public Peptide GetFullPeptide()
{
var aminoAcids = new List <AminoAcidReference>();
foreach (var approximatedAminoAcid in approximatePeptide.AminoAcids)
{
var aminoAcid = AminoAcidLibrary.Get(approximatedAminoAcid.Name, approximatedAminoAcid.SequenceNumber);
PdbAminoAcidAtomNamer.AssignNames(aminoAcid);
var nitrogen = aminoAcid.GetAtomFromName("N");
nitrogen.Position = approximatedAminoAcid.NitrogenPosition;
nitrogen.IsPositionFixed = true;
var carbonAlpha = aminoAcid.GetAtomFromName("CA");
carbonAlpha.Position = approximatedAminoAcid.CarbonAlphaPosition;
carbonAlpha.IsPositionFixed = true;
var carbon = aminoAcid.GetAtomFromName("C");
carbon.Position = approximatedAminoAcid.CarbonPosition;
carbon.IsPositionFixed = true;
aminoAcid.Molecule.PositionAtoms();
aminoAcids.Add(aminoAcid);
}
var peptide = PeptideBuilder.PeptideFromAminoAcids(aminoAcids);
peptide.Molecule.PositionAtoms();
return(peptide);
}
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));
}
public void ProlineNamedCorrectly()
{
var aminoAcidReference = AminoAcidLibrary.Proline(1);
PdbAminoAcidAtomNamer.AssignNames(aminoAcidReference);
var moleculeStructure = aminoAcidReference.Molecule.MoleculeStructure;
var nitrogen = moleculeStructure.GetVertexFromId(aminoAcidReference.FirstAtomId).Object;
Assume.That(nitrogen.Element, Is.EqualTo(ElementName.Nitrogen));
Assert.That(nitrogen.AminoAcidAtomName, Is.EqualTo("N"));
var carbonEnd = moleculeStructure.GetVertexFromId(aminoAcidReference.LastAtomId).Object;
Assume.That(carbonEnd.Element, Is.EqualTo(ElementName.Carbon));
Assert.That(carbonEnd.AminoAcidAtomName, Is.EqualTo("C"));
var remainingNonHydrogenAtoms = moleculeStructure.Vertices
.Select(v => v.Object)
.Where(atom => atom.Element != ElementName.Hydrogen)
.Except(new[] { nitrogen, carbonEnd })
.ToList();
Assert.That(remainingNonHydrogenAtoms.Count, Is.EqualTo(5));
var oxygen = remainingNonHydrogenAtoms.Single(atom => atom.Element == ElementName.Oxygen);
Assert.That(oxygen.AminoAcidAtomName, Is.EqualTo("O"));
var sideChainCarbons = remainingNonHydrogenAtoms.Where(atom => atom.Element == ElementName.Carbon).ToList();
Assert.That(sideChainCarbons.Count, Is.EqualTo(4));
Assert.That(sideChainCarbons.Select(atom => atom.AminoAcidAtomName), Is.EquivalentTo(new[] { "CA", "CB", "CG", "CD" }));
}
private static string SerializeAtoms(Peptide peptide)
{
var output = "";
var atomIdx = 1;
var chainId = 'A';
var aminoAcids = peptide.AminoAcids;
for (int residueIdx = 0; residueIdx < aminoAcids.Count; residueIdx++)
{
var aminoAcid = aminoAcids[residueIdx];
PdbAminoAcidAtomNamer.AssignNames(aminoAcid);
var aminoAcidVertices = aminoAcid.VertexIds
.Select(vId => aminoAcid.Molecule.MoleculeStructure.GetVertexFromId(vId));
var residueName = aminoAcid.Name.ToThreeLetterCode();
var sequenceNumber = aminoAcid.SequenceNumber;
foreach (var vertex in aminoAcidVertices)
{
var atom = aminoAcid.Molecule.GetAtom(vertex.Id);
if (atom.Element == ElementName.Hydrogen)
{
continue;
}
if (atom.Position == null)
{
continue;
}
var atomName = atom.AminoAcidAtomName ?? atom.Element.ToElementSymbol().ToString();
var x = (1e10 * atom.Position.X).ToString("F3");
var y = (1e10 * atom.Position.Y).ToString("F3");
var z = (1e10 * atom.Position.Z).ToString("F3");
var occupancy = 1.0.ToString("F2");
var temperatureFactor = 0.0.ToString("F2");
var elementSymbol = atom.Element.ToElementSymbol();
var charge = "";
if (atomIdx > 1)
{
output += Environment.NewLine;
}
output += $"ATOM {atomIdx,5} {atomName,4} {residueName,3} {chainId}{sequenceNumber,4} " +
$"{x,8}{y,8}{z,8}{occupancy,6}{temperatureFactor,6} " +
$"{elementSymbol,2}{charge,2}";
atomIdx++;
}
}
output += Environment.NewLine;
output += $"TER {atomIdx,5} {aminoAcids.Last().Name.ToThreeLetterCode()} {chainId}{aminoAcids.Count-1,4}".PadRight(80);
return(output);
}
public void Psi90PlusMeasuredCorrectly()
{
var peptide = PeptideBuilder.PeptideFromString("GG");
var firstAminoAcid = peptide.AminoAcids.First();
var lastAminoAcid = peptide.AminoAcids.Last();
PdbAminoAcidAtomNamer.AssignNames(firstAminoAcid);
PdbAminoAcidAtomNamer.AssignNames(lastAminoAcid);
var N1 = firstAminoAcid.GetAtomFromName("N");
var Ca1 = firstAminoAcid.GetAtomFromName("CA");
var C1 = firstAminoAcid.GetAtomFromName("C");
var N2 = lastAminoAcid.GetAtomFromName("N");
var Ca2 = lastAminoAcid.GetAtomFromName("CA");
