cct.interfaces
Interface MoleculeInterface

All Known Implementing Classes:

Molecule

public interface MoleculeInterface

Title:

Description:

Copyright: Copyright (c) 2006

Company: ANU

Field Summary

static java.lang.Integer	BALL_AND_STICKS
static java.lang.String	CCSDEnergyProperty
static java.lang.String	CCSDTEnergyProperty
static java.lang.String	ChargeProperty
static java.lang.String	DipoleMomentProperty
static java.lang.String	EnergyThermCorrProperty
static java.lang.String	EnthalpyThermCorrProperty
static java.lang.String	ESPChargesProperty
static java.lang.String	FrameGroupProperty
static java.lang.String	GibbsThermCorrProperty
static java.lang.String	ImaginaryFreqsProperty
static java.lang.String	LATTICE_PARAMETERS
static java.lang.String	LATTICE_VECTORS
static java.lang.String	MP2EnergyProperty
static java.lang.String	MP3EnergyProperty
static java.lang.String	MP4DEnergyProperty
static java.lang.String	MP4DQEnergyProperty
static java.lang.String	MP4SDQEnergyProperty
static java.lang.String	MullikenChargesProperty
static java.lang.String	MultiplicityProperty
static java.lang.String	NotesProperty
static java.lang.String	OUTPUT_RESULTS
static java.lang.String	PeriodicBox
static java.lang.String	PolarizabilityProperty
static java.lang.String	ProgramProperty
static java.lang.String	RenderingStyle
static java.lang.String	S_SquaredProperty
static java.lang.String	SCFEnergyProperty
static java.lang.Integer	SPACEFILL
static java.lang.Integer	STICKS
static java.lang.String	VersionProperty
static java.lang.String	VIBRATION_RENDERER
static java.lang.Integer	WIREFRAME
static java.lang.String	ZeroPointCorrProperty

Method Summary

void	addAtom(AtomInterface a)
void	addAtom(AtomInterface a, int monomer_number)
void	addAtom(AtomInterface a, int n, java.lang.String name)
void	addBond(BondInterface b)
void	addMonomer(java.lang.String monomer_name)
void	addProperty(java.lang.String propName, java.lang.Object value)
void	appendMolecule(MoleculeInterface mol) Adds COPIES of atoms from molecule "mol"
void	centerMolecule(float x, float y, float z)
AtomInterface	deleteAtom(int n)
BondInterface	deleteBond(BondInterface bond_to_delete)
int	getAtomIndex(AtomInterface a)
AtomInterface	getAtomInterface(int i)
int	getBondIndex(BondInterface b)
BondInterface	getBondInterface(int i)
MoleculeInterface	getInstance()
java.util.ArrayList	getMolecularSubstructure()
MonomerInterface	getMonomerInterface(int n)
java.lang.String	getName()
AtomInterface	getNewAtomInstance()
BondInterface	getNewBondInstance()
BondInterface	getNewBondInstance(AtomInterface a, AtomInterface b)
int	getNumberOfAtoms()
int	getNumberOfBonds()
int	getNumberOfMonomers()
java.util.HashMap	getProperties()
java.lang.Object	getProperty(java.lang.String key)
float	getXmax()
float	getXmin()
float	getYmax()
float	getYmin()
float	getZmax()
float	getZmin()
void	guessCovalentBondsBetweenMonomers(int n, int m)
void	guessCovalentBondsInMonomer(int n)
void	mergeMolecule(MoleculeInterface mol) Adds atoms from molecule "mol" (not their copies)
void	setName(java.lang.String name)

Field Detail

WIREFRAME

static final java.lang.Integer WIREFRAME

STICKS

static final java.lang.Integer STICKS

BALL_AND_STICKS

static final java.lang.Integer BALL_AND_STICKS

SPACEFILL

static final java.lang.Integer SPACEFILL

OUTPUT_RESULTS

static final java.lang.String OUTPUT_RESULTS

See Also:

Constant Field Values

VIBRATION_RENDERER

static final java.lang.String VIBRATION_RENDERER

See Also:

Constant Field Values

RenderingStyle

static final java.lang.String RenderingStyle

See Also:

Constant Field Values

ChargeProperty

static final java.lang.String ChargeProperty

See Also:

Constant Field Values

MultiplicityProperty

static final java.lang.String MultiplicityProperty

See Also:

Constant Field Values

SCFEnergyProperty

static final java.lang.String SCFEnergyProperty

See Also:

Constant Field Values

MP2EnergyProperty

static final java.lang.String MP2EnergyProperty

See Also:

Constant Field Values

MP3EnergyProperty

static final java.lang.String MP3EnergyProperty

See Also:

Constant Field Values

MP4DEnergyProperty

static final java.lang.String MP4DEnergyProperty

See Also:

Constant Field Values

MP4DQEnergyProperty

static final java.lang.String MP4DQEnergyProperty

See Also:

