Index

A

ABF (class in pysages.methods.abf) ABFState (class in pysages.methods.abf) Acylindricity (class in pysages.colvars.shape) acylindricity() (in module pysages.colvars.shape) Angle (class in pysages.colvars.angles)

angle() (in module pysages.colvars.angles) ANN (class in pysages.methods.ann) ANNState (class in pysages.methods.ann) Asphericity (class in pysages.colvars.shape) asphericity() (in module pysages.colvars.shape) AxisCV (class in pysages.colvars.core)

B

barycenter() (in module pysages.colvars.coordinates) basin_sampling() (in module pysages.methods.ffs) bias (pysages.methods.abf.ABFState attribute) (pysages.methods.ann.ANNState attribute) (pysages.methods.ffs.FFSState attribute) (pysages.methods.funn.FUNNState attribute) (pysages.methods.harmonic_bias.HarmonicBiasState attribute) (pysages.methods.metad.MetadynamicsState attribute)

build() (in module pysages.colvars.core) (pysages.methods.abf.ABF method) (pysages.methods.core.SamplingMethod method) build_bias_grad_evaluator() (in module pysages.methods.metad) build_force_estimator() (in module pysages.methods.abf) (in module pysages.methods.funn) build_free_energy_grad_learner() (in module pysages.methods.funn) build_free_energy_learner() (in module pysages.methods.ann) build_gaussian_accumulator() (in module pysages.methods.metad)

C

calc_local_reference_systems() (in module pysages.colvars.orientation) centers (pysages.methods.metad.MetadynamicsState attribute) (pysages.methods.metad.PartialMetadynamicsState attribute)

check_input() (in module pysages.methods.ffs) CollectiveVariable (class in pysages.colvars.core) Component (class in pysages.colvars.coordinates)

D

dihedral_angle() (in module pysages.colvars.angles) DihedralAngle (class in pysages.colvars.angles) Displacement (class in pysages.colvars.coordinates)

displacement() (in module pysages.colvars.coordinates) Distance (class in pysages.colvars.coordinates) distance() (in module pysages.colvars.coordinates)

E

ERMSD (class in pysages.colvars.orientation) ermsd() (in module pysages.colvars.orientation)

ermsd_cg() (in module pysages.colvars.orientation) ermsd_core() (in module pysages.colvars.orientation) ERMSDCG (class in pysages.colvars.orientation)

F

F (pysages.methods.funn.FUNNState attribute) FFS (class in pysages.methods.ffs) FFSState (class in pysages.methods.ffs) force (pysages.methods.abf.ABFState attribute) FourPointCV (class in pysages.colvars.core) Fsum (pysages.methods.abf.ABFState attribute) (pysages.methods.funn.FUNNState attribute) (pysages.methods.funn.PartialFUNNState attribute) function (pysages.colvars.angles.Angle property) (pysages.colvars.angles.DihedralAngle property) (pysages.colvars.angles.RingAmplitude property) (pysages.colvars.angles.RingPhaseAngle property) (pysages.colvars.core.CollectiveVariable property) (pysages.colvars.shape.Acylindricity property) (pysages.colvars.shape.Asphericity property) (pysages.colvars.shape.PrincipalMoment property) (pysages.colvars.shape.RadiusOfGyration property) (pysages.colvars.shape.ShapeAnisotropy property)

FUNN (class in pysages.methods.funn) FUNNState (class in pysages.methods.funn)

G

g_vector() (in module pysages.colvars.orientation) get_cov() (pysages.methods.utils.HistogramLogger method) get_histograms() (pysages.methods.utils.HistogramLogger method) get_means() (pysages.methods.utils.HistogramLogger method) grid_gradient (pysages.methods.metad.MetadynamicsState attribute) (pysages.methods.metad.PartialMetadynamicsState attribute)

grid_idx (pysages.methods.metad.PartialMetadynamicsState attribute) grid_potential (pysages.methods.metad.MetadynamicsState attribute) (pysages.methods.metad.PartialMetadynamicsState attribute) GriddedSamplingMethod (class in pysages.methods.core) gyration_tensor() (in module pysages.colvars.shape)

H

HarmonicBias (class in pysages.methods.harmonic_bias) HarmonicBiasState (class in pysages.methods.harmonic_bias) heights (pysages.methods.metad.MetadynamicsState attribute) (pysages.methods.metad.PartialMetadynamicsState attribute)

hist (pysages.methods.abf.ABFState attribute) (pysages.methods.ann.ANNState attribute) (pysages.methods.funn.FUNNState attribute) (pysages.methods.funn.PartialFUNNState attribute) HistogramLogger (class in pysages.methods.utils)

I

idx (pysages.methods.metad.MetadynamicsState attribute) (pysages.methods.metad.PartialMetadynamicsState attribute)

ind (pysages.methods.funn.PartialFUNNState attribute) infer_base_coordinates() (in module pysages.colvars.orientation) initial_flow() (in module pysages.methods.ffs)

