modeller.py

"""
modeller.py: Provides tools for editing molecular models

This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.

Portions copyright (c) 2012-2016 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import division
from __future__ import absolute_import

__author__ = "Peter Eastman"
__version__ = "1.0"

from simtk.openmm.app import Topology, PDBFile, ForceField
from simtk.openmm.app.forcefield import HAngles, AllBonds, CutoffNonPeriodic, _createResidueSignature, _matchResidue, DrudeGenerator
from simtk.openmm.app.topology import Residue
from simtk.openmm.vec3 import Vec3
from simtk.openmm import System, Context, NonbondedForce, CustomNonbondedForce, HarmonicBondForce, HarmonicAngleForce, VerletIntegrator, LocalEnergyMinimizer
from simtk.unit import nanometer, molar, elementary_charge, amu, gram, liter, degree, sqrt, acos, is_quantity, dot, norm
import simtk.unit as unit
from . import element as elem
import os
import random
import xml.etree.ElementTree as etree
from copy import deepcopy
from math import ceil, floor

class Modeller(object):
    """Modeller provides tools for editing molecular models, such as adding water or missing hydrogens.

    To use it, create a Modeller object, specifying the initial Topology and atom positions.  You can
    then call various methods to change the model in different ways.  Each time you do, a new Topology
    and list of coordinates is created to represent the changed model.  Finally, call getTopology()
    and getPositions() to get the results.
    """

    _residueHydrogens = {}
    _hasLoadedStandardHydrogens = False

    def __init__(self, topology, positions):
        """Create a new Modeller object

        Parameters
        ----------
        topology : Topology
            the initial Topology of the model
        positions : list
            the initial atomic positions
        """
        ## The Topology describing the structure of the system
        self.topology = topology
        if not is_quantity(positions):
            positions = positions*nanometer
        ## The list of atom positions
        self.positions = positions

    def getTopology(self):
        """Get the Topology of the model."""
        return self.topology

    def getPositions(self):
        """Get the atomic positions."""
        return self.positions

    def add(self, addTopology, addPositions):
        """Add chains, residues, atoms, and bonds to the model.

        Specify what to add by providing a new Topology object and the
        corresponding atomic positions. All chains, residues, atoms, and bonds
        contained in the Topology are added to the model.

        Parameters
        ----------
        addTopology : Topology
            a Topology whose contents should be added to the model
        addPositions : list
            the positions of the atoms to add
        """
        # Copy over the existing model.

        newTopology = Topology()
        newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
        newAtoms = {}
        newPositions = []*nanometer
        for chain in self.topology.chains():
            newChain = newTopology.addChain(chain.id)
            for residue in chain.residues():
                newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
                for atom in residue.atoms():
                    newAtom = newTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
                    newAtoms[atom] = newAtom
                    newPositions.append(deepcopy(self.positions[atom.index]))
        for bond in self.topology.bonds():
            newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])

        # Add the new model

        newAtoms = {}
        for chain in addTopology.chains():
            newChain = newTopology.addChain(chain.id)
            for residue in chain.residues():
                newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
                for atom in residue.atoms():
                    newAtom = newTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
                    newAtoms[atom] = newAtom
                    newPositions.append(deepcopy(addPositions[atom.index]))
        for bond in addTopology.bonds():
            newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
        self.topology = newTopology
        self.positions = newPositions

    def delete(self, toDelete):
        """Delete chains, residues, atoms, and bonds from the model.

        You can specify objects to delete at any granularity: atoms, residues, or chains.  Passing
        in an Atom object causes that Atom to be deleted.  Passing in a Residue object causes that
        Residue and all Atoms it contains to be deleted.  Passing in a Chain object causes that
        Chain and all Residues and Atoms it contains to be deleted.

        In all cases, when an Atom is deleted, any bonds it participates in are also deleted.
        You also can specify a bond (as a tuple of Atom objects) to delete just that bond without
        deleting the Atoms it connects.

