Index

_

__init__() (msmbuilder.clustering.Clarans method) (msmbuilder.clustering.HybridKMedoids method) (msmbuilder.clustering.KCenters method) (msmbuilder.clustering.SubsampledClarans method) (msmbuilder.metrics.AtomPairs method) (msmbuilder.metrics.BooleanContact method) (msmbuilder.metrics.ContinuousContact method) (msmbuilder.metrics.Dihedral method) (msmbuilder.metrics.RMSD method) (msmbuilder.metrics.baseclasses.Vectorized method) _assign() (in module msmbuilder.clustering) _clarans() (in module msmbuilder.clustering)

_hybrid_kmedoids() (in module msmbuilder.clustering) _kcenters() (in module msmbuilder.clustering)

A

AbstractDistanceMetric (class in msmbuilder.metrics.baseclasses) add_argument() (in module msmbuilder.arglib) (msmbuilder.arglib.ArgumentParser method) add_argument_group() (msmbuilder.arglib.ArgumentParser method) add_subparsers() (msmbuilder.arglib.ArgumentParser method) all_pairwise() (msmbuilder.metrics.AtomPairs method) (msmbuilder.metrics.BooleanContact method) (msmbuilder.metrics.ContinuousContact method) (msmbuilder.metrics.Dihedral method) (msmbuilder.metrics.RMSD method) (msmbuilder.metrics.baseclasses.AbstractDistanceMetric method) (msmbuilder.metrics.baseclasses.Vectorized method) all_to_all() (msmbuilder.metrics.AtomPairs method) (msmbuilder.metrics.BooleanContact method) (msmbuilder.metrics.ContinuousContact method) (msmbuilder.metrics.Dihedral method) (msmbuilder.metrics.baseclasses.Vectorized method) append_frames_to_file() (msmbuilder.Trajectory.Trajectory class method) AppendPDB() (msmbuilder.Trajectory.Trajectory method)

apply_mapping_to_assignments() (in module msmbuilder.MSMLib) apply_mapping_to_vector() (in module msmbuilder.MSMLib) are_all_dimensions_same() (in module msmbuilder.msm_analysis) ArgumentParser (class in msmbuilder.arglib) assign_in_memory() (in module msmbuilder.assigning) assign_with_checkpoint() (in module msmbuilder.assigning) AtomPairs (class in msmbuilder.metrics)

B

BaseFlatClusterer (class in msmbuilder.clustering) BooleanContact (class in msmbuilder.metrics)

build_msm() (in module msmbuilder.MSMLib)

C

calc_expectation_timeseries() (in module msmbuilder.msm_analysis) calculate_all_hub_scores() (in module msmbuilder.tpt) calculate_all_to_all_mfpt() (in module msmbuilder.tpt) calculate_avg_TP_time() (in module msmbuilder.tpt) calculate_committors() (in module msmbuilder.tpt) calculate_ensemble_mfpt() (in module msmbuilder.tpt) calculate_fluxes() (in module msmbuilder.tpt) calculate_fraction_visits() (in module msmbuilder.tpt) calculate_hub_score() (in module msmbuilder.tpt) calculate_mfpt() (in module msmbuilder.tpt) calculate_net_fluxes() (in module msmbuilder.tpt)

check_assignment_array_input() (in module msmbuilder.utils) check_dimensions() (in module msmbuilder.msm_analysis) check_for_bad_eigenvalues() (in module msmbuilder.msm_analysis) check_transition() (in module msmbuilder.msm_analysis) Clarans (class in msmbuilder.clustering) concatenate_trajectories() (in module msmbuilder.clustering) contact_reaction_coordinate() (in module msmbuilder.cfep) ContinuousContact (class in msmbuilder.metrics) Counter (class in msmbuilder.utils) CutCoordinate (class in msmbuilder.cfep)

D

deprecated() (in module msmbuilder.utils) deterministic_subsample() (in module msmbuilder.clustering) die_if_path_exists() (in module msmbuilder.arglib)

Dihedral (class in msmbuilder.metrics) Dijkstra() (in module msmbuilder.tpt)

