pyPESTO
v0.0.4
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Index
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A
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C
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D
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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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_
__call__() (pypesto.objective.Objective method)
__init__() (pypesto.engine.MultiProcessEngine method)
(pypesto.engine.OptimizerTask method)
(pypesto.engine.SingleCoreEngine method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.Objective method)
(pypesto.objective.ObjectiveOptions method)
(pypesto.objective.PetabImporter method)
(pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.OptimizeOptions method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.OptimizerResult method)
(pypesto.optimize.ScipyOptimizer method)
(pypesto.problem.Problem method)
(pypesto.profile.ProfileOptions method)
(pypesto.profile.ProfilerResult method)
(pypesto.result.OptimizeResult method)
(pypesto.result.ProfileResult method)
(pypesto.result.Result method)
(pypesto.result.SampleResult method)
(pypesto.visualize.ReferencePoint method)
A
add_profile() (pypesto.result.ProfileResult method)
AmiciObjective (class in pypesto.objective)
append() (pypesto.result.OptimizeResult method)
append_profile_point() (pypesto.profile.ProfilerResult method)
as_dataframe() (pypesto.result.OptimizeResult method)
as_list() (pypesto.result.OptimizeResult method)
assert_instance() (pypesto.objective.ObjectiveOptions static method)
(pypesto.optimize.OptimizeOptions static method)
assign_clustered_colors() (in module pypesto.visualize)
assign_clusters() (in module pypesto.visualize)
assign_colors() (in module pypesto.visualize)
assign_startpoints() (in module pypesto.startpoint)
auto_color (pypesto.visualize.ReferencePoint attribute)
C
check_grad() (pypesto.objective.Objective method)
check_sensi_orders() (pypesto.objective.Objective method)
color (pypesto.visualize.ReferencePoint attribute)
compile_model() (pypesto.objective.PetabImporter method)
create_edatas() (pypesto.objective.PetabImporter method)
create_instance() (pypesto.profile.ProfileOptions static method)
create_model() (pypesto.objective.PetabImporter method)
create_new_profile() (pypesto.result.ProfileResult method)
create_new_profile_list() (pypesto.result.ProfileResult method)
create_objective() (pypesto.objective.PetabImporter method)
create_problem() (pypesto.objective.PetabImporter method)
create_references() (in module pypesto.visualize)
create_solver() (pypesto.objective.PetabImporter method)
D
dim (pypesto.problem.Problem attribute)
DlibOptimizer (class in pypesto.optimize)
E
execute() (pypesto.engine.MultiProcessEngine method)
(pypesto.engine.OptimizerTask method)
(pypesto.engine.SingleCoreEngine method)
exitflag (pypesto.optimize.OptimizerResult attribute)
exitflag_path (pypesto.profile.ProfilerResult attribute)
F
finalize_history() (pypesto.objective.Objective method)
fix_parameters() (pypesto.problem.Problem method)
flip_profile() (pypesto.profile.ProfilerResult method)
from_folder() (pypesto.objective.PetabImporter static method)
fval (pypesto.optimize.OptimizerResult attribute)
(pypesto.visualize.ReferencePoint attribute)
fval_path (pypesto.profile.ProfilerResult attribute)
G
get_bound_fun() (pypesto.objective.AmiciObjective method)
get_bound_res() (pypesto.objective.AmiciObjective method)
get_current_profile() (pypesto.result.ProfileResult method)
get_default_options() (pypesto.optimize.DlibOptimizer static method)
(pypesto.optimize.Optimizer static method)
(pypesto.optimize.ScipyOptimizer static method)
get_error_output() (pypesto.objective.AmiciObjective method)
get_for_key() (pypesto.result.OptimizeResult method)
get_full_matrix() (pypesto.problem.Problem method)
get_full_vector() (pypesto.problem.Problem method)
get_fval() (pypesto.objective.Objective method)
get_grad() (pypesto.objective.Objective method)
get_hess() (pypesto.objective.Objective method)
get_reduced_matrix() (pypesto.problem.Problem method)
get_reduced_vector() (pypesto.problem.Problem method)
get_res() (pypesto.objective.Objective method)
get_sres() (pypesto.objective.Objective method)
gradnorm_path (pypesto.profile.ProfilerResult attribute)
H
has_fun (pypesto.objective.Objective attribute)
has_grad (pypesto.objective.Objective attribute)
has_hess (pypesto.objective.Objective attribute)
