biotite-dev / molmarbles

A bridge between Biotite and OpenMM

Molmarbles

This small package allows conversion between structures objects from Biotite (AtomArray and AtomArrayStack) and System, Topology, Context or State objects from OpenMM. This allows for data preparation, MD simulation and trajectory analysis from the same script without intermediate files.

Note The development of this package is work in progress. The API will probably change in the future.

Installation

Molmarbles can be installed via pip, either from PyPI...

$ pip install molmarbles

or a local repository clone.

$ pip install .

Note that OpenMM must also be installed for Molmarbles to work. OpenMM is not distributed via PyPI and must installed via Conda.

$ conda install -c conda-forge openmm

Usage

AtomArray and AtomArrayStack objects can be converted to the respective OpenMM objects with

• to_system()
• to_topology()

and vice versa with

• from_topology()
• from_context()
• from_states()
• from_state()

Detailed description of parameters and return values is provided by the respective docstring.

Example

A short MD simulation of lysozyme

import os
from os.path import isdir, join
import numpy as np
import matplotlib.pyplot as plt
import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.io.mmtf as mmtf
import molmarbles
import openmm
import openmm.app as app
from openmm.unit import nanometer, angstrom, kelvin, picosecond


BUFFER = 10
TIME_STEP = 0.004
FRAME_STEP = 0.1
N_FRAMES = 100


molecule = mmtf.get_structure(
    mmtf.MMTFFile.read(rcsb.fetch("1aki", "mmtf")),
    model=1,
    include_bonds=True
)
# Remove solvent, as proper solvent addition is handled by OpenMM
molecule = molecule[struc.filter_amino_acids(molecule)]
# Create a box with some buffer around the protein
# This box represents the
box_dim = np.max(molecule.coord, axis=0) - np.min(molecule.coord, axis=0)
molecule.box = np.diag(box_dim + BUFFER)

# Create an OpenMM Topology from the AtomArray
topology = molmarbles.to_topology(molecule)


force_field = openmm.app.ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
# Add hydrogen atoms and water
modeller = app.Modeller(topology, molecule.coord * angstrom)
modeller.addHydrogens(force_field)
modeller.addSolvent(force_field)
topology = modeller.topology

system = force_field.createSystem(
    topology, nonbondedMethod=app.PME,
    nonbondedCutoff=1*nanometer, constraints=app.HBonds
)
integrator = openmm.LangevinMiddleIntegrator(300*kelvin, 1/picosecond, TIME_STEP*picosecond)
simulation = app.Simulation(topology, system, integrator)
simulation.context.setPositions(modeller.positions)
simulation.minimizeEnergy()

# Run simulation and record the current state (the coordinates)
# every FRAME_STEP picoseconds
states = []
states.append(simulation.context.getState(getPositions=True))
for i in range(N_FRAMES):
    simulation.step(FRAME_STEP // TIME_STEP)
    states.append(simulation.context.getState(getPositions=True))


# Transfer the trajectory back to Biotite
# The topology was changed in the process of adding hydrogen and solvent
# -> Update the structure
template = molmarbles.from_topology(topology)
trajectory = molmarbles.from_states(template, states)
# Center protein in box
trajectory.coord -= struc.centroid(
    trajectory.coord[:, struc.filter_amino_acids(trajectory)]
)[:, np.newaxis, :]
trajectory.coord += np.sum(trajectory.box / 2, axis=-2)[:, np.newaxis, :]
# Remove segmentation over periodic boundary
trajectory = struc.remove_pbc(trajectory)

Visualization with Ammolite and PyMOL

example.mp4

Testing

Molmarbles uses pytest for running its tests.