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 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();
}