def generateTopologyFromOEMol(molecule):
"""
Generate an OpenMM Topology object from an OEMol molecule.
Parameters
----------
molecule : openeye.oechem.OEMol
The molecule from which a Topology object is to be generated.
Returns
-------
topology : simtk.openmm.app.Topology
The Topology object generated from `molecule`.
"""
# Create a Topology object with one Chain and one Residue.
from simtk.openmm.app import Topology
topology = Topology()
chain = topology.addChain()
resname = molecule.GetTitle()
residue = topology.addResidue(resname, chain)
# Create atoms in the residue.
for atom in molecule.GetAtoms():
name = atom.GetName()
element = Element.getByAtomicNumber(atom.GetAtomicNum())
atom = topology.addAtom(name, element, residue)
# Create bonds.
atoms = { atom.name : atom for atom in topology.atoms() }
for bond in molecule.GetBonds():
topology.addBond(atoms[bond.GetBgn().GetName()], atoms[bond.GetEnd().GetName()])
return topology
def generateTopologyFromOEMol(molecule):
"""
Generate an OpenMM Topology object from an OEMol molecule.
Parameters
----------
molecule : openeye.oechem.OEMol
The molecule from which a Topology object is to be generated.
Returns
-------
topology : simtk.openmm.app.Topology
The Topology object generated from `molecule`.
"""
# Create a Topology object with one Chain and one Residue.
from simtk.openmm.app import Topology
topology = Topology()
chain = topology.addChain()
resname = molecule.GetTitle()
residue = topology.addResidue(resname, chain)
# Create atoms in the residue.
for atom in molecule.GetAtoms():
name = atom.GetName()
element = Element.getByAtomicNumber(atom.GetAtomicNum())
atom = topology.addAtom(name, element, residue)
# Create bonds.
atoms = {atom.name: atom for atom in topology.atoms()}
for bond in molecule.GetBonds():
topology.addBond(atoms[bond.GetBgn().GetName()],
atoms[bond.GetEnd().GetName()])
return topology
def _find_nonsolvent_atoms(self, topology: app.Topology) -> List[int]:
solvent_residue_names = ["WAT", "SOL", "H2O", "HOH"]
nonsolvent_atoms = []
for atom in topology.atoms():
if not atom.residue.name in solvent_residue_names:
nonsolvent_atoms.append(atom.index)
return nonsolvent_atoms
def __init__(self, file):
"""Load a prmtop file."""
top = Topology()
## The Topology read from the prmtop file
self.topology = top
# Load the prmtop file
prmtop = amber_file_parser.PrmtopLoader(file)
self._prmtop = prmtop
# Add atoms to the topology
PDBFile._loadNameReplacementTables()
lastResidue = None
c = top.addChain()
for index in range(prmtop.getNumAtoms()):
resNumber = prmtop.getResidueNumber(index)
if resNumber != lastResidue:
lastResidue = resNumber
resName = prmtop.getResidueLabel(iAtom=index).strip()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
atomName = prmtop.getAtomName(index).strip()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Try to guess the element.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
top.addAtom(atomName, element, r)
# Add bonds to the topology
atoms = list(top.atoms())
for bond in prmtop.getBondsWithH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
for bond in prmtop.getBondsNoH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
# Set the periodic box size.
if prmtop.getIfBox():
top.setUnitCellDimensions(tuple(x.value_in_unit(unit.nanometer) for x in prmtop.getBoxBetaAndDimensions()[1:4])*unit.nanometer)
def generateTopologyFromOEMol(molecule):
"""
Generate an OpenMM Topology object from an OEMol molecule.
Parameters
----------
molecule : openeye.oechem.OEMol
The molecule from which a Topology object is to be generated.
Returns
-------
topology : simtk.openmm.app.Topology
The Topology object generated from `molecule`.
"""
# Avoid manipulating the molecule
mol = OEMol(molecule)
# Create a Topology object with one Chain and one Residue.
from simtk.openmm.app import Topology
topology = Topology()
chain = topology.addChain()
resname = mol.GetTitle()
residue = topology.addResidue(resname, chain)
# Make sure the atoms have names, otherwise bonds won't be created properly below
if any([atom.GetName() == '' for atom in mol.GetAtoms()]):
oechem.OETriposAtomNames(mol)
# Check names are unique; non-unique names will also cause a problem
atomnames = [atom.GetName() for atom in mol.GetAtoms()]
if any(atomnames.count(atom.GetName()) > 1 for atom in mol.GetAtoms()):
raise Exception(
"Error: Reference molecule must have unique atom names in order to create a Topology."
)
# Create atoms in the residue.
for atom in mol.GetAtoms():
name = atom.GetName()
element = elem.Element.getByAtomicNumber(atom.GetAtomicNum())
openmm_atom = topology.addAtom(name, element, residue)
# Create bonds.
atoms = {atom.name: atom for atom in topology.atoms()}
for bond in mol.GetBonds():
aromatic = None
if bond.IsAromatic(): aromatic = 'Aromatic'
# Add bond, preserving order assessed by OEChem
topology.addBond(atoms[bond.GetBgn().GetName()],
atoms[bond.GetEnd().GetName()],
type=aromatic,
order=bond.GetOrder())
return topology
class OpenMMAmberParm(AmberParm):
"""
OpenMM-compatible subclass of AmberParm. This object should still work with
the ParmEd API while also being compatible with OpenMM's environment
"""
# Define default force groups for all of the bonded terms. This allows them
# to be turned on and off selectively. This is a way to implement per-term
# energy decomposition to compare individual components
BOND_FORCE_GROUP = 0
ANGLE_FORCE_GROUP = 1
DIHEDRAL_FORCE_GROUP = 2
NONBONDED_FORCE_GROUP = 3
GB_FORCE_GROUP = 3
def openmm_LJ(self):
"""
Same as fill_LJ, except it uses 0.5 for the LJ radius for H-atoms with
no vdW parameters (per OpenMM's standard)
Returns:
list, list : The 1st list is the list of all Rmin/2 terms. The
2nd is the list of all epsilon (or well depth) terms.