E

empty_trajectory_like() (in module msmbuilder.clustering) ensure_path_exists() (in module msmbuilder.arglib) enum_chunks_from_hdf() (msmbuilder.Trajectory.Trajectory class method) enum_chunks_from_lhdf() (msmbuilder.Trajectory.Trajectory class method)

ergodic_trim() (in module msmbuilder.MSMLib) estimate_rate_matrix() (in module msmbuilder.MSMLib) estimate_transition_matrix() (in module msmbuilder.MSMLib) evaluate_partition_functions() (msmbuilder.cfep.CutCoordinate method)

F

fast_cdist() (in module msmbuilder.metrics.core) fast_pdist() (in module msmbuilder.metrics.core) find_path_bottleneck() (in module msmbuilder.tpt) find_top_paths() (in module msmbuilder.tpt)

flatten() (in module msmbuilder.msm_analysis) format_block() (in module msmbuilder.utils) future_warning() (in module msmbuilder.utils)

G

get_assignments() (msmbuilder.clustering.BaseFlatClusterer method) (msmbuilder.clustering.Clarans method) (msmbuilder.clustering.Hierarchical method) (msmbuilder.clustering.HybridKMedoids method) (msmbuilder.clustering.KCenters method) (msmbuilder.clustering.SubsampledClarans method) get_count_matrix_from_assignments() (in module msmbuilder.MSMLib) get_counts_from_traj() (in module msmbuilder.MSMLib) get_distances() (msmbuilder.clustering.BaseFlatClusterer method) (msmbuilder.clustering.Clarans method) (msmbuilder.clustering.HybridKMedoids method) (msmbuilder.clustering.KCenters method) (msmbuilder.clustering.SubsampledClarans method) get_eigenvectors() (in module msmbuilder.msm_analysis) get_generators_as_traj() (msmbuilder.clustering.BaseFlatClusterer method) (msmbuilder.clustering.Clarans method) (msmbuilder.clustering.HybridKMedoids method) (msmbuilder.clustering.KCenters method) (msmbuilder.clustering.SubsampledClarans method)

get_implied_timescales() (in module msmbuilder.msm_analysis) GetEnumeratedAtomID() (msmbuilder.Trajectory.Trajectory method) GetEnumeratedResidueID() (msmbuilder.Trajectory.Trajectory method) GetNumberOfAtoms() (msmbuilder.Trajectory.Trajectory method) GetNumberOfResidues() (msmbuilder.Trajectory.Trajectory method)

H

Hierarchical (class in msmbuilder.clustering) highlight() (in module msmbuilder.utils) Hybrid (class in msmbuilder.metrics.hybrid)

HybridKMedoids (class in msmbuilder.clustering) HybridPNorm (class in msmbuilder.metrics.hybrid)

I

invert_assignments() (in module msmbuilder.MSMLib)

is_transition_matrix() (in module msmbuilder.msm_analysis)

K

KCenters (class in msmbuilder.clustering)

keynat() (in module msmbuilder.utils)

L

load_from_dcd() (msmbuilder.Trajectory.Trajectory class method) load_from_disk() (msmbuilder.clustering.Hierarchical class method) load_from_hdf() (msmbuilder.Trajectory.Trajectory class method) load_from_lhdf() (msmbuilder.Trajectory.Trajectory class method) load_from_pdb() (msmbuilder.Trajectory.Trajectory class method) load_from_pdbList() (msmbuilder.Trajectory.Trajectory class method)

load_from_trr() (msmbuilder.Trajectory.Trajectory class method) load_from_xtc() (msmbuilder.Trajectory.Trajectory class method) load_trajectory_file() (msmbuilder.Trajectory.Trajectory class method) log_likelihood() (in module msmbuilder.MSMLib) lru_cache() (in module msmbuilder.utils)

