Index

_

_angle() (poreana.sample.Sample method) _angle_data() (poreana.sample.Sample method) _bin_ex() (poreana.sample.Sample method) _bin_in() (poreana.sample.Sample method) _bin_in_const_A() (poreana.sample.Sample method) _bin_mc() (poreana.sample.Sample method) _bin_window() (poreana.sample.Sample method) _calc_profile() (poreana.model.CosineModel method) (poreana.model.Model method) (poreana.model.StepModel method) _cosine_model() (poreana.model.CosineModel method) _create_basis_border() (poreana.model.CosineModel method) (poreana.model.StepModel method) _create_basis_center() (poreana.model.CosineModel method) (poreana.model.StepModel method) _density() (poreana.sample.Sample method) _density_data() (poreana.sample.Sample method) _diffusion_bin() (poreana.sample.Sample method) _diffusion_bin_data() (poreana.sample.Sample method)

_diffusion_bin_step() (poreana.sample.Sample method) _diffusion_mc() (poreana.sample.Sample method) _diffusion_mc_data() (poreana.sample.Sample method) _gyration() (poreana.sample.Sample method) _gyration_data() (poreana.sample.Sample method) _init_model() (poreana.model.CosineModel method) (poreana.model.StepModel method) _init_profiles() (poreana.model.CosineModel method) (poreana.model.Model method) (poreana.model.StepModel method) _init_rate_matrix_pbc() (poreana.mc.MC method) _init_stats() (poreana.mc.MC method) _log_likelihood_z() (poreana.mc.MC method) _mcmove_df() (poreana.mc.MC method) _mcmove_diffusion() (poreana.mc.MC method) _run_helper() (poreana.mc.MC method) _sample_helper() (poreana.sample.Sample method) _step_model() (poreana.model.StepModel method) _update_movewidth_mc() (poreana.mc.MC method)

A

angle() (in module poreana.geometry)

B

bins() (in module poreana.density) (in module poreana.diffusion) bins_plot() (in module poreana.angle) (in module poreana.density) (in module poreana.diffusion) (in module poreana.gyration)

C

calculate() (in module poreana.adsorption) column() (in module poreana.utils)

CosineModel (class in poreana.model) cross_product() (in module poreana.geometry) cui() (in module poreana.diffusion)

D

dot_product() (in module poreana.geometry)

F

file_to_text() (in module poreana.utils)

I

init_angle() (poreana.sample.Sample method) init_density() (poreana.sample.Sample method)

init_diffusion_bin() (poreana.sample.Sample method) init_diffusion_mc() (poreana.sample.Sample method) init_gyration() (poreana.sample.Sample method)

L

length() (in module poreana.geometry)

load() (in module poreana.utils)

M

MC (class in poreana.mc) mc_fit() (in module poreana.diffusion) mc_inputs() (in module poreana.tables) mc_lag_time() (in module poreana.tables) mc_model() (in module poreana.tables) mc_profile() (in module poreana.diffusion) (in module poreana.freeenergy) mc_results() (in module poreana.tables) mc_statistics() (in module poreana.tables) mc_trans_mat() (in module poreana.diffusion) mean() (in module poreana.density) (in module poreana.diffusion) mkdirp() (in module poreana.utils) mmol_g_to_mumol_m2() (in module poreana.utils)

mmol_l_to_mols() (in module poreana.utils) Model (class in poreana.model) module poreana.adsorption poreana.angle poreana.density poreana.diffusion poreana.freeenergy poreana.geometry poreana.gyration poreana.tables poreana.utils mols_to_mmol_l() (in module poreana.utils) mols_to_mumol_m2() (in module poreana.utils) mumol_m2_to_mols() (in module poreana.utils)

N

num_dens_to_mass_dens() (in module poreana.utils)

P

poreana.adsorption module poreana.angle module poreana.density module poreana.diffusion module poreana.freeenergy module

poreana.geometry module poreana.gyration module poreana.tables module poreana.utils module

R

run() (poreana.mc.MC method)

S

Sample (class in poreana.sample) sample() (poreana.sample.Sample method)

save() (in module poreana.utils) StepModel (class in poreana.model)

T

tic() (in module poreana.utils)

toc() (in module poreana.utils)

U

unit() (in module poreana.geometry)

V

vector() (in module poreana.geometry)