Constant Field Values

MP4SDQEnergyProperty

static final java.lang.String MP4SDQEnergyProperty

See Also:

Constant Field Values

CCSDEnergyProperty

static final java.lang.String CCSDEnergyProperty

See Also:

Constant Field Values

CCSDTEnergyProperty

static final java.lang.String CCSDTEnergyProperty

See Also:

Constant Field Values

DipoleMomentProperty

static final java.lang.String DipoleMomentProperty

See Also:

Constant Field Values

PolarizabilityProperty

static final java.lang.String PolarizabilityProperty

See Also:

Constant Field Values

MullikenChargesProperty

static final java.lang.String MullikenChargesProperty

See Also:

Constant Field Values

ESPChargesProperty

static final java.lang.String ESPChargesProperty

See Also:

Constant Field Values

FrameGroupProperty

static final java.lang.String FrameGroupProperty

See Also:

Constant Field Values

S_SquaredProperty

static final java.lang.String S_SquaredProperty

See Also:

Constant Field Values

ZeroPointCorrProperty

static final java.lang.String ZeroPointCorrProperty

See Also:

Constant Field Values

EnergyThermCorrProperty

static final java.lang.String EnergyThermCorrProperty

See Also:

Constant Field Values

EnthalpyThermCorrProperty

static final java.lang.String EnthalpyThermCorrProperty

See Also:

Constant Field Values

GibbsThermCorrProperty

static final java.lang.String GibbsThermCorrProperty

See Also:

Constant Field Values

ImaginaryFreqsProperty

static final java.lang.String ImaginaryFreqsProperty

See Also:

Constant Field Values

NotesProperty

static final java.lang.String NotesProperty

See Also:

Constant Field Values

ProgramProperty

static final java.lang.String ProgramProperty

See Also:

Constant Field Values

VersionProperty

static final java.lang.String VersionProperty

See Also:

Constant Field Values

PeriodicBox

static final java.lang.String PeriodicBox

See Also:

Constant Field Values

LATTICE_VECTORS

static final java.lang.String LATTICE_VECTORS

See Also:

Constant Field Values

LATTICE_PARAMETERS

static final java.lang.String LATTICE_PARAMETERS

See Also:

Constant Field Values

Method Detail

addAtom

void addAtom(AtomInterface a)

addAtom

void addAtom(AtomInterface a,
             int monomer_number)

addAtom

void addAtom(AtomInterface a,
             int n,
             java.lang.String name)

addBond

void addBond(BondInterface b)

addMonomer

void addMonomer(java.lang.String monomer_name)

addProperty

void addProperty(java.lang.String propName,
                 java.lang.Object value)

mergeMolecule

void mergeMolecule(MoleculeInterface mol)

Adds atoms from molecule "mol" (not their copies)

Parameters:

mol - MoleculeInterface

appendMolecule

void appendMolecule(MoleculeInterface mol)

Adds COPIES of atoms from molecule "mol"

Parameters:

mol - MoleculeInterface

centerMolecule

void centerMolecule(float x,
                    float y,
                    float z)

deleteAtom

AtomInterface deleteAtom(int n)

deleteBond

BondInterface deleteBond(BondInterface bond_to_delete)

getAtomIndex

int getAtomIndex(AtomInterface a)

getAtomInterface

AtomInterface getAtomInterface(int i)

getBondIndex

int getBondIndex(BondInterface b)

getBondInterface

BondInterface getBondInterface(int i)

getMonomerInterface

MonomerInterface getMonomerInterface(int n)

getName

java.lang.String getName()

getNewAtomInstance

AtomInterface getNewAtomInstance()
                                 throws java.lang.NullPointerException

Throws:

java.lang.NullPointerException

getNewBondInstance

BondInterface getNewBondInstance()
                                 throws java.lang.NullPointerException

Throws:

java.lang.NullPointerException

getNewBondInstance

BondInterface getNewBondInstance(AtomInterface a,
                                 AtomInterface b)
                                 throws java.lang.NullPointerException

Throws:

java.lang.NullPointerException

getNumberOfAtoms

int getNumberOfAtoms()

getNumberOfBonds

int getNumberOfBonds()

getNumberOfMonomers

int getNumberOfMonomers()

getMolecularSubstructure

java.util.ArrayList getMolecularSubstructure()

getProperties

java.util.HashMap getProperties()

getProperty

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

getXmax

float getXmax()

getXmin

float getXmin()

getYmax

float getYmax()

getYmin

float getYmin()

getZmax

float getZmax()

getZmin

float getZmin()

getInstance

MoleculeInterface getInstance()

guessCovalentBondsBetweenMonomers

void guessCovalentBondsBetweenMonomers(int n,
                                       int m)

guessCovalentBondsInMonomer

void guessCovalentBondsInMonomer(int n)

setName

void setName(java.lang.String name)