Simple program to quickly prepare 3D SDF/MOL2/PDBQT files from SMILES for ligands using rdkit & openbabel.
Also, split sdf and convert formats sdf<->pdbqt for Autodock Vina
pip install LigPrepper
LigPrepper.smiles2sdf('c1ccncc1', labels='pyridine')
LigPrepper.smiles2mol2('c1ccncc1', labels='pyridine')
LigPrepper.smiles2pdbqt('c1ccncc1', labels='pyridine')
LigPrepper.smiles2sdf(smiles_list, labels=labels_list, mergesdf=False)
LigPrepper.smiles2sdf(smiles_list, labels=labels_list, ref='ref.sdf', mergesdf=False)
sdf2pdbqt
pdbqt2sdf
splitsdf
LigPrepper.smiles2png(smiles_list, labels=labels_list)
LigPrepper.smiles2png(smiles_list, labels=labels_list, ref='ref smiles')
LigPrepper.smiles2png(smiles_list, labels=labels_list, ref='ref.sdf')