PySAGES

Overview

This documentation and software are under development. The API and implementation may change in the future.

Details

PySAGES: Python Suite for Advanced General Ensemble Simulations

Modules

• Advanced Sampling Methods
  • pysages.methods.abf
    • ABFState
    • ABF
    • build_force_estimator()
  • pysages.methods.ann
    • ANNState
    • ANN
    • build_free_energy_learner()
  • pysages.methods.ffs
    • FFSState
    • FFS
    • check_input()
    • basin_sampling()
    • initial_flow()
  • pysages.methods.funn
    • FUNNState
    • PartialFUNNState
    • FUNN
    • build_free_energy_grad_learner()
    • build_force_estimator()
  • pysages.methods.harmonic_bias
    • HarmonicBiasState
    • HarmonicBias
  • pysages.methods.metad
    • MetadynamicsState
    • PartialMetadynamicsState
    • Metadynamics
    • build_gaussian_accumulator()
    • build_bias_grad_evaluator()
    • sum_of_gaussians()
  • pysages.methods.umbrella_integration
    • UmbrellaIntegration
  • Spline String Method
    • SplineString
  • pysages.methods.utils
    • SerialExecutor
    • ReplicasConfiguration
    • HistogramLogger
    • MetaDLogger
    • listify()
    • numpyfy_vals()
  • pysages.methods.core
    • Result
    • SamplingMethod
    • GriddedSamplingMethod
    • NNSamplingMethod
    • run()
  • Advanced Sampling Methods
• Collective Variables
  • Angles as collective variables
    • Angle
    • angle()
    • DihedralAngle
    • dihedral_angle()
    • RingPuckeringCoordinates
    • ring_puckering_coordinates()
    • RingPhaseAngle
    • ring_phase_angle()
    • RingAmplitude
    • ring_amplitude()
  • Shapes as collective Variables
    • RadiusOfGyration
    • radius_of_gyration()
    • weighted_radius_of_gyration()
    • PrincipalMoment
    • gyration_tensor()
    • weighted_gyration_tensor()
    • principal_moments()
    • Asphericity
    • asphericity()
    • Acylindricity
    • acylindricity()
    • ShapeAnisotropy
    • shape_anisotropy()
  • Cartesian Coordinate Collective Variables
    • barycenter()
    • weighted_barycenter()
    • Component
    • Distance
    • distance()
    • Displacement
    • displacement()
  • Abstract Collective Variables
    • CollectiveVariable
    • AxisCV
    • TwoPointCV
    • ThreePointCV
    • FourPointCV
    • multicomponent()
    • build()
  • Orientation as collective variables
    • kabsch()
    • rmsd()
    • RMSD
    • ERMSD
    • calc_local_reference_systems()
    • g_vector()
    • reshape_coordinates()
    • ermsd_core()
    • ermsd()
    • ERMSDCG
    • infer_base_coordinates()
    • ermsd_cg()