get_graph_structure_node_feature {DeepPINCS} | R Documentation |
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.
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"))
smiles |
SMILES strings |
max_atoms |
maximum number of atoms |
element_list |
list of atom symbols |
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 |
Dongmin Jung
Balakin, K. V. (2009). Pharmaceutical data mining: approaches and applications for drug discovery. Wiley.
matlab::padarray, purrr::chuck, rcdk::get.adjacency.matrix, rcdk::get.atoms, rcdk::get.hydrogen.count, rcdk::get.symbol rcdk::parse.smiles
get_graph_structure_node_feature(example_cpi[1, 1], 10)