def add_interactions(self, state: interfaces.IState, system: mm.System,
topology: app.Topology) -> mm.System:
if self.active:
if self.use_pbc:
cartesian_force = mm.CustomExternalForce(
"0.5 * cart_force_const * r_eff^2;"
"r_eff = max(0.0, r - cart_delta);"
"r = periodicdistance(x, y, z, cart_x, cart_y, cart_z)")
else:
cartesian_force = mm.CustomExternalForce(
"0.5 * cart_force_const * r_eff^2;"
"r_eff = max(0.0, r - cart_delta);"
"r = sqrt(dx*dx + dy*dy + dz*dz);"
"dx = x - cart_x;"
"dy = y - cart_y;"
"dz = z - cart_z;")
cartesian_force.addPerParticleParameter("cart_x")
cartesian_force.addPerParticleParameter("cart_y")
cartesian_force.addPerParticleParameter("cart_z")
cartesian_force.addPerParticleParameter("cart_delta")
cartesian_force.addPerParticleParameter("cart_force_const")
# add the atoms
for r in self.restraints:
weight = r.force_const
cartesian_force.addParticle(r.atom_index,
[r.x, r.y, r.z, r.delta, weight])
system.addForce(cartesian_force)
self.force = cartesian_force
return system
def setup_system_non_bonded(self, system: mm.System, cutoff: Quantity):
if self.non_bonded_function_type != NB_FUNCTION_LENNARD_JONES:
# TODO: Implement Buckingham potential
raise NotImplementedError(
f'Non bonded function {self.non_bonded_function_type} '
'is not implemented.')
if self.combination_rule in '1':
potential = potentials.create_c6c12(cutoff=cutoff)
elif self.combination_rule in '2':
potential = potentials.create_epsilon_sigma(cutoff=cutoff)
else:
# TODO: implement combination rule 3
raise NotImplementedError(
f'Combination rule {self.combination_rule} is not implemented.'
)
for molecule_name, number_of_molecule_copies in self.molecules:
molecule = self.molecule_types[molecule_name]
for _ in range(number_of_molecule_copies):
for atom in molecule.atoms.values():
ptype = self.atom_types[atom.type_]
potential.addParticle([ptype.v, ptype.w])
system.addForce(potential)
return potential
def add_reaction_coordinate(
system: openmm.System,
host_index: List[int],
guest_index: List[int],
k_z: simtk_unit.Quantity,
z_0: simtk_unit.Quantity,
force_group: Optional[int] = 11,
):
"""
Applies the umbrella reaction coordinate to the guest molecule
"""
# Simple umbrella potential string expression
reaction = openmm.CustomCentroidBondForce(
2, "0.5 * k_z * (r_z - z_0)^2;" "r_z = z2 - z1;"
)
reaction.setUsesPeriodicBoundaryConditions(False)
reaction.setForceGroup(force_group)
# Umbrella parameters
reaction.addPerBondParameter("k_z", k_z)
reaction.addPerBondParameter("z_0", z_0)
# Add host and guest indices
g1 = reaction.addGroup(host_index)
g2 = reaction.addGroup(guest_index)
# Add bond
reaction.addBond([g1, g2], [k_z, z_0])
# Add force to system
system.addForce(reaction)
def add_harmonic_restraints(system: mm.System, args: ListOfArgs):
"""Restraints format is different here than in SM webservice.
Example record: :10 :151\n
or
:10 :151 0.1 30000\n
:i :j distance energy
"""
print(" Adding harmonic restraints")
if args.HR_USE_FLAT_BOTTOM_FORCE:
contact_force = mm.CustomBondForce('step(r-r0) * (k/2) * (r-r0)^2')
contact_force.addPerBondParameter('r0')
contact_force.addPerBondParameter('k')
else:
contact_force = mm.HarmonicBondForce()
system.addForce(contact_force)
with open(args.HR_RESTRAINTS_PATH) as input_file:
counter = 0
for line in input_file:
columns = line.split()
atom_index_i = int(columns[0][1:]) - 1
atom_index_j = int(columns[1][1:]) - 1
try:
r0 = float(columns[2])
k = float(columns[3]) * args.HR_K_SCALE
except IndexError:
r0 = args.HR_R0_PARAM
k = args.HR_K_PARAM
if args.HR_USE_FLAT_BOTTOM_FORCE:
contact_force.addBond(atom_index_i, atom_index_j, [r0, k])
else:
contact_force.addBond(atom_index_i, atom_index_j, r0, k)
counter += 1
print(f" {counter} restraints added.")
