cct.interfaces
Interface AtomInterface

All Superinterfaces:
java.lang.Cloneable, Point3fInterface
All Known Implementing Classes:
gAtom, vAtom

public interface AtomInterface
extends Point3fInterface, java.lang.Cloneable

Title: Computational Chemsitry Tookit

Description:

Copyright: Copyright (c) 2005-2007 Dr. Vladislav Vassiliev

Company: ANU


Field Summary
static java.lang.String AMBER_NAME
           
static java.lang.String AMBER_TYPE_INDEX
           
static java.lang.String AMBIENT_RGB_COLOR
           
static java.lang.String ATOMIC_CHARGE
           
static java.lang.String CCT_ATOM_TYPE
           
static float COVALENT_TO_GRADIUS_FACTOR
           
static java.lang.String DIFFUSE_RGB_COLOR
           
static java.lang.String GR_RADIUS
           
static java.lang.String NAME
           
static java.lang.String PICKABILITY
           
static int RENDER_POINT
           
static int RENDER_SMART_POINT
           
static int RENDER_SPHERE
           
static java.lang.String RENDERING_STYLE
           
static java.lang.String RGB_COLOR
           
static java.lang.String SPECULAR_RGB_COLOR
           
static java.lang.String SYBYL_TYPE
           
static java.lang.String VISIBLE
           
 
Method Summary
 float getAtomicMass()
           
 int getAtomicNumber()
           
 java.util.ArrayList getBondedToAtoms()
           
 java.util.ArrayList getBondIndex()
           
 BondInterface getBondToAtom(AtomInterface a)
           
 java.lang.String getName()
           
 AtomInterface getNewAtomInstance()
           
 AtomInterface getNewAtomInstance(AtomInterface a)
           
 int getNumberOfBondedAtoms()
           
 java.util.HashMap getProperties()
           
 java.lang.Object getProperty(java.lang.String key)
           
 int getSubstructureNumber()
           
 boolean isBondedTo(AtomInterface a)
           
 boolean isDynamic()
           
 boolean isSelected()
           
 boolean removeBond(BondInterface bond)
           
 void setAtomicMass(float mass)
           
 void setAtomicNumber(int anumber)
           
 void setBondedTo(AtomInterface a, boolean set_bond)
           
 void setBondIndex(BondInterface a)
           
 void setName(java.lang.String aName)
           
 void setProperty(java.lang.Object prop, java.lang.Object value)
           
 void setSelected(boolean select)
           
 void setSubstructureNumber(int n)
           
 
Methods inherited from interface cct.interfaces.Point3fInterface
distanceTo, getInstance, getInstance, getInstance, getX, getY, getZ, setX, setXYZ, setXYZ, setY, setZ, subtract
 

Field Detail

COVALENT_TO_GRADIUS_FACTOR

static final float COVALENT_TO_GRADIUS_FACTOR
See Also:
Constant Field Values

RENDER_SPHERE

static final int RENDER_SPHERE
See Also:
Constant Field Values

RENDER_POINT

static final int RENDER_POINT
See Also:
Constant Field Values

RENDER_SMART_POINT

static final int RENDER_SMART_POINT
See Also:
Constant Field Values

NAME

static final java.lang.String NAME
See Also:
Constant Field Values

SYBYL_TYPE

static final java.lang.String SYBYL_TYPE
See Also:
Constant Field Values

CCT_ATOM_TYPE

static final java.lang.String CCT_ATOM_TYPE
See Also:
Constant Field Values

AMBER_NAME

static final java.lang.String AMBER_NAME
See Also:
Constant Field Values

AMBER_TYPE_INDEX

static final java.lang.String AMBER_TYPE_INDEX
See Also:
Constant Field Values

ATOMIC_CHARGE

static final java.lang.String ATOMIC_CHARGE
See Also:
Constant Field Values

GR_RADIUS

static final java.lang.String GR_RADIUS
See Also:
Constant Field Values

RGB_COLOR

static final java.lang.String RGB_COLOR
See Also:
Constant Field Values

AMBIENT_RGB_COLOR

static final java.lang.String AMBIENT_RGB_COLOR
See Also:
Constant Field Values

DIFFUSE_RGB_COLOR

static final java.lang.String DIFFUSE_RGB_COLOR
See Also:
Constant Field Values

SPECULAR_RGB_COLOR

static final java.lang.String SPECULAR_RGB_COLOR
See Also:
Constant Field Values

PICKABILITY

static final java.lang.String PICKABILITY
See Also:
Constant Field Values

VISIBLE

static final java.lang.String VISIBLE
See Also:
Constant Field Values

RENDERING_STYLE

static final java.lang.String RENDERING_STYLE
See Also:
Constant Field Values
Method Detail

getAtomicMass

float getAtomicMass()

getAtomicNumber

int getAtomicNumber()

getBondedToAtoms

java.util.ArrayList getBondedToAtoms()

getBondIndex

java.util.ArrayList getBondIndex()

getNumberOfBondedAtoms

int getNumberOfBondedAtoms()

getProperties

java.util.HashMap getProperties()

getProperty

java.lang.Object getProperty(java.lang.String key)

setAtomicNumber

void setAtomicNumber(int anumber)

getBondToAtom

BondInterface getBondToAtom(AtomInterface a)

getName

java.lang.String getName()

getSubstructureNumber

int getSubstructureNumber()

isBondedTo

boolean isBondedTo(AtomInterface a)

isSelected

boolean isSelected()

isDynamic

boolean isDynamic()

removeBond

boolean removeBond(BondInterface bond)

setAtomicMass

void setAtomicMass(float mass)

setBondedTo

void setBondedTo(AtomInterface a,
                 boolean set_bond)

setBondIndex

void setBondIndex(BondInterface a)

setProperty

void setProperty(java.lang.Object prop,
                 java.lang.Object value)

setName

void setName(java.lang.String aName)

setSubstructureNumber

void setSubstructureNumber(int n)

setSelected

void setSelected(boolean select)

getNewAtomInstance

AtomInterface getNewAtomInstance()

getNewAtomInstance

AtomInterface getNewAtomInstance(AtomInterface a)