Order parameters for specific membrane region

class gorder.geometry.And(a, b, invert=False)

Combine two geometry selections with logical AND. Bonds will only be selected if they fulfill both selections.

Parameters:
class gorder.geometry.Cuboid(xdim=Ellipsis, ydim=Ellipsis, zdim=Ellipsis, reference=None, invert=False)

Calculate order parameters inside a cuboid.

Parameters:

  • xdim (Optional[Sequence[float]]) – Span of the cuboid along the x-axis [nm]. Defaults to infinite if not specified.

  • ydim (Optional[Sequence[float]]) – Span of the cuboid along the y-axis [nm]. Defaults to infinite if not specified.

  • zdim (Optional[Sequence[float]]) – Span of the cuboid along the z-axis [nm]. Defaults to infinite if not specified.

  • reference (Optional[Union[Sequence[float],str]]) – Reference point for the cuboid position. Defaults to [0.0, 0.0, 0.0].

  • invert (Optional[bool]) – Should the geometry selection be inverted? Defaults to False.

Raises:

ConfigError – If any dimension is invalid.

class gorder.geometry.Cylinder(radius, orientation, span=Ellipsis, reference=None, invert=False)

Calculate order parameters inside a cylinder.

Parameters:

  • radius (float) – Radius of the cylinder [nm].

  • orientation (str) – Orientation of the cylinder’s main axis. Expected values are x, y, or z.

  • span (Optional[Sequence[float]]) – Span along the main axis [nm]. Defaults to infinite if not specified.

  • reference (Optional[Union[Sequence[float],str]]) – Reference point for position and size. Defaults to [0.0, 0.0, 0.0].

  • invert (Optional[bool]) – Should the geometry selection be inverted? Defaults to False.

Raises:

ConfigError – If radius is not positive, span is invalid, or orientation is not recognized.

class gorder.geometry.Not(a, invert=False)

Invert a geometry selection with logical NOT. Bonds will be selected if they are not inside the given geometry. This is equivalent to the invert keyword.

Parameters:

a (Union[Cuboid, Cylinder, Sphere, And, Or, Not]) – Geometry selection to invert.

class gorder.geometry.Or(a, b, invert=False)

Combine two geometry selections with logical OR. Bonds will be selected if they fulfill any of the two selections.

Parameters:
class gorder.geometry.Sphere(radius, reference=None, invert=False)

Calculate order parameters inside a sphere.

Parameters:

  • radius (float) – Radius of the sphere [nm].

  • reference (Optional[Union[Sequence[float],str]]) – Center of the sphere. Defaults to [0.0, 0.0, 0.0].

  • invert (Optional[bool]) – Should the geometry selection be inverted? Defaults to False.

Raises:

ConfigError – If radius is not positive.