Colloids

Overview

hoobas.Colloid.Colloid	Object meant for holding CompositeObject comprised of both rigid and flexible parts.
hoobas.Colloid.SimpleColloid	This is the class used for simple rigid bodies, i.e., polyhedra, with a single surface atom type.

Details

class hoobas.Colloid.Colloid(center_type='W', surface_type='P', shape=None, **kwargs)

Object meant for holding CompositeObject comprised of both rigid and flexible parts.

Args:

center_type (str): Additional rigid beadtype prefixed to the colloid

surface_type (str): Beadtype to use when creating bead lists from the shape

shape (GenShape.Shape): Shape to use for constructing the rigid body

relative_positions()

Retrieve relative positions with respect to particle center. This is meant to produce tuples for hoomd rigid body constraints command

Returns:list[tuple]

class hoobas.Colloid.ComplexColloid(**kwargs)

Provides an object to build complex colloids defined by shells. This is generally used in conjunction with hoobas.GenShape.PDBProtein.

class hoobas.Colloid.FromComposite(composite, units=None)

Creates a rigid body out of a hoobas.Composite.CompositeObject prototype

relative_positions()

Retrieve relative positions with respect to particle center. This is meant to produce tuples for hoomd rigid body constraints command

Returns:list[tuple]

class hoobas.Colloid.MultiDisperseColloid(shape_property_function, **kwargs)

Class for colloids requiring dispersity in multiple variables. For instance rods with aspect ratios and sizes, which may have non-zero covariance.

Args:

shape_property_function: function which yields properties of the shape in a dict, must at least return a key for size

class hoobas.Colloid.SimpleColloid(size, **kwargs)

This is the class used for simple rigid bodies, i.e., polyhedra, with a single surface atom type. A single polydispersity can be supplied, which is obtained by passing a function for the size