Molecular properties

apparent_valence(mol::SimpleMolGraph) -> Vector{Int}

Return a vector of size $n$ representing the number of total bond order incident to 1 to $n$th atoms of the given molecule.

atom_counter(mol::SimpleMolGraph) -> Dict{Symbol,Int}

Count the number of atoms and return symbol => count dict.

atom_symbol(mol::MolGraph) -> Vector{Symbol}

Return a vector of size $n$ representing atom symbols of 1 to $n$th atoms of the given molecule.

bond_order(mol::MolGraph) -> Vector{Int}

Return a vector of size $n$ representing bond order of 1 to $n$th bonds of the given molecule.

charge(mol::MolGraph) -> Vector{Int}

Return a vector of size $n$ representing atom charges of 1 to $n$th atoms of the given molecule.

connectivity(mol::SimpleMolGraph) -> Vector{Int}

Return a vector of size $n$ representing the number of total atoms (implicit and explicit) connected to 1 to $n$th atoms of the given molecule.

This property corresponds to SMARTS X query.

edge_which_ring(mol::SimpleMolGraph) -> Vector{Vector{Int}}

Return a vector of size $n$ representing sssr membership of 1 to $n$th bonds of the given molecule.

SSSR membership is represented as a set of SSSR indices assigned to each rings. This means bonds that have the same SSSR index belong to the same SSSR.

empirical_formula(mol::MolGraph) -> String

Return the empirical formula in Hill system.

explicit_hydrogens(mol::SimpleMolGraph) -> Vector{Int}

Return a vector of size $n$ representing the number of explicit hydrogens connected to 1 to $n$th atoms of the given molecule.

"Explicit" means hydrogens are explicitly represented as graph nodes.

fused_rings(mol::SimpleMolGraph{T}) -> Vector{Vector{T}}

Return vectors of fused ring node sets.

A fused ring is defined as a 2-edge connected components in terms of graph theory. Spirocyclic structures are considered to be part of a fused ring.

heavy_atom_count(mol::SimpleMolGraph) -> Int

Return the total number of non-hydrogen atoms.

heavy_atoms(mol::SimpleMolGraph) -> Vector{Int}

Return a vector of size $n$ representing the number of non-hydrogen atoms connected to 1 to $n$th atoms of the given molecule.

hybridization(mol::SimpleMolGraph) -> Vector{Int}

Returns a vector of size $n$ representing the orbital hybridization symbols (:sp3, :sp2, :sp or :none) of 1 to $n$th atoms of the given molecule.

The hybridization value in inorganic atoms and non-typical organic atoms will be :none (e.g. s, sp3d and sp3d2 orbitals). Note that this is a simplified geometry descriptor for substructure matching and does not reflect actual molecular orbital hybridization.

hydrogen_acceptor_count(mol::SimpleMolGraph) -> Int

Return the total number of hydrogen bond acceptors (N, O and F).

hydrogen_donor_count(mol::SimpleMolGraph) -> Int

Return the total number of hydrogen bond donors (O and N attached to hydrogens).

implicit_hydrogens(mol::SimpleMolGraph) -> Vector{Int}

Return a vector of size $n$ representing the number of implicit hydrogens connected to 1 to $n$th atoms of the given molecule.

"Implicit" means hydrogens are not represented as graph nodes, but it can be infered from the intrinsic valence of typical organic atoms.

is_aromatic(mol::SimpleMolGraph) -> Vector{Bool}

Returns a vector of size $n$ representing whether 1 to $n$th atoms of the given molecule belong to an aromatic ring or not.

See is_ring_aromatic.

is_edge_aromatic(mol::SimpleMolGraph) -> Vector{Bool}

Returns a vector of size $n$ representing whether 1 to $n$th bonds of the given molecule belong to an aromatic ring or not.

