SYMBOL INDEX (234 symbols across 26 files)

FILE: examples/constant-force-optical-trap/extract-data.py
  function main (line 45) | def main():

FILE: examples/constant-force-optical-trap/force-bias-optical-trap.py
  function construct_nonuniform_bins (line 55) | def construct_nonuniform_bins(x_n, nbins):
  function main (line 124) | def main():

FILE: examples/harmonic-oscillators/harmonic-oscillators.py
  function stddev_away (line 39) | def stddev_away(namex, errorx, dx):
  function get_analytical (line 46) | def get_analytical(beta, K, O, observables):
  function generate_fes_data (line 674) | def generate_fes_data(

FILE: examples/heat-capacity/heat-capacity.py
  function parse_cli (line 21) | def parse_cli():
  function read_total_energies (line 107) | def read_total_energies(pathname, colnum):
  function read_simulation_temps (line 151) | def read_simulation_temps(pathname, num_temps):
  function print_results (line 179) | def print_results(string, E, dE, Cv, dCv, types):

FILE: examples/parallel-tempering-2dfes/parallel-tempering-2dfes.py
  function read_file (line 58) | def read_file(filename):

FILE: examples/umbrella-sampling-fes/umbrella-sampling-advanced-fes.py
  function bias_potential (line 205) | def bias_potential(x, k):
  function deltag (line 214) | def deltag(c, scalef=1, n=nspline):
  function ddeltag (line 223) | def ddeltag(c, scalef=1, n=nspline):
  function dddeltag (line 247) | def dddeltag(c, scalef=1, n=nspline):

FILE: pymbar/confidenceintervals.py
  function order_replicates (line 32) | def order_replicates(replicates, K):
  function anderson_darling (line 76) | def anderson_darling(replicates, K):
  function qq_plot (line 127) | def qq_plot(replicates, K, title="Generic Q-Q plot", filename="qq.pdf"):
  function generate_confidence_intervals (line 225) | def generate_confidence_intervals(replicates, K):

FILE: pymbar/fes.py
  class FES (line 47) | class FES:
    method __init__ (line 74) | def __init__(self, u_kn, N_k, verbose=False, mbar_options=None, timing...
    method generate_fes (line 221) | def generate_fes(
    method _setup_fes_histogram (line 440) | def _setup_fes_histogram(self, histogram_parameters):
    method _generate_fes_histogram (line 476) | def _generate_fes_histogram(self, b, x_n, w_nb, log_w_nb):
    method _setup_fes_kde (line 602) | def _setup_fes_kde(self, kde_parameters):
    method _generate_fes_kde (line 650) | def _generate_fes_kde(self, b, x_n, w_n):
    method _setup_fes_spline (line 701) | def _setup_fes_spline(self, spline_parameters):
    method _get_initial_spline_points (line 809) | def _get_initial_spline_points(self):
    method _get_initial_spline (line 883) | def _get_initial_spline(self, xinit, yinit):
    method _generate_fes_spline (line 971) | def _generate_fes_spline(self, b, x_n, w_n):
    method _calculate_information_criteria (line 1101) | def _calculate_information_criteria(nparameters, minus_log_likelihood,...
    method get_information_criteria (line 1136) | def get_information_criteria(self, type="akaike"):
    method get_fes (line 1167) | def get_fes(
    method get_mbar (line 1233) | def get_mbar(self):
    method get_kde (line 1245) | def get_kde(self):
    method _get_fes_histogram (line 1263) | def _get_fes_histogram(
    method _get_fes_kde (line 1523) | def _get_fes_kde(
    method _get_fes_spline (line 1611) | def _get_fes_spline(
    method sample_parameter_distribution (line 1696) | def sample_parameter_distribution(
    method get_confidence_intervals (line 1859) | def get_confidence_intervals(self, xplot, plow, phigh, reference="zero"):
    method get_mc_data (line 1928) | def get_mc_data(self):
    method _get_MC_loglikelihood (line 1954) | def _get_MC_loglikelihood(self, x_n, w_n, spline_weights, spline, xran...
    method _MC_step (line 2012) | def _MC_step(self, x_n, w_n, stepsize, xrange, spline_weights, logprior):
    method _bspline_calculate_f (line 2102) | def _bspline_calculate_f(self, xi, x_n, w_n):
    method _bspline_calculate_g (line 2188) | def _bspline_calculate_g(self, xi, x_n, w_n):
    method _bspline_calculate_h (line 2308) | def _bspline_calculate_h(self, xi, x_n, w_n):
    method _integrate (line 2419) | def _integrate(func, xlow, xhigh, args=(), method="quad"):  # could ad...
    method _val_to_spline (line 2430) | def _val_to_spline(self, x, form=None):