def add_interactions(self, state: interfaces.IState,
openmm_system: mm.System,
topology: app.Topology) -> mm.System:
if not self._active:
return openmm_system
cmap_force = mm.CMAPTorsionForce()
cmap_force.addMap(self._gly_map.shape[0], self._gly_map.flatten())
cmap_force.addMap(self._pro_map.shape[0], self._pro_map.flatten())
cmap_force.addMap(self._ala_map.shape[0], self._ala_map.flatten())
cmap_force.addMap(self._gen_map.shape[0], self._gen_map.flatten())
# loop over all of the contiguous chains of amino acids
for chain in self._iterate_cmap_chains():
# loop over the interior residues
n_res = len(chain)
for i in range(1, n_res - 1):
map_index = residue_to_map[chain[i].res_name]
c_prev = chain[i - 1].index_C
n = chain[i].index_N
ca = chain[i].index_CA
c = chain[i].index_C
n_next = chain[i + 1].index_N
cmap_force.addTorsion(map_index, c_prev, n, ca, c, n, ca, c,
n_next)
openmm_system.addForce(cmap_force)
return openmm_system
def add_interactions(
self, state: interfaces.IState, system: mm.System, topology: app.Topology
) -> mm.System:
if self.active:
# create the confinement force
if self.use_pbc:
confinement_force = mm.CustomExternalForce(
"step(r - radius) * force_const * (radius - r)^2;"
"r = periodicdistance(x, y, z, 0, 0 ,0)"
)
else:
confinement_force = mm.CustomExternalForce(
"step(r - radius) * force_const * (radius - r)^2;"
"r=sqrt(x*x + y*y + z*z)"
)
confinement_force.addPerParticleParameter("radius")
confinement_force.addPerParticleParameter("force_const")
# add the atoms
for r in self.restraints:
weight = r.force_const
confinement_force.addParticle(r.atom_index, [r.radius, weight])
system.addForce(confinement_force)
self.force = confinement_force
return system
def add_interactions(self, state: interfaces.IState, system: mm.System,
topology: app.Topology) -> mm.System:
if self.active:
meld_force = MeldForce()
# Add all of the always-on restraints
if self.always_on:
group_list = []
for rest in self.always_on:
rest_index = _add_meld_restraint(self.tracker, rest,
meld_force, 0, 0)
# Each restraint goes in its own group.
group_index = meld_force.addGroup([rest_index], 1)
group_list.append(group_index)
# Add the group to the tracker, but as None, so
# we won't update it.
self.tracker.groups.append(None)
# All of the always-on restraints go in a single collection
meld_force.addCollection(group_list, len(group_list))
# Add this collection to the tracker, but as
# None, so we won't update it
self.tracker.collections.append(None)
# Add the selectively active restraints
for coll in self.selective_on:
group_indices = []
for group in coll.groups:
restraint_indices = []
for rest in group.restraints:
rest_index = _add_meld_restraint(
self.tracker, rest, meld_force, 0, 0)
restraint_indices.append(rest_index)
# Create the group in the meldplugin
group_num_active = self._handle_num_active(
group.num_active, state)
group_index = meld_force.addGroup(restraint_indices,
group_num_active)
group_indices.append(group_index)
# Add the group to the tracker so we can update it
self.tracker.groups.append(group)
# Create the collection in the meldplugin
coll_num_active = self._handle_num_active(
group.num_active, state)
meld_force.addCollection(group_indices, coll_num_active)
# Add the collection to the tracker so we can update it
self.tracker.collections.append(coll)
system.addForce(meld_force)
self.force = meld_force
return system
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_funnel_potential(
system: openmm.System,
host_index: List[int],
guest_index: List[int],
k_xy: Optional[simtk_unit.Quantity] = 10.0
* simtk_unit.kilocalorie_per_mole
/ simtk_unit.angstrom ** 2,
z_cc: Optional[simtk_unit.Quantity] = 11.0 * simtk_unit.angstrom,
alpha: Optional[simtk_unit.Quantity] = 35.0 * simtk_unit.degrees,
R_cylinder: Optional[simtk_unit.Quantity] = 1.0 * simtk_unit.angstrom,
force_group: Optional[int] = 10,
):
"""
Applies a funnel potential to a guest molecule
"""
# Funnel potential string expression
funnel = openmm.CustomCentroidBondForce(
2,
"U_funnel + U_cylinder;"
"U_funnel = step(z_cc - abs(r_z))*step(r_xy - R_funnel)*Wall;"
"U_cylinder = step(abs(r_z) - z_cc)*step(r_xy - R_cylinder)*Wall;"
"Wall = 0.5 * k_xy * r_xy^2;"
"R_funnel = (z_cc-abs(r_z))*tan(alpha) + R_cylinder;"
"r_xy = sqrt((x2 - x1)^2 + (y2 - y1)^2);"
"r_z = z2 - z1;",
)
funnel.setUsesPeriodicBoundaryConditions(False)
funnel.setForceGroup(force_group)
# Funnel parameters
funnel.addGlobalParameter("k_xy", k_xy)
funnel.addGlobalParameter("z_cc", z_cc)
funnel.addGlobalParameter("alpha", alpha)
funnel.addGlobalParameter("R_cylinder", R_cylinder)
# Add host and guest indices
g1 = funnel.addGroup(host_index)
g2 = funnel.addGroup(guest_index)
# Add bond
funnel.addBond([g1, g2], [])
# Add force to system
system.addForce(funnel)
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)
def add_interactions(self, state: interfaces.IState, system: mm.System,
topology: app.Topology) -> mm.System:
if self.active:
rest = self.restraints[0]
