org.wallerlab.yoink.cube.domain

Class SimpleCube

java.lang.Object

org.wallerlab.yoink.cube.domain.SimpleCube

All Implemented Interfaces:

Cube

@Component
public class SimpleCube
extends java.lang.Object
implements Cube

Cube domain Model stores all information about cube. Constructing a cube needs the coordinate of the origin grid point, number of steps along x/y/z axis, and also step size along x/y/z axis.

Constructor Summary

Constructors

Constructor and Description
SimpleCube() default cube constructor
SimpleCube(double[] xyzStepSize) use xyz step sizes construct a cube and convert the unit of step size from angstrom to bohr
SimpleCube(int cubeSize) Construct when size is known, or use setter to set number of size

Method Summary

Modifier and Type	Method and Description
java.util.Set<Atom>	getAtoms() get all atoms in the cube
java.util.List<Coord>	getCoordinates() get the coordinates of grid points in the cube
java.util.List<DensityPoint.DensityType>	getDensityTypes() get the value of density types of the cube
Coord	getGridOrigin() get the value of origin coordinate of the cube
java.util.Set<Molecule>	getMolecules() get the molecules in the cube
java.lang.String	getName() get the name of the cube
int[]	getNumberOfXYZSteps() get the number of steps along xyz axes
int	getSize() get the number of grid points in the cube
java.util.List<java.lang.Double>	getValues() get the values of grid points in the cube
double[]	getXyzStepSize() get the step size along xyz axes
void	setCoordinates(java.util.List<Coord> coordinates) set the coordinates of grid points in the cube
void	setDensityTypes(java.util.List<DensityPoint.DensityType> densityTypes) set the value of density types of the cube
void	setGridOrigin(Coord gridOrigin) set the value of origin coordinate of the cube
void	setMolecules(java.util.Set<Molecule> molecules) set the value of molecules in the cube
void	setName(java.lang.String name) set the name of the cube
void	setNumberOfXYZSteps(int[] numberOfXYZSteps) set the number of steps along xyz axes
void	setSize(int size) set the number of grid points in the cube
void	setValues(java.util.List<java.lang.Double> values) set teh values of grid points in the cube

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleCube

public SimpleCube(double[] xyzStepSize)

use xyz step sizes construct a cube and convert the unit of step size from angstrom to bohr

Parameters:

xyzStepSize - -a double array with xyz step sizes

SimpleCube

public SimpleCube(int cubeSize)

Construct when size is known, or use setter to set number of size

Parameters:

cubeSize - , the total number of grid points in the cube

SimpleCube

public SimpleCube()

default cube constructor

Method Detail

getGridOrigin

public Coord getGridOrigin()

Description copied from interface: Cube

get the value of origin coordinate of the cube

Specified by:

getGridOrigin in interface Cube

Returns:

Coord

setGridOrigin

public void setGridOrigin(Coord gridOrigin)

Description copied from interface: Cube

set the value of origin coordinate of the cube

Specified by:

setGridOrigin in interface Cube

Parameters:

gridOrigin - -Coord

getNumberOfXYZSteps

public int[] getNumberOfXYZSteps()

Description copied from interface: Cube

get the number of steps along xyz axes

Specified by:

getNumberOfXYZSteps in interface Cube

Returns:

an int array

setNumberOfXYZSteps

public void setNumberOfXYZSteps(int[] numberOfXYZSteps)

Description copied from interface: Cube

set the number of steps along xyz axes

Specified by:

setNumberOfXYZSteps in interface Cube

Parameters:

numberOfXYZSteps - , an int array with 3 elements

getXyzStepSize

public double[] getXyzStepSize()

Description copied from interface: Cube

get the step size along xyz axes

Specified by:

getXyzStepSize in interface Cube

Returns:

a double array

getMolecules

public java.util.Set<Molecule> getMolecules()

Description copied from interface: Cube

get the molecules in the cube

Specified by:

getMolecules in interface Cube

Returns:

a Set of molecules. - Molecule

getAtoms

public java.util.Set<Atom> getAtoms()

get all atoms in the cube

Specified by:

getAtoms in interface Cube

Returns:

a Set of atoms.- Atom

setMolecules

public void setMolecules(java.util.Set<Molecule> molecules)

Description copied from interface: Cube

set the value of molecules in the cube

Specified by:

setMolecules in interface Cube

Parameters:

molecules - -a Set of molecules. Molecule

getName

public java.lang.String getName()

Description copied from interface: Cube

get the name of the cube

Specified by:

getName in interface Cube

Returns:

name -String

setName

public void setName(java.lang.String name)

Description copied from interface: Cube

set the name of the cube

Specified by:

setName in interface Cube

Parameters:

name - -String

getDensityTypes

@Value(value="#{\'${yoink.cube.densityTypes}\'.split(\',\')}")
public java.util.List<DensityPoint.DensityType> getDensityTypes()

Description copied from interface: Cube

get the value of density types of the cube

Specified by:

getDensityTypes in interface Cube

Returns:

a DensityPoint.DensityType List

setDensityTypes

public void setDensityTypes(java.util.List<DensityPoint.DensityType> densityTypes)

Description copied from interface: Cube

set the value of density types of the cube

Specified by:

setDensityTypes in interface Cube

Parameters:

densityTypes - -a DensityPoint.DensityType List

getSize

public int getSize()

Description copied from interface: Cube

get the number of grid points in the cube

Specified by:

getSize in interface Cube

Returns:

number of grid points -Integer

setSize

public void setSize(int size)

Description copied from interface: Cube

set the number of grid points in the cube

Specified by:

setSize in interface Cube

Parameters:

size - , number of grid points -Integer

getCoordinates

public java.util.List<Coord> getCoordinates()

Description copied from interface: Cube

get the coordinates of grid points in the cube

Specified by:

getCoordinates in interface Cube

Returns:

a Coord List

setCoordinates

public void setCoordinates(java.util.List<Coord> coordinates)

Description copied from interface: Cube

set the coordinates of grid points in the cube

Specified by:

setCoordinates in interface Cube

Parameters:

coordinates - , a Coord List

getValues

public java.util.List<java.lang.Double> getValues()

Description copied from interface: Cube

get the values of grid points in the cube

Specified by:

getValues in interface Cube

Returns:

a Double List

setValues

public void setValues(java.util.List<java.lang.Double> values)

Description copied from interface: Cube

set teh values of grid points in the cube

Specified by:

setValues in interface Cube

Parameters:

values - , a Double List