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

Class Perturbation

java.lang.Object

edu.duke.cs.osprey.dof.DegreeOfFreedom

edu.duke.cs.osprey.dof.deeper.perts.Perturbation

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

Backrub, LoopClosureAdjustment, PartialStructureSwitch, Shear

public abstract class Perturbation
extends DegreeOfFreedom

A perturbation, as in DEEPer Note: This DEEPer package, unlike the rest of the software, consists of perturbations specific to proteins and so it will make explicit reference to protein atoms outside HardCodedResidueInfo DEEPer perturbations can be used in the protein part of a mixed protein-nonprotein system

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
Perturbation(ArrayList<Residue> resDirectlyAffected)

Method Summary

Modifier and Type	Method	Description
void	apply(double paramVal)
abstract Perturbation	copyForNewMolecule(Molecule mol, PerturbationBlock block)
abstract boolean	doPerturbationMotion(double paramVal)
DOFBlock	getBlock()
String	getName()

Methods inherited from class edu.duke.cs.osprey.dof.DegreeOfFreedom

copy, getCurVal, getResidue, nameToIndexMap, setMolecule

Methods inherited from class java.lang.Object

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

Constructor Details

Perturbation

public Perturbation(ArrayList<Residue> resDirectlyAffected)

Method Details

apply

public void apply(double paramVal)

Specified by:

apply in class DegreeOfFreedom

doPerturbationMotion

public abstract boolean doPerturbationMotion(double paramVal)

copyForNewMolecule

public abstract Perturbation copyForNewMolecule(Molecule mol,
 PerturbationBlock block)

getBlock

public DOFBlock getBlock()

Specified by:

getBlock in class DegreeOfFreedom

getName

public String getName()

Specified by:

getName in class DegreeOfFreedom