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atesa package
atesa
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Index
A
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B
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C
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E
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F
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G
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H
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I
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J
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M
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O
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P
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R
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S
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T
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U
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V
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W
A
AdaptAmber (class in atesa.mdengine)
AdaptPBS (class in atesa.batchsystem)
AdaptSimple (class in atesa.taskmanager)
AdaptSlurm (class in atesa.batchsystem)
add_pathway_restraints() (atesa.jobtype.UmbrellaSampling method)
AimlessShooting (class in atesa.jobtype)
algorithm() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
atesa (module)
atesa.batchsystem (module)
atesa.boltzmann_weight (module)
atesa.configure (module)
atesa.factory (module)
atesa.information_error (module)
atesa.interpret (module)
atesa.jobtype (module)
atesa.lmax (module)
atesa.main (module)
atesa.mdengine (module)
atesa.process (module)
atesa.rc_eval (module)
atesa.resample_and_inferr (module)
atesa.taskmanager (module)
atesa.tests (module)
atesa.tests.test_information_error (module)
atesa.tests.test_jobtype (module)
atesa.tests.test_lmax (module)
atesa.tests.test_main (module)
atesa.tests.test_process (module)
atesa.tests.test_rc_eval (module)
atesa.tests.test_utilities (module)
atesa.utilities (module)
B
BatchSystem (class in atesa.batchsystem)
batchsystem_factory() (in module atesa.factory)
C
cancel_job() (atesa.batchsystem.AdaptPBS method)
(atesa.batchsystem.AdaptSlurm method)
(atesa.batchsystem.BatchSystem method)
(atesa.main.Thread method)
check_commit() (in module atesa.utilities)
check_for_successful_step() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
check_termination() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
cleanup() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
CommittorAnalysis (class in atesa.jobtype)
config_equilibrium_path_sampling() (in module atesa.tests.test_jobtype)
configure() (in module atesa.configure)
E
EquilibriumPathSampling (class in atesa.jobtype)
eval_rc() (in module atesa.lmax)
evaluate_rc() (in module atesa.utilities)
F
FindTS (class in atesa.jobtype)
G
gatekeeper() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
(atesa.main.Thread method)
get_batch_template() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
(atesa.main.Thread method)
get_cvs() (in module atesa.utilities)
get_frame() (atesa.main.Thread method)
(atesa.mdengine.AdaptAmber method)
(atesa.mdengine.MDEngine method)
get_initial_coordinates() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
get_inpcrd() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
get_input_file() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
get_next_step() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
(atesa.main.Thread method)
get_status() (atesa.batchsystem.AdaptPBS method)
(atesa.batchsystem.AdaptSlurm method)
(atesa.batchsystem.BatchSystem method)
(atesa.main.Thread method)
get_submit_command() (atesa.batchsystem.AdaptPBS method)
(atesa.batchsystem.AdaptSlurm method)
(atesa.batchsystem.BatchSystem method)
H
handle_loop_exception() (in module atesa.main)
I
init_threads() (in module atesa.main)
interpret() (atesa.main.Thread method)
(in module atesa.interpret)
interpret_cv() (in module atesa.utilities)
J
JobType (class in atesa.jobtype)
jobtype_factory() (in module atesa.factory)
M
main() (in module atesa.boltzmann_weight)
(in module atesa.information_error)
(in module atesa.lmax)
(in module atesa.main)
(in module atesa.rc_eval)
(in module atesa.resample_and_inferr)
main_loop() (in module atesa.main)
MDEngine (class in atesa.mdengine)
mdengine_factory() (in module atesa.factory)
O
objective_function() (in module atesa.boltzmann_weight)
(in module atesa.lmax)
P
partial_full_cvs() (in module atesa.utilities)
plot_cvs_vs_rc() (in module atesa.utilities)
