Index

_

__init__() (bcc_build.BicontinuousCubicBuild method) (coordinate_trace.CoordinateTrace method) (correlation_function.Correlation method) (genmdp.SimulationMdp method) (gentop.SystemTopology method) (hbonds.System method) (hexagonal_build.BuildHexagonal method) (infinite_hidden_markov_model.InfiniteHMM method) (msd.Diffusivity method) (parameterize.Parameterize method) (physical.region method) (rdf.System method) (solvation_equilibration.System method) (stats.Cdf method) (timeseries.VectorAutoRegression method) (topology.LC method) (topology.ReadItp method) (topology.Residue method) (xlink.System method) (xlink.Topology method) (xlink_schemes.Dibrpyr14 method) (xlink_schemes.DieneScheme method) (xlink_schemes.XlinkReaction method)

A

acf() (in module timeseries) acf_slow() (in module timeseries) add_pull_groups() (genmdp.SimulationMdp method) add_residue() (gentop.SystemTopology method) approximate_discrete_powerlaw() (in module sampling)

assign_gaff_parameters() (parameterize.Parameterize method) assign_molcharge_charges() (parameterize.Parameterize method) atoms() (topology.ReadItp method) autocov() (in module timeseries) avg_pore_loc() (in module p2p) (in module physical)

B

BicontinuousCubicBuild (class in bcc_build) bootstrap() (msd.Diffusivity method) (rdf.System method) bootstrap_msd() (in module timeseries)

bootstrap_power_law() (msd.Diffusivity method) build_column() (hexagonal_build.BuildHexagonal method) build_com() (rdf.System method) build_spline() (rdf.System method) BuildHexagonal (class in hexagonal_build)

C

calculate() (msd.Diffusivity method) calculate_moving_average() (in module timeseries) calculate_pore_water() (solvation_equilibration.System method) Cdf (class in stats) cdf() (stats.Cdf method) cdf_exp() (in module fitting_functions) cdf_power_law() (in module fitting_functions)

center_of_mass() (in module physical) compdensity() (in module physical) conc() (in module physical) confidence_interval() (in module stats) convert_parameter_format() (parameterize.Parameterize method) CoordinateTrace (class in coordinate_trace) Correlation (class in correlation_function) correlograms() (in module timeseries)

D

determine_monomer_placement() (bcc_build.BicontinuousCubicBuild method) determine_reaction_type() (xlink_schemes.DieneScheme method) Dibrpyr14 (class in xlink_schemes)

DieneScheme (class in xlink_schemes) Diffusivity (class in msd) discrete_powerlaw_ccdf() (in module sampling) distance_from_pore_center() (in module physical)

E

energy_minimize() (parameterize.Parameterize method) equilibrate() (solvation_equilibration.System method)

exact_discrete_power_law_sample() (in module sampling) exponential_integrated() (in module fitting_functions)

F

file_rw (module) fit_linear() (msd.Diffusivity method) fit_power_law() (in module fitting_functions) (msd.Diffusivity method)

fitting_functions (module) fix_names() (in module topology) full_equilibration() (solvation_equilibration.System method)

G

gaussian_log_likelihood() (in module fitting_functions) gen_grid() (bcc_build.BicontinuousCubicBuild method) get_bonds() (topology.ReadItp method)

get_improper_dihedrals() (topology.ReadItp method) get_vsites() (topology.ReadItp method) gromacs (module) grps() (in module rdf)

H

head2tail() (xlink_schemes.DieneScheme method)

hexagonal_build (module) hurst_autocovariance() (in module fitting_functions)

I

identify_hbonds() (hbonds.System method) inference() (infinite_hidden_markov_model.InfiniteHMM method)

InfiniteHMM (class in infinite_hidden_markov_model) insert_molecules() (in module gromacs)

L

LC (class in topology) limits() (in module physical)

line() (in module fitting_functions) locate_pore_centers() (coordinate_trace.CoordinateTrace method) log_power_law() (in module fitting_functions)

