Package edu.duke.cs.osprey.dof.deeper

Class DEEPerSettings

java.lang.Object

edu.duke.cs.osprey.dof.deeper.DEEPerSettings

All Implemented Interfaces:

Serializable

public class DEEPerSettings
extends Object
implements Serializable

Holds parameters that control a DEEPer run

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
DEEPerSettings()
DEEPerSettings(boolean doPerturbations, String pertFileName, boolean selectPerturbations, String startingPertFile, boolean onlyStarting, double maxShearParam, double maxBackrubParam, boolean selectLCAs, ArrayList<String> flexibleRes, String PDBFile, boolean doRamaCheck, ResidueTemplateLibrary templateLib)

Method Summary

Modifier and Type	Method	Description
boolean	doPerturbations()
ArrayList<ArrayList<double[]>>	getPertIntervals()
ArrayList<ArrayList<int[]>>	getPertStates(int pos)
void	loadPertFile(ResidueTermini termini)
DEEPerSettings	makeDiscreteVersion()
ArrayList<Perturbation>	makePerturbations(Molecule m)

Methods inherited from class java.lang.Object

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

Constructor Details

DEEPerSettings

public DEEPerSettings()

DEEPerSettings

public DEEPerSettings(boolean doPerturbations,
 String pertFileName,
 boolean selectPerturbations,
 String startingPertFile,
 boolean onlyStarting,
 double maxShearParam,
 double maxBackrubParam,
 boolean selectLCAs,
 ArrayList<String> flexibleRes,
 String PDBFile,
 boolean doRamaCheck,
 ResidueTemplateLibrary templateLib)

Method Details

doPerturbations

public boolean doPerturbations()

loadPertFile

public void loadPertFile(ResidueTermini termini)

makePerturbations

public ArrayList<Perturbation> makePerturbations(Molecule m)

getPertIntervals

public ArrayList<ArrayList<double[]>> getPertIntervals()

getPertStates

public ArrayList<ArrayList<int[]>> getPertStates(int pos)

makeDiscreteVersion

public DEEPerSettings makeDiscreteVersion()