has_hessp (pypesto.objective.Objective attribute)
has_res (pypesto.objective.Objective attribute)
has_sres (pypesto.objective.Objective attribute)
history (pypesto.objective.Objective attribute)
I
init_preequilibration_edatas() (pypesto.objective.AmiciObjective method)
is_least_squares() (pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.ScipyOptimizer method)
L
latin_hypercube() (in module pypesto.startpoint)
legend (pypesto.visualize.ReferencePoint attribute)
M
message (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
minimize() (in module pypesto.optimize)
(pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.ScipyOptimizer method)
MODEL_BASE_DIR (pypesto.objective.PetabImporter attribute)
MultiProcessEngine (class in pypesto.engine)
N
n_fval (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
n_grad (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
n_hess (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
n_procs (pypesto.engine.MultiProcessEngine attribute)
normalize_input() (pypesto.problem.Problem method)
O
Objective (class in pypesto.objective)
ObjectiveOptions (class in pypesto.objective)
optimize_result (pypesto.result.Result attribute)
OptimizeOptions (class in pypesto.optimize)
Optimizer (class in pypesto.optimize)
optimizer_history() (in module pypesto.visualize)
optimizer_history_lowlevel() (in module pypesto.visualize)
OptimizeResult (class in pypesto.result)
OptimizerResult (class in pypesto.optimize)
OptimizerTask (class in pypesto.engine)
output_to_dict() (pypesto.objective.Objective static method)
output_to_tuple() (pypesto.objective.Objective static method)
P
parameter_profile() (in module pypesto.profile)
parameters() (in module pypesto.visualize)
parameters_lowlevel() (in module pypesto.visualize)
PetabImporter (class in pypesto.objective)
postprocess (pypesto.objective.Objective attribute)
postprocess_preequilibration() (pypesto.objective.AmiciObjective method)
preprocess (pypesto.objective.Objective attribute)
preprocess_preequilibration() (pypesto.objective.AmiciObjective method)
print_parameter_summary() (pypesto.problem.Problem method)
Problem (class in pypesto.problem)
problem (pypesto.result.Result attribute)
process_offset_y() (in module pypesto.visualize)
process_result_list() (in module pypesto.visualize)
process_y_limits() (in module pypesto.visualize)
profile_lowlevel() (in module pypesto.visualize)
profile_result (pypesto.result.Result attribute)
ProfileOptions (class in pypesto.profile)
ProfileResult (class in pypesto.result)
ProfilerResult (class in pypesto.profile)
profiles() (in module pypesto.visualize)
profiles_lowlevel() (in module pypesto.visualize)
pypesto.engine (module)
pypesto.objective (module)
pypesto.optimize (module)
pypesto.problem (module)
pypesto.profile (module)
pypesto.result (module)
pypesto.sample (module)
pypesto.startpoint (module)
pypesto.visualize (module)
R
ratio_path (pypesto.profile.ProfilerResult attribute)
rdatas_to_measurement_df() (pypesto.objective.PetabImporter method)
rebind_fun() (pypesto.objective.AmiciObjective method)
rebind_res() (pypesto.objective.AmiciObjective method)
ReferencePoint (class in pypesto.visualize)
res_to_chi2() (in module pypesto.objective)
reset() (pypesto.objective.Objective method)
reset_history() (pypesto.objective.Objective method)
Result (class in pypesto.result)
run_preequilibration() (pypesto.objective.AmiciObjective method)
S
sample_result (pypesto.result.Result attribute)
SampleResult (class in pypesto.result)
ScipyOptimizer (class in pypesto.optimize)
sensitivity_orders (pypesto.objective.Objective attribute)
set_par_sim_for_condition() (pypesto.objective.AmiciObjective method)
set_parameter_scale() (pypesto.objective.AmiciObjective method)
SingleCoreEngine (class in pypesto.engine)
sort() (pypesto.result.OptimizeResult method)
sres_to_schi2() (in module pypesto.objective)
T
time_path (pypesto.profile.ProfilerResult attribute)
time_total (pypesto.profile.ProfilerResult attribute)
U
unfix_parameters() (pypesto.problem.Problem method)
uniform() (in module pypesto.startpoint)
update_from_problem() (pypesto.objective.Objective method)
W
waterfall() (in module pypesto.visualize)
waterfall_lowlevel() (in module pypesto.visualize)
X
x (pypesto.optimize.OptimizerResult attribute)
(pypesto.visualize.ReferencePoint attribute)
x_free_indices (pypesto.problem.Problem attribute)
x_path (pypesto.profile.ProfilerResult attribute)
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