public void VolumeAsExpected()
{
var aa1 = new ApproximatedAminoAcid(AminoAcidName.Alanine, 1);
var aa2 = new ApproximatedAminoAcid(AminoAcidName.Alanine, 2);
var aa3 = new ApproximatedAminoAcid(AminoAcidName.Alanine, 3);
var peptide = new ApproximatePeptide(new List <ApproximatedAminoAcid> {
aa1, aa2, aa3
});
// Set positions
aa1.NitrogenPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, 0, 0);
aa1.CarbonAlphaPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 1, 0, 0);
aa1.CarbonPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 1, 1, 0);
aa2.NitrogenPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, 1, 0);
aa2.CarbonAlphaPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, 1, 1);
aa2.CarbonPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 1, 1, 1);
aa3.NitrogenPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 1, 0, 1);
aa3.CarbonAlphaPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, 0, 1);
aa3.CarbonPosition = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0.5, 0.5, 0.5);
var result = CompactnessMeasurer.Measure(peptide);
var volume = result.Volume.Value;
var picoMultiplier = SIPrefix.Pico.GetMultiplier();
var cubicPicoMultiplier = picoMultiplier * picoMultiplier * picoMultiplier;
Assert.That(volume / cubicPicoMultiplier, Is.EqualTo(1).Within(1e-6));
}
public static ApproximatePeptide FromPeptide(Peptide peptide)
{
var dihedralAngles = AminoAcidAngleMeasurer.MeasureAngles(peptide);
var approximateAminoAcids = new List <ApproximatedAminoAcid>();
foreach (var aminoAcid in peptide.AminoAcids)
{
PdbAminoAcidAtomNamer.AssignNames(aminoAcid);
var nitrogen = aminoAcid.GetAtomFromName("N");
var carbonAlpha = aminoAcid.GetAtomFromName("CA");
var carbon = aminoAcid.GetAtomFromName("C");
var aminoAcidDihedralAngles = dihedralAngles[aminoAcid];
var approximateAminoAcid = new ApproximatedAminoAcid(aminoAcid.Name, aminoAcid.SequenceNumber)
{
NitrogenPosition = nitrogen.Position,
CarbonAlphaPosition = carbonAlpha.Position,
CarbonPosition = carbon.Position,
OmegaAngle = aminoAcidDihedralAngles.Omega,
PhiAngle = aminoAcidDihedralAngles.Phi,
PsiAngle = aminoAcidDihedralAngles.Psi,
IsFrozen = true
};
approximateAminoAcids.Add(approximateAminoAcid);
}
return(new ApproximatePeptide(approximateAminoAcids));
}
private void CalculateBondLengthForces(ApproximatedAminoAcid previousAminoAcid, ApproximatedAminoAcid aminoAcid,
Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces> bondForces)
{
var nitrogenCarbonBondLength = BondLengthCalculator.CalculateApproximate(ElementName.Nitrogen, ElementName.Carbon);
var carbonCarbonBondLength = BondLengthCalculator.CalculateApproximate(ElementName.Carbon, ElementName.Carbon);
var aminoAcidForces = bondForces[aminoAcid];
// Carbon - nitrogen bond
if (previousAminoAcid != null)
{
var carbonNitrogenForceVector = CalculateBondLengthForce(previousAminoAcid.CarbonPosition,
aminoAcid.NitrogenPosition,
nitrogenCarbonBondLength);
var previousAminoAcidForces = bondForces[previousAminoAcid];
previousAminoAcidForces.CarbonForce += carbonNitrogenForceVector;
aminoAcidForces.NitrogenForce += -carbonNitrogenForceVector;
}
// Nitrogen - carbon alpha bond
var nitrogenCarbonAlphaForceVector = CalculateBondLengthForce(aminoAcid.NitrogenPosition,