        Parameters
        ----------
        toDelete : list
            a list of Atoms, Residues, Chains, and bonds (specified as tuples of
            Atoms) to delete
        """
        newTopology = Topology()
        newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
        newAtoms = {}
        newPositions = []*nanometer
        deleteSet = set(toDelete)
        for chain in self.topology.chains():
            if chain not in deleteSet:
                needNewChain = True;
                for residue in chain.residues():
                    if residue not in deleteSet:
                        needNewResidue = True
                        for atom in residue.atoms():
                            if atom not in deleteSet:
                                if needNewChain:
                                    newChain = newTopology.addChain(chain.id)
                                    needNewChain = False;
                                if needNewResidue:
                                    newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
                                    needNewResidue = False;
                                newAtom = newTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
                                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:
                if bond not in deleteSet and (bond[1], bond[0]) not in deleteSet:
                    newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
        self.topology = newTopology
        self.positions = newPositions

    def deleteWater(self):
        """Delete all water molecules from the model."""
        self.delete(res for res in self.topology.residues() if res.name == "HOH")

    def convertWater(self, model='tip3p'):
        """Convert all water molecules to a different water model.

        @deprecated Use addExtraParticles() instead.  It performs the same
        function but in a more general way.

        Parameters
        ----------
        model : string='tip3p'
            the water model to convert to.  Supported values are 'tip3p',
            'spce', 'tip4pew', and 'tip5p'.
        """
        if model in ('tip3p', 'spce'):
            sites = 3
        elif model == 'tip4pew':
            sites = 4
        elif model == 'tip5p':
            sites = 5
        else:
            raise ValueError('Unknown water model: %s' % model)
        newTopology = Topology()
        newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
        newAtoms = {}
        newPositions = []*nanometer
        for chain in self.topology.chains():
            newChain = newTopology.addChain(chain.id)
            for residue in chain.residues():
                newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
                if residue.name == "HOH":
                    # Copy the oxygen and hydrogens
                    oatom = [atom for atom in residue.atoms() if atom.element == elem.oxygen]
                    hatoms = [atom for atom in residue.atoms() if atom.element == elem.hydrogen]
                    if len(oatom) != 1 or len(hatoms) != 2:
                        raise ValueError('Illegal water molecule (residue %d): contains %d oxygen(s) and %d hydrogen(s)' % (residue.index, len(oatom), len(hatoms)))
                    o = newTopology.addAtom(oatom[0].name, oatom[0].element, newResidue)
                    h1 = newTopology.addAtom(hatoms[0].name, hatoms[0].element, newResidue)
                    h2 = newTopology.addAtom(hatoms[1].name, hatoms[1].element, newResidue)
                    newAtoms[oatom[0]] = o
                    newAtoms[hatoms[0]] = h1
                    newAtoms[hatoms[1]] = h2
                    po = deepcopy(self.positions[oatom[0].index])
                    ph1 = deepcopy(self.positions[hatoms[0].index])
                    ph2 = deepcopy(self.positions[hatoms[1].index])
                    newPositions.append(po)
                    newPositions.append(ph1)
                    newPositions.append(ph2)

                    # Add virtual sites.

                    if sites == 4:
                        newTopology.addAtom('M', None, newResidue)
                        newPositions.append(0.786646558*po + 0.106676721*ph1 + 0.106676721*ph2)
                    elif sites == 5:
                        newTopology.addAtom('M1', None, newResidue)
                        newTopology.addAtom('M2', None, newResidue)
                        v1 = (ph1-po).value_in_unit(nanometer)
                        v2 = (ph2-po).value_in_unit(nanometer)
                        cross = Vec3(v1[1]*v2[2]-v1[2]*v2[1], v1[2]*v2[0]-v1[0]*v2[2], v1[0]*v2[1]-v1[1]*v2[0])
                        newPositions.append(po - (0.34490826*v1 - 0.34490826*v2 - 6.4437903*cross)*nanometer)
                        newPositions.append(po - (0.34490826*v1 - 0.34490826*v2 + 6.4437903*cross)*nanometer)
                else:
                    # Just copy the residue over.
                    for atom in residue.atoms():
                        newAtom = newTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
                        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]])
        self.topology = newTopology
        self.positions = newPositions

    def addSolvent(self, forcefield, model='tip3p', boxSize=None, boxVectors=None, padding=None, numAdded=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True):
        """Add solvent (both water and ions) to the model to fill a rectangular box.

        The algorithm works as follows:

        1. Water molecules are added to fill the box.
        2. Water molecules are removed if their distance to any solute atom is less than the sum of their van der Waals radii.
        3. If the solute is charged and neutralize=True, enough positive or negative ions are added to neutralize it.  Each ion is added by
           randomly selecting a water molecule and replacing it with the ion.
        4. Ion pairs are added to give the requested total ionic strength.  Note that only monovalent ions are currently supported.