"""
LJ_radius = [] # empty LJ_radii so it can be re-filled
LJ_depth = [] # empty LJ_depths so it can be re-filled
one_sixth = 1 / 6 # we need to raise some numbers to the 1/6th power
ntypes = self.pointers['NTYPES']
acoef = self.parm_data['LENNARD_JONES_ACOEF']
bcoef = self.parm_data['LENNARD_JONES_BCOEF']
for i in range(ntypes):
lj_index = self.parm_data["NONBONDED_PARM_INDEX"][ntypes*i+i] - 1
if acoef[lj_index] < 1.0e-10:
LJ_radius.append(0.5)
LJ_depth.append(0)
else:
factor = (2 * acoef[lj_index] / bcoef[lj_index])
LJ_radius.append(pow(factor, one_sixth) * 0.5)
LJ_depth.append(bcoef[lj_index] / 2 / factor)
# Now check that we haven't modified any off-diagonals, since that will
# not work with OpenMM
for i in range(ntypes):
for j in range(ntypes):
idx = self.parm_data['NONBONDED_PARM_INDEX'][ntypes*i+j] - 1
rij = LJ_radius[i] + LJ_radius[j]
wdij = sqrt(LJ_depth[i] * LJ_depth[j])
a = acoef[idx]
b = bcoef[idx]
if a == 0 or b == 0:
if a != 0 or b != 0 or (wdij != 0 and rij != 0):
raise OpenMMError('Off-diagonal LJ modifications '
'detected. These are incompatible '
'with the OpenMM API')
elif (abs((a - (wdij * rij**12)) / a) > 1e-6 or
abs((b - (2 * wdij * rij**6)) / b) > 1e-6):
raise OpenMMError(
'Off-diagonal LJ modifications detected. These are '
'incompatible with the OpenMM API. Acoef=%s; '
'computed=%s. Bcoef=%s; computed=%s' %
(acoef, wdij*rij**12, bcoef, 2*wdij*rij**6)
)
return LJ_radius, LJ_depth
def openmm_14_LJ(self):
"""
Returns the radii and depths for the LJ interactions between 1-4 pairs.
For Amber topology files this is the same as the normal LJ parameters,
but is done here so that OpenMMChamberParm can inherit and override this
behavior without having to duplicate all of the system creation code.
"""
return self.openmm_LJ()
@property
def topology(self):
"""
The OpenMM Topology object. Cached when possible, but any changes to the
topology object lists results in the topology being deleted and rebuilt
"""
# If anything changed, rebuild the topology
if not self._topology_changed():
try:
return self._topology
except AttributeError:
pass
else:
self.remake_parm()
self._topology = Topology()
# Add all of the atoms to the topology file in the same chain
chain = self._topology.addChain()
last_residue = None
for i, atm in enumerate(self.atom_list):
resnum = atm.residue.idx
if last_residue != resnum:
last_residue = resnum
resname = atm.residue.resname
res = self._topology.addResidue(resname, chain)
elem = element.get_by_symbol(pt.Element[atm.element])
self._topology.addAtom(atm.atname, elem, res)
# Add bonds to the topology (both with and without hydrogen)
atoms = list(self._topology.atoms())
for bnd in self.bonds_inc_h + self.bonds_without_h:
self._topology.addBond(atoms[bnd.atom1.starting_index],
atoms[bnd.atom2.starting_index])
# Set the box dimensions
if self.ptr('ifbox'):
if hasattr(self, 'rst7'):
self._topology.setUnitCellDimensions(
self.rst7.box[:3]*u.angstrom
)
else:
self._topology.setUnitCellDimensions(
self.parm_data['BOX_DIMENSIONS'][1:4]*u.angstrom
)
return self._topology
def _get_gb_params(self, gb_model=HCT):
""" Gets the GB parameters. Need this method to special-case GB neck """
if gb_model is GBn:
screen = [0.5 for atom in self.atom_list]
for i, atom in enumerate(self.atom_list):
if atom.element == 6:
screen[i] = 0.48435382330
elif atom.element == 1:
screen[i] = 1.09085413633
elif atom.element == 7:
screen[i] = 0.700147318409
elif atom.element == 8:
screen[i] = 1.06557401132
elif atom.element == 16:
screen[i] = 0.602256336067
elif gb_model is GBn2:
# Add non-optimized values as defaults
alpha = [1.0 for i in self.atom_list]
beta = [0.8 for i in self.atom_list]
gamma = [4.85 for i in self.atom_list]
screen = [0.5 for i in self.atom_list]
for i, atom in enumerate(self.atom_list):
if atom.element == 6:
screen[i] = 1.058554
alpha[i] = 0.733756
beta[i] = 0.506378
gamma[i] = 0.205844
elif atom.element == 1:
screen[i] = 1.425952
alpha[i] = 0.788440
beta[i] = 0.798699
gamma[i] = 0.437334
elif atom.element == 7:
screen[i] = 0.733599
alpha[i] = 0.503364
beta[i] = 0.316828
gamma[i] = 0.192915
elif atom.element == 8:
screen[i] = 1.061039
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
elif atom.element == 16:
screen[i] = -0.703469
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
else:
screen = self.parm_data['SCREEN']
length_conv = u.angstrom.conversion_factor_to(u.nanometer)
radii = [rad * length_conv for rad in self.parm_data['RADII']]
if gb_model is GBn2:
return zip(radii, screen, alpha, beta, gamma)
return zip(radii, screen)
def createSystem(self, nonbondedMethod=ff.NoCutoff,
nonbondedCutoff=1.0*u.nanometer,
constraints=None,
rigidWater=True,
implicitSolvent=None,
implicitSolventKappa=None,
implicitSolventSaltConc=0.0*u.moles/u.liter,
temperature=298.15*u.kelvin,
soluteDielectric=1.0,
solventDielectric=78.5,
removeCMMotion=True,
hydrogenMass=None,
ewaldErrorTolerance=0.0005,
flexibleConstraints=True,
verbose=False):
"""
Construct an OpenMM System representing the topology described by the
prmtop file.