aminoAcid.CarbonAlphaPosition,
nitrogenCarbonBondLength);
aminoAcidForces.NitrogenForce += nitrogenCarbonAlphaForceVector;
aminoAcidForces.CarbonAlphaForce += -nitrogenCarbonAlphaForceVector;
// Carbon alpha - carbon bond
var carbonAlphaCarbonForceVector = CalculateBondLengthForce(aminoAcid.CarbonAlphaPosition,
aminoAcid.CarbonPosition,
carbonCarbonBondLength);
aminoAcidForces.CarbonAlphaForce += carbonAlphaCarbonForceVector;
aminoAcidForces.CarbonForce += -carbonAlphaCarbonForceVector;
}
private void CalculateBondAngleForces(ApproximatedAminoAcid previousAminoAcid, ApproximatedAminoAcid aminoAcid,
Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces> bondForces)
{
const double RestoreForceScaling = 1e-10;
var aminoAcidForces = bondForces[aminoAcid];
var nitrogenCarbonAlphaVector = aminoAcid.NitrogenPosition.VectorTo(aminoAcid.CarbonAlphaPosition);
if (previousAminoAcid != null)
{
var previousAminoAcidForces = bondForces[previousAminoAcid];
// Carbon alpha - carbon - nitrogen bond pair
var carbonAlphaCarbonVector = previousAminoAcid.CarbonAlphaPosition
.VectorTo(previousAminoAcid.CarbonPosition);
var carbonNitrogenVector = previousAminoAcid.CarbonPosition
.VectorTo(aminoAcid.NitrogenPosition);
var cacnAngle = 180.To(Unit.Degree) - carbonAlphaCarbonVector.AngleWith(carbonNitrogenVector);
var cacnPlaneNormal = carbonAlphaCarbonVector.CrossProduct(carbonNitrogenVector);
var cacnForceMagnitude = RestoreForceScaling *
(cacnAngle.In(Unit.Degree) - AminoAcidBondAngles.CaCNAngle.In(Unit.Degree))
.To(Unit.Newton);
var carbonAlpha1ForceDirection = -carbonAlphaCarbonVector.CrossProduct(cacnPlaneNormal).Normalize().ToVector3D();
var nitrogenForceDirection = -carbonNitrogenVector.CrossProduct(cacnPlaneNormal).Normalize().ToVector3D();
previousAminoAcidForces.CarbonAlphaForce += cacnForceMagnitude * carbonAlpha1ForceDirection;
previousAminoAcidForces.CarbonForce += -(cacnForceMagnitude * carbonAlpha1ForceDirection
+ cacnForceMagnitude * nitrogenForceDirection);
aminoAcidForces.NitrogenForce += cacnForceMagnitude * nitrogenForceDirection;
// Carbon - nitrogen - carbon alpha bond pair
var cncaAngle = 180.To(Unit.Degree) - carbonNitrogenVector.AngleWith(nitrogenCarbonAlphaVector);
var cncaPlaneNormal = carbonNitrogenVector.CrossProduct(nitrogenCarbonAlphaVector);
var cncaForceMagnitude = RestoreForceScaling *
(cncaAngle.In(Unit.Degree) - AminoAcidBondAngles.CNCaAngle.In(Unit.Degree))
.To(Unit.Newton);
var carbonForceDirection = -carbonNitrogenVector.CrossProduct(cncaPlaneNormal).Normalize().ToVector3D();
var carbonAlpha2ForceDirection = -nitrogenCarbonAlphaVector.CrossProduct(cncaPlaneNormal).Normalize().ToVector3D();
previousAminoAcidForces.CarbonForce += cncaForceMagnitude * carbonForceDirection;
aminoAcidForces.NitrogenForce += -(cncaForceMagnitude * carbonForceDirection +
cncaForceMagnitude * carbonAlpha2ForceDirection);
aminoAcidForces.CarbonAlphaForce += cncaForceMagnitude * carbonAlpha2ForceDirection;
}
// Nitrogen - carbon alpha - carbon bond pair
var carbonAlphaCarbon2Vector = aminoAcid.CarbonAlphaPosition.VectorTo(aminoAcid.CarbonPosition);
var ncacAngle = 180.To(Unit.Degree) - nitrogenCarbonAlphaVector.AngleWith(carbonAlphaCarbon2Vector);
var ncacPlaneNormal = nitrogenCarbonAlphaVector.CrossProduct(carbonAlphaCarbon2Vector);