process() (atesa.main.Thread method)
(in module atesa.process)
R
resample() (in module atesa.utilities)
rev_vels() (in module atesa.utilities)
run_main() (in module atesa.main)
S
setup_method() (atesa.tests.test_information_error.Tests method)
(atesa.tests.test_jobtype.Tests method)
(atesa.tests.test_lmax.Tests method)
(atesa.tests.test_main.Tests method)
(atesa.tests.test_process.Tests method)
(atesa.tests.test_rc_eval.Tests method)
(atesa.tests.test_utilities.Tests method)
submit_batch() (atesa.taskmanager.AdaptSimple method)
(atesa.taskmanager.TaskManager method)
T
TaskManager (class in atesa.taskmanager)
taskmanager_factory() (in module atesa.factory)
teardown_method() (atesa.tests.test_information_error.Tests class method)
(atesa.tests.test_jobtype.Tests class method)
(atesa.tests.test_lmax.Tests class method)
(atesa.tests.test_main.Tests class method)
(atesa.tests.test_process.Tests class method)
(atesa.tests.test_rc_eval.Tests class method)
(atesa.tests.test_utilities.Tests class method)
test_algorithm_aimless_shooting_init() (atesa.tests.test_jobtype.Tests method)
test_algorithm_aimless_shooting_prod_accepted() (atesa.tests.test_jobtype.Tests method)
test_algorithm_aimless_shooting_prod_always_new_not_accepted() (atesa.tests.test_jobtype.Tests method)
test_algorithm_aimless_shooting_prod_not_always_new_not_accepted() (atesa.tests.test_jobtype.Tests method)
test_algorithm_equilibrium_path_sampling_init() (atesa.tests.test_jobtype.Tests method)
test_algorithm_equilibrium_path_sampling_prod_accepted() (atesa.tests.test_jobtype.Tests method)
test_algorithm_equilibrium_path_sampling_prod_not_accepted() (atesa.tests.test_jobtype.Tests method)
test_algorithm_equilibrium_path_sampling_prod_not_accepted_no_accepted_yet() (atesa.tests.test_jobtype.Tests method)
test_atesa_v2_imported() (atesa.tests.test_main.Tests method)
test_check_commit_bwd() (atesa.tests.test_utilities.Tests method)
test_check_commit_fwd() (atesa.tests.test_utilities.Tests method)
test_check_commit_none() (atesa.tests.test_utilities.Tests method)
test_check_commit_traj() (atesa.tests.test_utilities.Tests method)
test_check_commit_value_errors() (atesa.tests.test_utilities.Tests method)
test_check_for_successful_step_aimless_shooting_init() (atesa.tests.test_jobtype.Tests method)
test_check_for_successful_step_aimless_shooting_prod() (atesa.tests.test_jobtype.Tests method)
test_check_for_successful_step_committor_analysis() (atesa.tests.test_jobtype.Tests method)
test_check_for_successful_step_equilibrium_path_sampling() (atesa.tests.test_jobtype.Tests method)
test_check_termination_aimless_shooting_init() (atesa.tests.test_jobtype.Tests method)
test_check_termination_aimless_shooting_prod() (atesa.tests.test_jobtype.Tests method)
test_check_termination_committor_analysis() (atesa.tests.test_jobtype.Tests method)
test_check_termination_equilibrium_path_sampling_global() (atesa.tests.test_jobtype.Tests method)
test_check_termination_equilibrium_path_sampling_thread() (atesa.tests.test_jobtype.Tests method)
test_configure_broken() (atesa.tests.test_main.Tests method)
test_configure_directory() (atesa.tests.test_main.Tests method)
test_evaluate_rc() (atesa.tests.test_utilities.Tests method)
test_extrema_mdtraj() (atesa.tests.test_rc_eval.Tests method)
test_extrema_pytraj() (atesa.tests.test_rc_eval.Tests method)
test_gatekeep_aimless_shooting() (atesa.tests.test_jobtype.Tests method)
test_gatekeep_committor_analysis() (atesa.tests.test_jobtype.Tests method)
test_gatekeep_equilibrium_path_sampling() (atesa.tests.test_jobtype.Tests method)
test_get_batch_file_aimless_shooting_amber() (atesa.tests.test_jobtype.Tests method)
test_get_batch_file_aimless_shooting_broken() (atesa.tests.test_jobtype.Tests method)
test_get_batch_file_equilibrium_path_sampling_amber() (atesa.tests.test_jobtype.Tests method)
test_get_batch_file_equilibrium_path_sampling_broken() (atesa.tests.test_jobtype.Tests method)
test_get_batch_template_committor_analysis() (atesa.tests.test_jobtype.Tests method)
test_get_cvs_no_qdot() (atesa.tests.test_utilities.Tests method)
test_get_cvs_no_qdot_reduce() (atesa.tests.test_utilities.Tests method)
test_get_cvs_with_qdot() (atesa.tests.test_utilities.Tests method)
test_get_cvs_with_qdot_broken() (atesa.tests.test_utilities.Tests method)
test_get_initial_coordinates_aimless_shooting() (atesa.tests.test_jobtype.Tests method)
test_get_initial_coordinates_committor_analysis_rc_out() (atesa.tests.test_jobtype.Tests method)
test_get_initial_coordinates_committor_analysis_rc_out_does_not_exist() (atesa.tests.test_jobtype.Tests method)
