ProGAL.proteins.beltaStructure.loop
Class LoopStructure

java.lang.Object
  extended by ProGAL.proteins.beltaStructure.loop.LoopStructure
All Implemented Interfaces:
PartialStructure

public class LoopStructure
extends java.lang.Object
implements PartialStructure


Field Summary
 SecondaryStructure secondaryStructure
           
 SecondaryStructure.SSSegment segment1
           
 SecondaryStructure.SSSegment segment2
           
 Atom[] targetAtoms
           
 
Constructor Summary
LoopStructure(SecondaryStructure ss, int seg1, int seg2)
           
LoopStructure(SecondaryStructure ss, int seg1, int seg2, Atom[] targetAtoms)
           
 
Method Summary
 void enforceClosureAnalytically()
           
 void enforceClosureCCD()
           
 void enforceClosureJacobian()
           
 boolean isClosed()
          Indicates if the loop is closed, ie.
 void rebuildACO()
           
 void rebuildAnalytically()
           
 void rebuildCCD()
           
 void rebuildJacobian()
           
 void setFirstTransform(Matrix m)
           
 java.lang.String toString()
           
 void updateAtoms(AminoAcidChain chain)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

secondaryStructure

public final SecondaryStructure secondaryStructure

segment1

public final SecondaryStructure.SSSegment segment1

segment2

public final SecondaryStructure.SSSegment segment2

targetAtoms

public Atom[] targetAtoms
Constructor Detail

LoopStructure

public LoopStructure(SecondaryStructure ss,
                     int seg1,
                     int seg2,
                     Atom[] targetAtoms)

LoopStructure

public LoopStructure(SecondaryStructure ss,
                     int seg1,
                     int seg2)
Method Detail

setFirstTransform

public void setFirstTransform(Matrix m)

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

isClosed

public boolean isClosed()
Indicates if the loop is closed, ie. if the end of the loop matches up with the target atoms.


enforceClosureCCD

public void enforceClosureCCD()

enforceClosureAnalytically

public void enforceClosureAnalytically()

enforceClosureJacobian

public void enforceClosureJacobian()

rebuildCCD

public void rebuildCCD()

rebuildAnalytically

public void rebuildAnalytically()

rebuildJacobian

public void rebuildJacobian()

rebuildACO

public void rebuildACO()

updateAtoms

public void updateAtoms(AminoAcidChain chain)
Specified by:
updateAtoms in interface PartialStructure