FILE: pymbar/mbar.py
  class MBAR (line 65) | class MBAR:
    method __init__ (line 86) | def __init__(
    method W_nk (line 468) | def W_nk(self):
    method weights (line 482) | def weights(self):
    method compute_effective_sample_number (line 497) | def compute_effective_sample_number(self, verbose=False):
    method compute_overlap (line 564) | def compute_overlap(self):
    method compute_free_energy_differences (line 621) | def compute_free_energy_differences(
    method compute_expectations_inner (line 733) | def compute_expectations_inner(
    method compute_covariance_of_sums (line 1034) | def compute_covariance_of_sums(self, d_ij, K, a):
    method compute_expectations (line 1125) | def compute_expectations(
    method compute_multiple_expectations (line 1316) | def compute_multiple_expectations(
    method compute_perturbed_free_energies (line 1443) | def compute_perturbed_free_energies(
    method compute_entropy_and_enthalpy (line 1525) | def compute_entropy_and_enthalpy(
    method _ErrorOfDifferences (line 1688) | def _ErrorOfDifferences(self, cov, warning_cutoff=1.0e-10):
    method _pseudoinverse (line 1718) | def _pseudoinverse(self, A, tol=1.0e-10):
    method _zerosamestates (line 1740) | def _zerosamestates(self, A):
    method _computeAsymptoticCovarianceMatrix (line 1757) | def _computeAsymptoticCovarianceMatrix(self, W, N_k, method=None):
    method _initializeFreeEnergies (line 1869) | def _initializeFreeEnergies(self, verbose=False, method="zeros", f_k_i...
    method _computeUnnormalizedLogWeights (line 1920) | def _computeUnnormalizedLogWeights(self, u_n):
    method _initialize_with_bar (line 1937) | def _initialize_with_bar(self, u_kn, f_k_init=None):

FILE: pymbar/mbar_solvers.py
  function _setup_jax_acceleration (line 18) | def _setup_jax_acceleration():
  function jit_or_passthrough (line 96) | def jit_or_passthrough(fn):
  function _mbar_loss_and_grad_numba_python (line 115) | def _mbar_loss_and_grad_numba_python(
  function _mbar_loss_and_grad_numba_wrapper (line 207) | def _mbar_loss_and_grad_numba_wrapper(
  function jit_or_pass_after_bitsize (line 299) | def jit_or_pass_after_bitsize(jitable_fn):
  function validate_inputs (line 331) | def validate_inputs(u_kn, N_k, f_k):
  function self_consistent_update (line 363) | def self_consistent_update(u_kn, N_k, f_k, states_with_samples=None):
  function _jit_self_consistent_update (line 389) | def _jit_self_consistent_update(u_kn, N_k, f_k):
  function jax_self_consistent_update (line 402) | def jax_self_consistent_update(u_kn, N_k, f_k, states_with_samples=None):
  function mbar_gradient (line 417) | def mbar_gradient(u_kn, N_k, f_k):
  function jax_mbar_gradient (line 442) | def jax_mbar_gradient(u_kn, N_k, f_k):
  function mbar_objective (line 452) | def mbar_objective(u_kn, N_k, f_k):
  function jax_mbar_objective (line 485) | def jax_mbar_objective(u_kn, N_k, f_k):
  function jax_mbar_objective_and_gradient (line 499) | def jax_mbar_objective_and_gradient(u_kn, N_k, f_k):
  function mbar_objective_and_gradient (line 515) | def mbar_objective_and_gradient(u_kn, N_k, f_k):
  function jax_mbar_hessian (line 553) | def jax_mbar_hessian(u_kn, N_k, f_k):
  function mbar_hessian (line 571) | def mbar_hessian(u_kn, N_k, f_k):
  function jax_mbar_log_W_nk (line 597) | def jax_mbar_log_W_nk(u_kn, N_k, f_k):
  function mbar_log_W_nk (line 609) | def mbar_log_W_nk(u_kn, N_k, f_k):
  function jax_mbar_W_nk (line 634) | def jax_mbar_W_nk(u_kn, N_k, f_k):
  function mbar_W_nk (line 643) | def mbar_W_nk(u_kn, N_k, f_k):
  function adaptive (line 667) | def adaptive(u_kn, N_k, f_k, tol=1.0e-8, options=None):
  function jax_core_adaptive (line 828) | def jax_core_adaptive(u_kn, N_k, f_k, gamma):
  function jax_precondition_u_kn (line 855) | def jax_precondition_u_kn(u_kn, N_k, f_k):
  function precondition_u_kn (line 867) | def precondition_u_kn(u_kn, N_k, f_k):
  function solve_mbar_once (line 895) | def solve_mbar_once(
  function solve_mbar (line 1069) | def solve_mbar(u_kn_nonzero, N_k_nonzero, f_k_nonzero, solver_protocol=N...
  function solve_mbar_for_all_states (line 1160) | def solve_mbar_for_all_states(u_kn, N_k, f_k, states_with_samples, solve...

