private static Dictionary <Orbital, Vector3D> CalculateLonePairRepulsion(Graph <Atom, SimpleBond> graph,
IDictionary <uint, Vector3D> forceLookup)
{
var lonePairForceLookup = graph.Vertices
.Select(v => (AtomWithOrbitals)v.Object)
.SelectMany(atom => atom.LonePairs)
.ToDictionary(o => o, o => new Vector3D(0, 0, 0));
foreach (var vertex in graph.Vertices)
{
var adjacentVertices = GraphAlgorithms.GetAdjacentVertices(graph, vertex).Cast <IVertex <Atom> >().ToList();
var currentAtom = (AtomWithOrbitals)vertex.Object;
var filledOuterOrbitals = currentAtom.OuterOrbitals.Where(o => o.IsFull).ToList();
var orbitalNeighborVertexMap = MapBondOrbitalToNeighborVertex(
filledOuterOrbitals, currentAtom, adjacentVertices);
for (var orbitalIdx1 = 0; orbitalIdx1 < filledOuterOrbitals.Count; orbitalIdx1++)
{
var orbital1 = filledOuterOrbitals[orbitalIdx1];
for (var orbitalIdx2 = orbitalIdx1 + 1; orbitalIdx2 < filledOuterOrbitals.Count; orbitalIdx2++)
{
var orbital2 = filledOuterOrbitals[orbitalIdx2];
var repulsiveForce = CalculateRepulsiveForce(orbital1, orbital2);
var orbtial1Vector = currentAtom.Position
.VectorTo(orbital1.MaximumElectronDensityPosition)
.Normalize();
var orbital1ParallelForce = repulsiveForce.ProjectOnto(orbtial1Vector);
var orbital1RepulsiveForce = (repulsiveForce - orbital1ParallelForce).ToVector3D();
var orbtial2Vector = currentAtom.Position
.VectorTo(orbital2.MaximumElectronDensityPosition)
.Normalize();
var orbital2ParallelForce = repulsiveForce.ProjectOnto(orbtial2Vector);
var orbital2RepulsiveForce = (repulsiveForce - orbital2ParallelForce).ToVector3D();
if (orbital1.IsPartOfBond)
{
var neighborVertex = orbitalNeighborVertexMap[orbital1];
forceLookup[neighborVertex.Id] += orbital1RepulsiveForce;
}
else
{
lonePairForceLookup[orbital1] += orbital1RepulsiveForce;
}
if (orbital2.IsPartOfBond)
{
var neighborVertex = orbitalNeighborVertexMap[orbital2];
forceLookup[neighborVertex.Id] += -orbital2RepulsiveForce;
}
else
{
lonePairForceLookup[orbital2] += -orbital2RepulsiveForce;
}
}
}
}
return(lonePairForceLookup);
}
private static IEnumerable <IVertex <Atom> > PositionNeighborsAndLonePairs(Molecule molecule, IVertex <Atom> vertex)
{
var currentAtom = (AtomWithOrbitals)vertex.Object;
var vertextEdges = vertex.EdgeIds.Select(edgeId => molecule.MoleculeStructure.GetEdgeById(edgeId)).ToList();
var adjacentVertices = GraphAlgorithms.GetAdjacentVertices(molecule.MoleculeStructure, vertex).Cast <IVertex <Atom> >().ToList();
var unpositionedNeighbors = adjacentVertices.Where(v => !v.Object.IsPositioned).ToList();
var evenlyDistributedPoints = GetAtomSpherePoints(currentAtom, adjacentVertices);
var evenlySpacePointsQueue = new Queue <Point3D>(evenlyDistributedPoints);
var neighborsReadyForPositioning = new List <IVertex <Atom> >();
foreach (var neighbor in unpositionedNeighbors)
{
var atom = neighbor.Object;
if (atom.IsPositioned)
{
continue;
}
neighborsReadyForPositioning.Add(neighbor);
if (atom.IsPositionFixed)
{
atom.IsPositioned = true;
continue;
}
var connectingEdges = vertextEdges.Where(edge => edge.HasVertex(neighbor.Id)).ToList();
var bonds = connectingEdges.Select(edge => (OrbitalBond)edge.Object);
var bondLength = bonds.Select(bond => bond.BondLength.Value).Average();
var bondDirection = evenlySpacePointsQueue.Dequeue().ToVector3D();
var neighborPosition = currentAtom.Position + bondLength * bondDirection;
atom.Position = neighborPosition.To(SIPrefix.Pico, Unit.Meter);
atom.IsPositioned = true;
}
var lonePairs = currentAtom.OuterOrbitals.Where(o => o.IsFull && !o.IsPartOfBond).ToList();
