get_graph_structure_node_feature: Graph structure and node features from SMILES strings

In dongminjung/DeepPINCS: Protein Interactions and Networks with Compounds based on Sequences using Deep Learning

Description

In molecular graph representations, nodes represent atoms and edges represent bonds. For molecular features, the Chemistry Development Kit (CDK) is used as a cheminformatics tool. The degree of an atom in the graph representation and the atomic symbol and implicit hydrogen count for an atom are used as molecular features.

Usage

get_graph_structure_node_feature(smiles, max_atoms,
    element_list = c(
        "C", "N", "O", "S", "F", "Si", "P", "Cl",
        "Br", "Mg", "Na", "Ca", "Fe",  "Al", "I",
        "B", "K", "Se", "Zn", "H", "Cu", "Mn"))

Arguments

smiles	SMILES strings
max_atoms	maximum number of atoms
element_list	list of atom symbols

Value

A_pad	a padded or turncated adjacency matrix for each SMILES string
X_pad	a padded or turncated node features for each SMILES string
feature_dim	dimension of node features
element_list	list of atom symbols

Author(s)

Dongmin Jung

References

Balakin, K. V. (2009). Pharmaceutical data mining: approaches and applications for drug discovery. Wiley.

See Also

matlab::padarray, purrr::chuck, rcdk::get.adjacency.matrix, rcdk::get.atoms, rcdk::get.hydrogen.count, rcdk::get.symbol rcdk::parse.smiles

Examples

get_graph_structure_node_feature(example_cpi[1, 1], 10)

dongminjung/DeepPINCS documentation built on Dec. 20, 2021, 12:13 a.m.