        The box size can be specified in any of several ways:

        1. You can explicitly give the vectors defining the periodic box to use.
        2. Alternatively, for a rectangular box you can simply give the dimensions of the unit cell.
        3. You can give a padding distance.  The largest dimension of the solute (along the x, y, or z axis) is determined, and a cubic
           box of size (largest dimension)+2*padding is used.
        4. You can specify the total number of molecules (both waters and ions) to add.  A cubic box is then created whose size is
           just large enough hold the specified amount of solvent.
        5. Finally, if none of the above options is specified, the existing Topology's box vectors are used.

        Parameters
        ----------
        forcefield : ForceField
            the ForceField to use for determining van der Waals radii and atomic charges
        model : str='tip3p'
            the water model to use.  Supported values are 'tip3p', 'spce', 'tip4pew', and 'tip5p'.
        boxSize : Vec3=None
            the size of the box to fill with water
        boxVectors : tuple of Vec3=None
            the vectors defining the periodic box to fill with water
        padding : distance=None
            the padding distance to use
        numAdded : int=None
            the total number of molecules (waters and ions) to add
        positiveIon : string='Na+'
            the type of positive ion to add.  Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
        negativeIon : string='Cl-'
            the type of negative ion to add.  Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'. Be aware
            that not all force fields support all ion types.
        ionicStrength : concentration=0*molar
            the total concentration of ions (both positive and negative) to add.  This
            does not include ions that are added to neutralize the system.
            Note that only monovalent ions are currently supported.
        neutralize : bool=True
            whether to add ions to neutralize the system
        """
        if len([x for x in (boxSize, boxVectors, padding, numAdded) if x is not None]) > 1:
            raise ValueError('At most one of the following arguments may be specified: boxSize, boxVectors, padding, numAdded')

        # Load the pre-equilibrated water box.

        vdwRadiusPerSigma = 0.5612310241546864907
        if model == 'tip3p':
            waterRadius = 0.31507524065751241*vdwRadiusPerSigma
        elif model == 'spce':
            waterRadius = 0.31657195050398818*vdwRadiusPerSigma
        elif model == 'tip4pew':
            waterRadius = 0.315365*vdwRadiusPerSigma
        elif model == 'tip5p':
            waterRadius = 0.312*vdwRadiusPerSigma
        else:
            raise ValueError('Unknown water model: %s' % model)
        pdb = PDBFile(os.path.join(os.path.dirname(__file__), 'data', model+'.pdb'))
        pdbTopology = pdb.getTopology()
        pdbPositions = pdb.getPositions().value_in_unit(nanometer)
        pdbResidues = list(pdbTopology.residues())
        pdbBoxSize = pdbTopology.getUnitCellDimensions().value_in_unit(nanometer)

        # Pick a unit cell size.

        if numAdded is not None:
            # Select a padding distance which is guaranteed to give more than the specified number of molecules.

            padding = 1.1*(numAdded/((len(pdbResidues)/pdbBoxSize[0]**3)*8))**(1.0/3.0)
            if padding < 0.5:
                padding = 0.5 # Ensure we have enough when adding very small numbers of molecules
        if boxVectors is not None:
            if is_quantity(boxVectors[0]):
                boxVectors = (boxVectors[0].value_in_unit(nanometer), boxVectors[1].value_in_unit(nanometer), boxVectors[2].value_in_unit(nanometer))
            box = Vec3(boxVectors[0][0], boxVectors[1][1], boxVectors[2][2])
            vectors = boxVectors
        elif boxSize is not None:
            if is_quantity(boxSize):
                boxSize = boxSize.value_in_unit(nanometer)
            box = Vec3(boxSize[0], boxSize[1], boxSize[2])
            vectors = (Vec3(boxSize[0], 0, 0), Vec3(0, boxSize[1], 0), Vec3(0, 0, boxSize[2]))
        elif padding is not None:
            if is_quantity(padding):
                padding = padding.value_in_unit(nanometer)
            if len(self.positions) == 0:
                maxSize = 0
            else:
                maxSize = max(max((pos[i] for pos in self.positions))-min((pos[i] for pos in self.positions)) for i in range(3))
                maxSize = maxSize.value_in_unit(nanometer)
            box = (maxSize+2*padding)*Vec3(1, 1, 1)
            vectors = (Vec3(maxSize+2*padding, 0, 0), Vec3(0, maxSize+2*padding, 0), Vec3(0, 0, maxSize+2*padding))
        else:
            box = self.topology.getUnitCellDimensions().value_in_unit(nanometer)
            vectors = self.topology.getPeriodicBoxVectors().value_in_unit(nanometer)
            if box is None:
                raise ValueError('Neither the box size, box vectors, nor padding was specified, and the Topology does not define unit cell dimensions')
        invBox = Vec3(1.0/box[0], 1.0/box[1], 1.0/box[2])

