• Docs »

---

Index

_

__init__() (msmbuilder.arglib.ArgumentParser method) (msmbuilder.cfep.CutCoordinate method), [1] (msmbuilder.cfep.VariableCoordinate method), [1] (msmbuilder.clustering.BaseFlatClusterer method) (msmbuilder.clustering.Clarans method) (msmbuilder.clustering.Hierarchical method) (msmbuilder.clustering.HybridKMedoids method) (msmbuilder.clustering.KCenters method) (msmbuilder.reduce.tICA.tICA method)

A

add_argument() (in module msmbuilder.arglib) apply_mapping_to_assignments() (in module msmbuilder.MSMLib) apply_mapping_to_vector() (in module msmbuilder.MSMLib)

ArgumentParser (class in msmbuilder.arglib) assign_in_memory() (in module msmbuilder.assigning) assign_with_checkpoint() (in module msmbuilder.assigning)

B

BaseFlatClusterer (class in msmbuilder.clustering)

build_msm() (in module msmbuilder.MSMLib)

C

calc_expectation_timeseries() (in module msmbuilder.msm_analysis) Clarans (class in msmbuilder.clustering) concatenate_prep_trajectories() (in module msmbuilder.clustering) concatenate_trajectories() (in module msmbuilder.clustering)

ConstructRateFromParams() (in module msmbuilder.SCRE) contact_reaction_coordinate() (in module msmbuilder.cfep), [1] ConvertTIntoK() (in module msmbuilder.SCRE) CutCoordinate (class in msmbuilder.cfep), [1]

D

deterministic_subsample() (in module msmbuilder.clustering)

die_if_path_exists() (in module msmbuilder.arglib)

E

ensure_path_exists() (in module msmbuilder.arglib) ergodic_trim() (in module msmbuilder.MSMLib) ergodic_trim_indices() (in module msmbuilder.MSMLib)

estimate_rate_matrix() (in module msmbuilder.MSMLib) estimate_transition_matrix() (in module msmbuilder.MSMLib)

F

FixEntry() (in module msmbuilder.SCRE)

G

get_count_matrix_from_assignments() (in module msmbuilder.MSMLib) get_counts_from_traj() (in module msmbuilder.MSMLib) get_eigenvectors() (in module msmbuilder.msm_analysis) get_epsilon_neighborhoods() (in module msmbuilder.drift)

get_implied_timescales() (in module msmbuilder.msm_analysis) get_reversible_eigenvectors() (in module msmbuilder.msm_analysis) GetFormat() (in module msmbuilder.SCRE)

H

Hierarchical (class in msmbuilder.clustering) hitting_time() (in module msmbuilder.drift)

HybridKMedoids (class in msmbuilder.clustering)

I

initialize() (msmbuilder.reduce.tICA.tICA method) invert_assignments() (in module msmbuilder.MSMLib)

is_transition_matrix() (in module msmbuilder.msm_analysis)

K

KCenters (class in msmbuilder.clustering)

L

log_likelihood() (in module msmbuilder.MSMLib)

LogLikelihood() (in module msmbuilder.SCRE)

M

MaximizeRateLikelihood() (in module msmbuilder.SCRE) mle_reversible_count_matrix() (in module msmbuilder.MSMLib) msm_acf() (in module msmbuilder.msm_analysis) msmbuilder.arglib (module) msmbuilder.assigning (module) msmbuilder.cfep (module)

msmbuilder.clustering (module) msmbuilder.drift (module) msmbuilder.msm_analysis (module) msmbuilder.MSMLib (module) msmbuilder.reduce.tICA (module) msmbuilder.SCRE (module)

P

p_norm() (in module msmbuilder.clustering) permute_mat() (in module msmbuilder.MSMLib) PlotRates() (in module msmbuilder.SCRE)

project() (msmbuilder.reduce.tICA.tICA method) project_observable_onto_transition_matrix() (in module msmbuilder.msm_analysis) propagate_model() (in module msmbuilder.msm_analysis)

R

renumber_states() (in module msmbuilder.MSMLib)

S

sample() (in module msmbuilder.msm_analysis) save() (msmbuilder.reduce.tICA.tICA method) solve() (msmbuilder.reduce.tICA.tICA method)

square_drift() (in module msmbuilder.drift) stochastic_subsample() (in module msmbuilder.clustering)

T

tarjan() (in module msmbuilder.MSMLib) tICA (class in msmbuilder.reduce.tICA)

train() (msmbuilder.reduce.tICA.tICA method) trim_states() (in module msmbuilder.MSMLib)

U

unconcatenate_trajectory() (in module msmbuilder.clustering)

V

VariableCoordinate (class in msmbuilder.cfep), [1]