Parameters:
- nonbondedMethod (object=NoCutoff) The method to use for nonbonded
interactions. Allowed values are NoCutoff, CutoffNonPeriodic,
CutoffPeriodic, Ewald, or PME.
- nonbondedCutoff (distance=1*nanometer) The cutoff distance to use
for nonbonded interactions.
- constraints (object=None) Specifies which bonds or angles should be
implemented with constraints. Allowed values are None, HBonds,
AllBonds, or HAngles.
- rigidWater (boolean=True) If true, water molecules will be fully
rigid regardless of the value passed for the constraints argument
- implicitSolvent (object=None) If not None, the implicit solvent
model to use. Allowed values are HCT, OBC1, OBC2, or GBn
- implicitSolventKappa (float=None): Debye screening parameter to
model salt concentrations in GB solvent.
- implicitSolventSaltConc (float=0.0*u.moles/u.liter): Salt
concentration for GB simulations. Converted to Debye length
`kappa'
- temperature (float=298.15*u.kelvin): Temperature used in the salt
concentration-to-kappa conversion for GB salt concentration term
- soluteDielectric (float=1.0) The solute dielectric constant to use
in the implicit solvent model.
- solventDielectric (float=78.5) The solvent dielectric constant to
use in the implicit solvent model.
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be
added to the System.
- hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to
heavy atoms. Any mass added to a hydrogen is subtracted from the
heavy atom to keep their total mass the same.
- ewaldErrorTolerance (float=0.0005) The error tolerance to use if the
nonbonded method is Ewald or PME.
- flexibleConstraints (bool=True) Are our constraints flexible or not?
- verbose (bool=False) Optionally prints out a running progress report
"""
# Rebuild the topology file if necessary, and flush the atom property
# data to the atom list
if self._topology_changed():
self.remake_parm()
else:
self.atom_list.refresh_data()
LJ_radius, LJ_depth = self.openmm_LJ() # Get our LJ parameters
LJ_14_radius, LJ_14_depth = self.openmm_14_LJ()
# Set the cutoff distance in nanometers
cutoff = None
if nonbondedMethod is not ff.NoCutoff:
cutoff = nonbondedCutoff
# Remove units from cutoff
if u.is_quantity(cutoff):
cutoff = cutoff.value_in_unit(u.nanometers)
if nonbondedMethod not in (ff.NoCutoff, ff.CutoffNonPeriodic,
ff.CutoffPeriodic, ff.Ewald, ff.PME):
raise ValueError('Illegal value for nonbonded method')
if self.ptr('ifbox') == 0 and nonbondedMethod in (ff.CutoffPeriodic,
ff.Ewald, ff.PME):
raise ValueError('Illegal nonbonded method for a '
'non-periodic system')
if implicitSolvent not in (HCT, OBC1, OBC2, GBn, GBn2, None):
raise ValueError('Illegal implicit solvent model choice.')
if not constraints in (None, ff.HAngles, ff.HBonds, ff.AllBonds):
raise ValueError('Illegal constraints choice')
# Define conversion factors
length_conv = u.angstrom.conversion_factor_to(u.nanometer)
_ambfrc = u.kilocalorie_per_mole/(u.angstrom*u.angstrom)
_openmmfrc = u.kilojoule_per_mole/(u.nanometer*u.nanometer)
bond_frc_conv = _ambfrc.conversion_factor_to(_openmmfrc)
_ambfrc = u.kilocalorie_per_mole/(u.radians*u.radians)
_openmmfrc = u.kilojoule_per_mole/(u.radians*u.radians)
angle_frc_conv = _ambfrc.conversion_factor_to(_openmmfrc)
dihe_frc_conv = u.kilocalorie_per_mole.conversion_factor_to(
u.kilojoule_per_mole)
ene_conv = dihe_frc_conv
# Create the system
system = mm.System()
if verbose: print('Adding particles...')
for mass in self.parm_data['MASS']:
system.addParticle(mass)
# Set up the constraints
if verbose and (constraints is not None and not rigidWater):
print('Adding constraints...')
if constraints in (ff.HBonds, ff.AllBonds, ff.HAngles):
for bond in self.bonds_inc_h:
system.addConstraint(bond.atom1.starting_index,
bond.atom2.starting_index,
bond.bond_type.req*length_conv)
if constraints in (ff.AllBonds, ff.HAngles):
for bond in self.bonds_without_h:
system.addConstraint(bond.atom1.starting_index,
bond.atom2.starting_index,
bond.bond_type.req*length_conv)
if rigidWater and constraints is None:
for bond in self.bonds_inc_h:
if (bond.atom1.residue.resname in WATNAMES and
bond.atom2.residue.resname in WATNAMES):
system.addConstraint(bond.atom1.starting_index,
bond.atom2.starting_index,
bond.bond_type.req*length_conv)
# Add Bond forces
if verbose: print('Adding bonds...')
