Ligand-based Pharmacophores

[Daniel-Ibarrola]

Description

Common pharmacophores can be obtained from a set of ligands with known activity using the LigandBasedPharmacophore class. Besides extraction of common pharmacophores, this class also impements a workflow to prepare the ligands for pharmacophore elucidation, for example, by adding hydrogens and generating conformers.

Pharmacophores can be found with just a few lines of code

from openpharmacophore import LigandBasedPharmacophore

lbp = LigandBasedPharmacophore()
lbp.load_ligands("ligands.smi")
lbp.add_hydrogens(ligands="all") 
lbp.generate_conformers(ligands="all", n_confs=100)
lbp.find_chem_feats()
lbp.extract(
        n_points=4, min_actives=len(lbp.ligands), max_pharmacophores=10
    )

Todos

• [ ] Add directionality to ligand-based pharmacophoric points.
• [ ] Creation of excluded volumes.

Status

• [x] Ready to go