Index

A

ASEExtendedXYZReader (class in thermolib.thermodynamics.trajectory) Average (class in thermolib.thermodynamics.cv)

average() (thermolib.thermodynamics.condprob.ConditionalProbability1D1D method) average_cv_constraint_other() (thermolib.thermodynamics.histogram.Histogram2D method)

B

BaseFreeEnergyProfile (class in thermolib.thermodynamics.fep) BaseProfile (class in thermolib.thermodynamics.fep) BaseRateFactor (class in thermolib.kinetics.rate)

BiasPotential1D (class in thermolib.thermodynamics.bias) BiasPotential2D (class in thermolib.thermodynamics.bias) blav() (in module thermolib.tools)

C

calc_fun_values() (thermolib.error.Propagator method) CenterOfMass (class in thermolib.thermodynamics.cv) CenterOfPosition (class in thermolib.thermodynamics.cv) ColVarReader (class in thermolib.thermodynamics.trajectory) compute() (thermolib.thermodynamics.cv.Average method) (thermolib.thermodynamics.cv.CenterOfMass method) (thermolib.thermodynamics.cv.CenterOfPosition method) (thermolib.thermodynamics.cv.CoordinationNumber method) (thermolib.thermodynamics.cv.Difference method) (thermolib.thermodynamics.cv.Distance method) (thermolib.thermodynamics.cv.DistanceCOP method) (thermolib.thermodynamics.cv.DotProduct method) (thermolib.thermodynamics.cv.LinearCombination method) (thermolib.thermodynamics.cv.Minimum method) (thermolib.thermodynamics.cv.NormalizedAxis method) (thermolib.thermodynamics.cv.NormalToPlane method) compute_rate() (thermolib.kinetics.rate.BaseRateFactor method)

ConditionalProbability1D1D (class in thermolib.thermodynamics.condprob) ConditionalProbability1D2D (class in thermolib.thermodynamics.condprob) CoordinationNumber (class in thermolib.thermodynamics.cv) copy() (thermolib.error.GaussianDistribution method) (thermolib.error.LogGaussianDistribution method) (thermolib.error.MultiGaussianDistribution method) (thermolib.error.MultiLogGaussianDistribution method) (thermolib.thermodynamics.fep.FreeEnergySurface2D method) (thermolib.thermodynamics.histogram.Histogram1D method) (thermolib.thermodynamics.histogram.Histogram2D method) corr() (thermolib.error.MultiDistribution method) corrtime_from_acf() (in module thermolib.tools) cov() (thermolib.error.MultiGaussianDistribution method) (thermolib.error.MultiLogGaussianDistribution method) crop() (thermolib.thermodynamics.fep.BaseProfile method) (thermolib.thermodynamics.fep.FreeEnergySurface2D method) CVComputer (class in thermolib.thermodynamics.trajectory)

D

decorrelate() (in module thermolib.tools) deproject() (thermolib.thermodynamics.condprob.ConditionalProbability1D1D method) (thermolib.thermodynamics.condprob.ConditionalProbability1D2D method) detect_clusters() (thermolib.thermodynamics.fep.FreeEnergySurface2D method)

Difference (class in thermolib.thermodynamics.cv) Distance (class in thermolib.thermodynamics.cv) DistanceCOP (class in thermolib.thermodynamics.cv) DistOrthProjOrig (class in thermolib.thermodynamics.cv) DotProduct (class in thermolib.thermodynamics.cv)

E

ErrorArray (class in thermolib.error) exp_from_gaussian() (thermolib.error.LogGaussianDistribution class method) (thermolib.error.MultiLogGaussianDistribution class method)

extract_polynomial_bias_info() (in module thermolib.tools)

F

finish() (thermolib.kinetics.rate.BaseRateFactor method) finish_error() (thermolib.thermodynamics.condprob.ConditionalProbability1D1D method) fisher_matrix_mle_probdens() (in module thermolib.tools) flower() (thermolib.thermodynamics.fep.BaseProfile method) (thermolib.thermodynamics.fep.FreeEnergySurface2D method) format_scientific() (in module thermolib.tools) FreeEnergySurface2D (class in thermolib.thermodynamics.fep) from_average() (thermolib.thermodynamics.fep.BaseProfile class method) (thermolib.thermodynamics.histogram.Histogram1D class method) (thermolib.thermodynamics.histogram.Histogram2D class method) from_base() (thermolib.thermodynamics.fep.SimpleFreeEnergyProfile class method) from_fep() (thermolib.thermodynamics.histogram.Histogram1D class method) from_fes() (thermolib.thermodynamics.histogram.Histogram2D class method) from_histogram() (thermolib.thermodynamics.fep.BaseFreeEnergyProfile class method) (thermolib.thermodynamics.fep.FreeEnergySurface2D class method)

