public void GeneratePdbForPeptide()
{
var peptide = PeptideBuilder.PeptideFromString(
"MQRSPLEKASVVSKLFFSWTRPILRKGYRQRLELSDIYQIPSVDSADNLSEKLEREWDRE"
+ "LASKKNPKLINALRRCFFWRFMFYGIFLYLGEVTKAVQPLLLGRIIASYDPDNKEERSIA"
+ "IYLGIGLCLLFIVRTLLLHPAIFGLHHIGMQMRIAMFSLIYKKTLKLSSRVLDKISIGQL"
+ "VSLLSNNLNKFDEGLALAHFVWIAPLQVALLMGLIWELLQASAFCGLGFLIVLALFQAGL"
+ "GRMMMKYRDQRAGKISERLVITSEMIENIQSVKAYCWEEAMEKMIENLRQTELKLTRKAA"
+ "YVRYFNSSAFFFSGFFVVFLSVLPYALIKGIILRKIFTTISFCIVLRMAVTRQFPWAVQT"
+ "WYDSLGAINKIQDFLQKQEYKTLEYNLTTTEVVMENVTAFWEEGFGELFEKAKQNNNNRK"
+ "TSNGDDSLFFSNFSLLGTPVLKDINFKIERGQLLAVAGSTGAGKTSLLMVIMGELEPSEG"
+ "KIKHSGRISFCSQFSWIMPGTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIV"
+ "LGEGGITLSGGQRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTR"
+ "ILVTSKMEHLKKADKILILHEGSSYFYGTFSELQNLQPDFSSKLMGCDSFDQFSAERRNS"
+ "ILTETLHRFSLEGDAPVSWTETKKQSFKQTGEFGEKRKNSILNPINSIRKFSIVQKTPLQ"
+ "MNGIEEDSDEPLERRLSLVPDSEQGEAILPRISVISTGPTLQARRRQSVLNLMTHSVNQG"
+ "QNIHRKTTASTRKVSLAPQANLTELDIYSRRLSQETGLEISEEINEEDLKECFFDDMESI"
+ "PAVTTWNTYLRYITVHKSLIFVLIWCLVIFLAEVAASLVVLWLLGNTPLQDKGNSTHSRN"
+ "NSYAVIITSTSSYYVFYIYVGVADTLLAMGFFRGLPLVHTLITVSKILHHKMLHSVLQAP"
+ "MSTLNTLKAGGILNRFSKDIAILDDLLPLTIFDFIQLLLIVIGAIAVVAVLQPYIFVATV"
+ "PVIVAFIMLRAYFLQTSQQLKQLESEGRSPIFTHLVTSLKGLWTLRAFGRQPYFETLFHK"
+ "ALNLHTANWFLYLSTLRWFQMRIEMIFVIFFIAVTFISILTTGEGEGRVGIILTLAMNIM"
+ "STLQWAVNSSIDVDSLMRSVSRVFKFIDMPTEGKPTKSTKPYKNGQLSKVMIIENSHVKK"
+ "DDIWPSGGQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRL"
+ "LNTEGEIQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLDPYEQWSDQEIWKVAD"
+ "EVGLRSVIEQFPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPVT"
+ "YQIIRRTLKQAFADCTVILCEHRIEAMLECQQFLVIEENKVRQYDSIQKLLNERSLFRQA"
+ "ISPSDRVKLFPHRNSSKCKSKPQIAALKEETEEEVQDTRL");
peptide.Molecule.PositionAtoms(peptide.MoleculeReference.FirstAtomId, peptide.MoleculeReference.LastAtomId);
File.WriteAllText(@"G:\Projects\HumanGenome\cftr.pdb", PdbSerializer.Serialize("cftr", peptide));
}
private static Peptide ExtractChain(
IList <string> modelLines,
IList <string> annotationLines,
char chainId,
PdbReaderOptions options)
{
var aminoAcidSequence = ExtractSequence(modelLines, chainId);
if (!aminoAcidSequence.Any())
{
return(new Peptide(new MoleculeReference(new Molecule()), new List <AminoAcidReference>()));
}
var peptide = PeptideBuilder.PeptideFromSequence(aminoAcidSequence, new PeptideBuilderOptions {
BuildMolecule = options.BuildMolecule
});
peptide.ChainId = chainId;
var annotations = ExtractAnnotations(annotationLines, chainId, peptide);
peptide.Annotations.AddRange(annotations);
if (options.BuildMolecule)
{
ReadAtomPositions(modelLines, chainId, peptide);
}
return(peptide);
}
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));
}
public void RunSimulation()
{
var molecule = PeptideBuilder.PeptideFromSequence(new[]
{
AminoAcidName.Proline,
AminoAcidName.Tyrosine,
AminoAcidName.Alanine,
AminoAcidName.Glutamine,
AminoAcidName.Glutamine,
AminoAcidName.Lysine
}).Molecule;
var customForces = new List <CustomAtomForce>();
var settings = new MoleculeDynamicsSimulationSettings
{
SimulationTime = 10.To(SIPrefix.Nano, Unit.Second),
TimeStep = 4.To(SIPrefix.Femto, Unit.Second)
};
var simulator = new MoleculeDynamicsSimulator(molecule, customForces, settings);
simulator.SimulationCompleted += Simulator_SimulationCompleted;
simulationCompletedEvent.Reset();
simulator.StartSimulation();
simulationCompletedEvent.WaitOne();
}
public static Peptide ReadFile(string filename)
{
var aminoAcidSequence = File.ReadAllLines(filename).Aggregate((a, b) => a + b);
return(PeptideBuilder.PeptideFromString(aminoAcidSequence));
}