edu.sdsc.mbt
Class Conformation

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

All Implemented Interfaces:

java.lang.Cloneable, java.io.Serializable

Direct Known Subclasses:

Coil, Helix, Strand, Turn

public abstract class Conformation

extends StructureComponent

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

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

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

Author:

John L. Moreland

See Also:

Atom, Structure, StructureComponent, StructureComponentIterator,

, Serialized Form

Field Summary

java.lang.String	end_chain This value corresponds to the end Atom.chain_id value.
java.lang.String	end_compound For example, "ALA", "GLU", "LYS", etc.
int	end_residue This value corresponds to the end Atom.residue_id value.
java.lang.String	name For example, "helix_BA", "turn_1A"
java.lang.String	start_chain This value corresponds to the start Atom.chain_id value.
java.lang.String	start_compound For example, "ALA", "GLU", "LYS", etc.
int	start_residue This value corresponds to the Atom.residue_id value.
static java.lang.String	TYPE_UNDEFINED If a residue conformation / chain fragment type is not defined, use this value.

Fields inherited from class edu.sdsc.mbt.StructureComponent

structure

Constructor Summary

Conformation()

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.

Methods inherited from class edu.sdsc.mbt.StructureComponent

getStructure, getStructureComponentType, isVisible, setStructure

Methods inherited from class java.lang.Object

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

Field Detail

TYPE_UNDEFINED

public static final java.lang.String TYPE_UNDEFINED

If a residue conformation / chain fragment type is not defined, use this value. That is, assign this value when secondary structure has not been assigned.

See Also:

Constant Field Values

name

public java.lang.String name

For example, "helix_BA", "turn_1A"

start_compound

public java.lang.String start_compound

For example, "ALA", "GLU", "LYS", etc.

start_chain

public java.lang.String start_chain

This value corresponds to the start Atom.chain_id value. For example, "A", "B", "D", etc.

start_residue

public int start_residue

This value corresponds to the Atom.residue_id value. For example, 22, 27, etc.

end_compound

public java.lang.String end_compound

For example, "ALA", "GLU", "LYS", etc.

end_chain

public java.lang.String end_chain

This value corresponds to the end Atom.chain_id value. For example, "A", "B", "D", etc.

end_residue

public int end_residue

This value corresponds to the end Atom.residue_id value. For example, 27, 137, etc.

Constructor Detail

Conformation

public Conformation()

Method Detail

copy

public void copy(StructureComponent structureComponent)

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

Specified by:

copy in class StructureComponent

clone

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

Clone this object.

Overrides:

clone in class StructureComponent

Throws:

java.lang.CloneNotSupportedException

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.