Model library¶
All the names of the models follow the rule: ‘[geometry][dimension][p]_[parameterization]_[…]_[model form]’, with the simplest case as ‘[geometry][dimension]’ (e.g., ring3D
). For example, dualEllipse3D_avgR_discrete
means a dualellipse geometry in 3D, parametrized by the average radius, in a discrete form.
Note
The individual components of the names

Arc¶
 class models.arc2D(varargin)¶
Bases:
@geometricModel.geometricModel
arc2D
is a 2D model that describes an arc geometry. Geometric parameters:
radius: (nm) the radius of the ring where the arc is derived.
theta: (degree) the closing anlge of the arc.
 Relavent biological structure:
Crosssection of a clathrin coat
 Preview:

Scale bar: 50 nm.
 reference(par, dx)¶
For details, see
reference()
.
 class models.arc2D_arcLen(varargin)¶
Bases:
@geometricModel.geometricModel
arc2D_arcLen
is a 2D model that describes an arc geometry. It describes the same geometry as byarc2D
but with a different parameterization. Geometric parameters:
arcLength: (nm) the length of the arc.
theta: (degree) the closing anlge of the arc.
 Relavent biological structure:
Crosssection of a clathrin coat
See also
 reference(par, dx)¶
For details, see
reference()
.
Bucket¶
 class models.bucket2D(varargin)¶
Bases:
@geometricModel.geometricModel
bucket2D
is a 2D model that describes a bucket geometry. It creates a bucket based on an arc. The bucket is created to contain the arc. Geometric parameters:
radius: (nm) the radius of the ring where the arc is derived.
theta: (°) the closing anlge of the arc.
See also
 reference(par, dx)¶
For details, see
reference()
.
 getDerivedPars(pars)¶
For details, see
getDerivedPars()
.
Ring¶
 class models.ring2D(varargin)¶
Bases:
@geometricModel.geometricModel
ring2D
is a 2D model that describes a ring geometry. Geometric parameters:
radius: (nm) the ring radius.
 Relavent biological structure:
Topview projections of the nuclear pore complex.
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
 class models.ellipse3D(varargin)¶
Bases:
@geometricModel.geometricModel
ellipse3D
describes a ellipse geometry in 3D. Geometric parameters:
a: (nm) the axis along the xaxis.
b: (nm) the axis along the yaxis.
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
 class models.ring3D(varargin)¶
Bases:
@geometricModel.geometricModel
The model class
ring3D
describes a ring geometry in 3D. Geometric parameters:
radius: (nm) the ring radius.
 Relavent biological structure:
Topview projections of the nuclear pore complex.
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
Spline¶
 class models.cspline3D_midPoint(varargin)¶
Bases:
@geometricModel.geometricModel
A cspline for describing a linear structure traversing in 3D space.
 Geometric parameters:
xMid, yMid, zMid: (nm) the xyz coordinates of the mid point.
dist: (nm): the distance between neighbouring control points
rotAzi[L/R]_n, rotEle[L/R]_n: (°) the azimuthal and elevation
angles or of the vector pointing to the [L/R]_n control point. [L/R] is either L (left) or R (right) with respect to the mid point. n indicates the order. For exmple, rotAziL1 means the azimuthal angle defining the 1st point on the left of the mid point.
 Relavent biological structure:
Actin filaments
The central axes of microtubules
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
 getThings2Plot(par)¶
The user can define what should be also displayed in the plots.
 Parameters
obj – a
@geometricModel.geometricModel
object. Returns
items – things to be plotted.
Tube and derivitives¶
 class models.csplineClosedTube3D_midPoint(varargin)¶
Bases:
@geometricModel.geometricModel
A cspline for describing a flexible tube that has its ends closed, traversing in 3D space.
 Geometric parameters:
xMid, yMid, zMid: (nm) the xyz coordinates of the mid point.
r: (nm) the radius of the tube.
dist: (nm): the distance between neighbouring control points
rotAzi[L/R]_n, rotEle[L/R]_n: (°) the azimuthal and elevation angles or of the vector pointing to the [L/R]_n control point. [L/R] is either L (left) or R (right) with respect to the mid point. n indicates the order. For exmple, rotAziL1 means the azimuthal angle defining the 1^{st} point on the left of the mid point.
 Relavent biological structure:
outer membrane of a mitochondria
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
 getThings2Plot(par, varargin)¶
The user can define what should be also displayed in the plots.