from_samples() (thermolib.error.GaussianDistribution class method) (thermolib.error.LogGaussianDistribution class method) (thermolib.error.MultiGaussianDistribution class method) (thermolib.error.MultiLogGaussianDistribution class method) (thermolib.error.SampleDistribution class method) from_single_trajectory() (thermolib.thermodynamics.histogram.Histogram1D class method) (thermolib.thermodynamics.histogram.Histogram2D class method) from_txt() (thermolib.thermodynamics.fep.BaseFreeEnergyProfile class method) (thermolib.thermodynamics.fep.BaseProfile class method) (thermolib.thermodynamics.fep.FreeEnergySurface2D class method) from_wham() (thermolib.thermodynamics.histogram.Histogram1D class method) (thermolib.thermodynamics.histogram.Histogram2D class method) from_wham_c() (thermolib.thermodynamics.histogram.Histogram1D class method) (thermolib.thermodynamics.histogram.Histogram2D class method) fupper() (thermolib.thermodynamics.fep.BaseProfile method) (thermolib.thermodynamics.fep.FreeEnergySurface2D method)

G

GaussianDistribution (class in thermolib.error)

gen_args_samples() (thermolib.error.Propagator method) get_distribution() (thermolib.error.Propagator method)

H

h5_read_dataset() (in module thermolib.tools) HDF5Reader (class in thermolib.thermodynamics.trajectory)

Histogram1D (class in thermolib.thermodynamics.histogram) Histogram2D (class in thermolib.thermodynamics.histogram)

I

Integrate (class in thermolib.thermodynamics.state) integrate() (in module thermolib.tools) integrate2d() (in module thermolib.tools)

interpolate() (thermolib.thermodynamics.fep.FreeEnergySurface2D method) interpolate_surface_2d() (in module thermolib.tools) invert_fisher_to_covariance() (in module thermolib.tools)

L

LinearCombination (class in thermolib.thermodynamics.cv) log_from_loggaussian() (thermolib.error.GaussianDistribution class method) (thermolib.error.MultiGaussianDistribution class method)

LogGaussianDistribution (class in thermolib.error)

M

Maximum (class in thermolib.thermodynamics.state) mean() (thermolib.error.ErrorArray method) (thermolib.error.GaussianDistribution method) (thermolib.error.LogGaussianDistribution method) (thermolib.error.MultiGaussianDistribution method) (thermolib.error.MultiLogGaussianDistribution method) (thermolib.error.SampleDistribution method) Minimum (class in thermolib.thermodynamics.cv) (class in thermolib.thermodynamics.state) module thermolib.error thermolib.ext thermolib.kinetics.rate thermolib.thermodynamics.bias thermolib.thermodynamics.condprob thermolib.thermodynamics.cv thermolib.thermodynamics.fep thermolib.thermodynamics.histogram thermolib.thermodynamics.state thermolib.thermodynamics.trajectory thermolib.tools

MultiDistribution (class in thermolib.error) MultiGaussianDistribution (class in thermolib.error) MultiLogGaussianDistribution (class in thermolib.error) MultipleBiasses1D (class in thermolib.thermodynamics.bias) multivariate_normal() (in module thermolib.tools)

N

NormalizedAxis (class in thermolib.thermodynamics.cv) NormalToPlane (class in thermolib.thermodynamics.cv) nsigma_conf_int() (thermolib.error.ErrorArray method) (thermolib.error.GaussianDistribution method) (thermolib.error.LogGaussianDistribution method) (thermolib.error.MultiGaussianDistribution method) (thermolib.error.MultiLogGaussianDistribution method)

O

OrthogonalDistanceToPore (class in thermolib.thermodynamics.cv)

P

Parabola1D (class in thermolib.thermodynamics.bias) Parabola2D (class in thermolib.thermodynamics.bias) plot() (thermolib.thermodynamics.bias.BiasPotential1D method) (thermolib.thermodynamics.bias.BiasPotential2D method) (thermolib.thermodynamics.fep.BaseProfile method) (thermolib.thermodynamics.fep.FreeEnergySurface2D method) (thermolib.thermodynamics.fep.SimpleFreeEnergyProfile method) (thermolib.thermodynamics.histogram.Histogram1D method) (thermolib.thermodynamics.histogram.Histogram2D method) plot_corr_matrix() (thermolib.error.MultiGaussianDistribution method) (thermolib.error.MultiLogGaussianDistribution method) (thermolib.thermodynamics.fep.BaseProfile method) plot_histograms() (in module thermolib.thermodynamics.histogram) plot_histograms_1d() (in module thermolib.tools) plot_histograms_overlap_1d() (in module thermolib.tools) plot_profiles() (in module thermolib.thermodynamics.fep) plower() (thermolib.thermodynamics.histogram.Histogram1D method) (thermolib.thermodynamics.histogram.Histogram2D method) PlumedSplinePotential1D (class in thermolib.thermodynamics.bias) Polynomial1D (class in thermolib.thermodynamics.bias) print() (thermolib.error.GaussianDistribution method) (thermolib.thermodynamics.bias.BiasPotential1D method) (thermolib.thermodynamics.bias.BiasPotential2D method) print_pars() (thermolib.thermodynamics.bias.BiasPotential1D method) (thermolib.thermodynamics.bias.BiasPotential2D method) (thermolib.thermodynamics.bias.MultipleBiasses1D method) (thermolib.thermodynamics.bias.Parabola1D method) (thermolib.thermodynamics.bias.Parabola2D method) (thermolib.thermodynamics.bias.PlumedSplinePotential1D method) (thermolib.thermodynamics.bias.Polynomial1D method)