        # Identify the ion types.

        posIonElements = {'Cs+':elem.cesium, 'K+':elem.potassium, 'Li+':elem.lithium, 'Na+':elem.sodium, 'Rb+':elem.rubidium}
        negIonElements = {'Cl-':elem.chlorine, 'Br-':elem.bromine, 'F-':elem.fluorine, 'I-':elem.iodine}
        if positiveIon not in posIonElements:
            raise ValueError('Illegal value for positive ion: %s' % positiveIon)
        if negativeIon not in negIonElements:
            raise ValueError('Illegal value for negative ion: %s' % negativeIon)
        positiveElement = posIonElements[positiveIon]
        negativeElement = negIonElements[negativeIon]

        # Have the ForceField build a System for the solute from which we can determine van der Waals radii.

        system = forcefield.createSystem(self.topology)
        nonbonded = None
        for i in range(system.getNumForces()):
            if isinstance(system.getForce(i), NonbondedForce):
                nonbonded = system.getForce(i)
        if nonbonded is None:
            raise ValueError('The ForceField does not specify a NonbondedForce')
        cutoff = [nonbonded.getParticleParameters(i)[1].value_in_unit(nanometer)*vdwRadiusPerSigma+waterRadius for i in range(system.getNumParticles())]
        waterCutoff = waterRadius
        if len(cutoff) == 0:
            maxCutoff = waterCutoff
        else:
            maxCutoff = max(waterCutoff, max(cutoff))

        # Copy the solute over.

        newTopology = Topology()
        newTopology.setPeriodicBoxVectors(vectors*nanometer)
        newAtoms = {}
        newPositions = []*nanometer
        for chain in self.topology.chains():
            newChain = newTopology.addChain(chain.id)
            for residue in chain.residues():
                newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
                for atom in residue.atoms():
                    newAtom = newTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
                    newAtoms[atom] = newAtom
                    newPositions.append(deepcopy(self.positions[atom.index]))
        for bond in self.topology.bonds():
            newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])

        # Sort the solute atoms into cells for fast lookup.

        if len(self.positions) == 0:
            positions = []
        else:
            positions = self.positions.value_in_unit(nanometer)
        cells = {}
        numCells = tuple((max(1, int(floor(box[i]/maxCutoff))) for i in range(3)))
        cellSize = tuple((box[i]/numCells[i] for i in range(3)))
        for i in range(len(positions)):
            cell = tuple((int(floor(positions[i][j]/cellSize[j]))%numCells[j] for j in range(3)))
            if cell in cells:
                cells[cell].append(i)
            else:
                cells[cell] = [i]

        # Create a generator that loops over atoms close to a position.

        def neighbors(pos):
            centralCell = tuple((int(floor(pos[i]/cellSize[i])) for i in range(3)))
            offsets = (-1, 0, 1)
            for i in offsets:
                for j in offsets:
                    for k in offsets:
                        cell = ((centralCell[0]+i+numCells[0])%numCells[0], (centralCell[1]+j+numCells[1])%numCells[1], (centralCell[2]+k+numCells[2])%numCells[2])
                        if cell in cells:
                            for atom in cells[cell]:
                                yield atom

        # Define a function to compute the distance between two points, taking periodic boundary conditions into account.

        def periodicDistance(pos1, pos2):
            delta = pos1-pos2
            delta -= vectors[2]*floor(delta[2]*invBox[2]+0.5)
            delta -= vectors[1]*floor(delta[1]*invBox[1]+0.5)
            delta -= vectors[0]*floor(delta[0]*invBox[0]+0.5)
            return norm(delta)

        # Find the list of water molecules to add.

        newChain = newTopology.addChain()
        if len(positions) == 0:
            center = Vec3(0, 0, 0)
        else:
            center = [(max((pos[i] for pos in positions))+min((pos[i] for pos in positions)))/2 for i in range(3)]
            center = Vec3(center[0], center[1], center[2])
        numBoxes = [int(ceil(box[i]/pdbBoxSize[i])) for i in range(3)]
        addedWaters = []
        for boxx in range(numBoxes[0]):
            for boxy in range(numBoxes[1]):
                for boxz in range(numBoxes[2]):
                    offset = Vec3(boxx*pdbBoxSize[0], boxy*pdbBoxSize[1], boxz*pdbBoxSize[2])
                    for residue in pdbResidues:
                        oxygen = [atom for atom in residue.atoms() if atom.element == elem.oxygen][0]
                        atomPos = pdbPositions[oxygen.index]+offset
                        if not any((atomPos[i] > box[i] for i in range(3))):
                            # This molecule is inside the box, so see how close to it is to the solute.