force = mm.HarmonicBondForce()
force.setForceGroup(self.BOND_FORCE_GROUP)
if flexibleConstraints or (constraints not in (ff.HBonds, ff.AllBonds,
ff.HAngles)):
for bond in self.bonds_inc_h:
force.addBond(bond.atom1.starting_index,
bond.atom2.starting_index,
bond.bond_type.req*length_conv,
2*bond.bond_type.k*bond_frc_conv)
if flexibleConstraints or (constraints not in (ff.AllBonds,ff.HAngles)):
for bond in self.bonds_without_h:
force.addBond(bond.atom1.starting_index,
bond.atom2.starting_index,
bond.bond_type.req*length_conv,
2*bond.bond_type.k*bond_frc_conv)
system.addForce(force)
# Add Angle forces
if verbose: print('Adding angles...')
force = mm.HarmonicAngleForce()
force.setForceGroup(self.ANGLE_FORCE_GROUP)
if constraints is ff.HAngles:
num_constrained_bonds = system.getNumConstraints()
atom_constraints = [[]] * system.getNumParticles()
for i in range(num_constrained_bonds):
c = system.getConstraintParameters(i)
dist = c[2].value_in_unit(u.nanometer)
atom_constraints[c[0]].append((c[1], dist))
atom_constraints[c[1]].append((c[0], dist))
for angle in self.angles_inc_h:
if constraints is ff.HAngles:
a1 = angle.atom1.element
a2 = angle.atom2.element
a3 = angle.atom3.element
nh = int(a1==1) + int(a2==1) + int(a3==1)
constrained = (nh >= 2 or (nh == 1 and a2 == 8))
else:
constrained = False # no constraints
if constrained:
l1 = l2 = None
for bond in angle.atom2.bonds:
if bond.atom1 is angle.atom1 or bond.atom2 is angle.atom1:
l1 = bond.bond_type.req * length_conv
elif bond.atom1 is angle.atom3 or bond.atom2 is angle.atom3:
l2 = bond.bond_type.req * length_conv
# Compute the distance between the atoms and add a constraint
length = sqrt(l1*l1 + l2*l2 - 2*l1*l2*
cos(angle.angle_type.theteq))
system.addConstraint(bond.atom1.starting_index,
bond.atom2.starting_index, length)
if flexibleConstraints or not constrained:
force.addAngle(angle.atom1.starting_index,
angle.atom2.starting_index,
angle.atom3.starting_index,
angle.angle_type.theteq,
2*angle.angle_type.k*angle_frc_conv)
for angle in self.angles_without_h:
force.addAngle(angle.atom1.starting_index,
angle.atom2.starting_index,
angle.atom3.starting_index,
angle.angle_type.theteq,
2*angle.angle_type.k*angle_frc_conv)
system.addForce(force)
# Add dihedral forces
if verbose: print('Adding torsions...')
force = mm.PeriodicTorsionForce()
force.setForceGroup(self.DIHEDRAL_FORCE_GROUP)
for tor in self.dihedrals_inc_h + self.dihedrals_without_h:
force.addTorsion(tor.atom1.starting_index,
tor.atom2.starting_index,
tor.atom3.starting_index,
tor.atom4.starting_index,
int(tor.dihed_type.per),
tor.dihed_type.phase,
tor.dihed_type.phi_k*dihe_frc_conv)
system.addForce(force)
# Add nonbonded terms now
if verbose: print('Adding nonbonded interactions...')
force = mm.NonbondedForce()
force.setForceGroup(self.NONBONDED_FORCE_GROUP)
if self.ptr('ifbox') == 0: # non-periodic
if nonbondedMethod is ff.NoCutoff:
force.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
elif nonbondedMethod is ff.CutoffNonPeriodic:
if cutoff is None:
raise ValueError('No cutoff value specified')
force.setNonbondedMethod(mm.NonbondedForce.CutoffNonPeriodic)
force.setCutoffDistance(cutoff)
else:
raise ValueError('Illegal nonbonded method for non-periodic '
'system')
else: # periodic
# Set up box vectors (from inpcrd if available, or fall back to
# prmtop definitions
system.setDefaultPeriodicBoxVectors(*self.box_vectors)
# Set cutoff
if cutoff is None:
# Compute cutoff automatically
box = self.box_lengths
min_box_width = min((box[0]/u.nanometers,
box[1]/u.nanometers,
box[2]/u.nanometers))
CLEARANCE_FACTOR = 0.97
cutoff = u.Quantity((min_box_width*CLEARANCE_FACTOR)/2.0,
u.nanometers)
if nonbondedMethod is not ff.NoCutoff:
force.setCutoffDistance(cutoff)