# create the expression for the energy
components = []
if "x" in rest.dims:
components.append("(x1-abscom_x)*(x1-abscom_x)")
if "y" in rest.dims:
components.append("(y1-abscom_y)*(y1-abscom_y)")
if "z" in rest.dims:
components.append("(z1-abscom_z)*(z1-abscom_z)")
dist_expr = "dist2={};".format(" + ".join(components))
energy_expr = "0.5 * com_k * dist2;"
expr = "\n".join([energy_expr, dist_expr])
# create the force
force = mm.CustomCentroidBondForce(1, expr)
force.addPerBondParameter("com_k")
force.addPerBondParameter("abscom_x")
force.addPerBondParameter("abscom_y")
force.addPerBondParameter("abscom_z")
# create the restraint with parameters
if rest.weights:
g1 = force.addGroup(rest.indices, rest.weights)
else:
g1 = force.addGroup(rest.indices)
force_const = rest.force_const
pos_x = rest.position[0]
pos_y = rest.position[1]
pos_z = rest.position[2]
force.addBond([g1], [force_const, pos_x, pos_y, pos_z])
system.addForce(force)
self.force = force
return system
def add_interactions(self, state: interfaces.IState, system: mm.System,
topology: app.Topology) -> mm.System:
if self.active:
rest = self.restraints[0]
# create the expression for the energy
components = []
if "x" in rest.dims:
components.append("(x1-x2)*(x1-x2)")
if "y" in rest.dims:
components.append("(y1-y2)*(y1-y2)")
if "z" in rest.dims:
components.append("(z1-z2)*(z1-z2)")
dist_expr = "dist = sqrt({});".format(" + ".join(components))
energy_expr = "0.5 * com_k * (dist - com_ref_dist)*(dist-com_ref_dist);"
expr = "\n".join([energy_expr, dist_expr])
# create the force
force = mm.CustomCentroidBondForce(2, expr)
force.addPerBondParameter("com_k")
force.addPerBondParameter("com_ref_dist")
# create the restraint with parameters
if rest.weights1:
g1 = force.addGroup(rest.indices1, rest.weights1)
else:
g1 = force.addGroup(rest.indices1)
if rest.weights2:
g2 = force.addGroup(rest.indices2, rest.weights2)
else:
g2 = force.addGroup(rest.indices2)
force_const = rest.force_const
pos = rest.positioner(0)
force.addBond([g1, g2], [force_const, pos])
system.addForce(force)
self.force = force
return system
from simtk.openmm import System
from ANN import *
system = System()
a = ANN_Force()
a.set_list_of_index_of_atoms_forming_dihedrals_from_index_of_backbone_atoms(
[1, 2, 3, 4, 5, 6])
system.addForce(a)
print "Python wrapper test passed!"
def addHydrogens(self, forcefield=None, pH=None, variants=None, platform=None):
"""Add missing hydrogens to the model.
This function automatically changes compatible residues into their constant-pH variant if no variant is specified.:
Aspartic acid:
AS4: Form with a 2 hydrogens on each one of the delta oxygens (syn,anti)
It has 5 titration states.
Alternative:
AS2: Has 2 hydrogens (syn, anti) on one of the delta oxygens
It has 3 titration states.
Cysteine:
CYS: Neutral form with a hydrogen on the sulfur
CYX: No hydrogen on the sulfur (either negatively charged, or part of a disulfide bond)
Glutamic acid:
GL4: Form with a 2 hydrogens on each one of the epsilon oxygens (syn,anti)
It has 5 titration states.
Histidine:
HIP: Positively charged form with hydrogens on both ND1 and NE2
It has 3 titration states.
The variant to use for each residue is determined by the following rules:
1. Any Cysteine that participates in a disulfide bond uses the CYX variant regardless of pH.
2. Other residues are all set to maximally protonated state, which can be updated using a proton drive
You can override these rules by explicitly specifying a variant for any residue. To do that, provide a list for the
'variants' parameter, and set the corresponding element to the name of the variant to use.
A special case is when the model already contains a hydrogen that should not be present in the desired variant.
If you explicitly specify a variant using the 'variants' parameter, the residue will be modified to match the
desired variant, removing hydrogens if necessary. On the other hand, for residues whose variant is selected
automatically, this function will only add hydrogens. It will never remove ones that are already present in the
model.
Definitions for standard amino acids and nucleotides are built in. You can call loadHydrogenDefinitions() to load
additional definitions for other residue types.
Parameters
----------
forcefield : ForceField=None
the ForceField to use for determining the positions of hydrogens.
If this is None, positions will be picked which are generally
reasonable but not optimized for any particular ForceField.
pH : None,
Kept for compatibility reasons. Has no effect.
variants : list=None
an optional list of variants to use. If this is specified, its
length must equal the number of residues in the model. variants[i]
is the name of the variant to use for residue i (indexed starting at
0). If an element is None, the standard rules will be followed to
select a variant for that residue.
platform : Platform=None
the Platform to use when computing the hydrogen atom positions. If
this is None, the default Platform will be used.