var ncacForceMagnitude = RestoreForceScaling *
(ncacAngle.In(Unit.Degree) - AminoAcidBondAngles.NCaCAngle.In(Unit.Degree))
.To(Unit.Newton);
var nitrogenForceDirection2 = -nitrogenCarbonAlphaVector.CrossProduct(ncacPlaneNormal).Normalize().ToVector3D();
var carbonForceDirection2 = -carbonAlphaCarbon2Vector.CrossProduct(ncacPlaneNormal).Normalize().ToVector3D();
aminoAcidForces.NitrogenForce += ncacForceMagnitude * nitrogenForceDirection2;
aminoAcidForces.CarbonAlphaForce += -(ncacForceMagnitude * nitrogenForceDirection2 +
ncacForceMagnitude * carbonForceDirection2);
aminoAcidForces.CarbonForce += ncacForceMagnitude * carbonForceDirection2;
}
public static void Position(IList <ApproximatedAminoAcid> aminoAcids, UnitPoint3D startPosition)
{
ApproximatedAminoAcid lastAminoAcid = null;
foreach (var aminoAcid in aminoAcids)
{
PositionAminoAcid(aminoAcid, lastAminoAcid, startPosition);
lastAminoAcid = aminoAcid;
}
}
public ApproximateAminoAcidVertex3D(ApproximatedAminoAcid aminoAcid)
{
AminoAcid = aminoAcid;
Id = Interlocked.Increment(ref lastId);
var carbonAlphaPosition = aminoAcid.CarbonAlphaPosition.In(SIPrefix.Pico, Unit.Meter);
var x = carbonAlphaPosition.X;
var y = carbonAlphaPosition.Y;
var z = carbonAlphaPosition.Z;
Position = new[] { x, y, z };
Point = new Point3D(x, y, z);
}
private static void ApplyOmegaDeviationForce(ApproximatedAminoAcid lastAminoAcid,
ApproximatedAminoAcid aminoAcid,
AminoAcidAngles aminoAcidAngles,
Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces> forceDictionary)
{
if (lastAminoAcid == null)
{
return;
}
var omegaDeviation = aminoAcidAngles.Omega.In(Unit.Degree) < 0
? -180 - aminoAcidAngles.Omega.In(Unit.Degree)
: 180 - aminoAcidAngles.Omega.In(Unit.Degree);
if (!forceDictionary.ContainsKey(aminoAcid))
{
forceDictionary.Add(aminoAcid, new ApproximateAminoAcidForces());
}
var aminoAcidForces = forceDictionary[aminoAcid];
if (!forceDictionary.ContainsKey(lastAminoAcid))
{
forceDictionary.Add(lastAminoAcid, new ApproximateAminoAcidForces());
}
var lastAminoAcidForces = forceDictionary[lastAminoAcid];
var carbonNitrogenVector = lastAminoAcid.CarbonPosition
.VectorTo(aminoAcid.NitrogenPosition)
.In(SIPrefix.Pico, Unit.Meter);
var previousCarbonCarbonAlphaVector = lastAminoAcid.CarbonPosition
.VectorTo(lastAminoAcid.CarbonAlphaPosition)
.In(SIPrefix.Pico, Unit.Meter);
var forceMagnitude1 = forceScaling * omegaDeviation * 1.0.To(Unit.Newton);
var forceDirection1 = previousCarbonCarbonAlphaVector
.CrossProduct(carbonNitrogenVector)
.Normalize()
.ToVector3D();
lastAminoAcidForces.CarbonAlphaForce += forceMagnitude1 * forceDirection1;
var nitrogenCarbonAlphaVector = aminoAcid.NitrogenPosition
.VectorTo(aminoAcid.CarbonAlphaPosition)
.In(SIPrefix.Pico, Unit.Meter);
var forceMagnitude2 = forceScaling * omegaDeviation * 1.0.To(Unit.Newton);
var forceDirection2 = -nitrogenCarbonAlphaVector
.CrossProduct(carbonNitrogenVector)
.Normalize()
.ToVector3D();
aminoAcidForces.CarbonAlphaForce += forceMagnitude2 * forceDirection2;
}
private void RecursiveAddAndPositionNewAminoAcid(
ApproximatePeptide peptide,
Stack <AminoAcidName> aminoAcidQueue,
MultiLevelGrowingFoldingSimulatorSettings settings)
{
var aminoAcidName = aminoAcidQueue.Pop();
