Package ffx.algorithms.optimize

Class ConformationScan

java.lang.Object

ffx.algorithms.optimize.ConformationScan

public class ConformationScan
extends Object

This class is for a configuration optimization of two small systems. The search consists of aligning heavy (except carbon) and hydrogen atoms at a h-bond distance with their center of masses behind them all on the z-axis in hopes that a global conformational minima will be found by allowing for strong h-bonds to occur. After aligning, an optional static torsion scan and NONE,DIRECT,MUTUAL minimizations are performed. A binding energy can be calculated with this by: ddEbind = dEbind (of two systems) - dEbind (of one system w/ itself) - dEbind (of the other system w/ itself)

Constructor Summary

Constructors

Constructor	Description
ConformationScan(MolecularAssembly molecularAssembly, Molecule[] systemOne, Molecule[] systemTwo, double minimizeEps, int minimizeMaxIterations, boolean staticTorsionScan, boolean excludeExtraHydrogen, boolean minimize)

Method Summary

Modifier and Type	Method	Description
double	getAverageEnergy()
double	getAverageEnergyNoOutlier()
ArrayList<Double>	getEnergies()
ArrayList<Double>	getEnergiesWithinEnergy(double energy)
double	getM1MinEnergy()
double	getM2MinEnergy()
double	getMinimumEnergy()
ArrayList<AssemblyState>	getStates()
ArrayList<AssemblyState>	getStatesAroundAverage(double averageE, double radialCutoff)
ArrayList<AssemblyState>	getStatesFilteredByRMSD(double rmsdCutoff)
ArrayList<AssemblyState>	getStatesWithinEnergy(double energy)
double	getStdOfEnergies()
double	getStdOfEnergiesNoOutlier()
double	getTotalMonomerMinimizedEnergy()
void	logAllEnergyInformation()
static ArrayList<Double>	logBindingEnergyCalculation(ConformationScan m1, ConformationScan m2, ConformationScan dimer)
void	scan()
boolean	writeStructuresToXYZ(File outputFile)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ConformationScan

public ConformationScan(MolecularAssembly molecularAssembly,
 Molecule[] systemOne,
 Molecule[] systemTwo,
 double minimizeEps,
 int minimizeMaxIterations,
 boolean staticTorsionScan,
 boolean excludeExtraHydrogen,
 boolean minimize)

Method Details

scan

public void scan()

logAllEnergyInformation

public void logAllEnergyInformation()

writeStructuresToXYZ

public boolean writeStructuresToXYZ(File outputFile)

logBindingEnergyCalculation

public static ArrayList<Double> logBindingEnergyCalculation(ConformationScan m1,
 ConformationScan m2,
 ConformationScan dimer)

getStates

public ArrayList<AssemblyState> getStates()

getStatesWithinEnergy

public ArrayList<AssemblyState> getStatesWithinEnergy(double energy)

getStatesFilteredByRMSD

public ArrayList<AssemblyState> getStatesFilteredByRMSD(double rmsdCutoff)

getStatesAroundAverage

public ArrayList<AssemblyState> getStatesAroundAverage(double averageE,
 double radialCutoff)

getEnergies

public ArrayList<Double> getEnergies()

getEnergiesWithinEnergy

public ArrayList<Double> getEnergiesWithinEnergy(double energy)

getM1MinEnergy

public double getM1MinEnergy()

getM2MinEnergy

public double getM2MinEnergy()

getTotalMonomerMinimizedEnergy

public double getTotalMonomerMinimizedEnergy()

getMinimumEnergy

public double getMinimumEnergy()

getAverageEnergy

public double getAverageEnergy()

getAverageEnergyNoOutlier

public double getAverageEnergyNoOutlier()

getStdOfEnergies

public double getStdOfEnergies()

getStdOfEnergiesNoOutlier

public double getStdOfEnergiesNoOutlier()