# Set nonbonded method.
if nonbondedMethod is ff.NoCutoff:
force.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
elif nonbondedMethod is ff.CutoffNonPeriodic:
force.setNonbondedMethod(mm.NonbondedForce.CutoffNonPeriodic)
elif nonbondedMethod is ff.CutoffPeriodic:
force.setNonbondedMethod(mm.NonbondedForce.CutoffPeriodic)
elif nonbondedMethod is ff.Ewald:
force.setNonbondedMethod(mm.NonbondedForce.Ewald)
elif nonbondedMethod is ff.PME:
force.setNonbondedMethod(mm.NonbondedForce.PME)
else:
raise ValueError('Cutoff method is not understood')
if ewaldErrorTolerance is not None:
force.setEwaldErrorTolerance(ewaldErrorTolerance)
# Add per-particle nonbonded parameters (LJ params)
sigma_scale = 2**(-1/6) * 2
for i, atm in enumerate(self.atom_list):
force.addParticle(atm.charge,
sigma_scale*LJ_radius[atm.nb_idx-1]*length_conv,
LJ_depth[atm.nb_idx-1]*ene_conv)
# Add 1-4 interactions
excluded_atom_pairs = set() # save these pairs so we don't zero them out
sigma_scale = 2**(-1/6)
for tor in self.dihedrals_inc_h + self.dihedrals_without_h:
if min(tor.signs) < 0: continue # multi-terms and impropers
charge_prod = (tor.atom1.charge * tor.atom4.charge /
tor.dihed_type.scee)
epsilon = (sqrt(LJ_14_depth[tor.atom1.nb_idx-1] * ene_conv *
LJ_14_depth[tor.atom4.nb_idx-1] * ene_conv) /
tor.dihed_type.scnb)
sigma = (LJ_14_radius[tor.atom1.nb_idx-1] +
LJ_14_radius[tor.atom4.nb_idx-1])*length_conv*sigma_scale
force.addException(tor.atom1.starting_index,
tor.atom4.starting_index,
charge_prod, sigma, epsilon)
excluded_atom_pairs.add(
min( (tor.atom1.starting_index, tor.atom4.starting_index),
(tor.atom4.starting_index, tor.atom1.starting_index) )
)
# Add excluded atoms
for atom in self.atom_list:
# Exclude all bonds and angles
for atom2 in atom.bond_partners:
if atom2.starting_index > atom.starting_index:
force.addException(atom.starting_index,
atom2.starting_index, 0.0, 0.1, 0.0)
for atom2 in atom.angle_partners:
if atom2.starting_index > atom.starting_index:
force.addException(atom.starting_index,
atom2.starting_index, 0.0, 0.1, 0.0)
for atom2 in atom.exclusion_partners:
if atom2.starting_index > atom.starting_index:
force.addException(atom.starting_index,
atom2.starting_index, 0.0, 0.1, 0.0)
for atom2 in atom.dihedral_partners:
if atom2.starting_index <= atom.starting_index: continue
if ((atom.starting_index, atom2.starting_index) in
excluded_atom_pairs):
continue
force.addException(atom.starting_index,
atom2.starting_index, 0.0, 0.1, 0.0)
system.addForce(force)
# Add virtual sites for water
# First tag the residues that have an extra point in them
for res in self.residue_list: res.has_ep = False
ep = [atom for atom in self.atom_list if atom.atname in EPNAMES]
for atom in ep: atom.residue.has_ep = True
if len(ep) > 0:
numRes = ep[-1].residue.idx + 1
waterO = [[] for i in range(numRes)]
waterH = [[] for i in range(numRes)]
waterEP = [[] for i in range(numRes)]
for atom in self.atom_list:
if atom.residue.has_ep:
if atom.element == 8:
waterO[res].append(atom)
elif atom.element == 1:
waterH[res].append(atom)
elif atom.element == 0:
waterEP[res].append(atom)
# Record bond lengths for faster access
distOH = [None] * numRes
distHH = [None] * numRes
distOE = [None] * numRes
for bond in self.bonds_inc_h + self.bonds_without_h:
a1 = bond.atom1
a2 = bond.atom2
if a1.residue.has_ep:
res = a1.residue.idx
if a1.element == 1 or a2.element == 1:
if a1.element == 1 and a2.element == 1:
distHH[res] = bond.bond_type.req * u.angstroms
if a1.element == 8 or a2.element == 8:
distOH[res] = bond.bond_type.req * u.angstroms
elif ((a1.element == 8 or a2.element == 8) and
(a1.element == 0 or a2.element == 0)):
distOE[res] = bond.bond_type.req * u.angstroms
# Loop over residues and add the virtual points
out_of_plane_angle = 54.735 * u.degrees
cosOOP = u.cos(out_of_plane_angle)
sinOOP = u.sin(out_of_plane_angle)
for residue in self.residue_list:
if not residue.has_ep: continue
res = residue.idx
if len(waterO[res]) == 1 and len(waterH[res]) == 2:
if len(waterEP[res]) == 1:
# 4-point water
weightH = distOE[res] / sqrt(distOH[res] * distOH[res] -
0.25 * distHH[res] * distHH[res])
system.setVirtualSite(
waterEP[res][0],
mm.ThreeParticleAverageSite(waterO[res][0],
waterH[res][0], waterH[res][1],
1-weightH, weightH/2, weightH/2)
)
elif len(waterEP[res]) == 2:
# 5-point water
weightH = (cosOOP * distOE[res] /
sqrt(distOH[res] * distOH[res] -
0.25 * distHH[res] * distHH[res])
)
angleHOH = 2 * asin(0.5 * distHH[res] / distOH[res])
lenCross = distOH[res] * distOH[res] * sin(angleHOH)
weightCross = sinOOP * distOE[res] / lenCross
site1 = mm.OutOfPlaneSite(waterO[res][0], waterH[res][0],
waterH[res][1], weightH/2, weightH/2, weightCross)
site2 = mm.OutOfPlaneSite(waterO[res][0], waterH[res][0],
waterH[res][1], weightH/2, weightH/2, -weightCross)
system.setVirtualSite(waterEP[res][0], site1)
system.setVirtualSite(waterEP[res][1], site2)
# Add GB model if we're doing one
if implicitSolvent is not None:
if verbose: print('Adding GB parameters...')
