Using with RDKit

RDKit integration in narupatools provides a couple of ASE forcefields, as well as access to the powerful tools allowing generating systems.

How do I…

… generate a system from one or more SMILES strings?

Systems can be generated from one or more SMILES strings using the narupatools.rdkit.generate_from_smiles functionality:

from narupatools.rdkit import generate_from_smiles

# Create an RDKit Mol object from the SMILES string for ethane
mol = generate_from_smiles("CC")

from narupa.trajectory import FrameData

# Create a Narupa FrameData from the SMILES string for two methanols
frame = generate_from_smiles("CO", "CO", output_type=FrameData)

from MDAnalysis import Universe

# Create an MDAnalysis universe from the SMILES string for ethylene without hydrogens
universe = generate_from_smiles("C=C", output_type=Universe, add_hydrogens=False)

… run ASE dynamics with the MMFF94 forcefield?

The narupatools.ase.rdkit.MMFF94Calculator allows the MMFF94 forcefield as implemented by RDKit to be used to provide forces and energies:

from narupatools.ase.rdkit import MMFF94Calculator

atoms.calc = MMFF94Calculator()

… run ASE dynamics with the UFF forcefield?

The narupatools.ase.rdkit.UFFCalculator allows the UFF forcefield to be used with ASE:

from narupatools.ase.rdkit import UFFCalculator

atoms.calc = UFFCalculator()

… ignore intermolecular forces with MMFF94 or UFF?

Both the MMFF94 and UFF calculators can ignore intermolecular forces by setting include_interatomic to False:

from narupatools.ase.rdkit import UFFCalculator

atoms.calc = UFFCalculator(include_interatomic=False)

… set a cutoff for nonbonded forces with MMFF94 or UFF?

Both forcefields support having a cutoff specified (in nanometers):

from narupatools.ase.rdkit import MMFF94Calculator

atoms.calc = MMFF94Calculator(nonbonded_cutoff=2.0)