var C2 = lastAminoAcid.GetAtomFromName("C");
N1.Position = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 0, 0, 0);
N1.IsPositionFixed = true;
Ca1.Position = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 100, 0, 0);
Ca1.IsPositionFixed = true;
C1.Position = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 100, 100, 0);
C1.IsPositionFixed = true;
N2.Position = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 100, 100, 100);
N2.IsPositionFixed = true;
Ca2.Position = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 200, 100, 100);
Ca2.IsPositionFixed = true;
C2.Position = new UnitPoint3D(SIPrefix.Pico, Unit.Meter, 200, 200, 100);
C2.IsPositionFixed = true;
var measurements = AminoAcidAngleMeasurer.MeasureAngles(peptide);
Assert.That(measurements.ContainsKey(firstAminoAcid));
Assert.That(measurements.ContainsKey(lastAminoAcid));
var firstAngles = measurements[firstAminoAcid];
var lastAngles = measurements[lastAminoAcid];
Assert.That(firstAngles.Omega, Is.Null);
Assert.That(firstAngles.Phi, Is.Null);
Assert.That(firstAngles.Psi, Is.Not.Null);
Assert.That(firstAngles.Psi.In(Unit.Degree), Is.EqualTo(90));
Assert.That(lastAngles.Omega, Is.Not.Null);
Assert.That(lastAngles.Omega.In(Unit.Degree), Is.EqualTo(90));
}
private static void ReadAtomPositions(IList <string> lines, char chainId, Peptide peptide)
{
var aminoAcidAtomGroups = lines
.Where(line => ReadLineCode(line) == "ATOM")
.Select(ParseAtomLine)
.Where(atom => atom.ChainId == chainId)
.Where(atom => atom.AlternateConformationId == ' ' || atom.AlternateConformationId == 'A')
.Where(atom => !atom.IsAlternative)
.GroupBy(atom => atom.ResidueNumber);
foreach (var aminoAcidAtomInfos in aminoAcidAtomGroups)
{
if (aminoAcidAtomInfos.Key < peptide.AminoAcids.First().SequenceNumber) // TODO: Log warning
{
continue;
}
if (aminoAcidAtomInfos.Key > peptide.AminoAcids.Last().SequenceNumber) // TODO: Log warning
{
continue;
}
var residueNumber = aminoAcidAtomInfos.Key;
var aminoAcid = peptide.AminoAcids.SingleOrDefault(aa => aa.SequenceNumber == residueNumber);
if (aminoAcid == null) // TODO: Log warning
{
continue;
}
PdbAminoAcidAtomNamer.AssignNames(aminoAcid);
foreach (var atomInfo in aminoAcidAtomInfos)
{
var correspondingAtom = aminoAcid.GetAtomFromName(atomInfo.Name);
if (correspondingAtom == null)
{
continue;
}
correspondingAtom.Position = new UnitPoint3D(SIPrefix.Pico, Unit.Meter,
100 * atomInfo.X,
100 * atomInfo.Y,
100 * atomInfo.Z);
correspondingAtom.IsPositioned = true;
correspondingAtom.IsPositionFixed = true;
}
}
}
public static Dictionary <AminoAcidReference, AminoAcidAngles> MeasureAngles(Peptide peptide)
{
var measurements = new Dictionary <AminoAcidReference, AminoAcidAngles>();
AminoAcidAngles lastAngles = null;
UnitPoint3D lastNitrogenPosition = null;
UnitPoint3D lastCarbonAlphaPosition = null;
UnitPoint3D lastCarbonPosition = null;
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 nitrogenPosition = nitrogen != null && nitrogen.IsPositionFixed
? nitrogen.Position
: null;
var carbonAlphaPosition = carbonAlpha != null && carbonAlpha.IsPositionFixed
? carbonAlpha.Position
: null;
var carbonPosition = carbon != null && carbon.IsPositionFixed
? carbon.Position
: null;
if (lastAngles != null &&
lastNitrogenPosition != null &&
lastCarbonAlphaPosition != null &&
lastCarbonPosition != null &&
nitrogenPosition != null)
{
var psi = DihedralAngleCalculator.Calculate(
lastNitrogenPosition,
lastCarbonAlphaPosition,
lastCarbonPosition,
nitrogenPosition);
lastAngles.Psi = psi;
}
UnitValue omega = null;
if (lastCarbonAlphaPosition != null &&
lastCarbonPosition != null &&
nitrogenPosition != null &&
carbonAlphaPosition != null)
{
omega = DihedralAngleCalculator.Calculate(
lastCarbonAlphaPosition,
lastCarbonPosition,
nitrogenPosition,
carbonAlphaPosition);
}
UnitValue phi = null;
if (lastCarbonPosition != null &&
nitrogenPosition != null &&
carbonAlphaPosition != null &&
carbonPosition != null)
{
phi = DihedralAngleCalculator.Calculate(
lastCarbonPosition,
nitrogenPosition,
carbonAlphaPosition,
carbonPosition);
}
var angles = new AminoAcidAngles
{
Omega = omega,
Phi = phi
};
measurements.Add(aminoAcid, angles);
lastNitrogenPosition = nitrogenPosition;
lastCarbonAlphaPosition = carbonAlphaPosition;
lastCarbonPosition = carbonPosition;
lastAngles = angles;
}
return(measurements);
}