gb_parms = self._get_gb_params(implicitSolvent)
# If implicitSolventKappa is None, compute it from salt
# concentration
if implicitSolventKappa is None:
if u.is_quantity(implicitSolventSaltConc):
sc = implicitSolventSaltConc.value_in_unit(u.moles/u.liter)
implicitSolventSaltConc = sc
if u.is_quantity(temperature):
temperature = temperature.value_in_unit(u.kelvin)
# The constant is 1 / sqrt( epsilon_0 * kB / (2 * NA * q^2 *
# 1000) ) where NA is avogadro's number, epsilon_0 is the
# permittivity of free space, q is the elementary charge (this
# number matches sander/pmemd's kappa conversion factor)
implicitSolventKappa = 50.33355 * sqrt(implicitSolventSaltConc /
solventDielectric / temperature)
# Multiply by 0.73 to account for ion exclusions, and multiply
# by 10 to convert to 1/nm from 1/angstroms
implicitSolventKappa *= 7.3
elif implicitSolvent is None:
implicitSolventKappa = 0.0
if u.is_quantity(implicitSolventKappa):
implicitSolventKappa = implicitSolventKappa.value_in_unit(
(1.0/u.nanometer).unit)
if implicitSolvent is HCT:
gb = GBSAHCTForce(solventDielectric, soluteDielectric, None,
cutoff, kappa=implicitSolventKappa)
elif implicitSolvent is OBC1:
gb = GBSAOBC1Force(solventDielectric, soluteDielectric, None,
cutoff, kappa=implicitSolventKappa)
elif implicitSolvent is OBC2:
gb = GBSAOBC2Force(solventDielectric, soluteDielectric, None,
cutoff, kappa=implicitSolventKappa)
elif implicitSolvent is GBn:
gb = GBSAGBnForce(solventDielectric, soluteDielectric, None,
cutoff, kappa=implicitSolventKappa)
elif implicitSolvent is GBn2:
gb = GBSAGBn2Force(solventDielectric, soluteDielectric, None,
cutoff, kappa=implicitSolventKappa)
for i, atom in enumerate(self.atom_list):
gb.addParticle([atom.charge] + list(gb_parms[i]))
# Set cutoff method
if nonbondedMethod is ff.NoCutoff:
gb.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
elif nonbondedMethod is ff.CutoffNonPeriodic:
gb.setNonbondedMethod(mm.NonbondedForce.CutoffNonPeriodic)
gb.setCutoffDistance(cutoff)
elif nonbondedMethod is ff.CutoffPeriodic:
gb.setNonbondedMethod(mm.NonbondedForce.CutoffPeriodic)
gb.setCutoffDistance(cutoff)
else:
raise ValueError('Illegal nonbonded method for use with GBSA')
gb.setForceGroup(self.GB_FORCE_GROUP)
system.addForce(gb)
force.setReactionFieldDielectric(1.0) # applies to NonbondedForce
# See if we repartition the hydrogen masses
if hydrogenMass is not None:
for bond in self.bonds_inc_h:
atom1, atom2 = bond.atom1, bond.atom2
if atom1.element == 1:
atom1, atom2 = atom2, atom1 # now atom2 is hydrogen for sure
if atom1.element != 1:
transfer_mass = hydrogenMass - atom2.mass
new_mass1 = (system.getParticleMass(atom1.index) -
transfer_mass)
system.setParticleMass(atom2.index, hydrogenMass)
system.setParticleMass(atom1.index, new_mass1)
# See if we want to remove COM motion
if removeCMMotion:
system.addForce(mm.CMMotionRemover())
# Cache our system for easy access
self._system = system
return system
@property
def system(self):
"""
Return the cached system class -- it needs to be initialized via
"createSystem" first!
"""
try:
return self._system
except AttributeError:
raise APIError('You must initialize the system with createSystem '
'before accessing the cached object.')
@property
def positions(self):
"""
Return the cached positions or create new ones from the atoms
"""
try:
if len(self._positions) == len(self.atom_list):
return self._positions
except AttributeError:
pass
self._positions = tuple([Vec3(a.xx, a.xy, a.xz)
for a in self.atom_list]) * u.angstroms
return self._positions
@positions.setter
def positions(self, stuff):
"""
Update the cached positions and assign the coordinates to the atoms
"""
self._positions = stuff
for i, pos in enumerate(stuff.value_in_unit(u.angstroms)):
i3 = i * 3
atom = self.atom_list[i]
atom.xx, atom.xy, atom.xz = pos
self.coords[i3], self.coords[i3+1], self.coords[i3+2] = pos
@property
def velocities(self):
""" Same as for positions, but for velocities """
try:
if len(self._velocities) == len(self.atom_list):
return self._velocities
except AttributeError:
pass
self._velocities = tuple([Vec3(a.vx, a.vy, a.vz)
for a in self.atom_list]) * (u.angstroms/u.picosecond)
return self._velocities
@velocities.setter
def velocities(self, stuff):
self._velocities = stuff
for atom, vel in zip(self.atom_list, stuff):
atom.vx, atom.vy, atom.vz = vel.value_in_unit(
u.angstroms/u.picoseconds)
@property
def box_vectors(self):
""" Return tuple of box vectors """
if hasattr(self, 'rst7'):
box = [x*u.angstrom for x in self.rst7.box[:3]]
ang = [self.rst7.box[3], self.rst7.box[4], self.rst7.box[5]]
return _box_vectors_from_lengths_angles(box[0], box[1], box[2],
ang[0], ang[1], ang[2])
else:
box = [x*u.angstrom for x in self.parm_data['BOX_DIMENSIONS'][1:]]
ang = [self.parm_data['BOX_DIMENSIONS'][0]] * 3
return _box_vectors_from_lengths_angles(box[0], box[1], box[2],
ang[0], ang[1], ang[2])
@property
def box_lengths(self):
""" Return tuple of 3 units """
if hasattr(self, 'rst7'):
box = [x*u.angstrom for x in self.rst7.box[:3]]
else:
box = [x*u.angstrom for x in self.parm_data['BOX_DIMENSIONS'][1:]]
return tuple(box)
def __init__(self, file):
"""Load a prmtop file."""