                            atomPos += center-box/2
                            for i in neighbors(atomPos):
                                if periodicDistance(atomPos, positions[i]) < cutoff[i]:
                                    break
                            else:
                                # Record this water molecule as one to add.

                                addedWaters.append((residue.index, atomPos))

        if numAdded is not None:
            # We added many more waters than we actually want.  Sort them based on distance to the nearest box edge and
            # only keep the ones in the middle.

            lowerBound = center-box/2
            upperBound = center+box/2
            distToEdge = (min(min(pos-lowerBound), min(upperBound-pos)) for index, pos in addedWaters)
            sortedIndex = [i[0] for i in sorted(enumerate(distToEdge), key=lambda x: -x[1])]
            addedWaters = [addedWaters[i] for i in sortedIndex[:numAdded]]

            # Compute a new periodic box size.

            maxSize = max(max((pos[i] for index, pos in addedWaters))-min((pos[i] for index, pos in addedWaters)) for i in range(3))
            newTopology.setUnitCellDimensions(Vec3(maxSize, maxSize, maxSize))
        else:
            # There could be clashes between water molecules at the box edges.  Find ones to remove.

            upperCutoff = center+box/2-Vec3(waterCutoff, waterCutoff, waterCutoff)
            lowerCutoff = center-box/2+Vec3(waterCutoff, waterCutoff, waterCutoff)
            lowerSkinPositions = [pos for index, pos in addedWaters if pos[0] < lowerCutoff[0] or pos[1] < lowerCutoff[1] or pos[2] < lowerCutoff[2]]
            filteredWaters = []
            cells = {}
            for i in range(len(lowerSkinPositions)):
                cell = tuple((int(floor(lowerSkinPositions[i][j]/cellSize[j]))%numCells[j] for j in range(3)))
                if cell in cells:
                    cells[cell].append(i)
                else:
                    cells[cell] = [i]
            for entry in addedWaters:
                pos = entry[1]
                if pos[0] < upperCutoff[0] and pos[1] < upperCutoff[1] and pos[2] < upperCutoff[2]:
                    filteredWaters.append(entry)
                else:
                    if not any((periodicDistance(lowerSkinPositions[i], pos) < waterCutoff and norm(lowerSkinPositions[i]-pos) > waterCutoff for i in neighbors(pos))):
                        filteredWaters.append(entry)
            addedWaters = filteredWaters

        # Add ions to neutralize the system.

        def addIon(element):
            # Replace a water by an ion.
            index = random.randint(0, len(addedWaters)-1)
            newResidue = newTopology.addResidue(element.symbol.upper(), newChain)
            newTopology.addAtom(element.symbol, element, newResidue)
            newPositions.append(addedWaters[index][1]*nanometer)
            del addedWaters[index]
        if neutralize:
            totalCharge = int(floor(0.5+sum((nonbonded.getParticleParameters(i)[0].value_in_unit(elementary_charge) for i in range(system.getNumParticles())))))
            if abs(totalCharge) > len(addedWaters):
                raise Exception('Cannot neutralize the system because the charge is greater than the number of available positions for ions')
            for i in range(abs(totalCharge)):
                addIon(positiveElement if totalCharge < 0 else negativeElement)

        # Add ions based on the desired ionic strength.

        numIons = len(addedWaters)*ionicStrength/(55.4*molar) # Pure water is about 55.4 molar (depending on temperature)
        numPairs = int(floor(numIons+0.5))
        for i in range(numPairs):
            addIon(positiveElement)
        for i in range(numPairs):
            addIon(negativeElement)