test_get_initial_coordinates_committor_analysis_rc_out_no_shooting_points() (atesa.tests.test_jobtype.Tests method)
test_get_initial_coordinates_equilibrium_path_sampling() (atesa.tests.test_jobtype.Tests method)
test_get_inpcrd_aimless_shooting_init() (atesa.tests.test_jobtype.Tests method)
test_get_inpcrd_aimless_shooting_prod() (atesa.tests.test_jobtype.Tests method)
test_get_inpcrd_committor_analysis() (atesa.tests.test_jobtype.Tests method)
test_get_inpcrd_equilibrium_path_sampling() (atesa.tests.test_jobtype.Tests method)
test_get_input_file_aimless_shooting() (atesa.tests.test_jobtype.Tests method)
test_get_input_file_committor_analysis() (atesa.tests.test_jobtype.Tests method)
test_get_input_file_equilibrium_path_sampling() (atesa.tests.test_jobtype.Tests method)
test_get_input_file_rxncor_umbrella_sampling() (atesa.tests.test_jobtype.Tests method)
test_get_next_step_aimless_shooting_init() (atesa.tests.test_jobtype.Tests method)
test_get_next_step_aimless_shooting_prod() (atesa.tests.test_jobtype.Tests method)
test_get_next_step_committor_analysis() (atesa.tests.test_jobtype.Tests method)
test_get_next_step_equilibrium_path_sampling_first() (atesa.tests.test_jobtype.Tests method)
test_get_next_step_equilibrium_path_sampling_init() (atesa.tests.test_jobtype.Tests method)
test_get_next_step_equilibrium_path_sampling_prod() (atesa.tests.test_jobtype.Tests method)
test_import_cvs() (atesa.tests.test_main.Tests method)
test_init_threads_new() (atesa.tests.test_main.Tests method)
test_init_threads_restart() (atesa.tests.test_main.Tests method)
test_interpret_cv() (atesa.tests.test_utilities.Tests method)
test_main() (atesa.tests.test_information_error.Tests method)
(atesa.tests.test_main.Tests method)
test_main_improper_input() (atesa.tests.test_lmax.Tests method)
test_main_k_and_f() (atesa.tests.test_lmax.Tests method)
test_main_k_f_and_p() (atesa.tests.test_lmax.Tests method)
test_main_k_f_and_q() (atesa.tests.test_lmax.Tests method)
test_main_mdtraj() (atesa.tests.test_rc_eval.Tests method)
test_main_non_existent_input() (atesa.tests.test_lmax.Tests method)
test_main_pytraj() (atesa.tests.test_rc_eval.Tests method)
test_main_running() (atesa.tests.test_lmax.Tests method)
test_main_two_line_test() (atesa.tests.test_lmax.Tests method)
test_objective_function() (atesa.tests.test_lmax.Tests method)
test_process_to_be_terminated() (atesa.tests.test_process.Tests method)
test_process_to_submit() (atesa.tests.test_process.Tests method)
test_resample() (atesa.tests.test_utilities.Tests method)
test_rev_vels() (atesa.tests.test_utilities.Tests method)
test_thread_get_frame_amber() (atesa.tests.test_main.Tests method)
test_two_line_test() (atesa.tests.test_lmax.Tests method)
test_update_history_aimless_shooting_init() (atesa.tests.test_jobtype.Tests method)
test_update_history_aimless_shooting_prod() (atesa.tests.test_jobtype.Tests method)
test_update_history_committor_analysis() (atesa.tests.test_jobtype.Tests method)
test_update_history_equilibrium_path_sampling_init() (atesa.tests.test_jobtype.Tests method)
test_update_history_equilibrium_path_sampling_out_of_bounds() (atesa.tests.test_jobtype.Tests method)
test_update_history_equilibrium_path_sampling_prod() (atesa.tests.test_jobtype.Tests method)
test_update_results_aimless_shooting_init() (atesa.tests.test_jobtype.Tests method)
test_update_results_aimless_shooting_prod() (atesa.tests.test_jobtype.Tests method)
test_update_results_committor_analysis() (atesa.tests.test_jobtype.Tests method)
test_update_results_equilibrium_path_sampling() (atesa.tests.test_jobtype.Tests method)
Tests (class in atesa.tests.test_information_error)
(class in atesa.tests.test_jobtype)
(class in atesa.tests.test_lmax)
(class in atesa.tests.test_main)
(class in atesa.tests.test_process)
(class in atesa.tests.test_rc_eval)
(class in atesa.tests.test_utilities)
Thread (class in atesa.main)
two_line_test_func() (in module atesa.lmax)
U
UmbrellaSampling (class in atesa.jobtype)
update_history() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
update_progress() (in module atesa.boltzmann_weight)
(in module atesa.lmax)
(in module atesa.rc_eval)
update_results() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
V
verify() (atesa.jobtype.AimlessShooting method)
(atesa.jobtype.CommittorAnalysis method)
(atesa.jobtype.EquilibriumPathSampling method)
(atesa.jobtype.FindTS method)
(atesa.jobtype.JobType method)
(atesa.jobtype.UmbrellaSampling method)
W
write_find_ts_restraint() (atesa.mdengine.AdaptAmber method)
(atesa.mdengine.MDEngine method)
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