (MDSimsEval.rmsf_baseline_models.KSDistance attribute) (MDSimsEval.rmsf_baseline_models.ResidueMajority attribute) summarize_rg() (in module MDSimsEval.rg_sasa_analysis) summarize_sasa() (in module MDSimsEval.rg_sasa_analysis)

U

uni (MDSimsEval.AnalysisActorClass.AnalysisActor attribute)