Data Structures

The primary building blocks in an mBuild hierarchy inherit from the Compound class. Compounds maintain an ordered set of children which are other Compounds. In addition, an independent, ordered dictionary of labels is maintained through which users can reference any other Compound in the hierarchy via descriptive strings. Every Compound knows its parent Compound, one step up in the hierarchy, and knows which Compounds reference it in their labels. Ports are a special type of Compound which are used internally to connect different Compounds using the equivalence transformations described below.

Compounds at the bottom of an mBuild hierarchy, the leafs of the tree, are referred to as Particles and can be instantiated as foo = mb.Particle(name='bar'). Note however, that this merely serves to illustrate that this Compound is at the bottom of the hierarchy; Particle is simply an alias for Compound which can be used to clarify the intended role of an object you are creating. The method Compound.particles() traverses the hierarchy to the bottom and yields those Compounds. Compound.root() returns the compound at the top of the hierarchy.