LatticePy

A python package for MCMC simulations of folding and phase separation in biomolecules on a lattice. LatticePy currently supports the simulation of amino acids and protein polymers on a lattice with any given number of units.

Installation

Stable Release

Run the following command in bash:

pip3 install LatticePy

Developers Release

Run the following command in bash:

pip3 install git+https://github.com/sohitmiglani/LatticePy#egg=LatticePy

Tutorial

- Import the package and initialize the lattice. You can customize the bounds of the lattice, the compactness energy, the beta (1/Temperature), and the lattice type.

from LatticePy import lattice
mylattice = lattice(bound=50, E_c=1.5, beta=0, lattice_type='simple_cubic')

- Add your polymer

• By a list of polarities

polymer = [-1, -1, -1, 1, 1, -1, -1, 1, -1, -1, -1, -1, 1, -1, 1, 1, 1, -1, 1, -1, 1, -1, 1, 1, 1, -1, -1]
mylattice.add_polymer(polymer, n_polymers=1, placement='straight') # to add it in a straight line
mylattice.add_polymer(polymer, n_polymers=1, placement='randomly') # to add it in a random fashion which may cause knots

• By sequence

sequence = 'MTKSHSEEVIVPEFNSSAKELPRPLAEKCPSIIKKFISAYDAKPDFVARSPGRVNLIGEH'
mylattice.add_protein(sequence, type='straight', n_polymers=1)

- Simulate your polymers with annealing

Change the parameters as you see fit

mylattice.simulate(n_mcmc=200000, 
                   interval=1000, 
                   record_intervals = True, 
                   anneal=True, 
                   beta_lower_bound=0, 
                   beta_upper_bound=2, 
                   beta_interval=0.05)

- Visualize the energy variation over all the MCMC steps

mylattice.energy_variation_graph()

- Visualize in an interactive 3-D lattice

mylattice.visualize()

You can see the interactive 3-D lattice for this run here.

- Get important statistics

mylattice.native_contacts

20

mylattice.energy

-58.7

mylattice.non_covalent_hydrophobic_contacts

9