A new small molecule quantifier using RDkit

[anupam-banerjee]

This module reads a multi-molecule SDF file and computes ligand efficiency plus basic ADME/physicochemical descriptors for each compound. It optionally standardizes molecules (cleanup, metal disconnection, reionization, normalization, tautomer canonicalization) before calculation. It extracts binding energy and minimized RMSD from SD fields (e.g. Pharmit’s minimizedAffinity and minimizedRMSD); if these fields are missing or invalid, the corresponding energy, RMSD, and LE entries are reported as None for that ligand. It then calculates descriptors such as MW, cLogP, TPSA, HBA/HBD, rotatable bonds, fSP3, aromaticity metrics, and simple HIA/BBB likelihood, and screens for PAINS/Brenk/NIH/ZINC alerts. Using these properties, it derives a ligand efficiency value (when energy is available), a weighted 0–10 “drug_score”, and a qualitative label (“Good”, “Medium”, “Poor”) to help prioritize screening hits.

[anupam-banerjee]

it can be tested by running-

from prody import *

calcLigandEfficiencyFromSDF("input.sdf", out_csv="input_le_adme.csv")

[anupam-banerjee]

An input file to test-
input_sdf.txt

Rename file to input.sdf and run