Index

A

accept_or_reject() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) analyze_REXEE_time() (in module ensemble_md.utils.utils)

analyze_transitions() (in module ensemble_md.analysis.clustering) average_weights() (in module ensemble_md.analysis.analyze_free_energy)

C

calc_equil_prob() (in module ensemble_md.analysis.analyze_matrix) calc_hist_rmse() (in module ensemble_md.analysis.analyze_traj) calc_prob_acc() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) calc_rmse() (in module ensemble_md.utils.utils) calc_spectral_gap() (in module ensemble_md.analysis.analyze_matrix) calc_t_relax() (in module ensemble_md.analysis.analyze_matrix) calc_transmtx() (in module ensemble_md.analysis.analyze_matrix)

calculate_df_rmse() (in module ensemble_md.analysis.analyze_free_energy) calculate_free_energy() (in module ensemble_md.analysis.analyze_free_energy) check_gmx_executable() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) cluster_traj() (in module ensemble_md.analysis.clustering) combine_weights() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) COMMENT (ensemble_md.utils.gmx_parser.MDP attribute) compare_MDPs() (in module ensemble_md.utils.gmx_parser) convert_npy2xvg() (in module ensemble_md.analysis.analyze_traj)

D

decide_lagtimes() (in module ensemble_md.analysis.msm_analysis)

E

ensemble_md.analysis.analyze_free_energy module ensemble_md.analysis.analyze_matrix module ensemble_md.analysis.analyze_traj module ensemble_md.analysis.clustering module ensemble_md.analysis.msm_analysis module ensemble_md.analysis.synthesize_data module

ensemble_md.replica_exchange_EE module ensemble_md.utils.exceptions module ensemble_md.utils.gmx_parser module ensemble_md.utils.utils module extract_final_dhdl_info() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) extract_final_log_info() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) extract_state_traj() (in module ensemble_md.analysis.analyze_traj)

F

flush() (ensemble_md.utils.utils.Logger method)

format_time() (in module ensemble_md.utils.utils)

G

get_averaged_weights() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) get_cluster_info() (in module ensemble_md.analysis.clustering) get_cluster_members() (in module ensemble_md.analysis.clustering) get_delta_w_updates() (in module ensemble_md.analysis.analyze_traj) get_dg_evolution() (in module ensemble_md.analysis.analyze_traj)

get_g_evolution() (in module ensemble_md.analysis.analyze_traj) get_ref_dist() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) get_swapping_pattern() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) get_swaps() (in module ensemble_md.analysis.analyze_traj) get_time_metrics() (in module ensemble_md.utils.utils)

H

histogram_correction() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method)

I

identify_swappable_pairs() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE static method)

initialize_MDP() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method)

L

Logger (class in ensemble_md.utils.utils)

M

MDP (class in ensemble_md.utils.gmx_parser) module ensemble_md.analysis.analyze_free_energy ensemble_md.analysis.analyze_matrix ensemble_md.analysis.analyze_traj ensemble_md.analysis.clustering ensemble_md.analysis.msm_analysis ensemble_md.analysis.synthesize_data ensemble_md.replica_exchange_EE ensemble_md.utils.exceptions ensemble_md.utils.gmx_parser ensemble_md.utils.utils

P

PARAMETER (ensemble_md.utils.gmx_parser.MDP attribute) ParameterError parse_log() (in module ensemble_md.utils.gmx_parser) ParseError plot_acf() (in module ensemble_md.analysis.msm_analysis) plot_dg_evolution() (in module ensemble_md.analysis.analyze_traj) plot_free_energy() (in module ensemble_md.analysis.analyze_free_energy) plot_g_vecs() (in module ensemble_md.analysis.analyze_traj) plot_its() (in module ensemble_md.analysis.msm_analysis)

plot_matrix() (in module ensemble_md.analysis.analyze_matrix) plot_rep_trajs() (in module ensemble_md.analysis.analyze_traj) plot_state_hist() (in module ensemble_md.analysis.analyze_traj) plot_state_trajs() (in module ensemble_md.analysis.analyze_traj) plot_swaps() (in module ensemble_md.analysis.analyze_traj) plot_transit_time() (in module ensemble_md.analysis.analyze_traj) preprocess_data() (in module ensemble_md.analysis.analyze_free_energy) print_params() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) propose_swap() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE static method)

R

read() (ensemble_md.utils.gmx_parser.MDP method) reformat_MDP() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE static method)

ReplicaExchangeEE (class in ensemble_md.replica_exchange_EE) run_gmx_cmd() (in module ensemble_md.utils.utils) run_REXEE() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method)

S

set_params() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) split_transmtx() (in module ensemble_md.analysis.analyze_matrix) stitch_time_series() (in module ensemble_md.analysis.analyze_traj)

stitch_time_series_for_sim() (in module ensemble_md.analysis.analyze_traj) stitch_xtc_trajs() (in module ensemble_md.analysis.analyze_traj) synthesize_traj() (in module ensemble_md.analysis.synthesize_data) synthesize_transmtx() (in module ensemble_md.analysis.synthesize_data)

T

traj2transmtx() (in module ensemble_md.analysis.analyze_traj)

U

update_MDP() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method)

W

weight_correction() (ensemble_md.replica_exchange_EE.ReplicaExchangeEE method) weighted_mean() (in module ensemble_md.utils.utils)

write() (ensemble_md.utils.gmx_parser.MDP method) (ensemble_md.utils.utils.Logger method)