FILE: pymbar/other_estimators.py
  function bar_zero (line 56) | def bar_zero(w_F, w_R, DeltaF):
  function bar (line 156) | def bar(
  function bar_overlap (line 534) | def bar_overlap(w_F, w_R):
  function exp (line 572) | def exp(w_F, compute_uncertainty=True, is_timeseries=False):
  function exp_gauss (line 650) | def exp_gauss(w_F, compute_uncertainty=True, is_timeseries=False):

FILE: pymbar/tests/test_bar.py
  function generate_ho (line 19) | def generate_ho(O_k=np.array([1.0, 2.0]), K_k=np.array([0.5, 2.0])):
  function generate_exp (line 23) | def generate_exp(rates=np.array([1.0, 4.0])):  # Rates, e.g. Lambda
  function bar_and_test (line 31) | def bar_and_test(request):
  function test_sample (line 48) | def test_sample(system_generator):
  function test_bar_free_energies (line 60) | def test_bar_free_energies(bar_and_test):
  function test_bar_overlap (line 101) | def test_bar_overlap():

FILE: pymbar/tests/test_covariance.py
  function _test (line 15) | def _test(statesa, statesb, test_system):

FILE: pymbar/tests/test_exp.py
  function generate_ho (line 18) | def generate_ho(O_k=np.array([1.0, 2.0]), K_k=np.array([0.5, 1.0])):
  function generate_exp (line 22) | def generate_exp(rates=np.array([1.0, 4.0])):  # Rates, e.g. Lambda
  function exp_and_test (line 30) | def exp_and_test(request):
  function test_sample (line 46) | def test_sample(system_generator):
  function test_EXP_free_energies (line 58) | def test_EXP_free_energies(exp_and_test):

FILE: pymbar/tests/test_fes.py
  function generate_fes_data (line 19) | def generate_fes_data(ndim=1, nsamples=1000, K0=20.0, Ku=100.0, gridscal...
  function fes_1d (line 99) | def fes_1d():
  function fes_2d (line 190) | def fes_2d():
  function test_1d_fes_histogram (line 319) | def test_1d_fes_histogram(fes_1d, reference_point):
  function base_1d_fes_kde (line 343) | def base_1d_fes_kde(fes_1d, gen_kwargs, reference_point):
  function test_1d_fes_kde (line 388) | def test_1d_fes_kde(fes_1d, gen_kwargs, reference_point):
  function test_1d_fes_kde_bootstraped (line 396) | def test_1d_fes_kde_bootstraped(fes_1d):
  function base_1d_fes_spline (line 402) | def base_1d_fes_spline(fes_1d, gen_kwargs, reference_point):
  function test_1d_fes_spline (line 464) | def test_1d_fes_spline(fes_1d, gen_kwargs, reference_point):
  function test_1d_fes_spline_bootstraped (line 468) | def test_1d_fes_spline_bootstraped(fes_1d):
  function test_2d_fes_histogram (line 483) | def test_2d_fes_histogram(fes_2d, reference_point):
  function test_2d_fes_kde (line 531) | def test_2d_fes_kde(fes_2d, gen_kwargs, reference_point):