        # Add the water molecules.

        for index, pos in addedWaters:
            newResidue = newTopology.addResidue(residue.name, newChain)
            residue = pdbResidues[index]
            oxygen = [atom for atom in residue.atoms() if atom.element == elem.oxygen][0]
            oPos = pdbPositions[oxygen.index]
            molAtoms = []
            for atom in residue.atoms():
                molAtoms.append(newTopology.addAtom(atom.name, atom.element, newResidue))
                newPositions.append((pos+pdbPositions[atom.index]-oPos)*nanometer)
            for atom1 in molAtoms:
                if atom1.element == elem.oxygen:
                    for atom2 in molAtoms:
                        if atom2.element == elem.hydrogen:
                            newTopology.addBond(atom1, atom2)
        self.topology = newTopology
        self.positions = newPositions

    class _ResidueData:
        """Inner class used to encapsulate data about the hydrogens for a residue."""
        def __init__(self, name):
            self.name = name
            self.variants = []
            self.hydrogens = []

    class _Hydrogen:
        """Inner class used to encapsulate data about a hydrogen atom."""
        def __init__(self, name, parent, maxph, variants, terminal):
            self.name = name
            self.parent = parent
            self.maxph = maxph
            self.variants = variants
            self.terminal = terminal

    @staticmethod
    def loadHydrogenDefinitions(file):
        """Load an XML file containing definitions of hydrogens that should be added by addHydrogens().

        The built in hydrogens.xml file containing definitions for standard amino acids and nucleotides is loaded automatically.
        This method can be used to load additional definitions for other residue types.  They will then be used in subsequent
        calls to addHydrogens().
        """
        tree = etree.parse(file)
        infinity = float('Inf')
        for residue in tree.getroot().findall('Residue'):
            resName = residue.attrib['name']
            data = Modeller._ResidueData(resName)
            Modeller._residueHydrogens[resName] = data
            for variant in residue.findall('Variant'):
                data.variants.append(variant.attrib['name'])
            for hydrogen in residue.findall('H'):
                maxph = infinity
                if 'maxph' in hydrogen.attrib:
                    maxph = float(hydrogen.attrib['maxph'])
                atomVariants = None
                if 'variant' in hydrogen.attrib:
                    atomVariants = hydrogen.attrib['variant'].split(',')
                terminal = None
                if 'terminal' in hydrogen.attrib:
                    terminal = hydrogen.attrib['terminal']
                data.hydrogens.append(Modeller._Hydrogen(hydrogen.attrib['name'], hydrogen.attrib['parent'], maxph, atomVariants, terminal))

    def addHydrogens(self, forcefield=None, 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
            HIN: Negatively charged form without a hydrogen on either ND1 or 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.  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, 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=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 : 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
        -------
        list
             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.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' 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
                    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 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():
                        # 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, nonbondedMethod=CutoffNonPeriodic)
            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)')
            nonbonded.setNonbondedMethod(CustomNonbondedForce.CutoffNonPeriodic);
            nonbonded.setCutoffDistance(1*nanometer)
            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, 100000.0)
                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 addExtraParticles(self, forcefield):
        """Add missing extra particles to the model that are required by a force
        field.

        Some force fields use "extra particles" that do not represent
        actual atoms, but still need to be included in the System.  Examples
        include lone pairs, Drude particles, and the virtual sites used in some
        water models to adjust the charge distribution.  Extra particles can be
        recognized by the fact that their element is None.

        This method is primarily used to add extra particles, but it can also
        remove them.  It tries to match every residue in the Topology to a
        template in the force field.  If there is no match, it will both add
        and remove extra particles as necessary to make it match.

        Parameters
        ----------
        forcefield : ForceField
            the ForceField defining what extra particles should be present
        """
        # Create copies of all residue templates that have had all extra points removed.

        templatesNoEP = {}
        for resName, template  in forcefield._templates.items():
            if any(atom.element is None for atom in template.atoms):
                index = 0
                newIndex = {}
                newTemplate = ForceField._TemplateData(resName)
                for i, atom in enumerate(template.atoms):
                    if atom.element is not None:
                        newIndex[i] = index
                        index += 1
                        newAtom = ForceField._TemplateAtomData(atom.name, atom.type, atom.element)
                        newAtom.externalBonds = atom.externalBonds
                        newTemplate.atoms.append(newAtom)
                for b1, b2 in template.bonds:
                    if b1 in newIndex and b2 in newIndex:
                        newTemplate.bonds.append((newIndex[b1], newIndex[b2]))
                        newTemplate.atoms[newIndex[b1]].bondedTo.append(newIndex[b2])
                        newTemplate.atoms[newIndex[b2]].bondedTo.append(newIndex[b1])
                for b in template.externalBonds:
                    if b in newIndex:
                        newTemplate.externalBonds.append(newIndex[b])
                templatesNoEP[template] = newTemplate

