Introduction

GitHub: https://www.github.com/andrewtarzia/SpinDry

spindry is a Monte Carlo-based host-guest conformer generator using cheap and unphysical potentials.

Please submit an issue with any questions or bugs!

SpinDry uses the Monte-Carlo/molecule interface provided by my other code MCHammer (https://github.com/andrewtarzia/MCHammer).

Usage with stk

spindry optimisers (Spinner) are available by default in stk as:

import stk

host = stk.ConstructedMolecule(
    topology_graph=stk.cage.FourPlusSix(
        building_blocks=(
            stk.BuildingBlock(
                smiles='NC1CCCCC1N',
                functional_groups=[
                    stk.PrimaryAminoFactory(),
                ],
            ),
            stk.BuildingBlock(
                smiles='O=Cc1cc(C=O)cc(C=O)c1',
                functional_groups=[stk.AldehydeFactory()],
            ),
        ),
        optimizer=stk.MCHammer(),
    ),
)
guest1 = stk.host_guest.Guest(
    building_block=stk.BuildingBlock('BrBr'),
    displacement=(0., 3., 0.),
)
guest2 = stk.host_guest.Guest(
    building_block=stk.BuildingBlock('C1CCCC1'),
)

hgcomplex = stk.ConstructedMolecule(
    topology_graph=stk.host_guest.Complex(
        host=stk.BuildingBlock.init_from_molecule(host),
        guests=(guest1, guest2),
        optimizer=stk.Spinner(),
    ),
)

Installation

Install using pip:

pip install spindry

Algorithm

SpinDry implements a simple Metropolis Monte-Carlo algorithm to translate and rotate the guest molecules. All atom positions/bond lengths within the host and guest are kept rigid and do not contribute to the potential energy. The algorithm uses, by default, a simple Lennard-Jones nonbonded potential to define the potential energy surface such that steric clashes are avoided. Atom radii are taken from STREUSSEL (https://github.com/hmsoregon/STREUSEL). Custom potential functions can also be defined now – see examples/custom_potential_function.py.

The default MC algorithm is as follows:

For step in N steps:

1. Define a translation of the guest by a random unit-vector and a random [-1, 1) step along the that vector.

2. Define a rotation of the guest by a random [-1, 1) * rotation_step_size angle and a random unit axis.

Compute system potential U_nb:

U_nb is the nonbonded potential, defined by the Lennard-Jones potential:

U_nb = sum_i,j (epsilon_nb * ((sigma / r_ij)^12 - (sigma / r_ij)^6)), where epsilon_nb defines the strength of the potential, sigma defines the position where the potential becomes repulsive and r_ij is the pairwise distance between atoms i and j.

Accept or reject move:

Accept if U_i < U_(i-1) or exp(-beta(U_i - U_(i-1)) > R, where R is a random number [0, 1) and beta is the inverse Boltzmann temperature. Reject otherwise.

If num_conformers is met, quit.

Examples

The workflow for a porous organic cage built using stk (<https://stk.readthedocs.io/>) is shown in examples/ for a single guest and multiple guests.

The Spinner class yields a SupraMolecule conformer. Only conformers that pass the MC conditions are yielded. The examples in examples show how to access the structures of these conformers as .xyz files or stk molecules.

Contributors and Acknowledgements

I developed this code as a post doc in the Jelfs research group at Imperial College London (<http://www.jelfs-group.org/>, <https://github.com/JelfsMaterialsGroup>).

This code was reviewed and edited by: Lukas Turcani (<https://github.com/lukasturcani>)

License

This project is licensed under the MIT license.