Simple program to quickly prepare ligand 3d SDF/MOL2/PDBQT from smiles
Project description
LigPrepper
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
Installation:
pip install LigPrepper
Usage:
For single SMILES
LigPrepper.smiles2sdf('c1ccncc1', labels='pyridine')
LigPrepper.smiles2mol2('c1ccncc1', labels='pyridine')
LigPrepper.smiles2pdbqt('c1ccncc1', labels='pyridine')
For a list of SMILES
LigPrepper.smiles2sdf(smiles_list, labels=labels_list, mergesdf=False)
Want to align molecule to reference molecule in SDF format
LigPrepper.smiles2sdf(smiles_list, labels=labels_list, ref='ref.sdf', mergesdf=False)
convert formats
sdf2pdbqt
pdbqt2sdf
split sdf
splitsdf
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