var lastAminoAcid = peptide.AminoAcids.LastOrDefault();
var lastPosition = lastAminoAcid?.CarbonAlphaPosition ?? new UnitPoint3D(Unit.Meter, 0, 0, 0);
var influencingAminoAcids = peptide.AminoAcids
.Where(x => x.CarbonAlphaPosition.DistanceTo(lastPosition) < settings.InfluenceHorizont)
.ToList();
var ramachandranPlot = ramachandranPlotSource.Get(aminoAcidName);
var sequenceNumber = lastAminoAcid?.SequenceNumber + 1 ?? 0;
var isTimeForSecondaryStructureFolding =
sequenceNumber % settings.SecondaryStructureFoldingFrequency == 0;
if (isTimeForSecondaryStructureFolding)
{
FoldSecondaryStructure(peptide);
}
var remainingPositionAttempts = settings.PositioningAttempts;
do
{
try
{
var aminoAcid = new ApproximatedAminoAcid(aminoAcidName, sequenceNumber);
PositionAminoAcid(aminoAcid, lastAminoAcid, ramachandranPlot, influencingAminoAcids, settings);
peptide.Add(aminoAcid);
RecursiveAddAndPositionNewAminoAcid(peptide, aminoAcidQueue, settings);
return;
}
catch (AminoAcidCannotBePositionedException)
{
remainingPositionAttempts--;
}
} while (remainingPositionAttempts > 0);
aminoAcidQueue.Push(aminoAcidName);
throw new AminoAcidCannotBePositionedException(aminoAcidName, sequenceNumber);
}
private void ApplyForce(ApproximatedAminoAcid aminoAcid,
ApproximateAminoAcidForces resultingForces,
UnitValue timeStepSize,
UnitValue reservoirTemperature)
{
var scaling = 1e0;
var nitrogenForce = scaling * resultingForces.NitrogenForce;
var nitrogenMass = PeriodicTable.GetSingleAtomMass(ElementName.Nitrogen);
var nitrogenAcceleration = nitrogenForce / nitrogenMass;
var nitrogenVelocityChange = nitrogenAcceleration * timeStepSize;
aminoAcid.NitrogenVelocity += nitrogenVelocityChange;
aminoAcid.NitrogenVelocity = InteractWithReservoir(aminoAcid.NitrogenVelocity, nitrogenMass, reservoirTemperature);
aminoAcid.NitrogenPosition += aminoAcid.NitrogenVelocity * timeStepSize;
if (simulationSettings.ResetAtomVelocityAfterEachTimestep)
{
aminoAcid.NitrogenVelocity = new UnitVector3D(Unit.MetersPerSecond, 0, 0, 0);
}
var carbonAlphaForce = scaling * resultingForces.CarbonAlphaForce;
var carbonAlphaMass = PeriodicTable.GetSingleAtomMass(ElementName.Carbon) + AminoAcidSideChainMassLookup.SideChainMasses[aminoAcid.Name];
var carbonAlphaAcceleration = carbonAlphaForce / carbonAlphaMass;
var carbonAlphaVelocityChange = carbonAlphaAcceleration * timeStepSize;
aminoAcid.CarbonAlphaVelocity += carbonAlphaVelocityChange;
aminoAcid.CarbonAlphaVelocity = InteractWithReservoir(aminoAcid.CarbonAlphaVelocity, carbonAlphaMass, reservoirTemperature);
aminoAcid.CarbonAlphaPosition += aminoAcid.CarbonAlphaVelocity * timeStepSize;
if (simulationSettings.ResetAtomVelocityAfterEachTimestep)
{
aminoAcid.CarbonAlphaVelocity = new UnitVector3D(Unit.MetersPerSecond, 0, 0, 0);
}
var carbonForce = scaling * resultingForces.CarbonForce;
var carbonMass = PeriodicTable.GetSingleAtomMass(ElementName.Carbon);
var carbonAcceleration = carbonForce / carbonMass;
var carbonVelocityChange = carbonAcceleration * timeStepSize;
aminoAcid.CarbonVelocity += carbonVelocityChange;
aminoAcid.CarbonVelocity = InteractWithReservoir(aminoAcid.CarbonVelocity, carbonMass, reservoirTemperature);
aminoAcid.CarbonPosition += aminoAcid.CarbonVelocity * timeStepSize;
if (simulationSettings.ResetAtomVelocityAfterEachTimestep)
