graph_distance_index#
- skfp.descriptors.graph_distance_index(mol: Mol, distance_matrix: ndarray | None = None) int #
Graph Distance Index (GDI).
Calculates the Graph Distance Index [1], defined as the squared sum of all graph distance counts in the molecular graph’s distance matrix. The formula for calculating GDI is given as:
\[GDI = \sum_{k=1}^{D} \left(k \cdot f_k\right)^2\]where:
\(D\) is the topological diameter of the graph (the largest graph distance)
\(f_k\) is the total number of distances in the graph equal to \(k\)
- Parameters:
mol (RDKit
Mol
object) – The molecule for which the Graph Distance Index is to be calculated.distance_matrix (np.ndarray, optional) – Precomputed distance matrix. If not provided, it will be calculated using RDKit.
References
Examples
>>> from rdkit.Chem import MolFromSmiles >>> from skfp.descriptors import graph_distance_index >>> mol = MolFromSmiles("C1=CC=CC=C1") # Benzene >>> graph_distance_index(mol) 261