top = Topology()
## The Topology read from the prmtop file
self.topology = top
self.elements = []
# Load the prmtop file
prmtop = amber_file_parser.PrmtopLoader(file)
self._prmtop = prmtop
# Add atoms to the topology
PDBFile._loadNameReplacementTables()
lastResidue = None
c = top.addChain()
for index in range(prmtop.getNumAtoms()):
resNumber = prmtop.getResidueNumber(index)
if resNumber != lastResidue:
lastResidue = resNumber
resName = prmtop.getResidueLabel(iAtom=index).strip()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
atomName = prmtop.getAtomName(index).strip()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Get the element from the prmtop file if available
if prmtop.has_atomic_number:
try:
element = elem.Element.getByAtomicNumber(
int(prmtop._raw_data['ATOMIC_NUMBER'][index]))
except KeyError:
element = None
else:
# Try to guess the element from the atom name.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
elif upper.startswith('ZN'):
element = elem.zinc
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
top.addAtom(atomName, element, r)
self.elements.append(element)
# Add bonds to the topology
atoms = list(top.atoms())
for bond in prmtop.getBondsWithH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
for bond in prmtop.getBondsNoH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
# Set the periodic box size.
if prmtop.getIfBox():
top.setUnitCellDimensions(
tuple(
x.value_in_unit(unit.nanometer)
for x in prmtop.getBoxBetaAndDimensions()[1:4]) *
unit.nanometer)
def __init__(self, file):
"""Load a prmtop file."""
top = Topology()
## The Topology read from the prmtop file
self.topology = top
self.elements = []
# Load the prmtop file
prmtop = amber_file_parser.PrmtopLoader(file)
self._prmtop = prmtop
# Add atoms to the topology
PDBFile._loadNameReplacementTables()
lastResidue = None
c = top.addChain()
for index in range(prmtop.getNumAtoms()):
resNumber = prmtop.getResidueNumber(index)
if resNumber != lastResidue:
lastResidue = resNumber
resName = prmtop.getResidueLabel(iAtom=index).strip()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
atomName = prmtop.getAtomName(index).strip()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Get the element from the prmtop file if available
if prmtop.has_atomic_number:
try:
element = elem.Element.getByAtomicNumber(int(prmtop._raw_data['ATOMIC_NUMBER'][index]))
except KeyError:
element = None
else:
# Try to guess the element from the atom name.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
elif upper.startswith('ZN'):
element = elem.zinc
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
top.addAtom(atomName, element, r)
self.elements.append(element)
# Add bonds to the topology
atoms = list(top.atoms())
for bond in prmtop.getBondsWithH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
for bond in prmtop.getBondsNoH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
# Set the periodic box size.
if prmtop.getIfBox():
box = prmtop.getBoxBetaAndDimensions()
top.setPeriodicBoxVectors(computePeriodicBoxVectors(*(box[1:4] + box[0:1]*3)))
def remove_molecules(self, simulation_old, system_options, ensemble_options):
topology_old = simulation_old.topology
system_old = simulation_old.system
state = simulation_old.context.getState(getPositions=True, getVelocities=True)
positions_old = state.getPositions(asNumpy=True)
velocities_old = state.getVelocities(asNumpy=True)
periodic_box_vectors = state.getPeriodicBoxVectors(asNumpy=True)
# randomly determine which molecules are removed
removed_molecules = random.sample(range(topology_old.getNumChains()), self.numVoid)
# create new topology and dictionary mapping old atom indices to new atom indices
removed_atoms = []
topology_new = Topology()
old_to_new = {}
atom_index_new = 0
for chain_index, chain_old in enumerate(topology_old.chains()):
if chain_index not in removed_molecules:
chain_id = chain_old.id.split('-', 1)[-1]
chain_new = topology_new.addChain(id="{}-{}".format(topology_new.getNumChains()+1, chain_id))
for residue_old in chain_old.residues():
residue_new = topology_new.addResidue(residue_old.name, chain_new)
for atom_old in residue_old.atoms():
topology_new.addAtom(atom_old.name, atom_old.element, residue_new)
old_to_new[atom_old.index] = atom_index_new
atom_index_new += 1
else:
for atom_old in chain_old.atoms():
removed_atoms.append(atom_old.index)
# add bonds to new topology
atoms_new = list(topology_new.atoms())
for bond_old in topology_old.bonds():
atom1_index_old = bond_old[0].index
atom2_index_old = bond_old[1].index
try:
atom1_new = atoms_new[old_to_new[atom1_index_old]]
atom2_new = atoms_new[old_to_new[atom2_index_old]]
topology_new.addBond(atom1_new, atom2_new)
except KeyError:
pass
# set box vectors for topology
topology_new.setPeriodicBoxVectors(periodic_box_vectors)
# create system
system_new = system_options.create_system_with_new_topology(topology_new)
# check if old system had barostat and add to new system if applicable
if self._has_barostat(system_old):
barostat_old = self._get_barostat(system_old)
defaultPressure = barostat_old.getDefaultPressure()
defaultTemperature = barostat_old.getDefaultTemperature()
frequency = barostat_old.getFrequency()
if isinstance(barostat_old, MonteCarloAnisotropicBarostat):
scaleX = barostat_old.getScaleX()
scaleY = barostat_old.getScaleY()
scaleZ = barostat_old.getScaleZ()
barostat_new = MonteCarloAnisotropicBarostat(defaultPressure, defaultTemperature,
scaleX, scaleY, scaleZ, frequency)
else:
barostat_new = MonteCarloBarostat(defaultPressure, defaultTemperature, frequency)
system_new.addForce(barostat_new)
barostat_new.setForceGroup(system_new.getNumForces() - 1)
# create integrator
integrator = ensemble_options.create_integrator()
# create new positions and velocities arrays
positions_new = np.delete(positions_old, removed_atoms, axis=0)
velocities_new = np.delete(velocities_old, removed_atoms, axis=0)
# create new simulation
simulation_new = Simulation(topology_new, system_new, integrator)
simulation_new.context.setPositions(positions_new)
simulation_new.context.setVelocities(velocities_new)
simulation_new.context.setPeriodicBoxVectors(*periodic_box_vectors)
# move reporters from old simulation to new simulation
while simulation_old.reporters:
simulation_new.reporters.append(simulation_old.reporters.pop(0))
# create pdb file if specified
if self.file is not None:
PDBFile.writeFile(topology_new, positions_new, open(self.file, 'w'))
return simulation_new
def addHydrogens(self, forcefield, pH=7.0, variants=None, platform=None):
"""Add missing hydrogens to the model.