Returns
-------
list
a list of what variant was actually selected for each residue,
in the same format as the variants parameter
Notes
-----
This function does not use a pH specification. The argument is kept for compatibility reasons.
"""
# Check the list of variants.
if pH is not None:
print("Ignored pH argument provided for constant-pH residues.")
residues = list(self.topology.residues())
if variants is not None:
if len(variants) != len(residues):
raise ValueError(
"The length of the variants list must equal the number of residues"
)
else:
variants = [None] * len(residues)
actualVariants = [None] * len(residues)
# Load the residue specifications.
if not Modeller._hasLoadedStandardHydrogens:
Modeller.loadHydrogenDefinitions(
os.path.join(
os.path.dirname(__file__), "data", "hydrogens-amber10-constph.xml"
)
)
# Make a list of atoms bonded to each atom.
bonded = {}
for atom in self.topology.atoms():
bonded[atom] = []
for atom1, atom2 in self.topology.bonds():
bonded[atom1].append(atom2)
bonded[atom2].append(atom1)
# Define a function that decides whether a set of atoms form a hydrogen bond, using fairly tolerant criteria.
def isHbond(d, h, a):
if norm(d - a) > 0.35 * nanometer:
return False
deltaDH = h - d
deltaHA = a - h
deltaDH /= norm(deltaDH)
deltaHA /= norm(deltaHA)
return acos(dot(deltaDH, deltaHA)) < 50 * degree
# Loop over residues.
newTopology = Topology()
newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
newAtoms = {}
newPositions = [] * nanometer
newIndices = []
acceptors = [
atom
for atom in self.topology.atoms()
if atom.element in (elem.oxygen, elem.nitrogen)
]
for chain in self.topology.chains():
newChain = newTopology.addChain(chain.id)
for residue in chain.residues():
newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
isNTerminal = residue == chain._residues[0]
isCTerminal = residue == chain._residues[-1]
if residue.name in Modeller._residueHydrogens:
# Add hydrogens. First select which variant to use.
spec = Modeller._residueHydrogens[residue.name]
variant = variants[residue.index]
if variant is None:
if residue.name == "CYS":
# If this is part of a disulfide, use CYX.
sulfur = [
atom
for atom in residue.atoms()
if atom.element == elem.sulfur
]
if len(sulfur) == 1 and any(
(atom.residue != residue for atom in bonded[sulfur[0]])
):
variant = "CYX"
if residue.name == "HIS":
variant = "HIP"
if residue.name == "GLU":
variant = "GL4"
if residue.name == "ASP":
variant = "AS4"
if variant is not None and variant not in spec.variants:
raise ValueError(
"Illegal variant for %s residue: %s"
% (residue.name, variant)
)
actualVariants[residue.index] = variant
removeExtraHydrogens = variants[residue.index] is not None
# Make a list of hydrogens that should be present in the residue.
parents = [
atom
for atom in residue.atoms()
if atom.element != elem.hydrogen
]
parentNames = [atom.name for atom in parents]
hydrogens = [
h
for h in spec.hydrogens
if (variant is None)
or (h.variants is None)
or (h.variants is not None and variant in h.variants)
]
hydrogens = [
h
for h in hydrogens
if h.terminal is None
or (isNTerminal and h.terminal == "N")
or (isCTerminal and h.terminal == "C")
]
hydrogens = [h for h in hydrogens if h.parent in parentNames]
# Loop over atoms in the residue, adding them to the new topology along with required hydrogens.
for parent in residue.atoms():
# Check whether this is a hydrogen that should be removed.
if (
removeExtraHydrogens
and parent.element == elem.hydrogen
and not any(parent.name == h.name for h in hydrogens)
):
continue
# Add the atom.
newAtom = newTopology.addAtom(
parent.name, parent.element, newResidue
)
newAtoms[parent] = newAtom
newPositions.append(deepcopy(self.positions[parent.index]))
if parent in parents:
# Match expected hydrogens with existing ones and find which ones need to be added.
existing = [
atom
for atom in bonded[parent]
if atom.element == elem.hydrogen
]
expected = [h for h in hydrogens if h.parent == parent.name]
if len(existing) < len(expected):
# Try to match up existing hydrogens to expected ones.
matches = []
for e in existing:
match = [h for h in expected if h.name == e.name]
if len(match) > 0:
matches.append(match[0])
expected.remove(match[0])
else:
matches.append(None)
# If any hydrogens couldn't be matched by name, just match them arbitrarily.
for i in range(len(matches)):
if matches[i] is None:
matches[i] = expected[-1]
expected.remove(expected[-1])
# Add the missing hydrogens.
for h in expected:
newH = newTopology.addAtom(
h.name, elem.hydrogen, newResidue
)
newIndices.append(newH.index)
delta = Vec3(0, 0, 0) * nanometer
if len(bonded[parent]) > 0:
for other in bonded[parent]:
delta += (
self.positions[parent.index]
- self.positions[other.index]
)
else:
delta = (
Vec3(
random.random(),
random.random(),
random.random(),
)
* nanometer
)
delta *= 0.1 * nanometer / norm(delta)
delta += (
0.05
* Vec3(
random.random(),
random.random(),
random.random(),
)
* nanometer
)
delta *= 0.1 * nanometer / norm(delta)
newPositions.append(
self.positions[parent.index] + delta
)
newTopology.addBond(newAtom, newH)
else:
