Reference Guide

We here provide an overview of all modules, classes and routines included in ThermoLIB including their corresponding documentation provided in the source code.

• Thermodynamics – thermolib.thermodynamics
  • Free energy profiles – thermolib.thermodynamics.fep
    • BaseFreeEnergyProfile
      • BaseFreeEnergyProfile.from_histogram()
      • BaseFreeEnergyProfile.from_txt()
      • BaseFreeEnergyProfile.process_states()
      • BaseFreeEnergyProfile.recollect()
      • BaseFreeEnergyProfile.transform_function()
    • BaseProfile
      • BaseProfile.crop()
      • BaseProfile.flower()
      • BaseProfile.from_average()
      • BaseProfile.from_txt()
      • BaseProfile.fupper()
      • BaseProfile.plot()
      • BaseProfile.plot_corr_matrix()
      • BaseProfile.savetxt()
      • BaseProfile.set_ref()
    • FreeEnergySurface2D
      • FreeEnergySurface2D.copy()
      • FreeEnergySurface2D.crop()
      • FreeEnergySurface2D.detect_clusters()
      • FreeEnergySurface2D.flower()
      • FreeEnergySurface2D.from_histogram()
      • FreeEnergySurface2D.from_txt()
      • FreeEnergySurface2D.fupper()
      • FreeEnergySurface2D.interpolate()
      • FreeEnergySurface2D.plot()
      • FreeEnergySurface2D.project_average()
      • FreeEnergySurface2D.project_cv1()
      • FreeEnergySurface2D.project_cv2()
      • FreeEnergySurface2D.project_difference()
      • FreeEnergySurface2D.project_function()
      • FreeEnergySurface2D.recollect()
      • FreeEnergySurface2D.savetxt()
      • FreeEnergySurface2D.set_ref()
      • FreeEnergySurface2D.transform_function()
    • SimpleFreeEnergyProfile
      • SimpleFreeEnergyProfile.from_base()
      • SimpleFreeEnergyProfile.plot()
      • SimpleFreeEnergyProfile.print_states()
      • SimpleFreeEnergyProfile.process_states()
      • SimpleFreeEnergyProfile.set_ref()
      • SimpleFreeEnergyProfile.update_states()
    • plot_profiles()
  • Histograms – thermolib.thermodynamics.histogram
    • Histogram1D
      • Histogram1D.copy()
      • Histogram1D.from_average()
      • Histogram1D.from_fep()
      • Histogram1D.from_single_trajectory()
      • Histogram1D.from_wham()
      • Histogram1D.from_wham_c()
      • Histogram1D.plot()
      • Histogram1D.plower()
      • Histogram1D.pupper()
    • Histogram2D
      • Histogram2D.average_cv_constraint_other()
      • Histogram2D.copy()
      • Histogram2D.from_average()
      • Histogram2D.from_fes()
      • Histogram2D.from_single_trajectory()
      • Histogram2D.from_wham()
      • Histogram2D.from_wham_c()
      • Histogram2D.plot()
      • Histogram2D.plower()
      • Histogram2D.pupper()
    • plot_histograms()
  • Trajectory readers – thermolib.thermodynamics.trajectory
    • ASEExtendedXYZReader
    • CVComputer
    • ColVarReader
    • HDF5Reader
  • Bias potentials – thermolib.thermodynamics.bias
    • BiasPotential1D
      • BiasPotential1D.plot()
      • BiasPotential1D.print()
      • BiasPotential1D.print_pars()
    • BiasPotential2D
      • BiasPotential2D.plot()
      • BiasPotential2D.print()
      • BiasPotential2D.print_pars()
    • MultipleBiasses1D
      • MultipleBiasses1D.print_pars()
    • Parabola1D
      • Parabola1D.print_pars()
    • Parabola2D
      • Parabola2D.print_pars()
    • PlumedSplinePotential1D
      • PlumedSplinePotential1D.print_pars()
    • Polynomial1D
      • Polynomial1D.print_pars()
  • Collective variables – thermolib.thermodynamics.cv
    • Average
      • Average.compute()
    • CenterOfMass
      • CenterOfMass.compute()
    • CenterOfPosition
      • CenterOfPosition.compute()
    • CoordinationNumber
      • CoordinationNumber.compute()
    • Difference
      • Difference.compute()
    • DistOrthProjOrig
    • Distance
      • Distance.compute()
    • DistanceCOP
      • DistanceCOP.compute()
    • DotProduct
      • DotProduct.compute()
    • LinearCombination
      • LinearCombination.compute()
    • Minimum
      • Minimum.compute()
    • NormalToPlane
      • NormalToPlane.compute()
    • NormalizedAxis
      • NormalizedAxis.compute()
    • OrthogonalDistanceToPore