foreach (var lonePair in lonePairs)
{
var lonePairDirection = evenlySpacePointsQueue.Dequeue().ToVector3D();
var lonePairPosition = currentAtom.Position
+ currentAtom.Radius.Value * lonePairDirection;
lonePair.MaximumElectronDensityPosition = lonePairPosition;
}
return(neighborsReadyForPositioning);
}
private static void PositionSpecificNeighborAlongXAxis(Molecule molecule, IVertex <Atom> currentVertex, IVertex <Atom> neighborVertex)
{
var currentAtom = currentVertex.Object;
var neighborAtom = neighborVertex.Object;
if (neighborAtom.IsPositioned)
{
return;
}
if (neighborAtom.IsPositionFixed)
{
neighborAtom.IsPositioned = true;
return;
}
var adjacentVertices = GraphAlgorithms.GetAdjacentVertices(molecule.MoleculeStructure, currentVertex).Cast <IVertex <Atom> >().ToList();
var evenlyDistributedPoints = GetAtomSpherePoints((AtomWithOrbitals)currentAtom, adjacentVertices);
var edgesToNeighbor = currentVertex.EdgeIds
.Select(edgeId => molecule.MoleculeStructure.GetEdgeById(edgeId))
.Where(edge => edge.HasVertex(neighborVertex.Id))
.ToList();
if (!edgesToNeighbor.Any())
{
throw new ArgumentException("Vertex to be positioned is not a neighbor of the current vertex");
}
var bonds = edgesToNeighbor.Select(edge => (OrbitalBond)edge.Object);
var bondLength = bonds.Select(bond => bond.BondLength.Value).Average();
var candidateAtomPositions = evenlyDistributedPoints
.Select(bondDirection => currentAtom.Position + bondLength * bondDirection)
.ToList();
var pointsFurtherAlongX = candidateAtomPositions.Where(p => p.X > currentAtom.Position.X).ToList();
Point3D neighborPosition;
if (pointsFurtherAlongX.Any())
{
neighborPosition = pointsFurtherAlongX
.MinimumItem(p => p.DistanceToLine(new Point3D(0, 0, 0), new Point3D(1, 0, 0)));
}
else
{
neighborPosition = candidateAtomPositions
.MinimumItem(p => p.DistanceToLine(new Point3D(0, 0, 0), new Point3D(1, 0, 0)));
}
neighborAtom.Position = neighborPosition.To(SIPrefix.Pico, Unit.Meter);
neighborAtom.IsPositioned = true;
}
private static Graph <ApproximatedAminoAcid, OrbitalBond> ToGraph(ConvexHull <ApproximateAminoAcidVertex3D, DefaultConvexFace <ApproximateAminoAcidVertex3D> > convexHull)
{
var graph = new Graph <ApproximatedAminoAcid, OrbitalBond>();
// Add vertices
var convexHullToGraphVertexIdMap = new Dictionary <long, uint>();
foreach (var hullVertex in convexHull.Points)
{
var graphVertex = new Vertex <ApproximatedAminoAcid>(graph.GetUnusedVertexId())
{
Object = hullVertex.AminoAcid
};
graph.AddVertex(graphVertex);
convexHullToGraphVertexIdMap.Add(hullVertex.Id, graphVertex.Id);
}
// Connect vertices
foreach (var face in convexHull.Faces)
{
for (int v1Idx = 0; v1Idx < face.Vertices.Length - 1; v1Idx++)
{
var vertex1 = face.Vertices[v1Idx];
var vertex1GraphId = convexHullToGraphVertexIdMap[vertex1.Id];
for (int v2Idx = v1Idx + 1; v2Idx < face.Vertices.Length; v2Idx++)
{
var vertex2 = face.Vertices[v2Idx];
var vertex2GraphId = convexHullToGraphVertexIdMap[vertex2.Id];
var graphVertex1 = graph.GetVertexFromId(vertex1GraphId);
var adjacentVertices = GraphAlgorithms.GetAdjacentVertices(graph, graphVertex1);
if (!adjacentVertices.Select(v => v.Id).Contains(vertex2GraphId))
{
graph.AddEdge(new Edge <OrbitalBond>(graph.GetUnusedEdgeId(), vertex1GraphId, vertex2GraphId));
}
}
}
}
return(graph);
}
public Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces> Calculate(
CompactnessMeasurerResult compactnessMeasurerResult)
{
// VALIDATED: Forces point in the right direction, chain is compacted.