{
aminoAcid.CarbonVelocity = new UnitVector3D(Unit.MetersPerSecond, 0, 0, 0);
}
}
private void ApplyPsiDeviationForce(ApproximatedAminoAcid aminoAcid,
ApproximatedAminoAcid nextAminoAcid,
Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces> forceDictionary,
double psiDeviation)
{
var carbonAlphaCarbonVector = aminoAcid.CarbonAlphaPosition
.VectorTo(aminoAcid.CarbonPosition)
.In(SIPrefix.Pico, Unit.Meter);
if (!forceDictionary.ContainsKey(aminoAcid))
{
forceDictionary.Add(aminoAcid, new ApproximateAminoAcidForces());
}
var aminoAcidForces = forceDictionary[aminoAcid];
var carbonAlphaNitrogenVector = aminoAcid.CarbonAlphaPosition
.VectorTo(aminoAcid.NitrogenPosition)
.In(SIPrefix.Pico, Unit.Meter);
var forceMagnitude1 = -forceScaling * psiDeviation * 1.0.To(Unit.Newton);
var forceDirection1 = carbonAlphaCarbonVector
.CrossProduct(carbonAlphaNitrogenVector)
.Normalize()
.ToVector3D();
aminoAcidForces.NitrogenForce += forceMagnitude1 * forceDirection1;
if (nextAminoAcid != null) // Should be redundant, because psi is undefined if no next amino acid
{
if (!forceDictionary.ContainsKey(nextAminoAcid))
{
forceDictionary.Add(nextAminoAcid, new ApproximateAminoAcidForces());
}
var nextAminoAcidForces = forceDictionary[nextAminoAcid];
var carbonNitrogenVector = aminoAcid.CarbonPosition
.VectorTo(nextAminoAcid.NitrogenPosition)
.In(SIPrefix.Pico, Unit.Meter);
var forceMagnitude2 = forceScaling * psiDeviation * 1.0.To(Unit.Newton);
var forceDirection2 = carbonAlphaCarbonVector
.CrossProduct(carbonNitrogenVector)
.Normalize()
.ToVector3D();
nextAminoAcidForces.NitrogenForce += forceMagnitude2 * forceDirection2;
}
}
private void PositionAminoAcid(
ApproximatedAminoAcid aminoAcid,
ApproximatedAminoAcid lastAminoAcid,
RamachandranPlot ramachandranPlot,
List <ApproximatedAminoAcid> influencingAminoAcids,
MultiLevelGrowingFoldingSimulatorSettings settings)
{
var influencingCenter = CalculateCenter(influencingAminoAcids);
var positionAttempt = 1;
do
{
var aminoAcidAngles = ramachandranPlot.GetRandomPhiPsi();
aminoAcid.OmegaAngle = aminoAcidAngles.Omega;
aminoAcid.PhiAngle = aminoAcidAngles.Phi;
aminoAcid.PsiAngle = aminoAcidAngles.Psi;
ApproximateAminoAcidPositioner.PositionAminoAcid(aminoAcid, lastAminoAcid, new UnitPoint3D(Unit.Meter, 0, 0, 0));
// Note: Clashing distance was determined using MultiLevelGrowingFoldingSimulatorStudy.MeasureAverageAminoAcidDistance
var isClashingWithAnyInfluencingAminoAcid = influencingAminoAcids
.Any(otherAminoAcid => otherAminoAcid.CarbonAlphaPosition.DistanceTo(aminoAcid.CarbonAlphaPosition).In(SIPrefix.Nano, Unit.Meter) < 1.0);
if (isClashingWithAnyInfluencingAminoAcid)
{
positionAttempt++;
continue;
}
if (lastAminoAcid != null && influencingAminoAcids.Count > 0)
{
var isTooFarAway = aminoAcid.CarbonAlphaPosition.DistanceTo(influencingCenter) > lastAminoAcid.CarbonAlphaPosition.DistanceTo(influencingCenter) &&
aminoAcid.CarbonAlphaPosition.DistanceTo(influencingCenter) > 0.8 * settings.InfluenceHorizont;
if (isTooFarAway)
{
positionAttempt++;
continue;
}
}
return;
} while (positionAttempt < settings.PositioningAttempts);
throw new AminoAcidCannotBePositionedException(aminoAcid.Name, aminoAcid.SequenceNumber);
}
public void AminoAcidPositioningTest()
{