M

make_box() (parameterize.Parameterize method) make_slice() (correlation_function.Correlation method) map_atoms() (in module topology)

minimum_image_distance() (in module physical) monoclinic_to_cubic() (in module transform) msd() (in module timeseries) msd_straightforward() (in module timeseries)

O

organize_bonds() (topology.ReadItp method)

outliers() (in module stats)

P

p2p (module) p2p() (in module p2p) (in module physical) p2p_stats() (in module p2p) Parameterize (class in parameterize) partition() (in module physical) physical (module) place_monomers() (bcc_build.BicontinuousCubicBuild method) place_water_tails() (solvation_equilibration.System method) plot() (msd.Diffusivity method) (rdf.System method)

plot_autocorrelation() (msd.Diffusivity method) plot_hbonds() (hbonds.System method) plot_slice() (correlation_function.Correlation method) plot_trace() (coordinate_trace.CoordinateTrace method) power_law() (in module fitting_functions) power_law_discrete_log_likelihood() (in module fitting_functions) powerlaw_cutoff_mle() (in module fitting_functions) powerlaw_integrated() (in module fitting_functions) put_in_box() (in module physical)

Q

query_database() (solvation_equilibration.System method)

R

radial_distance_spline() (in module physical) radial_distances() (coordinate_trace.CoordinateTrace method) radial_distribution_function() (rdf.System method) radical_c2() (xlink_schemes.DieneScheme method) rand (module) random_exponential_dwell() (in module sampling) random_orientation() (in module transform) random_power_law_dwell() (in module sampling) random_sample() (stats.Cdf method) randombeta() (in module rand) randombetavariate() (in module rand) randombinomial() (in module rand) randomdirichlet() (in module rand) randomexponential() (in module rand) randomgamma() (in module rand) randomgammaint() (in module rand) randomnormal() (in module rand) rdf (module)

ReadItp (class in topology) region (class in physical) remove_residue() (gentop.SystemTopology method) reorder() (bcc_build.BicontinuousCubicBuild method) (hexagonal_build.BuildHexagonal method) rescale() (in module transform) Residue (class in topology) residue_center_of_mass() (in module physical) restrict_atoms() (in module p2p) restrict_to_pore() (msd.Diffusivity method) rotate_coords() (in module transform) rotate_coords_x() (in module transform) rotate_coords_z() (in module transform) rotate_vector() (in module transform) rotate_x() (in module transform) rotate_z() (in module transform) rotateplane() (in module transform) rotateplane_coords() (in module transform) Rvect2vect() (in module transform)

S

sampling (module) set_eligible() (hbonds.System method) simulate() (in module gromacs) SimulationMdp (class in genmdp) stationarity() (msd.Diffusivity method) stats (module) step_autocorrelation() (in module timeseries) (msd.Diffusivity method)

summarize_results() (infinite_hidden_markov_model.InfiniteHMM method) switch_points() (in module timeseries) System (class in hbonds) (class in rdf) (class in solvation_equilibration) (class in xlink) SystemTopology (class in gentop)

T

terminate() (xlink_schemes.DieneScheme method) thickness() (in module physical) timeseries (module) Topology (class in xlink)

topology (module) trace_pores() (in module physical) transform (module) translate() (in module transform)

U

update_cdf() (stats.Cdf method)

V

VectorAutoRegression (class in timeseries)

W

wrap_box() (in module physical) write_assembly() (in module file_rw) write_em_mdp() (genmdp.SimulationMdp method) (in module file_rw) write_final_pore_configuration() (solvation_equilibration.System method) write_gro() (hexagonal_build.BuildHexagonal method) (in module file_rw)

write_gro_pos() (in module file_rw) write_npt_mdp() (genmdp.SimulationMdp method) write_nve_mdp() (genmdp.SimulationMdp method) write_nvt_mdp() (genmdp.SimulationMdp method) write_top() (gentop.SystemTopology method) write_water_ndx() (in module file_rw)

X

XlinkReaction (class in xlink_schemes)

xyregion() (physical.region method)

Z

z_correlation() (in module hexagonal_build)

zeta() (in module fitting_functions)