The AtomGraph Type

AtomGraph is a type defined by ChemistryFeaturization.jl. It is a subtype of LightGraphs.AbstractGraph{Float32} (we've chosen to fix 32-bit floats for now to maintain compatibility with Flux.jl), and has all the required functions defined such that most of the LightGraphs API should "just work" on these objects.

Fields

• graph::SimpleWeightedGraph{Int32,Float32}: The actual graph object we are encoding.
• elements::Vector{String}: List of elemental symbols corresponding to nodes of the graph (length should be equal to nv(graph))
• lapl::Matrix{Float32}: Normalized laplacian of the graph, stored so that graph convolutional layers can be more computationally efficient by not needing to compute it themselves
• features::Matrix{Float32}: Feature matrix corresponding to this atomic graph. Its shape should be (# features, # nodes).
• featurization::Vector{AtomFeat}: Featurization scheme (see Terminology) in the form of a list of AtomFeat objects.

Note that it is possible to initialize an AtomGraph object without the final two fields being populated, but not to add only a feature matrix without its associated featurization scheme. This is to ensure that features are always invertible back to human-interpretable values!

Notable Functions

• Full constructor AtomGraph(gr::SimpleWeightedGraph{Int32,Float32}, el_list::Vector{String}, features::Matrix{Float32}, featurization::Vector{AtomFeat}), requiring inputs of all fields except for the laplacian, which will be computed. This constructor also verifies that the element list and feature matrix are of appropriate dimensions
• Constructor AtomGraph(gr::SimpleWeightedGraph{Int32,Float32}, el_list::Vector{String}) that requires only the graph and the element list, which does not initialize the feature matrix or featurization fields.
• add_features!(g::AtomGraph, features::Matrix{Float32}, featurization::Vector{AtomFeat}) to associate a feature matrix and featurization scheme with an AtomGraph that was initialized via the second constructor, OR to modify them for a fully-initialized case
• Several alternate signatures for add_features! that can build the features/featurization given requisite metadata
• visualize_graph(ag::AtomGraph) which simply calls GraphPlot.jl's gplot function with nodes labeled with their elemental symbol and edge widths drawn according to their weights