# Just copy over the residue.
for atom in residue.atoms():
newAtom = newTopology.addAtom(
atom.name, atom.element, newResidue
)
newAtoms[atom] = newAtom
newPositions.append(deepcopy(self.positions[atom.index]))
for bond in self.topology.bonds():
if bond[0] in newAtoms and bond[1] in newAtoms:
newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
# The hydrogens were added at random positions. Now perform an energy minimization to fix them up.
if forcefield is not None:
# Use the ForceField the user specified.
system = forcefield.createSystem(newTopology, rigidWater=False)
atoms = list(newTopology.atoms())
for i in range(system.getNumParticles()):
if atoms[i].element != elem.hydrogen:
# This is a heavy atom, so make it immobile.
system.setParticleMass(i, 0)
else:
# Create a System that restrains the distance of each hydrogen from its parent atom
# and causes hydrogens to spread out evenly.
system = System()
nonbonded = CustomNonbondedForce("100/((r/0.1)^4+1)")
bonds = HarmonicBondForce()
angles = HarmonicAngleForce()
system.addForce(nonbonded)
system.addForce(bonds)
system.addForce(angles)
bondedTo = []
for atom in newTopology.atoms():
nonbonded.addParticle([])
if atom.element != elem.hydrogen:
system.addParticle(0.0)
else:
system.addParticle(1.0)
bondedTo.append([])
for atom1, atom2 in newTopology.bonds():
if atom1.element == elem.hydrogen or atom2.element == elem.hydrogen:
bonds.addBond(atom1.index, atom2.index, 0.1, 100_000.0)
bondedTo[atom1.index].append(atom2)
bondedTo[atom2.index].append(atom1)
for residue in newTopology.residues():
if residue.name == "HOH":
# Add an angle term to make the water geometry correct.
atoms = list(residue.atoms())
oindex = [
i for i in range(len(atoms)) if atoms[i].element == elem.oxygen
]
if len(atoms) == 3 and len(oindex) == 1:
hindex = list(set([0, 1, 2]) - set(oindex))
angles.addAngle(
atoms[hindex[0]].index,
atoms[oindex[0]].index,
atoms[hindex[1]].index,
1.824,
836.8,
)
else:
# Add angle terms for any hydroxyls.
for atom in residue.atoms():
index = atom.index
if (
atom.element == elem.oxygen
and len(bondedTo[index]) == 2
and elem.hydrogen in (a.element for a in bondedTo[index])
):
angles.addAngle(
bondedTo[index][0].index,
index,
bondedTo[index][1].index,
1.894,
460.24,
)
if platform is None:
context = Context(system, VerletIntegrator(0.0))
else:
context = Context(system, VerletIntegrator(0.0), platform)
context.setPositions(newPositions)
LocalEnergyMinimizer.minimize(context, 1.0, 50)
self.topology = newTopology
self.positions = context.getState(getPositions=True).getPositions()
del context
return actualVariants
def __simulate(
positions: unit.Quantity,
box_vectors: Optional[unit.Quantity],
omm_topology: app.Topology,
omm_system: openmm.System,
n_steps: int,
temperature: unit.Quantity,
pressure: Optional[unit.Quantity],
platform: Literal["Reference", "OpenCL", "CUDA", "CPU"] = "Reference",
):
"""
Parameters
----------
positions
The starting coordinates of the molecules in the system.
box_vectors
The box vectors to use. These will overwrite the topology box vectors.
omm_topology
The topology detailing the system to simulate.
omm_system
The object which defines the systems hamiltonian.
n_steps
The number of steps to simulate for.
temperature
The temperature to simulate at.
pressure
The pressure to simulate at.
platform
The platform to simulate using.
"""
"""A helper function for simulating a system with OpenMM."""
with open("input.pdb", "w") as file:
app.PDBFile.writeFile(omm_topology, positions, file)
with open("system.xml", "w") as file:
file.write(openmm.XmlSerializer.serialize(omm_system))
if pressure is not None:
omm_system.addForce(
openmm.MonteCarloBarostat(pressure, temperature, 25))
integrator = openmm.LangevinIntegrator(
temperature, # simulation temperature,
1.0 / unit.picosecond, # friction
2.0 * unit.femtoseconds, # simulation timestep
)
platform = openmm.Platform.getPlatformByName(platform)
simulation = app.Simulation(omm_topology, omm_system, integrator, platform)
if box_vectors is not None:
simulation.context.setPeriodicBoxVectors(box_vectors[0, :],
box_vectors[1, :],
box_vectors[2, :])
simulation.context.setPositions(positions)
simulation.context.computeVirtualSites()
simulation.minimizeEnergy()
# Randomize the velocities from a Boltzmann distribution at a given temperature.
simulation.context.setVelocitiesToTemperature(temperature * unit.kelvin)
# Configure the information in the output files.
pdb_reporter = openmm.app.DCDReporter("trajectory.dcd",
int(0.05 * n_steps))
state_data_reporter = openmm.app.StateDataReporter(
"data.csv",
int(0.05 * n_steps),
step=True,
potentialEnergy=True,
temperature=True,
density=True,
)
simulation.reporters.append(pdb_reporter)
simulation.reporters.append(state_data_reporter)
logger.debug("Starting simulation")
start = time.process_time()
# Run the simulation
simulation.step(n_steps)
end = time.process_time()
logger.debug("Elapsed time %.2f seconds" % (end - start))
logger.debug("Done!")
