oddt.toolkits.extras package

Submodules

oddt.toolkits.extras.rdkit module

oddt.toolkits.extras.rdkit.MolFromPDBBlock(molBlock, sanitize=True, removeHs=True, flavor=0)

oddt.toolkits.extras.rdkit.MolFromPDBQTBlock(block, sanitize=True, removeHs=True)

Read PDBQT block to a RDKit Molecule

Parameters:

block: string

Residue name which explicitly pint to a ligand(s).

sanitize: bool (default=True)

Should the sanitization be performed

removeHs: bool (default=True)

Should hydrogens be removed when reading molecule.

Returns:

mol: rdkit.Chem.rdchem.Mol

Molecule read from PDBQT

oddt.toolkits.extras.rdkit.MolToPDBQTBlock(mol, flexible=True, addHs=False, computeCharges=False)

Write RDKit Molecule to a PDBQT block

Parameters:

mol: rdkit.Chem.rdchem.Mol

Molecule with a protein ligand complex

flexible: bool (default=True)

Should the molecule encode torsions. Ligands should be flexible, proteins in turn can be rigid.

addHs: bool (default=False)

The PDBQT format requires at least polar Hs on donors. By default Hs are added.

computeCharges: bool (default=False)

Should the partial charges be automatically computed. If the Hs are added the charges must and will be recomputed. If there are no partial charge information, they are set to 0.0.

Returns:

block: str

String wit PDBQT encoded molecule

oddt.toolkits.extras.rdkit.PDBQTAtomLines(mol, donors, acceptors)

Create a list with PDBQT atom lines for each atom in molecule. Donors and acceptors are given as a list of atom indices.

Module contents