FILE: pymbar/tests/test_mbar.py
  function generate_ho (line 19) | def generate_ho(O_k=np.array([1.0, 2.0, 3.0, 4.0]), K_k=np.array([0.5, 1...
  function generate_exp (line 23) | def generate_exp(rates=np.array([1.0, 2.0, 3.0, 4.0])):  # Rates, e.g. L...
  function convert_to_differences (line 27) | def convert_to_differences(x_ij, dx_ij, xa):
  function mbar_and_test (line 45) | def mbar_and_test(request):
  function mbar_and_test_harmonic (line 55) | def mbar_and_test_harmonic():
  function mbar_and_test_kln (line 65) | def mbar_and_test_kln():
  function fixed_harmonic_sample (line 75) | def fixed_harmonic_sample():
  function single_harmonic_u_kn (line 81) | def single_harmonic_u_kn(fixed_harmonic_sample):
  function free_energies_almost_equal (line 86) | def free_energies_almost_equal(mbar_fe, err_fe, analytical_fe):
  function test_ukln (line 95) | def test_ukln(mbar_and_test_kln):
  function test_duplicate_state (line 104) | def test_duplicate_state(fixed_harmonic_sample, caplog):
  function test_x_kindices (line 116) | def test_x_kindices(fixed_harmonic_sample):
  function test_bad_inital_f_k (line 128) | def test_bad_inital_f_k(fixed_harmonic_sample):
  function test_covariance_of_sums_runs (line 133) | def test_covariance_of_sums_runs(mbar_and_test_kln):
  function test_analytical (line 143) | def test_analytical(system_generator):
  function test_sample (line 155) | def test_sample(system_generator):
  function test_mbar_free_energies (line 183) | def test_mbar_free_energies(mbar_and_test, uncertainty_method):
  function test_mbar_bad_bootstrap (line 197) | def test_mbar_bad_bootstrap(single_harmonic_u_kn, n_bootstrap):
  function test_mbar_initialization (line 207) | def test_mbar_initialization(fixed_harmonic_sample, method):
  function test_mbar_compute_expectations_position_averages (line 217) | def test_mbar_compute_expectations_position_averages(mbar_and_test):
  function test_mbar_compute_expectations_position_differences (line 231) | def test_mbar_compute_expectations_position_differences(mbar_and_test):
  function test_mbar_compute_expectations_position2 (line 243) | def test_mbar_compute_expectations_position2(mbar_and_test):
  function test_mbar_compute_expectations_potential (line 256) | def test_mbar_compute_expectations_potential(mbar_and_test):
  function test_mbar_compute_expectations_edges (line 283) | def test_mbar_compute_expectations_edges(
  function multiExpectationAssertion (line 315) | def multiExpectationAssertion(results, test, state=1):
  function test_mbar_compute_multiple_expectations (line 326) | def test_mbar_compute_multiple_expectations(mbar_and_test):
  function test_mbar_compute_multiple_expectations_more_dims (line 343) | def test_mbar_compute_multiple_expectations_more_dims(mbar_and_test_kln):
  function test_mbar_compute_entropy_and_enthalpy (line 362) | def test_mbar_compute_entropy_and_enthalpy(mbar_and_test, with_uxx=True):
  function test_mbar_compute_entropy_and_enthalpy_edges (line 404) | def test_mbar_compute_entropy_and_enthalpy_edges(
  function test_mbar_compute_effective_sample_number (line 414) | def test_mbar_compute_effective_sample_number(mbar_and_test):
  function test_mbar_compute_overlap_analytical (line 425) | def test_mbar_compute_overlap_analytical():
  function test_mbar_compute_overlap_nonanalytical (line 451) | def test_mbar_compute_overlap_nonanalytical(mbar_and_test):
  function test_mbar_weights (line 466) | def test_mbar_weights(mbar_and_test):
  function test_mbar_computePerturbedFreeEnergeies (line 484) | def test_mbar_computePerturbedFreeEnergeies(system_generator, mode, bad_n):
  function test_mbar_compute_expectations_inner (line 518) | def test_mbar_compute_expectations_inner(mbar_and_test):
  function test_mbar_bootstrap_deterministic_given_same_seed (line 534) | def test_mbar_bootstrap_deterministic_given_same_seed(fixed_harmonic_sam...
  function test_mbar_numba_solver_matches_default (line 548) | def test_mbar_numba_solver_matches_default(fixed_harmonic_sample):