def addHydrogens(self,
forcefield=None,
pH=None,
variants=None,
platform=None):
"""Add missing hydrogens to the model.
This function automatically changes compatible residues into their constant-pH variant if no variant is specified.:
Aspartic acid:
AS4: Form with a 2 hydrogens on each one of the delta oxygens (syn,anti)
It has 5 titration states.
Alternative:
AS2: Has 2 hydrogens (syn, anti) on one of the delta oxygens
It has 3 titration states.
Cysteine:
CYS: Neutral form with a hydrogen on the sulfur
CYX: No hydrogen on the sulfur (either negatively charged, or part of a disulfide bond)
Glutamic acid:
GL4: Form with a 2 hydrogens on each one of the epsilon oxygens (syn,anti)
It has 5 titration states.
Histidine:
HIP: Positively charged form with hydrogens on both ND1 and NE2
It has 3 titration states.
The variant to use for each residue is determined by the following rules:
1. Any Cysteine that participates in a disulfide bond uses the CYX variant regardless of pH.
2. Other residues are all set to maximally protonated state, which can be updated using a proton drive
You can override these rules by explicitly specifying a variant for any residue. To do that, provide a list for the
'variants' parameter, and set the corresponding element to the name of the variant to use.
A special case is when the model already contains a hydrogen that should not be present in the desired variant.
If you explicitly specify a variant using the 'variants' parameter, the residue will be modified to match the
desired variant, removing hydrogens if necessary. On the other hand, for residues whose variant is selected
automatically, this function will only add hydrogens. It will never remove ones that are already present in the
model.
Definitions for standard amino acids and nucleotides are built in. You can call loadHydrogenDefinitions() to load
additional definitions for other residue types.
Parameters
----------
forcefield : ForceField=None
the ForceField to use for determining the positions of hydrogens.
If this is None, positions will be picked which are generally
reasonable but not optimized for any particular ForceField.
pH : None,
Kept for compatibility reasons. Has no effect.
variants : list=None
an optional list of variants to use. If this is specified, its
length must equal the number of residues in the model. variants[i]
is the name of the variant to use for residue i (indexed starting at
0). If an element is None, the standard rules will be followed to
select a variant for that residue.
platform : Platform=None
the Platform to use when computing the hydrogen atom positions. If
this is None, the default Platform will be used.
Returns
-------
list
a list of what variant was actually selected for each residue,
in the same format as the variants parameter
Notes
-----
This function does not use a pH specification. The argument is kept for compatibility reasons.
"""
# Check the list of variants.
if pH is not None:
print("Ignored pH argument provided for constant-pH residues.")
residues = list(self.topology.residues())
if variants is not None:
if len(variants) != len(residues):
raise ValueError(
"The length of the variants list must equal the number of residues"
)
else:
variants = [None] * len(residues)
actualVariants = [None] * len(residues)
# Load the residue specifications.
if not Modeller._hasLoadedStandardHydrogens:
Modeller.loadHydrogenDefinitions(
os.path.join(os.path.dirname(__file__), "data",
"hydrogens-amber10-constph.xml"))
# Make a list of atoms bonded to each atom.
bonded = {}
for atom in self.topology.atoms():
bonded[atom] = []
for atom1, atom2 in self.topology.bonds():
bonded[atom1].append(atom2)
bonded[atom2].append(atom1)
# Define a function that decides whether a set of atoms form a hydrogen bond, using fairly tolerant criteria.
def isHbond(d, h, a):
if norm(d - a) > 0.35 * nanometer:
return False
deltaDH = h - d
deltaHA = a - h
deltaDH /= norm(deltaDH)
deltaHA /= norm(deltaHA)
return acos(dot(deltaDH, deltaHA)) < 50 * degree
# Loop over residues.
newTopology = Topology()
newTopology.setPeriodicBoxVectors(
self.topology.getPeriodicBoxVectors())
newAtoms = {}
newPositions = [] * nanometer
newIndices = []
acceptors = [
atom for atom in self.topology.atoms()
if atom.element in (elem.oxygen, elem.nitrogen)
]
for chain in self.topology.chains():
newChain = newTopology.addChain(chain.id)
for residue in chain.residues():
newResidue = newTopology.addResidue(residue.name, newChain,
residue.id)
isNTerminal = residue == chain._residues[0]
isCTerminal = residue == chain._residues[-1]
if residue.name in Modeller._residueHydrogens:
