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

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Constant Field Values

RENDER_SPHERE

static final int RENDER_SPHERE

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Constant Field Values

RENDER_POINT

static final int RENDER_POINT

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Constant Field Values

RENDER_SMART_POINT

static final int RENDER_SMART_POINT

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Constant Field Values

NAME

static final java.lang.String NAME

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Constant Field Values

SYBYL_TYPE

static final java.lang.String SYBYL_TYPE

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Constant Field Values

CCT_ATOM_TYPE

static final java.lang.String CCT_ATOM_TYPE

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Constant Field Values

AMBER_NAME

static final java.lang.String AMBER_NAME

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Constant Field Values

AMBER_TYPE_INDEX

static final java.lang.String AMBER_TYPE_INDEX

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Constant Field Values

ATOMIC_CHARGE

static final java.lang.String ATOMIC_CHARGE

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Constant Field Values

GR_RADIUS

static final java.lang.String GR_RADIUS

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Constant Field Values

RGB_COLOR

static final java.lang.String RGB_COLOR

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Constant Field Values

AMBIENT_RGB_COLOR

static final java.lang.String AMBIENT_RGB_COLOR

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Constant Field Values

DIFFUSE_RGB_COLOR

static final java.lang.String DIFFUSE_RGB_COLOR

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Constant Field Values

SPECULAR_RGB_COLOR

static final java.lang.String SPECULAR_RGB_COLOR

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Constant Field Values

PICKABILITY

static final java.lang.String PICKABILITY

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Constant Field Values

VISIBLE

static final java.lang.String VISIBLE

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Constant Field Values

RENDERING_STYLE

static final java.lang.String RENDERING_STYLE

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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)