        # Record which atoms are bonded to each other atom, with and without extra particles.

        bondedToAtom = []
        bondedToAtomNoEP = []
        for atom in self.topology.atoms():
            bondedToAtom.append(set())
            bondedToAtomNoEP.append(set())
        for atom1, atom2 in self.topology.bonds():
            bondedToAtom[atom1.index].add(atom2.index)
            bondedToAtom[atom2.index].add(atom1.index)
            if atom1.element is not None and atom2.element is not None:
                bondedToAtomNoEP[atom1.index].add(atom2.index)
                bondedToAtomNoEP[atom2.index].add(atom1.index)

        # If the force field has a DrudeForce, record the types of Drude particles and their parents since we'll
        # need them for picking particle positions.

        drudeTypeMap = {}
        for force in forcefield._forces:
            if isinstance(force, DrudeGenerator):
                for type in force.typeMap:
                    drudeTypeMap[type] = force.typeMap[type][0]

        # Create the new Topology.

        newTopology = Topology()
        newTopology.setPeriodicBoxVectors(self.topology.getPeriodicBoxVectors())
        newAtoms = {}
        newPositions = []*nanometer
        missingPositions = set()
        for chain in self.topology.chains():
            newChain = newTopology.addChain(chain.id)
            for residue in chain.residues():
                newResidue = newTopology.addResidue(residue.name, newChain, residue.id)

                # Look for a matching template.

                matchFound = False
                signature = _createResidueSignature([atom.element for atom in residue.atoms()])
                if signature in forcefield._templateSignatures:
                    for t in forcefield._templateSignatures[signature]:
                        if _matchResidue(residue, t, bondedToAtom, False) is not None:
                            matchFound = True
                if matchFound:
                    # Just copy the residue over.

                    for atom in residue.atoms():
                        newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
                        newAtoms[atom] = newAtom
                        newPositions.append(deepcopy(self.positions[atom.index]))
                else:
                    # There's no matching template.  Try to find one that matches based on everything except
                    # extra points.

                    template = None
                    residueNoEP = Residue(residue.name, residue.index, residue.chain, residue.id)
                    residueNoEP._atoms = [atom for atom in residue.atoms() if atom.element is not None]
                    if signature in forcefield._templateSignatures:
                        for t in forcefield._templateSignatures[signature]:
                            if t in templatesNoEP:
                                matches = _matchResidue(residueNoEP, templatesNoEP[t], bondedToAtomNoEP, False)
                                if matches is not None:
                                    template = t;
                                    # Record the corresponding atoms.
                                    matchingAtoms = {}
                                    for atom, match in zip(residueNoEP.atoms(), matches):
                                        templateAtomName = templatesNoEP[t].atoms[match].name
                                        for templateAtom in template.atoms:
                                            if templateAtom.name == templateAtomName:
                                                matchingAtoms[templateAtom] = atom
                                    break
                    if template is None:
                        raise ValueError('Residue %d (%s) does not match any template defined by the ForceField.' % (residue.index+1, residue.name))

                    # Add the regular atoms.

                    for atom in residue.atoms():
                        if atom.element is not None:
                            newAtoms[atom] = newTopology.addAtom(atom.name, atom.element, newResidue)
                            newPositions.append(deepcopy(self.positions[atom.index]))

                    # Add the extra points.

                    templateAtomPositions = len(template.atoms)*[None]
                    for index, atom in enumerate(template.atoms):
                        if atom in matchingAtoms:
                            templateAtomPositions[index] = self.positions[matchingAtoms[atom].index].value_in_unit(nanometer)
                    newExtraPoints = {}
                    for index, atom in enumerate(template.atoms):
                        if atom.element is None:
                            newExtraPoints[atom] = newTopology.addAtom(atom.name, None, newResidue)
                            position = None
                            for site in template.virtualSites:
                                if site.index == index:
                                    # This is a virtual site.  Compute its position by the correct rule.