# Add hydrogens. First select which variant to use.
spec = Modeller._residueHydrogens[residue.name]
variant = variants[residue.index]
if variant is None:
if residue.name == "CYS":
# If this is part of a disulfide, use CYX.
sulfur = [
atom for atom in residue.atoms()
if atom.element == elem.sulfur
]
if len(sulfur) == 1 and any(
(atom.residue != residue
for atom in bonded[sulfur[0]])):
variant = "CYX"
if residue.name == "HIS":
variant = "HIP"
if residue.name == "GLU":
variant = "GL4"
if residue.name == "ASP":
variant = "AS4"
if variant is not None and variant not in spec.variants:
raise ValueError("Illegal variant for %s residue: %s" %
(residue.name, variant))
actualVariants[residue.index] = variant
removeExtraHydrogens = variants[residue.index] is not None
# Make a list of hydrogens that should be present in the residue.
parents = [
atom for atom in residue.atoms()
if atom.element != elem.hydrogen
]
parentNames = [atom.name for atom in parents]
hydrogens = [
h for h in spec.hydrogens
if (variant is None) or (h.variants is None) or (
h.variants is not None and variant in h.variants)
]
hydrogens = [
h for h in hydrogens if h.terminal is None or (
isNTerminal and h.terminal == "N") or (
isCTerminal and h.terminal == "C")
]
hydrogens = [
h for h in hydrogens if h.parent in parentNames
]
# Loop over atoms in the residue, adding them to the new topology along with required hydrogens.
for parent in residue.atoms():
# Check whether this is a hydrogen that should be removed.
if (removeExtraHydrogens
and parent.element == elem.hydrogen
and not any(parent.name == h.name
for h in hydrogens)):
continue
# Add the atom.
newAtom = newTopology.addAtom(parent.name,
parent.element,
newResidue)
newAtoms[parent] = newAtom
newPositions.append(
deepcopy(self.positions[parent.index]))
if parent in parents:
# Match expected hydrogens with existing ones and find which ones need to be added.
existing = [
atom for atom in bonded[parent]
if atom.element == elem.hydrogen
]
expected = [
h for h in hydrogens if h.parent == parent.name
]
if len(existing) < len(expected):
# Try to match up existing hydrogens to expected ones.
matches = []
for e in existing:
match = [
h for h in expected if h.name == e.name
]
if len(match) > 0:
matches.append(match[0])
expected.remove(match[0])
else:
matches.append(None)
# If any hydrogens couldn't be matched by name, just match them arbitrarily.
for i in range(len(matches)):
if matches[i] is None:
matches[i] = expected[-1]
expected.remove(expected[-1])
# Add the missing hydrogens.
for h in expected:
newH = newTopology.addAtom(
h.name, elem.hydrogen, newResidue)
newIndices.append(newH.index)
delta = Vec3(0, 0, 0) * nanometer
if len(bonded[parent]) > 0:
for other in bonded[parent]:
delta += (
self.positions[parent.index] -
self.positions[other.index])
else:
delta = (Vec3(
random.random(),
random.random(),
random.random(),
) * nanometer)
delta *= 0.1 * nanometer / norm(delta)
delta += (0.05 * Vec3(
random.random(),
random.random(),
random.random(),
) * nanometer)
delta *= 0.1 * nanometer / norm(delta)
newPositions.append(
self.positions[parent.index] + delta)
newTopology.addBond(newAtom, newH)
else:
# Just copy over the residue.
for atom in residue.atoms():
newAtom = newTopology.addAtom(atom.name, atom.element,
newResidue)
newAtoms[atom] = newAtom
newPositions.append(
deepcopy(self.positions[atom.index]))
for bond in self.topology.bonds():
if bond[0] in newAtoms and bond[1] in newAtoms:
newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
# The hydrogens were added at random positions. Now perform an energy minimization to fix them up.
if forcefield is not None:
# Use the ForceField the user specified.
system = forcefield.createSystem(newTopology, rigidWater=False)
atoms = list(newTopology.atoms())
for i in range(system.getNumParticles()):
if atoms[i].element != elem.hydrogen:
# This is a heavy atom, so make it immobile.
system.setParticleMass(i, 0)
else:
# Create a System that restrains the distance of each hydrogen from its parent atom
# and causes hydrogens to spread out evenly.
system = System()
nonbonded = CustomNonbondedForce("100/((r/0.1)^4+1)")
bonds = HarmonicBondForce()
angles = HarmonicAngleForce()
system.addForce(nonbonded)
system.addForce(bonds)
system.addForce(angles)
bondedTo = []
for atom in newTopology.atoms():
nonbonded.addParticle([])
if atom.element != elem.hydrogen:
system.addParticle(0.0)
else:
system.addParticle(1.0)
bondedTo.append([])
for atom1, atom2 in newTopology.bonds():
if atom1.element == elem.hydrogen or atom2.element == elem.hydrogen:
bonds.addBond(atom1.index, atom2.index, 0.1, 100_000.0)
bondedTo[atom1.index].append(atom2)
bondedTo[atom2.index].append(atom1)
for residue in newTopology.residues():
if residue.name == "HOH":
