public static ApproximatePeptideFoldingSimulator Create(ApproximatePeptide peptide,
ApproximatePeptideSimulationSettings simulationSettings,
string ramachadranDataDirectory)
{
var compactnessForceCalculator = new CompactingForceCalculator();
var ramachandranPlotDistributionSource = new RamachandranPlotGradientDistributionFileSource(ramachadranDataDirectory);
var ramachadranForceCalculator = new RamachandranForceCalculator(ramachandranPlotDistributionSource);
var bondForceCalculator = new BondForceCalculator();
return(new ApproximatePeptideFoldingSimulator(peptide,
simulationSettings,
compactnessForceCalculator,
ramachadranForceCalculator,
bondForceCalculator));
}
public ApproximatePeptideFoldingSimulator(ApproximatePeptide peptide,
ApproximatePeptideSimulationSettings simulationSettings,
CompactingForceCalculator compactnessForceCalculator,
RamachandranForceCalculator ramachandranForceCalculator,
BondForceCalculator bondForceCalculator)
{
this.simulationSettings = simulationSettings;
this.compactnessForceCalculator = compactnessForceCalculator;
this.ramachandranForceCalculator = ramachandranForceCalculator;
this.bondForceCalculator = bondForceCalculator;
Peptide = peptide;
if (peptide.AminoAcids.Count <= 3)
{
simulationSettings.UseCompactingForce = false; // Cannot be done
}
}