See is_ring_aromatic.

is_edge_in_ring(mol::MolGraph) -> Vector{Bool}

Return a vector of size $n$ representing whether 1 to $n$th bonds of the given molecule belong to a ring or not.

is_in_ring(mol::MolGraph) -> Vector{Bool}

Return a vector of size $n$ representing whether 1 to $n$th atoms of the given molecule belong to a ring or not.

is_ring_aromatic(mol::SimpleMolGraph) -> Vector{Bool}

Returns a vector of size $n$ representing whether first to $n$-th rings of a given molecule are aromatic or not.

This is a binary descriptor based on a chemoinformatic algorithm and may not reflect actual molecular orbitals. Atypical aromaticities such as Moebius aromaticity are not considered.

is_rotatable(mol::SimpleMolGraph) -> Vector{Bool}

Return a vector of size $n$ representing whether 1 to $n$th bonds of the given molecule are rotatable or not.

lone_pair(mol::MolGraph) -> Vector{Int}

Return a vector of size $n$ representing the number of lone pairs of 1 to $n$th atoms of the given molecule.

molecular_formula(mol::MolGraph) -> String

Return the molecular formula in Hill system.

multiplicity(mol::MolGraph) -> Vector{Int}

Return a vector of size $n$ representing atom multiplicities of 1 to $n$th atoms of the given molecule (1: non-radical, 2: radical, 3: biradical).

pi_electron(mol::SimpleMolGraph) -> Vector{Int}

Returns a vector of size $n$ representing the number of $\pi$ electrons of 1 to $n$th atoms of the given molecule.

The number of $\pi$ electrons is calculated as valence - connectivity. Typically, each atom connected to double bonds adds one pi electron for each, and each atom connected to a triple bond adds two pi electrons.

ring_count(mol::MolGraph) -> Vector{Int}

Return a vector of size $n$ representing the number of sssr that 1 to $n$th atoms of the given molecule belong to.

This property corresponds to SMARTS R query.

rotatable_count(mol::SimpleMolGraph) -> Int

Return the total number of rotatable bonds.

smallest_ring(mol::SimpleMolGraph) -> Vector{Int}

Return a vector of size $n$ representing the size of the smallest sssr that 1 to $n$th atoms of the given molecule belong to.

If the node is not in a ring, the value would be 0. This property corresponds to SMARTS r query.

sssr(mol::SimpleMolGraph{T}) -> Vector{Vector{T}}

Return vectors of ring nodes representing small set of smallest rings (SSSR).

See mincyclebasis.

total_hydrogens(mol::SimpleMolGraph) -> Vector{Int}

Return a vector of size $n$ representing the number of total hydrogens (implicit and explicit) connected to 1 to $n$th atoms of the given molecule.

This property corresponds to SMARTS H query.

valence(mol::SimpleMolGraph) -> Vector{Int}

Return a vector of size $n$ representing the intrinsic valence of 1 to $n$th atoms of the given molecule.

The number of implicit hydrogens would be calculated based on the valence. The valence of a hypervalent atom or a non-organic atom is the same as its apparent_valence. This property corresponds to SMARTS v query.

which_fused_ring(mol::SimpleMolGraph) -> Vector{Vector{Int}}

Return a vector of size $n$ representing fused_rings membership of 1 to $n$th atoms of the given molecule.

Fused ring membership is represented as a set of fused ring indices assigned to each fused rings. This means atoms that have the same fused ring index belong to the same fused ring.

which_ring(mol::SimpleMolGraph) -> Vector{Vector{Int}}

Return a vector of size $n$ representing sssr membership of 1 to $n$th nodes of the given graph.

SSSR membership is represented as a vector of SSSR indices assigned to each rings. This means nodes that have the same SSSR index belong to the same SSSR.

wclogp(mol::GraphMol) -> Float64

Return predicted logP value calculated by using Wildman and Crippen method.

Reference

1. Wildman, S. A. and Crippen, G. M. (1999). Prediction of Physicochemical Parameters by Atomic Contributions. Journal of Chemical Information and Modeling, 39(5), 868–873. https://doi.org/10.1021/ci990307l

wclogptype(mol::MolGraph)

Return Wildman-Crippen LogP atom types.