                                    if site.type == 'average2':
                                        position = site.weights[0]*templateAtomPositions[site.atoms[0]] + site.weights[1]*templateAtomPositions[site.atoms[1]]
                                    elif site.type == 'average3':
                                        position = site.weights[0]*templateAtomPositions[site.atoms[0]] + site.weights[1]*templateAtomPositions[site.atoms[1]] + site.weights[2]*templateAtomPositions[site.atoms[2]]
                                    elif site.type == 'outOfPlane':
                                        v1 = templateAtomPositions[site.atoms[1]] - templateAtomPositions[site.atoms[0]]
                                        v2 = templateAtomPositions[site.atoms[2]] - templateAtomPositions[site.atoms[0]]
                                        cross = Vec3(v1[1]*v2[2]-v1[2]*v2[1], v1[2]*v2[0]-v1[0]*v2[2], v1[0]*v2[1]-v1[1]*v2[0])
                                        position = templateAtomPositions[site.atoms[0]] + site.weights[0]*v1 + site.weights[1]*v2 + site.weights[2]*cross
                                    elif site.type == 'localCoords':
                                        origin = templateAtomPositions[site.atoms[0]]*site.originWeights[0] + templateAtomPositions[site.atoms[1]]*site.originWeights[1] + templateAtomPositions[site.atoms[2]]*site.originWeights[2];
                                        xdir = templateAtomPositions[site.atoms[0]]*site.xWeights[0] + templateAtomPositions[site.atoms[1]]*site.xWeights[1] + templateAtomPositions[site.atoms[2]]*site.xWeights[2];
                                        ydir = templateAtomPositions[site.atoms[0]]*site.yWeights[0] + templateAtomPositions[site.atoms[1]]*site.yWeights[1] + templateAtomPositions[site.atoms[2]]*site.yWeights[2];
                                        zdir = Vec3(xdir[1]*ydir[2]-xdir[2]*ydir[1], xdir[2]*ydir[0]-xdir[0]*ydir[2], xdir[0]*ydir[1]-xdir[1]*ydir[0])
                                        xdir /= norm(xdir);
                                        zdir /= norm(zdir);
                                        ydir = Vec3(zdir[1]*xdir[2]-zdir[2]*xdir[1], zdir[2]*xdir[0]-zdir[0]*xdir[2], zdir[0]*xdir[1]-zdir[1]*xdir[0])
                                        position = origin + xdir*site.localPos[0] + ydir*site.localPos[1] + zdir*site.localPos[2];
                            if position is None and atom.type in drudeTypeMap:
                                # This is a Drude particle.  Put it on top of its parent atom.

                                for atom2, pos in zip(template.atoms, templateAtomPositions):
                                    if atom2.type in drudeTypeMap[atom.type]:
                                        position = deepcopy(pos)
                            if position is None:
                                # We couldn't figure out the correct position.  Put it at a random position near the center of the residue,
                                # and we'll try to fix it later based on bonds.

                                knownPositions = [x for x in templateAtomPositions if x is not None]
                                position = Vec3(random.gauss(0, 1), random.gauss(0, 1), random.gauss(0, 1))+(unit.sum(knownPositions)/len(knownPositions))
                                missingPositions.add(len(newPositions))
                            newPositions.append(position*nanometer)

                    # Add bonds involving the extra points.

                    for atom1, atom2 in template.bonds:
                        atom1 = template.atoms[atom1]
                        atom2 = template.atoms[atom2]
                        if atom1 in newExtraPoints or atom2 in newExtraPoints:
                            if atom1 in newExtraPoints:
                                a1 = newExtraPoints[atom1]
                            else:
                                a1 = newAtoms[matchingAtoms[atom1]]
                            if atom2 in newExtraPoints:
                                a2 = newExtraPoints[atom2]
                            else:
                                a2 = newAtoms[matchingAtoms[atom2]]
                            newTopology.addBond(a1, a2)

        for bond in self.topology.bonds():
            if bond[0] in newAtoms and bond[1] in newAtoms:
                newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])

        if len(missingPositions) > 0:
            # There were particles whose position we couldn't identify before, since they were neither virtual sites nor Drude particles.
            # Try to figure them out based on bonds.  First, use the ForceField to create a list of every bond involving one of them.

            system = forcefield.createSystem(newTopology, constraints=AllBonds)
            bonds = []
            for i in range(system.getNumConstraints()):
                bond = system.getConstraintParameters(i)
                if bond[0] in missingPositions or bond[1] in missingPositions:
                    bonds.append(bond)

            # Now run a few iterations of SHAKE to try to select reasonable positions.

            for iteration in range(15):
                for atom1, atom2, distance in bonds:
                    if atom1 in missingPositions:
                        if atom2 in missingPositions:
                            weights = (0.5, 0.5)
                        else:
                            weights = (1.0, 0.0)
                    else:
                        weights = (0.0, 1.0)
                    delta = newPositions[atom2]-newPositions[atom1]
                    length = norm(delta)
                    delta *= (distance-length)/length
                    newPositions[atom1] -= weights[0]*delta
                    newPositions[atom2] += weights[1]*delta

        self.topology = newTopology
        self.positions = newPositions