def _get_charges_from_openmm_system(omm_sys: openmm.System):
for force in omm_sys.getForces():
if type(force) == openmm.NonbondedForce:
break
for idx in range(omm_sys.getNumParticles()):
param = force.getParticleParameters(idx)
yield param[0].value_in_unit(simtk_unit.elementary_charge)
def add_constraints(system: mm.System, args: ListOfArgs):
print(" Adding constraints...")
print(f" r = {args.POL_CONSTRAINT_DISTANCE}")
counter = 0
for i in range(system.getNumParticles() - 1):
system.addConstraint(i, i + 1, args.POL_CONSTRAINT_DISTANCE)
counter += 1
print(f" {counter} constraints added.")
def _get_lj_params_from_openmm_system(omm_sys: openmm.System):
for force in omm_sys.getForces():
if type(force) == openmm.NonbondedForce:
break
n_particles = omm_sys.getNumParticles()
sigmas = np.asarray([*_get_sigma_from_nonbonded_force(n_particles, force)])
epsilons = np.asarray([*_get_epsilon_from_nonbonded_force(n_particles, force)])
return sigmas, epsilons
def add_harmonic_bond(system: mm.System, args: ListOfArgs):
print(" Adding harmonic bonds...")
print(f" r0 = {args.POL_HARMONIC_BOND_R0}")
print(f" k = {args.POL_HARMONIC_BOND_K} kJ/mol/nm^2")
bond_force = mm.HarmonicBondForce()
system.addForce(bond_force)
counter = 0
for i in range(system.getNumParticles() - 1):
bond_force.addBond(i, i + 1, args.POL_HARMONIC_BOND_R0, args.POL_HARMONIC_BOND_K)
counter += 1
print(f" {counter} harmonic bonds added.")
def add_harmonic_angle(system: mm.System, args: ListOfArgs):
print(" Adding harmonic angles...")
print(f" r0 = {args.POL_HARMONIC_ANGLE_R0}")
print(f" k = {args.POL_HARMONIC_ANGLE_K} kJ/mol/radian^2")
bond_force = mm.HarmonicAngleForce()
system.addForce(bond_force)
counter = 0
for i in range(system.getNumParticles() - 2):
bond_force.addAngle(i, i + 1, i + 2, args.POL_HARMONIC_ANGLE_R0, args.POL_HARMONIC_ANGLE_K)
counter += 1
print(f" {counter} harmonic bonds added.")
def add_excluded_volume(system: mm.System, args: ListOfArgs):
print(" Adding excluded volume...")
print(f" epsilon = {args.EV_EPSILON}")
print(f" sigma = {args.EV_SIGMA}")
ev_force = mm.CustomNonbondedForce('epsilon*((sigma1+sigma2)/r)^12')
ev_force.addGlobalParameter('epsilon', defaultValue=args.EV_EPSILON)
ev_force.addPerParticleParameter('sigma')
system.addForce(ev_force)
counter = 0
for i in range(system.getNumParticles()):
ev_force.addParticle([args.EV_SIGMA])
counter += 1
print(f" {counter} ev interactions added.")
def add_external_field(system: mm.System, args: ListOfArgs):
"""Add external forcefield for image-driven modelling purposes."""
print(' Adding external forcefield.')
size = os.stat(args.EF_PATH).st_size
print(f" Reading {args.EF_PATH} file ({sizeof_fmt(size)})...")
img = np.load(args.EF_PATH)
print(f" Array of shape {img.shape} loaded.")
print(f" Number of values: {img.size}")
print(f" Min: {np.min(img)}")
print(f" Max: {np.max(img)}")
if args.EF_NORMALIZE:
print(' [INFO] Field will be normalized to [0, -1]')
img = standardize_image(img)
print(f' [INFO] IMG min = {np.min(img)}, max = {np.max(img)}')
print(f' [INFO] Adding funnel like border to image')
mask_p = (img < -0.1)
mask_n = np.logical_not(mask_p)
img = add_funnel(img, mask_n)
print(" Creating a force based on density...")
