ConfCalc

This script provides you with the ability to calculate the energy of a molecule with variable dihedral angles via xtb.

How to use:

For correct calculation, xtb should be in PATH.

Firstly, you should create object of ConfCalc class and define some properties:

    from conf_calc import ConfCalc

    calculator = ConfCalc(mol_file_name="test.py", 
                          rotable_dihedral_idxs=[[0, 1, 2, 3],
                                                 [1, 2, 3, 4]])

or

    from conf_calc import ConfCalc

    calculator = ConfCalc(mol=some_mol, 
                          rotable_dihedral_idxs=[[0, 1, 2, 3],
                                                  1, 2, 3, 4])

Where some_mol - rdkit.Chem.Mol object, rotable_dihedral_idxs - list of idxs of atoms in rotable dihedrals. Next, to get energy of current conformer just type:

    calculator.get_energy([0., np.pi / 2])

It returns dictionary, where in field 'energy' will be current conformers' energy

To update normalization energy:

calculator.set_norm_en(0.)

If you need energy derivatives with respect to torsion angles, type this:

calculator.get_energy([0., 0., 0.], req_grad=True)

It will return dict with energy and list of gradients like this:

{
    'energy': 0.,
    'grads' : [([0, 1, 2, 3], 0.), 
               ([1, 2, 3, 4], 0.)]
}

Requirements

• rdkit *numpy

Reference

Wilson B-Matrix implementation is taken from @RMeli irc repo, and adapted to python