var aminoAcid1 = new ApproximatedAminoAcid(AminoAcidName.Glycine, 1)
{
OmegaAngle = 0.To(Unit.Degree),
PhiAngle = 0.To(Unit.Degree),
PsiAngle = -120.To(Unit.Degree)
};
var aminoAcid2 = new ApproximatedAminoAcid(AminoAcidName.Glycine, 2)
{
OmegaAngle = 10.To(Unit.Degree),
PhiAngle = -70.To(Unit.Degree),
PsiAngle = 0.To(Unit.Degree)
};
var peptide = new ApproximatePeptide(new [] { aminoAcid1, aminoAcid2 });
var angles = AminoAcidAngleMeasurer.MeasureAngles(peptide);
var aminoAcid1Angles = angles[aminoAcid1];
var aminoAcid2Angles = angles[aminoAcid2];
Assert.That(aminoAcid1Angles.Psi.In(Unit.Radians), Is.EqualTo(aminoAcid1.PsiAngle.In(Unit.Radians)).Within(1e-9));
Assert.That(aminoAcid2Angles.Omega.In(Unit.Radians), Is.EqualTo(aminoAcid2.OmegaAngle.In(Unit.Radians)).Within(1e-9));
Assert.That(aminoAcid2Angles.Phi.In(Unit.Radians), Is.EqualTo(aminoAcid2.PhiAngle.In(Unit.Radians)).Within(1e-9));
}
public void CarbonAlphaDistancesMatchRealMeasurements()
{
var aminoAcid1 = new ApproximatedAminoAcid(AminoAcidName.Valine, 90)
{
OmegaAngle = 179.9.To(Unit.Degree),
PhiAngle = -35.9.To(Unit.Degree),
PsiAngle = -52.0.To(Unit.Degree)
};
var aminoAcid2 = new ApproximatedAminoAcid(AminoAcidName.Alanine, 91)
{
OmegaAngle = 179.9.To(Unit.Degree),
PhiAngle = -63.5.To(Unit.Degree),
PsiAngle = -59.7.To(Unit.Degree)
};
var peptide = new[] { aminoAcid1, aminoAcid2 };
ApproximateAminoAcidPositioner.Position(peptide, new UnitPoint3D(Unit.Meter, 0, 0, 0));
var carbonAlphaCarbonDistance = aminoAcid1.CarbonAlphaPosition
.DistanceTo(aminoAcid1.CarbonPosition);
Assert.That(carbonAlphaCarbonDistance.In(SIPrefix.Pico, Unit.Meter), Is.EqualTo(154).Within(0.1));
var carbonNitrogenDistance = aminoAcid1.CarbonPosition
.DistanceTo(aminoAcid2.NitrogenPosition);
Assert.That(carbonNitrogenDistance.In(SIPrefix.Pico, Unit.Meter), Is.EqualTo(152).Within(0.1));
var aminoAcidAngles = AminoAcidAngleMeasurer.MeasureAngles(new ApproximatePeptide(peptide));
Assert.That(aminoAcidAngles[aminoAcid1].Psi.Value - aminoAcid1.PsiAngle.Value, Is.EqualTo(0).Within(0.1));
Assert.That(aminoAcidAngles[aminoAcid2].Phi.Value - aminoAcid2.PhiAngle.Value, Is.EqualTo(0).Within(0.1));
// The bond length vary because we use theoretical bond length, which do not exactly match real bond lengths
//Assert.That(
// aminoAcid1.CarbonAlphaPosition.DistanceTo(aminoAcid2.CarbonAlphaPosition).In(SIPrefix.Pico, Unit.Meter),
// Is.EqualTo(380.3).Within(0.1));
}
public void AtomPositionsAsExpected()
{
var aminoAcid1 = new ApproximatedAminoAcid(AminoAcidName.Valine, 90)
{
OmegaAngle = 45.To(Unit.Degree),
PhiAngle = -60.To(Unit.Degree),
PsiAngle = 90.To(Unit.Degree)
};
var aminoAcid2 = new ApproximatedAminoAcid(AminoAcidName.Alanine, 91)
{
OmegaAngle = 0.To(Unit.Degree),
PhiAngle = -90.To(Unit.Degree),
PsiAngle = 90.To(Unit.Degree)
};
var peptide = new ApproximatePeptide(new[] { aminoAcid1, aminoAcid2 });
ApproximateAminoAcidPositioner.Position(peptide.AminoAcids, new UnitPoint3D(Unit.Meter, 0, 0, 0));
var angles = AminoAcidAngleMeasurer.MeasureAngles(peptide);
Assert.That(angles[aminoAcid1].Psi.In(Unit.Degree), Is.EqualTo(aminoAcid1.PsiAngle.In(Unit.Degree)).Within(1));
Assert.That(angles[aminoAcid2].Omega.In(Unit.Degree), Is.EqualTo(aminoAcid2.OmegaAngle.In(Unit.Degree)).Within(1));