// If force is reversed, chain is stretched out to a line.
var forceDictionary = new Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces>();
var convexHull = compactnessMeasurerResult.ConvexHull;
foreach (var vertex in convexHull.Vertices)
{
var aminoAcid = vertex.Object;
var vertexPosition = aminoAcid.CarbonAlphaPosition;
if (!forceDictionary.ContainsKey(aminoAcid))
{
forceDictionary.Add(aminoAcid, new ApproximateAminoAcidForces());
}
var adjacentVertices = GraphAlgorithms.GetAdjacentVertices(convexHull, vertex).Cast <IVertex <ApproximatedAminoAcid> >();
foreach (var adjacentVertex in adjacentVertices)
{
var adjacentAminoAcid = adjacentVertex.Object;
var adjacentPosition = adjacentAminoAcid.CarbonAlphaPosition;
var connectingVector = vertexPosition.VectorTo(adjacentPosition);
var distance = connectingVector.Magnitude();
var forceMagnitude = ForceScaling * (1.0 + ForceDistanceScaling * distance.In(SIPrefix.Pico, Unit.Meter));
var forceDirection = connectingVector.In(SIPrefix.Pico, Unit.Meter).Normalize().ToVector3D();
if (!forceDictionary.ContainsKey(adjacentAminoAcid))
{
forceDictionary.Add(adjacentAminoAcid, new ApproximateAminoAcidForces());
}
AddForce(forceDictionary[aminoAcid], forceDirection, forceMagnitude);
AddForce(forceDictionary[adjacentAminoAcid], -forceDirection, forceMagnitude);
}
}
return(forceDictionary);
}
public void RedistributeCharges(Molecule aminoAcid)
{
var newCharges = aminoAcid.MoleculeStructure.Vertices
.ToDictionary(vertex => vertex.Id, vertex => vertex.Object.EffectiveCharge);
double chargeChange;
do
{
var currentCharges = newCharges;
var vertices = aminoAcid.MoleculeStructure.Vertices;
foreach (var vertex in vertices)
{
var neighbors = GraphAlgorithms.GetAdjacentVertices(aminoAcid.MoleculeStructure, vertex)
.Cast <IVertex <Atom> >()
.Select(v => v.Object)
.ToList();
var atoms = new[] { vertex.Object }.Concat(neighbors).ToList();
var chargeSum = atoms.Sum(x => x.EffectiveCharge.In(Unit.ElementaryCharge))
- atoms.Count;
var electroNegativitySum = atoms.Sum(x => x.ElectroNegativity);
foreach (var atom in atoms)
{
atom.EffectiveCharge = (1 + chargeSum * (atom.ElectroNegativity / electroNegativitySum)).To(Unit.ElementaryCharge);
}
}
newCharges = aminoAcid.MoleculeStructure.Vertices
.ToDictionary(vertex => vertex.Id, vertex => vertex.Object.EffectiveCharge);
chargeChange = aminoAcid.MoleculeStructure.Vertices
.Select(v => v.Id)
.Select(vId => (newCharges[vId] - currentCharges[vId]).Abs().In(Unit.ElementaryCharge))
.Max();
//var effectiveCharges = aminoAcid.Atoms.OrderBy(atom => atom.EffectiveCharge)
// .Select(atom => new { Atom = atom, Charge = atom.EffectiveCharge.In(Unit.ElementaryCharge) })
// .ToList();
} while (chargeChange > 0.01);
}