  • State – thermolib.thermodynamics.state
    • Integrate
    • Maximum
    • Minimum
  • Conditional probability – thermolib.thermodynamics.condprob
    • ConditionalProbability1D1D
      • ConditionalProbability1D1D.average()
      • ConditionalProbability1D1D.deproject()
      • ConditionalProbability1D1D.finish_error()
      • ConditionalProbability1D1D.process_trajectory_cvs()
      • ConditionalProbability1D1D.process_trajectory_xyz()
      • ConditionalProbability1D1D.transform()
    • ConditionalProbability1D2D
      • ConditionalProbability1D2D.deproject()
      • ConditionalProbability1D2D.process_trajectory_cvs()
      • ConditionalProbability1D2D.process_trajectory_xyz()
• Kinetics – thermolib.kinetics
  • Rate constant – thermolib.kinetics.rate
    • BaseRateFactor
      • BaseRateFactor.compute_rate()
      • BaseRateFactor.finish()
      • BaseRateFactor.process_trajectory()
      • BaseRateFactor.read_results()
      • BaseRateFactor.result_blav()
      • BaseRateFactor.result_bootstrapping()
      • BaseRateFactor.result_no_statistics()
    • RateFactorEquilibrium
      • RateFactorEquilibrium.process_trajectory()
      • RateFactorEquilibrium.process_trajectory_h5()
• Error distributions – thermolib.error
  • ErrorArray
    • ErrorArray.mean()
    • ErrorArray.nsigma_conf_int()
    • ErrorArray.sample()
    • ErrorArray.std()
  • GaussianDistribution
    • GaussianDistribution.copy()
    • GaussianDistribution.from_samples()
    • GaussianDistribution.log_from_loggaussian()
    • GaussianDistribution.mean()
    • GaussianDistribution.nsigma_conf_int()
    • GaussianDistribution.print()
    • GaussianDistribution.sample()
    • GaussianDistribution.set_ref()
    • GaussianDistribution.shift()
    • GaussianDistribution.std()
  • LogGaussianDistribution
    • LogGaussianDistribution.copy()
    • LogGaussianDistribution.exp_from_gaussian()
    • LogGaussianDistribution.from_samples()
    • LogGaussianDistribution.mean()
    • LogGaussianDistribution.nsigma_conf_int()
    • LogGaussianDistribution.sample()
    • LogGaussianDistribution.set_ref()
    • LogGaussianDistribution.shift()
    • LogGaussianDistribution.std()
  • MultiDistribution
    • MultiDistribution.corr()
  • MultiGaussianDistribution
    • MultiGaussianDistribution.copy()
    • MultiGaussianDistribution.cov()
    • MultiGaussianDistribution.from_samples()
    • MultiGaussianDistribution.log_from_loggaussian()
    • MultiGaussianDistribution.mean()
    • MultiGaussianDistribution.nsigma_conf_int()
    • MultiGaussianDistribution.plot_corr_matrix()
    • MultiGaussianDistribution.sample()
    • MultiGaussianDistribution.set_ref()
    • MultiGaussianDistribution.std()
  • MultiLogGaussianDistribution
    • MultiLogGaussianDistribution.copy()
    • MultiLogGaussianDistribution.cov()
    • MultiLogGaussianDistribution.exp_from_gaussian()
    • MultiLogGaussianDistribution.from_samples()
    • MultiLogGaussianDistribution.mean()
    • MultiLogGaussianDistribution.nsigma_conf_int()
    • MultiLogGaussianDistribution.plot_corr_matrix()
    • MultiLogGaussianDistribution.sample()
    • MultiLogGaussianDistribution.std()
  • Propagator
    • Propagator.calc_fun_values()
    • Propagator.gen_args_samples()
    • Propagator.get_distribution()
    • Propagator.reset()
  • SampleDistribution
    • SampleDistribution.from_samples()
    • SampleDistribution.mean()
    • SampleDistribution.sample()
    • SampleDistribution.set_ref()
    • SampleDistribution.shift()
    • SampleDistribution.std()
• Tools – thermolib.tools
  • blav()
  • corrtime_from_acf()
  • decorrelate()
  • extract_polynomial_bias_info()
  • fisher_matrix_mle_probdens()
  • format_scientific()
  • h5_read_dataset()
  • integrate()
  • integrate2d()
  • interpolate_surface_2d()
  • invert_fisher_to_covariance()
  • multivariate_normal()
  • plot_histograms_1d()
  • plot_histograms_overlap_1d()
  • read_wham_input()
  • rolling_average()
• Extensions – thermolib.ext
  • wham1d_bias()
  • wham1d_error()
  • wham1d_hs()
  • wham1d_scf()
  • wham2d_bias()
  • wham2d_error()
  • wham2d_hs()
  • wham2d_scf()