Molecular graph models

atom_charge(atom::AbstractAtom) -> Int

Return atomic charge of the given atom.

atom_number(atom::AbstractAtom) -> Int

Return an atomic number of the given atom or the atomic symbol.

atom_symbol(atom::AbstractAtom) -> Symbol

Return an atomic symbol of the given atom or the atomic number.

bond_order(bond::AbstractBond) -> Int

Return bond order of the given bond.

edge_neighbors(g::SimpleGraph{T}, u::Integer, v::Integer) where T -> Tuple{Vector{T},Vector{T}}
edge_neighbors(g::SimpleGraph{T}, e::Edge) where T -> Tuple{Vector{T},Vector{T}}

Return neighbors of the source and destination vertices of the edge, respectively.

eproptype(::Type{AbstractMolGraph}) -> Type
eproptype(mol::AbstractMolGraph) -> Type

Return the type of edge properties

multiplicity(atom::AbstractAtom) -> Int

Return multiplicity (num of radicals + 1) of the given atom.

This is experimental feature - free radical chemistry is still not introduced to this library. This does nothing for now, but for example, you can set multiplicity=2 to molecular oxygens manually.

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::SimpleMolGraph{T}, src, dst) where T -> Edge{T}

A workaround for UndirectedEdge that are not yet implemented in SimpleGraph

vproptype(::Type{AbstractMolGraph}) -> Type
vproptype(mol::AbstractMolGraph) -> Type

Return the type of vertex properties

AbstractAtom <: AbstractElement

The base class of vertex properties (atom).

AbstractBond <: AbstractElement

The base class of edge properties (bond).

QueryTree{T<:Integer,U<:AbstractQueryNode} <: AbstractElement

The base class of molecular query trees.

Reaction{T<:AbstractMolGraph}

Reaction type.

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

Basic molecular graph type.

Usually MolGraphs are not directly constructed, but constructed by molecule reader methods such as smilestomol or sdfilereader. Atom and Bond properties of MolGraph are specific to the type of morecular reader (e.g. sdfilereader generates MolGraph{Int,SDFAtom,SDFBond} instances).

atom_number(atomsymbol::Symbol) -> Int

Return an atomic number of the given atom or the atomic symbol.

atom_symbol(n::Int) -> Symbol

Return an atomic symbol of the given atom or the atomic number.

CommonChemAtom

CommonChem atom property type.

SDFAtom

SDFile (CTAB) atom property type.

SMILESAtom

SMILES atom property type.

CommonChemBond

CommonChem bond 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.