edu.sdsc.mbt
Class Strand

java.lang.Object
  edu.sdsc.mbt.StructureComponent
      edu.sdsc.mbt.Conformation
          edu.sdsc.mbt.Strand

All Implemented Interfaces:

java.lang.Cloneable, java.io.Serializable

public class Strand

extends Conformation

implements java.lang.Cloneable, java.io.Serializable

Implements a StructureComponent container for Strand conformation (secondary structure) data.

IMPORTANT!: Each individual SHEET record in most data sources (eg: PDB and mmCIF files) really represents a single STRAND. And, it takes multiple SHEET records in order to fully specify a sheet structure. So, in this toolkit, we treat each individual sheet record as a Strand.

See the "PROGRAMMING NOTE" section of the StructureComponent class.

Author:

John L. Moreland

See Also:

Structure, Conformation,

, Serialized Form

Field Summary

Fields inherited from class edu.sdsc.mbt.Conformation

end_chain, end_compound, end_residue, name, start_chain, start_compound, start_residue, TYPE_UNDEFINED

Fields inherited from class edu.sdsc.mbt.StructureComponent

structure

Constructor Summary

Strand()
Creates a new Strand object.

Method Summary

java.lang.Object	clone() Clone this object.
void	copy(StructureComponent structureComponent) Copy all of the field values from the parameter object into "this".
static java.lang.String	getClassName() This method returns the fully qualified name of this class.
java.lang.String	getStructureComponentType() This method returns the fully qualified name of this class.
boolean	isVisible()

Methods inherited from class edu.sdsc.mbt.StructureComponent

getStructure, setStructure

Methods inherited from class java.lang.Object

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

Constructor Detail

Strand

public Strand()

Creates a new Strand object.

Method Detail

getClassName

public static java.lang.String getClassName()

Description copied from class: StructureComponent

This method returns the fully qualified name of this class. Sub-classes must override this method (This method should really be declared abstract, but unfortunately Java does not allow a method to be both static AND abstract). Instead, this base class implementation will through an UnsupportedOperationException.

This name is used by the StructureComponentRegistry class to enable dynamic registration and discovery of new StructureComponent sub-classes/types. The name is also used to create instances of any sublcass dynamically from this name.

getStructureComponentType

public java.lang.String getStructureComponentType()

This method returns the fully qualified name of this class.

Specified by:

getStructureComponentType in class StructureComponent

copy

public void copy(StructureComponent structureComponent)

Copy all of the field values from the parameter object into "this".

Overrides:

copy in class Conformation

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Clone this object.

Overrides:

clone in class Conformation

Throws:

java.lang.CloneNotSupportedException

isVisible

public boolean isVisible()

Specified by:

isVisible in class StructureComponent