LigPrepper 0.4.5

Simple program to quickly prepare ligand 3d SDF/MOL2/PDBQT from smiles

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

Draw 2D structures

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')