org.strbio.mol
Class AtomNode

java.lang.Object
  org.strbio.mol.Atom
      org.strbio.mol.AtomNode

All Implemented Interfaces:

DLinkedList.Node

public class AtomNode
extends Atom
implements DLinkedList.Node

Class to represent a node in a list of atoms.

 Version 1.1, 4/16/98 - uses DlinkedList class, renamed from AtomList to AtomNode
 Version 1.0, 3/31/98 - original version
 

Version:

1.1, 4/16/98

Author:

JMC

See Also:

Atom, Molecule, Monomer, Residue, Protein

Field Summary

AtomNode	next the next atom in the list
AtomNode	prev the previous atom in the list

Fields inherited from class org.strbio.mol.Atom

altLoc, coord, n, name, occupancy, tempFactor

Constructor Summary

AtomNode()
constructor sets next, prev to null

AtomNode(Atom x)
when constructed from an Atom, it makes a new copy of the data in the Atom, but doesn't set next, prev.

Method Summary

DLinkedList.Node	copyNode() Return a node with a copy of the same atom.
void	insertNodeQuickly(AtomNode x) Inserts another AtomNode in the linked list after this atom, without going through the DLinkedList routines.
DLinkedList.Node	next() return the next AtomNode
DLinkedList.Node	prev() return the previous AtomNode
void	removeQuickly() Removes this atom from the linked list, without going through the DLinkedList routines.
void	setNext(DLinkedList.Node x) set the next AtomNode
void	setPrev(DLinkedList.Node x) set the previous AtomNode

Methods inherited from class org.strbio.mol.Atom

bondAngle, dihedralAngle, distance, find4, find4, readPDB, rotate, transform, translate, writePDB, x, y, z

Methods inherited from class java.lang.Object

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

Field Detail

next

public AtomNode next

the next atom in the list

prev

public AtomNode prev

the previous atom in the list

Constructor Detail

AtomNode

public AtomNode()

constructor sets next, prev to null

AtomNode

public AtomNode(Atom x)

when constructed from an Atom, it makes a new copy of the data in the Atom, but doesn't set next, prev. There's no constructor from AtomNode because I can't think of why anybody would want to copy all aspects of an AtomNode.

Method Detail

copyNode

public DLinkedList.Node copyNode()

Return a node with a copy of the same atom.

Specified by:

copyNode in interface DLinkedList.Node

next

public DLinkedList.Node next()

return the next AtomNode

Specified by:

next in interface DLinkedList.Node

prev

public DLinkedList.Node prev()

return the previous AtomNode

Specified by:

prev in interface DLinkedList.Node

setNext

public void setNext(DLinkedList.Node x)

set the next AtomNode

Specified by:

setNext in interface DLinkedList.Node

setPrev

public void setPrev(DLinkedList.Node x)

set the previous AtomNode

Specified by:

setPrev in interface DLinkedList.Node

removeQuickly

public final void removeQuickly()

Removes this atom from the linked list, without going through the DLinkedList routines.

insertNodeQuickly

public final void insertNodeQuickly(AtomNode x)

Inserts another AtomNode in the linked list after this atom, without going through the DLinkedList routines.