Some residues can exist in multiple forms depending on the pH and properties of the local environment. These
variants differ in the presence or absence of particular hydrogens. In particular, the following variants
are supported:
Aspartic acid:
ASH: Neutral form with a hydrogen on one of the delta oxygens
ASP: Negatively charged form without a hydrogen on either delta oxygen
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:
GLH: Neutral form with a hydrogen on one of the epsilon oxygens
GLU: Negatively charged form without a hydrogen on either epsilon oxygen
Histidine:
HID: Neutral form with a hydrogen on the ND1 atom
HIE: Neutral form with a hydrogen on the NE2 atom
HIP: Positively charged form with hydrogens on both ND1 and NE2
Lysine:
LYN: Neutral form with two hydrogens on the zeta nitrogen
LYS: Positively charged form with three hydrogens on the zeta nitrogen
The variant to use for each residue is determined by the following rules:
1. The most common variant at the specified pH is selected.
2. Any Cysteine that participates in a disulfide bond uses the CYX variant regardless of pH.
3. For a neutral Histidine residue, the HID or HIE variant is selected based on which one forms a better hydrogen bond.
You can override these rules by explicitly specifying a variant for any residue. Also keep in mind that this
function will only add hydrogens. It will never remove ones that are already present in the model, regardless
of the specified pH.
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) the ForceField to use for determining the positions of hydrogens
- pH (float=7.0) the pH based on which to select variants
- 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: a list of what variant was actually selected for each residue, in the same format as the variants parameter
"""
# Check the list of variants.
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.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.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
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()
for residue in chain.residues():
newResidue = newTopology.addResidue(residue.name, newChain)
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' and pH > 6.5:
# See if either nitrogen already has a hydrogen attached.
nd1 = [atom for atom in residue.atoms() if atom.name == 'ND1']
ne2 = [atom for atom in residue.atoms() if atom.name == 'NE2']
if len(nd1) != 1 or len(ne2) != 1:
raise ValueError('HIS residue (%d) has the wrong set of atoms' % residue.index)
nd1 = nd1[0]
ne2 = ne2[0]
nd1HasHydrogen = any((atom.element == elem.hydrogen for atom in bonded[nd1]))
ne2HasHydrogen = any((atom.element == elem.hydrogen for atom in bonded[ne2]))
if nd1HasHydrogen and ne2HasHydrogen:
variant = 'HIP'
elif nd1HasHydrogen:
variant = 'HID'
elif ne2HasHydrogen:
variant = 'HIE'
else:
# Estimate the hydrogen positions.
nd1Pos = self.positions[nd1.index]
ne2Pos = self.positions[ne2.index]
hd1Delta = Vec3(0, 0, 0)*nanometer
for other in bonded[nd1]:
hd1Delta += nd1Pos-self.positions[other.index]
hd1Delta *= 0.1*nanometer/norm(hd1Delta)
hd1Pos = nd1Pos+hd1Delta
he2Delta = Vec3(0, 0, 0)*nanometer
for other in bonded[ne2]:
he2Delta += ne2Pos-self.positions[other.index]
he2Delta *= 0.1*nanometer/norm(he2Delta)
he2Pos = ne2Pos+he2Delta
# See whether either hydrogen would form a hydrogen bond.
nd1IsBonded = False
ne2IsBonded = False
for acceptor in acceptors:
if acceptor.residue != residue:
acceptorPos = self.positions[acceptor.index]
if isHbond(nd1Pos, hd1Pos, acceptorPos):
nd1IsBonded = True
break
if isHbond(ne2Pos, he2Pos, acceptorPos):
ne2IsBonded = True
if ne2IsBonded and not nd1IsBonded:
variant = 'HIE'
else:
variant = 'HID'
elif residue.name == 'HIS':
variant = 'HIP'
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
# 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 and pH <= h.maxph) or (h.variants is None and pH <= h.maxph) 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():
# 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 use the ForceField to fix them up.
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)
if platform is None:
context = Context(system, VerletIntegrator(0.0))
else:
context = Context(system, VerletIntegrator(0.0), platform)
context.setPositions(newPositions)
LocalEnergyMinimizer.minimize(context)
self.topology = newTopology
self.positions = context.getState(getPositions=True).getPositions()
return actualVariants
