Index

A

add_disulfide_bond() (SimulationBox method) af2rave.colvar module af2rave.feature.analysis module af2rave.feature.utils module af2rave.simulation.reporter module af2rave.simulation.simulation module

af2rave.simulation.utils module af2rave.spib.spib module af2rave.spib.spib_result module apparent_bias (SPIBResult property) apparent_weight (SPIBResult property) apply_filter() (FeatureSelection method) atom_name() (in module af2rave.feature.utils) atom_pairs (FeatureSelection property)

B

bias (SPIBResult property)

C

chain() (in module af2rave.feature.utils) chimera_representation() (in module af2rave.feature.utils) choose() (Colvar method)

Colvar (class in af2rave.colvar) create_box() (SimulationBox method) CVReporter (class in af2rave.simulation.reporter)

D

data (Colvar property)

describeNextReport() (CVReporter method) dt (SPIBResult property)

F

feature_array (FeatureSelection property) features (FeatureSelection property)

FeatureSelection (class in af2rave.feature.analysis) from_file() (Colvar class method) (SPIBResult class method)

G

get_chimera_plotscript() (FeatureSelection method) get_free_energy() (SPIBResult method) get_latent_representation() (SPIBResult method)

get_probability_distribution() (SPIBResult method) get_rmsd() (FeatureSelection method) get_state_label() (SPIBResult method) get_traj_label() (SPIBResult method)

H

header (Colvar property)

K

kappend() (Colvar method)

M

map() (Colvar method) map_atom_index (SimulationBox property) map_atom_index() (TopologyMap method) MinimizationReporter (class in af2rave.simulation.reporter) minimum_nonbonded_distance (FeatureSelection property) module af2rave.colvar af2rave.feature.analysis af2rave.feature.utils af2rave.simulation.reporter af2rave.simulation.simulation af2rave.simulation.utils af2rave.spib.spib af2rave.spib.spib_result

N

n_converged_states (SPIBResult property) n_input_labels (SPIBResult property)

n_traj (SPIBResult property) nonbonded_pairs (FeatureSelection property)

P

pca() (FeatureSelection method) pdb_name (FeatureSelection property) peptide_bond_filter() (FeatureSelection method) peptide_bond_stats (FeatureSelection property)

pos (UnbiasedSimulation property) project() (SPIBResult method) project_colvar() (SPIBResult method) project_state_label() (SPIBResult method)

R

rank_feature() (FeatureSelection method) read() (Colvar method) ref_pdb (FeatureSelection property) regular_space_clustering() (FeatureSelection method) report() (CVReporter method) (MinimizationReporter method)

representation() (in module af2rave.feature.utils) resid() (in module af2rave.feature.utils) resname() (in module af2rave.feature.utils) restart() (UnbiasedSimulation method) rmsd_filter() (FeatureSelection method) run() (SPIBProcess method) (UnbiasedSimulation method)

S

save_checkpoint() (UnbiasedSimulation method) save_pdb() (SimulationBox method) (UnbiasedSimulation method) shape (Colvar property)

SimulationBox (class in af2rave.simulation.utils) SPIBProcess (class in af2rave.spib.spib) SPIBResult (class in af2rave.spib.spib_result) steric_clash_filter() (FeatureSelection method) stride() (Colvar method)

T

tappend() (Colvar method) time (Colvar property) to_file() (SPIBResult method)

top (FeatureSelection property) TopologyMap (class in af2rave.simulation.utils) traj (FeatureSelection property)

U

UnbiasedSimulation (class in af2rave.simulation.simulation)

W

weight (SPIBResult property)

write() (Colvar method)