 Parameters
obj – a
@geometricModel.geometricModel
object. Returns
items – things to be plotted.
 getDerivedPars(pars)¶
Exports a empty variable when no derived parameters.
 class models.csplineTube3D_midPoint(varargin)¶
Bases:
@geometricModel.geometricModel
A cspline for describing a flexible tube traversing in 3D space.
 Geometric parameters:
xMid, yMid, zMid: (nm) the xyz coordinates of the mid point.
r: (nm) the radius of the tube.
dist: (nm): the distance between neighbouring control points
rotAzi[L/R]_n, rotEle[L/R]_n: (°) the azimuthal and elevation angles or of the vector pointing to the [L/R]_n control point. [L/R] is either L (left) or R (right) with respect to the mid point. n indicates the order. For exmple, rotAziL1 means the azimuthal angle defining the 1^{st} point on the left of the mid point.
 Relavent biological structure:
actin filaments
the central axes of microtubules
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
 getThings2Plot(par, varargin)¶
The user can define what should be also displayed in the plots.
 Parameters
obj – a
@geometricModel.geometricModel
object. Returns
items – things to be plotted.
 getDerivedPars(pars)¶
Exports a empty variable when no derived parameters.
 class models.csplineTube3D_xyz(varargin)¶
Bases:
@geometricModel.geometricModel
A cspline for describing a linear structure traversing in 3D space. It describe the same geometry as
csplineTube3D_midPoint
but with a different parameterization. Geometric parameters:
x_n, y_n, z_n: (nm) the xyz coordinates of the n^{th} control point.
r: (nm) the radius of the tube.
 Relavent biological structure:
Actin filaments
The central axes of microtubules
See also
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
set additional parameters of the model
 getThings2Plot(par)¶
The user can define what should be also displayed in the plots.
 Parameters
obj – a
@geometricModel.geometricModel
object. Returns
items – things to be plotted.
Dual rings and derivitives¶
 class models.dualEllipse3D_discrete(varargin)¶
Bases:
@geometricModel.geometricModel
dualEllipse3D_discrete
describes two parallel ellipse in 3D. The ellipse have the same xy positions and short/long axes. Geometric parameters:
ringDistance: (nm) the distance between the two parallel rings.
azimuthalShift: (°) the twist angle between the two parallel rings.
a: (nm) the length of the long axis.
ellipticity: (no unit) or e, is defined as e = 1b/a, where a and b are the long and short axes.
aDir: (°) the rotational offset between the first corner and the long axis a.
cornerDegree: (°) the rotational offset between two copies per corner.
 Relavent biological structure:
deformed nuclear pore complex
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
 class models.dualEllipse3D_avgR_discrete(varargin)¶
Bases:
@geometricModel.geometricModel
dualEllipse3D_avgR_discrete
describes two parallel ellipse in 3D. The ellipse have the same xy positions and short/long axes. It describe the same geometry asdualEllipse3D_discrete
but with a different parameterization. Geometric parameters:
ringDistance: (nm) the distance between the two parallel rings.
azimuthalShift: (°) the twist angle between the two parallel rings.
avgR: (nm) the average of the short and long axes.
ellipticity: (no unit) or e, is defined as e = 1b/a, where a and b are the long and short axes.
aDir: (°) the rotational offset between the first corner and the long axis a.
cornerDegree: (°) the rotational offset between two copies per corner.
 Relavent biological structure:
deformed nuclear pore complex
See also
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
 class models.dualRing3D_discrete(varargin)¶
Bases:
@geometricModel.geometricModel
dualRing3D_discrete
describes two parallel rings in 3D. The rings have the same xy position and radius. Geometric parameters:
ringDistance: (nm) the distance between the two parallel rings.
azimuthalShift: (°) the twist angle between the two parallel rings.
radius: (nm) the radius of the rings.
cornerDegree: (°) the rotational offset between two copies per corner.
 Internal settings:
copyPerCorner: (integer values) the copy number of the protein per corner. For example, 2 (default).
cornerNum: (integer values) the number of corners. For example, 8 (default).
useSecondRing: (logical) true if the second ring is to be used in the model. For example, true (default).
 Relavent biological structure:
the nuclear pore complex
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
Sperical model and derivitives¶
 class models.sphericalCap3D_surfaceArea(varargin)¶
Bases:
@geometricModel.geometricModel
sphericalCap3D_surfaceArea
describes the geometry of a spherical cap in 3D. Geometric parameters:
surfaceArea: (10^{4} nm^{2}) the surface area of the spherical cap.
closeAngle: (°) the angle from the pole to the edge of the cap.