FILE: pymbar/tests/test_mbar_solvers.py
  function base_oscillator (line 14) | def base_oscillator():
  function more_oscillators (line 20) | def more_oscillators():
  function test_solvers (line 30) | def test_solvers(statesa, statesb, test_system):
  function run_mbar_protocol (line 44) | def run_mbar_protocol(oscillator_bundle, protocol):
  function test_protocols (line 75) | def test_protocols(base_oscillator, more_oscillators, protocol):
  class TestPymbarJaxDisabled (line 94) | class TestPymbarJaxDisabled:
    method test_env_values (line 117) | def test_env_values(self, monkeypatch, env_value, expected):
    method test_unset_variable (line 122) | def test_unset_variable(self, monkeypatch):

FILE: pymbar/tests/test_timeseries.py
  function data (line 22) | def data(N=10000, K=10):
  function test_statistical_inefficiency_single (line 36) | def test_statistical_inefficiency_single(data):
  function test_statistical_inefficiency_multiple (line 50) | def test_statistical_inefficiency_multiple(data):
  function test_statistical_inefficiency_fft (line 61) | def test_statistical_inefficiency_fft(data):
  function test_statistical_inefficiency_fft_gaussian (line 77) | def test_statistical_inefficiency_fft_gaussian():
  function test_detectEquil (line 107) | def test_detectEquil():
  function test_detectEquil_binary (line 113) | def test_detectEquil_binary():
  function test_compare_detectEquil (line 119) | def test_compare_detectEquil(show_hist=False):
  function test_detectEquil_constant_trailing (line 147) | def test_detectEquil_constant_trailing():
  function test_correlationFunctionMultiple (line 161) | def test_correlationFunctionMultiple():

FILE: pymbar/tests/test_utils.py
  function test_logsumexp (line 13) | def test_logsumexp():
  function test_logsumexp_single_infinite (line 24) | def test_logsumexp_single_infinite():
  function test_logsumexp_b (line 31) | def test_logsumexp_b():
  function test_logsum (line 43) | def test_logsum():
  function test_non_normalized_w_badrow (line 51) | def test_non_normalized_w_badrow():
  function test_non_normalized_w_badcol (line 58) | def test_non_normalized_w_badcol():
  function test_type_ensure (line 195) | def test_type_ensure(fn_args_and_kwargs, expected, warn):
  function test_kln_to_nk_to_k (line 209) | def test_kln_to_nk_to_k(n_k):

FILE: pymbar/testsystems/exponential_distributions.py
  class ExponentialTestCase (line 4) | class ExponentialTestCase(object):
    method __init__ (line 41) | def __init__(self, rates=(1, 2, 3, 4, 5), beta=1.0):
    method analytical_free_energies (line 62) | def analytical_free_energies(self):
    method analytical_means (line 66) | def analytical_means(self):
    method analytical_variances (line 69) | def analytical_variances(self):
    method analytical_standard_deviations (line 72) | def analytical_standard_deviations(self):
    method analytical_observable (line 75) | def analytical_observable(self, observable="position"):
    method analytical_entropies (line 86) | def analytical_entropies(self):
    method analytical_x_squared (line 92) | def analytical_x_squared(self):
    method sample (line 95) | def sample(self, N_k=(10, 20, 30, 40, 50), mode="u_kln", seed=None):
    method evenly_spaced_exponentials (line 201) | def evenly_spaced_exponentials(

FILE: pymbar/testsystems/gaussian_work.py
  function gaussian_work_example (line 4) | def gaussian_work_example(N_F=200, N_R=200, mu_F=2.0, DeltaF=None, sigma...