# Add an angle term to make the water geometry correct.
atoms = list(residue.atoms())
oindex = [
i for i in range(len(atoms))
if atoms[i].element == elem.oxygen
]
if len(atoms) == 3 and len(oindex) == 1:
hindex = list(set([0, 1, 2]) - set(oindex))
angles.addAngle(
atoms[hindex[0]].index,
atoms[oindex[0]].index,
atoms[hindex[1]].index,
1.824,
836.8,
)
else:
# Add angle terms for any hydroxyls.
for atom in residue.atoms():
index = atom.index
if (atom.element == elem.oxygen
and len(bondedTo[index]) == 2 and elem.hydrogen
in (a.element for a in bondedTo[index])):
angles.addAngle(
bondedTo[index][0].index,
index,
bondedTo[index][1].index,
1.894,
460.24,
)
if platform is None:
context = Context(system, VerletIntegrator(0.0))
else:
context = Context(system, VerletIntegrator(0.0), platform)
context.setPositions(newPositions)
LocalEnergyMinimizer.minimize(context, 1.0, 50)
self.topology = newTopology
self.positions = context.getState(getPositions=True).getPositions()
del context
return actualVariants
def add_interactions(self, state: interfaces.IState, system: mm.System,
topology: app.Topology) -> mm.System:
# The approach we use is based on
# Habeck, Nilges, Rieping, J. Biomol. NMR., 2007, 135-144.
#
# Rather than solving for the exact alignment tensor
# every step, we sample from a distribution of alignment
# tensors.
#
# We encode the five components of the alignment tensor in
# the positions of two dummy atoms relative to the center
# of mass. The value of kappa should be scaled so that the
# components of the alignment tensor are approximately unity.
#
# There is a restraint on the z-component of the seocnd dummy
# particle to ensure that it does not diffuse off to ininity,
# which could cause precision issues.
if self.active:
rdc_force = mm.CustomCentroidBondForce(
5,
"Erest + z_scaler*Ez;"
"Erest = (1 - step(dev - quadcut)) * quad + step(dev - quadcut) * linear;"
"linear = 0.5 * k_rdc * quadcut^2 + k_rdc * quadcut * (dev - quadcut);"
"quad = 0.5 * k_rdc * dev^2;"
"dev = max(0, abs(d_obs - dcalc) - flat);"
"dcalc=2/3 * kappa_rdc/r^5 * (s1*(rx^2-ry^2) + s2*(3*rz^2-r^2) + s3*2*rx*ry + s4*2*rx*rz + s5*2*ry*rz);"
"r=distance(g4, g5);"
"rx=x4-x5;"
"ry=y4-y5;"
"rz=z4-z5;"
"s1=x2-x1;"
"s2=y2-y1;"
"s3=z2-z1;"
"s4=x3-x1;"
"s5=y3-y1;"
"Ez=(z3-z1)^2;",
)
rdc_force.addPerBondParameter("d_obs")
rdc_force.addPerBondParameter("kappa_rdc")
rdc_force.addPerBondParameter("k_rdc")
rdc_force.addPerBondParameter("flat")
rdc_force.addPerBondParameter("quadcut")
rdc_force.addPerBondParameter("z_scaler")
for experiment in self.expt_dict:
# find the set of all atoms involved in this experiment
com_ind = set()
for r in self.expt_dict[experiment]:
com_ind.add(r.atom_index_1)
com_ind.add(r.atom_index_2)
# add groups for the COM and dummy particles
s1 = self.expt_dict[experiment][0].s1_index
s2 = self.expt_dict[experiment][0].s2_index
g1 = rdc_force.addGroup(list(com_ind))
g2 = rdc_force.addGroup([s1])
g3 = rdc_force.addGroup([s2])
# add non-bonded exclusions between dummy particles and all other atoms
nb_forces = [
f for f in system.getForces()
if isinstance(f, mm.NonbondedForce)
or isinstance(f, mm.CustomNonbondedForce)
]
for nb_force in nb_forces:
n_parts = nb_force.getNumParticles()
for i in range(n_parts):
if isinstance(nb_force, mm.NonbondedForce):
if i != s1:
nb_force.addException(i,
s1,
0.0,
0.0,
0.0,
replace=True)
if i != s2:
nb_force.addException(i,
s2,
0.0,
0.0,
0.0,
replace=True)
else:
if i != s1:
nb_force.addExclusion(i, s1)
if i != s2:
nb_force.addExclusion(i, s2)
for r in self.expt_dict[experiment]:
# add groups for the atoms involved in the RDC
g4 = rdc_force.addGroup([r.atom_index_1])
g5 = rdc_force.addGroup([r.atom_index_2])
rdc_force.addBond(
[g1, g2, g3, g4, g5],
[
r.d_obs,
r.kappa,
0.0,
r.tolerance,
r.quadratic_cut,
0,
], # z_scaler initial value shouldn't matter
)
system.addForce(rdc_force)
self.force = rdc_force
return system