Molecular graph models

to_dict(mol::MolGraph) -> Dict{String,Any}

Convert molecule object into JSON compatible dictionary.

to_json(mol::MolGraph) -> String

Convert molecule object into JSON String.

u_edge(::Type{T}, src, dst) where T <: Integer -> Edge{T}
u_edge(g::SimpleGraph{T}, src, dst) where T -> Edge{T}
u_edge(mol::AbstractMolGraph{T}, src, dst) where T -> Edge{T}

A workaround for UndirectedEdge that are not yet implemented in SimpleGraph

Reaction{T}

Reaction type.

MolGraph{T,V,E} <: SimpleMolGraph{T,V,E}

Basic molecular graph type.

atomnumber(atomsymbol::Symbol) -> Int

Return atom number.

atomsymbol(n::Int) -> Symbol

Return atom symbol of given atomic number.

SDFAtom

SDFile (CTAB) atom property type.

SMILESAtom

SMILES atom property type.

SDFBond

SDFile (CTAB) bond property type.

• SDFile bond notation
  • Single bond
    • 0: u - v
    • 1: u ◀ v (Up-arrow)
    • 4: u ~ v (Up or down)
    • 6: u ◁ v (Down-arrow)
  • Double bond
    • 0: v = u
    • 3: u x v (Cis-Trans Unknown)

SMILESBond

SMILES bond property type.