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)

Install using pip:

pip install spindry

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. 3. 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.

4. 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.

5. If num_conformers is met, quit.

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.

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>)

This project is licensed under the MIT license.