voxel_size = np.array((args.EF_VOXEL_SIZE_X, args.EF_VOXEL_SIZE_Y, args.EF_VOXEL_SIZE_Z))
real_size = img.shape * voxel_size
density_fun_args = dict(
xsize=img.shape[2],
ysize=img.shape[1],
zsize=img.shape[0],
values=img.flatten().astype(np.float64),
xmin=0 * simtk.unit.angstrom - 0.5 * voxel_size[0],
ymin=0 * simtk.unit.angstrom - 0.5 * voxel_size[1],
zmin=0 * simtk.unit.angstrom - 0.5 * voxel_size[2],
xmax=(img.shape[0] - 1) * voxel_size[0] + 0.5 * voxel_size[0],
ymax=(img.shape[1] - 1) * voxel_size[1] + 0.5 * voxel_size[1],
zmax=(img.shape[2] - 1) * voxel_size[2] + 0.5 * voxel_size[2])
print(f' [INFO] Voxel size: ({args.EF_VOXEL_SIZE_X}, {args.EF_VOXEL_SIZE_Y}, {args.EF_VOXEL_SIZE_Z})')
print(f' [INFO] Real size (Shape * voxel size): ({real_size[0]}, {real_size[1]}, {real_size[2]})')
print(
f" [INFO] begin coords: ({density_fun_args['xmin']}, {density_fun_args['ymin']}, {density_fun_args['zmin']})")
print(
f" [INFO] end coords: ({density_fun_args['xmax']}, {density_fun_args['ymax']}, {density_fun_args['zmax']})")
center_x = (density_fun_args['xmax'] - density_fun_args['xmin']) / 2 + density_fun_args['xmin']
center_y = (density_fun_args['ymax'] - density_fun_args['ymin']) / 2 + density_fun_args['ymin']
center_z = (density_fun_args['zmax'] - density_fun_args['zmin']) / 2 + density_fun_args['zmin']
print(f" [INFO] Image central point: ({center_x}, {center_y}, {center_z}) ")
field_function = mm.Continuous3DFunction(**density_fun_args)
field_force = mm.CustomCompoundBondForce(1, 'ksi*fi(x1,y1,z1)')
field_force.addTabulatedFunction('fi', field_function)
field_force.addGlobalParameter('ksi', args.EF_SCALING_FACTOR)
print(" Adding force to the system...")
for i in range(system.getNumParticles()):
field_force.addBond([i], [])
system.addForce(field_force)
def add_spherical_container(system: mm.System, args: ListOfArgs):
print(" Adding spherical container...")
container_force = mm.CustomExternalForce(
'{}*max(0, r-{})^2; r=sqrt((x-{})^2+(y-{})^2+(z-{})^2)'.format(args.SC_SCALE,
args.SC_RADIUS,
args.SC_CENTER_X,
args.SC_CENTER_Y,
args.SC_CENTER_Z,
))
system.addForce(container_force)
for i in range(system.getNumParticles()):
container_force.addParticle(i, [])
print(f" Spherical container added.")
print(f" radius: {args.SC_RADIUS} nm")
print(f" scale: {args.SC_SCALE} ")
print(f" center: ({args.SC_CENTER_X}, {args.SC_CENTER_Y}, {args.SC_CENTER_Z})")
def _add_restraints(system: openmm.System, reference_pdb: openmm_app.PDBFile,
stiffness: unit.Unit, rset: str,
exclude_residues: Sequence[int]):
"""Adds a harmonic potential that restrains the system to a structure."""
assert rset in ["non_hydrogen", "c_alpha"]
force = openmm.CustomExternalForce(
"0.5 * k * ((x-x0)^2 + (y-y0)^2 + (z-z0)^2)")
force.addGlobalParameter("k", stiffness)
for p in ["x0", "y0", "z0"]:
force.addPerParticleParameter(p)
for i, atom in enumerate(reference_pdb.topology.atoms()):
if atom.residue.index in exclude_residues:
continue
if will_restrain(atom, rset):
force.addParticle(i, reference_pdb.positions[i])
logger.info("Restraining %d / %d particles.", force.getNumParticles(),
system.getNumParticles())
system.addForce(force)