K

kabsch() (in module pysages.colvars.orientation)

kspring (pysages.methods.harmonic_bias.HarmonicBias property)

L

listify() (in module pysages.methods.utils)

M

MetaDLogger (class in pysages.methods.utils) Metadynamics (class in pysages.methods.metad) MetadynamicsState (class in pysages.methods.metad) module pysages pysages.colvars pysages.colvars.angles pysages.colvars.coordinates pysages.colvars.core pysages.colvars.orientation pysages.colvars.shape pysages.methods pysages.methods.abf pysages.methods.ann pysages.methods.core pysages.methods.ffs pysages.methods.funn pysages.methods.harmonic_bias pysages.methods.metad pysages.methods.spline_string pysages.methods.umbrella_integration pysages.methods.utils

multicomponent (pysages.colvars.core.CollectiveVariable property) multicomponent() (in module pysages.colvars.core)

N

ncalls (pysages.methods.abf.ABFState attribute) (pysages.methods.ann.ANNState attribute) (pysages.methods.ffs.FFSState attribute) (pysages.methods.funn.FUNNState attribute) (pysages.methods.harmonic_bias.HarmonicBiasState attribute) (pysages.methods.metad.MetadynamicsState attribute)

nn (pysages.methods.ann.ANNState attribute) (pysages.methods.funn.FUNNState attribute) (pysages.methods.funn.PartialFUNNState attribute) NNSamplingMethod (class in pysages.methods.core) numpyfy_vals() (in module pysages.methods.utils)

P

PartialFUNNState (class in pysages.methods.funn) PartialMetadynamicsState (class in pysages.methods.metad) phi (pysages.methods.ann.ANNState attribute) pred (pysages.methods.funn.PartialFUNNState attribute) principal_moments() (in module pysages.colvars.shape) PrincipalMoment (class in pysages.colvars.shape) prob (pysages.methods.ann.ANNState attribute) pysages module pysages.colvars module pysages.colvars.angles module pysages.colvars.coordinates module pysages.colvars.core module pysages.colvars.orientation module pysages.colvars.shape module

pysages.methods module pysages.methods.abf module pysages.methods.ann module pysages.methods.core module pysages.methods.ffs module pysages.methods.funn module pysages.methods.harmonic_bias module pysages.methods.metad module pysages.methods.spline_string module pysages.methods.umbrella_integration module pysages.methods.utils module

R

radius_of_gyration() (in module pysages.colvars.shape) RadiusOfGyration (class in pysages.colvars.shape) ReplicasConfiguration (class in pysages.methods.utils) reset() (pysages.methods.utils.HistogramLogger method) reshape_coordinates() (in module pysages.colvars.orientation) Result (class in pysages.methods.core) ring_amplitude() (in module pysages.colvars.angles)

ring_phase_angle() (in module pysages.colvars.angles) ring_puckering_coordinates() (in module pysages.colvars.angles) RingAmplitude (class in pysages.colvars.angles) RingPhaseAngle (class in pysages.colvars.angles) RingPuckeringCoordinates (class in pysages.colvars.angles) RMSD (class in pysages.colvars.orientation) rmsd() (in module pysages.colvars.orientation) run() (in module pysages.methods.core)

S

SamplingMethod (class in pysages.methods.core) save_hills() (pysages.methods.utils.MetaDLogger method) SerialExecutor (class in pysages.methods.utils) shape_anisotropy() (in module pysages.colvars.shape) ShapeAnisotropy (class in pysages.colvars.shape) sigmas (pysages.methods.metad.MetadynamicsState attribute) (pysages.methods.metad.PartialMetadynamicsState attribute)

snapshot_flags (pysages.methods.abf.ABF attribute) (pysages.methods.ffs.FFS attribute) SplineString (class in pysages.methods.spline_string) submit() (pysages.methods.utils.SerialExecutor method) sum_of_gaussians() (in module pysages.methods.metad)

T

ThreePointCV (class in pysages.colvars.core)

TwoPointCV (class in pysages.colvars.core)

U

UmbrellaIntegration (class in pysages.methods.umbrella_integration)

W

weighted_barycenter() (in module pysages.colvars.coordinates) weighted_gyration_tensor() (in module pysages.colvars.shape) weighted_radius_of_gyration() (in module pysages.colvars.shape)

Wp (pysages.methods.abf.ABFState attribute) (pysages.methods.funn.FUNNState attribute) Wp_ (pysages.methods.abf.ABFState attribute) (pysages.methods.funn.FUNNState attribute)

X

xi (pysages.methods.abf.ABFState attribute) (pysages.methods.ann.ANNState attribute) (pysages.methods.ffs.FFSState attribute) (pysages.methods.funn.FUNNState attribute) (pysages.methods.funn.PartialFUNNState attribute) (pysages.methods.harmonic_bias.HarmonicBiasState attribute) (pysages.methods.metad.MetadynamicsState attribute) (pysages.methods.metad.PartialMetadynamicsState attribute)