Assert.That(angles[aminoAcid2].Phi.In(Unit.Degree), Is.EqualTo(aminoAcid2.PhiAngle.In(Unit.Degree)).Within(1));
//Assert.That(
// aminoAcid1.NitrogenPosition.DistanceTo(new UnitPoint3D(Unit.Meter, 0, 0, 0)).In(SIPrefix.Pico, Unit.Meter),
// Is.EqualTo(0).Within(1e-3));
//Assert.That(
// aminoAcid1.CarbonAlphaPosition.DistanceTo(new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 152, 0, 0)).In(SIPrefix.Pico, Unit.Meter),
// Is.EqualTo(0).Within(1e-3));
//Assert.That(
// aminoAcid1.CarbonPosition.DistanceTo(new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 152, 154, 0)).In(SIPrefix.Pico, Unit.Meter),
// Is.EqualTo(0).Within(1e-3));
//Assert.That(
// aminoAcid2.NitrogenPosition.DistanceTo(new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 152, 154, 152)).In(SIPrefix.Pico, Unit.Meter),
// Is.EqualTo(0).Within(1e-3));
}
public static void PositionAminoAcid(ApproximatedAminoAcid aminoAcid,
ApproximatedAminoAcid lastAminoAcid = null,
UnitPoint3D startPosition = null)
{
if (lastAminoAcid == null && startPosition == null)
{
throw new ArgumentNullException("Either last amino acid or start position must be non-null");
}
var nitrogenCarbonDistance = PeriodicTable.GetCovalentRadius(ElementName.Nitrogen) +
PeriodicTable.GetCovalentRadius(ElementName.Carbon);
var CaCDistance = 2 * PeriodicTable.GetCovalentRadius(ElementName.Carbon);
UnitPoint3D carbonPosition;
UnitPoint3D carbonAlphaPosition;
Vector3D carbonAlphaCarbonBondDirection;
Vector3D nitrogenCarbonAlphaBondDirection;
if (lastAminoAcid == null)
{
carbonPosition = startPosition;
carbonAlphaPosition = startPosition + new UnitPoint3D(SIPrefix.Pico, Unit.Meter, -CaCDistance.In(SIPrefix.Pico, Unit.Meter), 0, 0);
carbonAlphaCarbonBondDirection = carbonAlphaPosition.VectorTo(carbonPosition);
nitrogenCarbonAlphaBondDirection = new Vector3D(0, 1, 0);
}
else
{
carbonPosition = lastAminoAcid.CarbonPosition;
carbonAlphaPosition = lastAminoAcid.CarbonAlphaPosition;
carbonAlphaCarbonBondDirection = carbonAlphaPosition
.VectorTo(carbonPosition);
nitrogenCarbonAlphaBondDirection = lastAminoAcid.NitrogenPosition
.VectorTo(carbonAlphaPosition);
}
var omega = aminoAcid.OmegaAngle ?? Math.PI.To(Unit.Radians);
var phi = aminoAcid.PhiAngle ?? 0.To(Unit.Radians);
var psi = lastAminoAcid?.PsiAngle ?? 0.To(Unit.Radians);
var nitrogenPosition = CalculateAtomPosition(carbonPosition,
carbonAlphaCarbonBondDirection,
nitrogenCarbonAlphaBondDirection,
nitrogenCarbonDistance,
AminoAcidBondAngles.CaCNAngle,
psi);
carbonAlphaPosition = CalculateAtomPosition(nitrogenPosition,
carbonPosition.VectorTo(nitrogenPosition),
carbonAlphaCarbonBondDirection,
nitrogenCarbonDistance,
AminoAcidBondAngles.CNCaAngle,
omega);
carbonPosition = CalculateAtomPosition(carbonAlphaPosition,
nitrogenPosition.VectorTo(carbonAlphaPosition),
carbonPosition.VectorTo(nitrogenPosition),
CaCDistance,
AminoAcidBondAngles.NCaCAngle,
phi);
aminoAcid.NitrogenPosition = nitrogenPosition;
aminoAcid.CarbonAlphaPosition = carbonAlphaPosition;
aminoAcid.CarbonPosition = carbonPosition;
if (aminoAcid.OmegaAngle == null)
{
aminoAcid.OmegaAngle = omega;
}
if (aminoAcid.PhiAngle == null)
{
aminoAcid.PhiAngle = phi;
}
if (lastAminoAcid != null && lastAminoAcid.PsiAngle == null)
{
lastAminoAcid.PsiAngle = psi;
}
}
