Models#

DeerLab provides a wide selection of built-in models. These are instances of the deerlab.Model object class and can be manipulated and expanded as described in the Modelling guide.

These are models particularly oriented towards the modelling of dipolar EPR spectroscopy data.

Experiment models#

These generator functions model different dipolar EPR experiments, and provide the means to refine the dipolar signal models by introducing experimental information.

ex_3pdeer

Generate a 3-pulse DEER dipolar experiment model.

ex_4pdeer

Generate a 4-pulse DEER dipolar experiment model.

ex_rev5pdeer

Generate a reverse 5-pulse DEER dipolar experiment model.

ex_fwd5pdeer

Generate a forward 5-pulse DEER dipolar experiment model.

ex_sifter

Generate a SIFTER dipolar experiment model.

ex_ridme

Generate a RIDME dipolar experiment model.

Distance distribution models#

These models provide parametrizations of the interspin distance distributions.

Basis functions

This group of distribution models is based on functions that can serve as basis functions for modeling more general distributions.

dd_gauss

Gaussian distribution model

dd_gauss2

Sum of two Gaussian distributions model

dd_gauss3

Sum of three Gaussian distributions model

dd_rice

3D-Rice distribution model

dd_rice2

Sum of two 3D-Rice distributions model

dd_rice3

Sum of two 3D-Rice distributions model

dd_gengauss

Generalized Gaussian distribution model

dd_skewgauss

Skew Gaussian distribution model

dd_cos

Raised-cosine parametric model

Disordered physical models

This group of distribution models represents spin labels attached to disordered macromolecular structures.

dd_wormchain

Worm-like chain model near the rigid limit.

dd_wormgauss

Worm-like chain model near the rigid limit with Gaussian convolution.

dd_randcoil

Random-coil model for an unfolded peptide/protein

Sphere/shell models

This group of distribution models represents spin labels in simple partitions of 3D space.

dd_sphere

Particles uniformly distributed on a sphere.

dd_spheresurf

Particles uniformly distributed on a sphere's surface.

dd_spherepoint

One particle distanced from particles uniformly distributed on a sphere

dd_shell

Uniform distribution of particles on a spherical shell

dd_shellshell

Particles uniformly distributed on a spherical shell and on another concentric spherical shell.

dd_shellsphere

Particles uniformly distributed on a sphere and on an outer spherical shell.

dd_shellvoidshell

Particles uniformly distributed on a spherical shell and on another concentric spherical shell separated by a void.

dd_shellvoidsphere

Particles uniformly distributed on a sphere and on a concentric outer spherical shell separated by a void.

Toy models

This group contains distribution models that have absolutely no physical relevance. They are useful for testing numerical algorithms.

dd_circle

Semicircle distribution model

dd_triangle

Triangular distribution model.

dd_uniform

Uniform distribution model.

Background models#

These models provide parametrizations of the signal contribution arising from intermolecular dipolar interactions.

Physical models

This category involves models that describe particular distributions of spin labels in space. These models depend on physical parameters such as spin concentration, exclusion distances, and dimensionality.

bg_hom3d

Background from a homogeneous distribution of spins in a 3D medium

bg_hom3dex

Background from a homogeneous distribution of spins with excluded volume

bg_homfractal

Background from homogeneous spin distribution in a space of fractal dimension

Additionally, the following models describe the time-dependent phase-shifts arising from these particular distributions of spin labels in space.

bg_hom3d_phase

Phase shift from a homogeneous distribution of spins in a 3D medium

bg_hom3dex_phase

Phase shift from a homogeneous distribution of spins with excluded volume

bg_homfractal_phase

Phase shift from a homogeneous distribution of spins in a fractal medium

Phenomenological models

This category comprises phenomenological models that represent various mathematical functions that are intended to mimic the background decay, without reference to a particular spatial distribution of spins. The parameters of these models do no have direct physical meaning.

bg_exp

Exponential background model

bg_strexp

Stretched exponential background model

bg_sumstrexp

Sum of two stretched exponentials background model

bg_prodstrexp

Product of two stretched exponentials background model

bg_poly1

Polynomial 1st-order background model

bg_poly2

Polynomial 2nd-order background model

bg_poly3

Polynomial 3rd-order background model