edu.sdsc.mbt
Class Atom

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

All Implemented Interfaces:

java.lang.Cloneable, java.io.Serializable

public class Atom

extends StructureComponent

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

Implements a StructureComponent container for atom data.

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

Author:

John L. Moreland

See Also:

StructureComponent, Structure,

, Serialized Form

Field Summary

boolean	backbone Whether this atom is a part of the protein backbone
java.lang.String	chain_id Chain/Asymetric unit ID.
java.lang.String	compound Compound 3-letter code.
double[]	coordinate The x,y,z coordinate in angstroms.
short	element The element symbol.
java.lang.String	forceFieldType Force field type indicates the kind of atom depending on the atoms it's bonded to
short	formalCharge
short	hybridization Atomic orbital hybridization state.
java.lang.String	name The macromolecular ID (element name).
int	number The atom serial number.
float	partialCharge Partial Charge (-1.0 - 3.0).
short	quality
short	render Inidcates whether this atom is ionized, hence which radius should be used for rendering
Residue	residue
int	residue_id Residue/Sequence ID.
static short	SP
static short	SP2
static short	SP3
boolean	visible

Fields inherited from class edu.sdsc.mbt.StructureComponent

structure

Constructor Summary

Atom()
Creates a new Atom object and initializes the StructureComponent "structure" field.

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	getElement()
java.lang.String	getStructureComponentType() This method returns the fully qualified name of this class.
boolean	isVisible()
void	setElement(java.lang.String symbol)

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

Field Detail

SP3

public static short SP3

SP2

public static short SP2

SP

public static short SP

element

public short element

The element symbol. For example, "C", "O", "N", "H", etc.

name

public java.lang.String name

The macromolecular ID (element name). For example, "CA", "CB", "OG1", "N", etc.

number

public int number

The atom serial number.

compound

public java.lang.String compound

Compound 3-letter code. For example, "VAL", "THR", "ILE", etc.

formalCharge

public short formalCharge

chain_id

public java.lang.String chain_id

Chain/Asymetric unit ID. For example, "A", "B", "C", etc.

residue_id

public int residue_id

Residue/Sequence ID. Must be a positive integer. For example, "10", "11", "13", etc.

residue

public Residue residue

coordinate

public double[] coordinate

The x,y,z coordinate in angstroms. For example, (21.023, 30.128, 12.340).

backbone

public boolean backbone

Whether this atom is a part of the protein backbone

partialCharge

public float partialCharge

Partial Charge (-1.0 - 3.0). For example, "0.3", "1.1", etc.

hybridization

public short hybridization

Atomic orbital hybridization state. Needed for molecular mechanics calculations

forceFieldType

public java.lang.String forceFieldType

Force field type indicates the kind of atom depending on the atoms it's bonded to

render

public short render

Inidcates whether this atom is ionized, hence which radius should be used for rendering

quality

public short quality

visible

public boolean visible

Constructor Detail

Atom

public Atom()

Creates a new Atom object and initializes the StructureComponent "structure" field.

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.

getStructureComponentType

public java.lang.String getStructureComponentType()

This method returns the fully qualified name of this class.

Specified by:

getStructureComponentType in class StructureComponent

getElement

public java.lang.String getElement()

setElement

public void setElement(java.lang.String symbol)

isVisible

public boolean isVisible()

Specified by:

isVisible in class StructureComponent