M

make_methods_pickable() (in module msmbuilder.utils) many_to_many() (msmbuilder.metrics.AtomPairs method) (msmbuilder.metrics.BooleanContact method) (msmbuilder.metrics.ContinuousContact method) (msmbuilder.metrics.Dihedral method) (msmbuilder.metrics.baseclasses.Vectorized method) mle_reversible_count_matrix() (in module msmbuilder.MSMLib) msmbuilder.clustering (module)

msmbuilder.MSMLib (module) msmbuilder.tpt (module) msmbuilder.utils (module)

O

one_to_all() (msmbuilder.metrics.AtomPairs method) (msmbuilder.metrics.BooleanContact method) (msmbuilder.metrics.ContinuousContact method) (msmbuilder.metrics.Dihedral method) (msmbuilder.metrics.RMSD method) (msmbuilder.metrics.baseclasses.AbstractDistanceMetric method) (msmbuilder.metrics.baseclasses.Vectorized method) one_to_many() (msmbuilder.metrics.AtomPairs method) (msmbuilder.metrics.BooleanContact method) (msmbuilder.metrics.ContinuousContact method) (msmbuilder.metrics.Dihedral method) (msmbuilder.metrics.RMSD method) (msmbuilder.metrics.baseclasses.AbstractDistanceMetric method) (msmbuilder.metrics.baseclasses.Vectorized method)

optimize() (msmbuilder.cfep.VariableCoordinate method)

P

p_norm() (in module msmbuilder.clustering) parse_args() (msmbuilder.arglib.ArgumentParser method) plot() (msmbuilder.cfep.CutCoordinate method)

prepare_trajectory() (msmbuilder.metrics.AtomPairs method) (msmbuilder.metrics.BooleanContact method) (msmbuilder.metrics.ContinuousContact method) (msmbuilder.metrics.Dihedral method) (msmbuilder.metrics.RMSD method) (msmbuilder.metrics.baseclasses.AbstractDistanceMetric method) (msmbuilder.metrics.baseclasses.Vectorized method) project_observable_onto_transition_matrix() (in module msmbuilder.msm_analysis) propagate_model() (in module msmbuilder.msm_analysis)

R

reaction_mfpt() (msmbuilder.cfep.CutCoordinate method) read_dcd_frame() (msmbuilder.Trajectory.Trajectory class method) read_frame() (msmbuilder.Trajectory.Trajectory class method) read_hdf_frame() (msmbuilder.Trajectory.Trajectory class method) read_lhdf_frame() (msmbuilder.Trajectory.Trajectory class method)

read_xtc_frame() (msmbuilder.Trajectory.Trajectory class method) renumber_states() (in module msmbuilder.MSMLib) rescale_to_natural_coordinate() (msmbuilder.cfep.CutCoordinate method) restrict_atom_indices() (msmbuilder.Trajectory.Trajectory method) RMSD (class in msmbuilder.metrics)

S

sample() (in module msmbuilder.msm_analysis) save() (msmbuilder.Trajectory.Trajectory method) save_to_disk() (msmbuilder.clustering.Hierarchical method) save_to_lhdf() (msmbuilder.Trajectory.Trajectory method) save_to_pdb() (msmbuilder.Trajectory.Trajectory method) save_to_xtc() (msmbuilder.Trajectory.Trajectory method) save_to_xyz() (msmbuilder.Trajectory.Trajectory method) set_coordinate_as_committors() (msmbuilder.cfep.CutCoordinate method)

set_coordinate_as_eigvector2() (msmbuilder.cfep.CutCoordinate method) set_coordinate_values() (msmbuilder.cfep.CutCoordinate method) split() (in module msmbuilder.clustering) stochastic_subsample() (in module msmbuilder.clustering) streaming_assign_with_checkpoint() (in module msmbuilder.assigning) subsample() (msmbuilder.Trajectory.Trajectory method) SubsampledClarans (class in msmbuilder.clustering)

T

tarjan() (in module msmbuilder.MSMLib)

Trajectory (class in msmbuilder.Trajectory)

U

unconcatenate_trajectory() (in module msmbuilder.clustering)

uneven_zip() (in module msmbuilder.utils)

V

VariableCoordinate (class in msmbuilder.cfep)

Vectorized (class in msmbuilder.metrics.baseclasses)