FILE: pymbar/testsystems/harmonic_oscillators.py
  class HarmonicOscillatorsTestCase (line 4) | class HarmonicOscillatorsTestCase(object):
    method __init__ (line 41) | def __init__(self, O_k=(0, 1, 2, 3, 4), K_k=(1, 2, 4, 8, 16), beta=1.0):
    method analytical_means (line 73) | def analytical_means(self):
    method analytical_variances (line 76) | def analytical_variances(self):
    method analytical_standard_deviations (line 79) | def analytical_standard_deviations(self):
    method analytical_observable (line 82) | def analytical_observable(self, observable="position"):
    method analytical_free_energies (line 92) | def analytical_free_energies(self, subtract_component=0):
    method analytical_entropies (line 98) | def analytical_entropies(self, subtract_component=0):
    method sample (line 103) | def sample(self, N_k=(10, 20, 30, 40, 50), mode="u_kn", seed=None):
    method evenly_spaced_oscillators (line 210) | def evenly_spaced_oscillators(

FILE: pymbar/testsystems/timeseries.py
  function correlated_timeseries_example (line 4) | def correlated_timeseries_example(N=10000, tau=5.0, seed=None):

FILE: pymbar/timeseries.py
  function statistical_inefficiency (line 83) | def statistical_inefficiency(A_n, B_n=None, fast=False, mintime=3, fft=F...
  function statistical_inefficiency_multiple (line 209) | def statistical_inefficiency_multiple(A_kn, fast=False, return_correlati...
  function integrated_autocorrelation_time (line 371) | def integrated_autocorrelation_time(A_n, B_n=None, fast=False, mintime=3):
  function integrated_autocorrelation_timeMultiple (line 388) | def integrated_autocorrelation_timeMultiple(A_kn, fast=False):
  function normalized_fluctuation_correlation_function (line 405) | def normalized_fluctuation_correlation_function(A_n, B_n=None, N_max=Non...
  function normalized_fluctuation_correlation_function_multiple (line 509) | def normalized_fluctuation_correlation_function_multiple(
  function subsample_correlated_data (line 664) | def subsample_correlated_data(A_t, g=None, fast=False, conservative=Fals...
  function detect_equilibration (line 771) | def detect_equilibration(A_t, fast=True, nskip=1):
  function statistical_inefficiency_fft (line 839) | def statistical_inefficiency_fft(A_n, mintime=3):
  function detect_equilibration_binary_search (line 901) | def detect_equilibration_binary_search(A_t, bs_nodes=10):

FILE: pymbar/utils.py
  class TypeCastPerformanceWarning (line 36) | class TypeCastPerformanceWarning(RuntimeWarning):
  function kln_to_kn (line 40) | def kln_to_kn(kln, N_k=None, cleanup=False):
  function kn_to_n (line 77) | def kn_to_n(kn, N_k=None, cleanup=False):
  function ensure_type (line 116) | def ensure_type(
  function _logsum (line 234) | def _logsum(a_n):
  function logsumexp (line 278) | def logsumexp(a, axis=None, b=None, use_numexpr=True):
  function check_w_normalized (line 339) | def check_w_normalized(W, N_k, tolerance=1.0e-4):
  class ParameterError (line 400) | class ParameterError(Exception):
  class ConvergenceError (line 406) | class ConvergenceError(Exception):
  class BoundsError (line 412) | class BoundsError(Exception):
  class DataError (line 418) | class DataError(Exception):

FILE: pymbar/utils_for_testing.py
  function oscillators (line 62) | def oscillators(n_states, n_samples, provide_test=False):
  function exponentials (line 75) | def exponentials(n_states, n_samples, provide_test=False):