get_graph_structure_node_feature {DeepPINCS} | R Documentation

## Graph structure and node features from SMILES strings

### 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)

[Package DeepPINCS version 1.2.2 Index]