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)