print_states() (thermolib.thermodynamics.fep.SimpleFreeEnergyProfile method) process_states() (thermolib.thermodynamics.fep.BaseFreeEnergyProfile method) (thermolib.thermodynamics.fep.SimpleFreeEnergyProfile method) process_trajectory() (thermolib.kinetics.rate.BaseRateFactor method) (thermolib.kinetics.rate.RateFactorEquilibrium method) process_trajectory_cvs() (thermolib.thermodynamics.condprob.ConditionalProbability1D1D method) (thermolib.thermodynamics.condprob.ConditionalProbability1D2D method) process_trajectory_h5() (thermolib.kinetics.rate.RateFactorEquilibrium method) process_trajectory_xyz() (thermolib.thermodynamics.condprob.ConditionalProbability1D1D method) (thermolib.thermodynamics.condprob.ConditionalProbability1D2D method) project_average() (thermolib.thermodynamics.fep.FreeEnergySurface2D method) project_cv1() (thermolib.thermodynamics.fep.FreeEnergySurface2D method) project_cv2() (thermolib.thermodynamics.fep.FreeEnergySurface2D method) project_difference() (thermolib.thermodynamics.fep.FreeEnergySurface2D method) project_function() (thermolib.thermodynamics.fep.FreeEnergySurface2D method) Propagator (class in thermolib.error) pupper() (thermolib.thermodynamics.histogram.Histogram1D method) (thermolib.thermodynamics.histogram.Histogram2D method)

R

RateFactorEquilibrium (class in thermolib.kinetics.rate) read_results() (thermolib.kinetics.rate.BaseRateFactor method) read_wham_input() (in module thermolib.tools) recollect() (thermolib.thermodynamics.fep.BaseFreeEnergyProfile method) (thermolib.thermodynamics.fep.FreeEnergySurface2D method)

reset() (thermolib.error.Propagator method) result_blav() (thermolib.kinetics.rate.BaseRateFactor method) result_bootstrapping() (thermolib.kinetics.rate.BaseRateFactor method) result_no_statistics() (thermolib.kinetics.rate.BaseRateFactor method) rolling_average() (in module thermolib.tools)

S

sample() (thermolib.error.ErrorArray method) (thermolib.error.GaussianDistribution method) (thermolib.error.LogGaussianDistribution method) (thermolib.error.MultiGaussianDistribution method) (thermolib.error.MultiLogGaussianDistribution method) (thermolib.error.SampleDistribution method) SampleDistribution (class in thermolib.error) savetxt() (thermolib.thermodynamics.fep.BaseProfile method) (thermolib.thermodynamics.fep.FreeEnergySurface2D method) set_ref() (thermolib.error.GaussianDistribution method) (thermolib.error.LogGaussianDistribution method) (thermolib.error.MultiGaussianDistribution method) (thermolib.error.SampleDistribution method) (thermolib.thermodynamics.fep.BaseProfile method) (thermolib.thermodynamics.fep.FreeEnergySurface2D method) (thermolib.thermodynamics.fep.SimpleFreeEnergyProfile method)

shift() (thermolib.error.GaussianDistribution method) (thermolib.error.LogGaussianDistribution method) (thermolib.error.SampleDistribution method) SimpleFreeEnergyProfile (class in thermolib.thermodynamics.fep) std() (thermolib.error.ErrorArray method) (thermolib.error.GaussianDistribution method) (thermolib.error.LogGaussianDistribution method) (thermolib.error.MultiGaussianDistribution method) (thermolib.error.MultiLogGaussianDistribution method) (thermolib.error.SampleDistribution method)

T

thermolib.error module thermolib.ext module thermolib.kinetics.rate module thermolib.thermodynamics.bias module thermolib.thermodynamics.condprob module thermolib.thermodynamics.cv module

thermolib.thermodynamics.fep module thermolib.thermodynamics.histogram module thermolib.thermodynamics.state module thermolib.thermodynamics.trajectory module thermolib.tools module transform() (thermolib.thermodynamics.condprob.ConditionalProbability1D1D method) transform_function() (thermolib.thermodynamics.fep.BaseFreeEnergyProfile method) (thermolib.thermodynamics.fep.FreeEnergySurface2D method)

U

update_states() (thermolib.thermodynamics.fep.SimpleFreeEnergyProfile method)

W

wham1d_bias() (in module thermolib.ext) wham1d_error() (in module thermolib.ext) wham1d_hs() (in module thermolib.ext) wham1d_scf() (in module thermolib.ext)

wham2d_bias() (in module thermolib.ext) wham2d_error() (in module thermolib.ext) wham2d_hs() (in module thermolib.ext) wham2d_scf() (in module thermolib.ext)