 Relavent biological structure:
mammalian endocytic coat
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
 getDerivedPars(pars)¶
For details, see
getDerivedPars()
.
 class models.sphericalCap3Dp_surfaceArea(varargin)¶
Bases:
@parametricModel.parametricModel
sphericalCap3Dp_surfaceArea
describes a geometry of spherical cap in 3D. It describe the same geometry with the same parameterization assphericalCap3D_surfaceArea
but in a parametric form. Geometric parameters:
surfaceArea: (10^{4} nm^{2}) the surface area of the spherical cap.
closeAngle: (°) the angle from the pole to the edge of the cap.
 Relavent biological structure:
mammalian endocytic coat
See also
 Preview:
 getDerivedPars(pars)¶
For details, see
getDerivedPars()
.
 class models.spheroid3Dp_surfaceArea(varargin)¶
Bases:
models.spheroidCap3Dp_surfaceArea
spheroid3Dp_surfaceArea
describes the geometry of spheroid in 3D. It is parametric. Spheroid is a sphere flattened at the poles.Important
Here the flattening is applied along the zaxis, not the yaxis.
 Geometric parameters:
 surfaceArea: (10^{4} nm^{2}) the surface area of the spherical cap.
flattening: (no unit) or f, is defined as 1c/a, where a and c are the two distinct axis lengths. c lines on the yaxis.
 Relavent biological structure:
deformed vesicle
See also
 Preview:
Note
It will be available soon.
 getDerivedPars(par)¶
For details, see
getDerivedPars()
.
 class models.spheroidCap3Dp_surfaceArea(varargin)¶
Bases:
@parametricModel.parametricModel
sphericalCap3Dp_surfaceArea
describes the geometry of spheroid cap in 3D. It is parametric. Spheroid cap is a spherial cap flattened at the poles.Important
Here the flattening is applied along the yaxis, not the zaxis.
 Geometric parameters:
surfaceArea: (10^{4} nm^{2}) the surface area of the spherical cap.
 closeAngle: (°) the angle from the pole to the edge of the cap.
flattening: (no unit) or f, is defined as 1c/a, where a and c are the two distinct axis lengths. c lines on the yaxis.
 Relavent biological structure:
mammalian endocytic coat
See also
 Preview:
Note
It will be available soon.
 getDerivedPars(pars)¶
For details, see
getDerivedPars()
.
2D projection of 3D geometry¶
 class models.hemispheroid2D(varargin)¶
Bases:
@geometricModel.geometricModel
hemispheroid2D
describes the sideview projection of a hemispheroid. Geometric parameters:
a: (nm) the axis along the yaxis.
b: (nm) the axis along the xaxis.
xcenter: (nm) [obsolete] please set it to zero.
ycenter: (nm) [obsolete] please set it to zero.
 Relavent biological structure:
actin network at the endocytic site
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
 class models.thickRing2D(varargin)¶
Bases:
@geometricModel.geometricModel
thickRing2D
describes the sideview projection of a thick ring. Geometric parameters:
innerRadius: (nm) the inner radius of the ring.
outerRadius: (nm) the outer radius of the ring.
thickness: (nm) the thickness of the ring.
xcenter: (nm) [obsolete] please set it to zero.
ycenter: (nm) [obsolete] please set it to zero.
 Relavent biological structure:
actin network at the endocytic site
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.
Random geometry¶
 class models.locsBG3D(varargin)¶
Bases:
@geometricModel.geometricModel
locsBG3D
is usually used for simulations. It allows generating localizations in 3D at random positions. Geometric parameters:
density: (μm^{2}) density of background localizations in the xy plane.
depth: (nm) the depth of the ROI.
 class models.gaussianCluster2D(varargin)¶
Bases:
@geometricModel.geometricModel
sphericalCap3Dp_surfaceArea
describes a geometry of spherical cap in 3D. It describe the same geometry with the same parameterization assphericalCap3D_surfaceArea
but in a parametric form. Geometric parameters:
x0: (nm) the x position of the cluster.
y0: (nm) the y position of the cluster.
Important
The parameter sigma of the gaussian cluster is determined by the extrinsic parameter variation.
 Relavent biological structure:
a protein cluster on the plasma membrane
 Preview:
Note
It will be available soon.
 reference(par, dx)¶
For details, see
reference()
.