OpenBabel interface

OpenBabel is described as a chemical toolbox for speaking the many languages of chemical data. It's an open-source project that has long been useful for converting between file formats and many other things.

ASH features a simple interface to using OpenBabel as a theory-level, currently only for the purpose of using the built-in FF options in OpenBabel. The interface hence allows one to utilize the simple MMFF94, UFF, GAFF and Ghemical forcefields. These can be useful in ASH as e.g pre-optimizer or useful on their own if accurate enough.

Note that the interface can not be used as MM-theory in a hybrid QM/MM context. However, it should work within a hybrid ONIOM scheme.

OpenBabelTheory class:

class OpenBabelTheory():
    def __init__(self, forcefield="UFF", chargemodel=None, label="OpenBabelTheory",
                printlevel=2, user_atomcharges=None):

Keyword	Type	Default value	Details
printlevel	integer	2	Printlevel
forcefield	string	'UFF'	Options: 'UFF', 'GAFF', 'MMFF94', 'Ghemical'

OpenBabel installation

Refer to installation instructions here: https://openbabel.org/docs/Installation/install.html

A conda-forge installation (https://anaconda.org/conda-forge/openbabel) has worked for us:

mamba install openbabel

Forcefield options

Please refer to the manual about the FF implementations https://open-babel.readthedocs.io/en/latest/Forcefields/Overview.html

Note: While in principle different charge models can be used to modify the electrostatic interactions that the FF may use, in practice this is not enabled yet.

Example usage.

from ash import *

# Define fragment
frag = Fragment(xyzfile="cowley_full.xyz", charge=0, mult=1)
# Define OpenBabelTheory object
# forcefield options : 'UFF', 'MMFF94', 'GAFF', 'Ghemical'
theory = OpenBabelTheory(forcefield="UFF")

# Optimize
Optimizer(theory=theory, fragment=frag)

Other OpenBabel features in ASH

OpenBabel is also occasionally used by ASH for other features. The ability to define an ASH fragment via a SMILES string alone (see Coordinates and fragments) is e.g. enabled by OpenBabel.

ASH has also wrapped some OpenBabel library functionality into special functions:

#Function to convert Mol file to PDB-file via OpenBabel
def mol_to_pdb(file):

#Function to convert SDF file to PDB-file via OpenBabel
def sdf_to_pdb(file):

#Function to read in PDB-file and write new one with CONECT lines (geometry needs to be sensible)
def writepdb_with_connectivity(file):

#Function to read in XYZ-file (small molecule) and create PDB-file with CONECT lines (geometry needs to be sensible)
def xyz_to_pdb_with_connectivity(file, resname="UNL"):

#Function to convert PDB-file to SMILES string
def pdb_to_smiles(fname: str) -> str:

#Function to convert SMILES string to coordinates
def smiles_to_coords(smiles_string):