java.lang.Object
- org.jmol.quantum.QuantumCalculation
- - org.jmol.quantum.QuantumPlaneCalculation
  - - org.jmol.quantum.NciCalculation

public class NciCalculation
extends QuantumPlaneCalculation

Field Summary

Fields
Modifier and Type	Field	Description
`private BS`	`bsOK`
`private static double`	`c`
`private static double[]`	`coef1`
`private static double[]`	`coef2`
`private static double[]`	`coef3`
`private boolean`	`dataIsReducedDensity`
`private float`	`dataScaling`
`private double`	`DEFAULT_RHOPARAM`
`private double`	`DEFAULT_RHOPLOT_PRO`
`private double`	`DEFAULT_RHOPLOT_SCF`
`private static double[]`	`dMax`
`private javajs.util.Eigen`	`eigen`
`private float[]`	`eigenValues`
`private double`	`grad`
`private double`	`gxTemp`
`private double`	`gxxTemp`
`private double`	`gxyTemp`
`private double`	`gxzTemp`
`private double`	`gyTemp`
`private double`	`gyyTemp`
`private double`	`gyzTemp`
`private double`	`gzTemp`
`private double`	`gzzTemp`
`private boolean`	`havePoints`
`private double[][]`	`hess`
`private boolean`	`isPromolecular`
`private boolean`	`isReducedDensity`
`private int`	`nMolecules`
`private static double`	`NO_VALUE`
`private boolean`	`noValuesAtAll`
`private float[]`	`p0`
`private float[]`	`p1`
`private float[]`	`p2`
`private double`	`rhoMin`
`private double[]`	`rhoMolecules`
`private double`	`rhoParam`
`private double`	`rhoPlot`
`private static double`	`rpower`
`(package private) double`	`test1`
`private int`	`type`
`private static int`	`TYPE_ALL`
`private static int`	`TYPE_INTER`
`private static int`	`TYPE_INTRA`
`private static int`	`TYPE_LIGAND`
`private boolean`	`useAbsolute`
`private int`	`yzCount`
`private float[][]`	`yzPlanesRaw`
`private float[][]`	`yzPlanesRho`
`private static double[]`	`zeta1`
`private static double[]`	`zeta2`
`private static double[]`	`zeta3`

Fields inherited from class org.jmol.quantum.QuantumCalculation
atomIndex, bohr_per_angstrom, bsExcluded, countsXYZ, doDebug, firstAtomOffset, nX, nY, nZ, originBohr, points, qmAtoms, rangeBohrOrAngstroms, stepBohr, thisAtom, unitFactor, vd, volume, voxelData, voxelDataTemp, X, X2, xBohr, xMax, xMin, Y, Y2, yBohr, yMax, yMin, Z, Z2, zBohr, zMax, zMin

Constructor Summary

Constructors
Constructor Description

NciCalculation()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`calcPlane(int x, float[] plane)`	For reduced density only; coloring is done point by point.
`void`	`createCube()`
`private void`	`getBsOK()`	grid-based discrete SCF calculation needs to know which atoms to consider inter and which intramolecular
`float`	`getNoValue()`	Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.
`private static double`	`getParameter(float[] parameters, int i, double def, java.lang.String name)`
`void`	`getPlane(int ix, float[] yzPlane)`
`private double`	`getPlaneValue(int vA)`	We always have four raw planes in hand; we just need to know which three to use in any particular case.
`private float`	`getValue(double rho, boolean isReducedDensity)`
`private void`	`initializeEigen()`
`protected void`	`initializeOnePoint()`
`protected void`	`process()`
`float`	`process(int vA, int vB, float f)`	Passing the grid points of the two ends of an edge and a fraction to this method returns the value at a triangle point.
`private double`	`processAtoms(int ix, int iy, int iz, int index)`	At each grid point we need to calculate the sum of the atom-based promolecular data.
`void`	`setPlanes(float[][] planes)`	Raw file data planes are passed to us here from VolumeFileReader
`boolean`	`setupCalculation(VolumeData volumeData, BS bsSelected, BS bsExcluded, BS[] bsMolecules, javajs.util.T3[] atomCoordAngstroms, int firstAtomOffset, boolean isReducedDensity, javajs.util.T3[] points, float[] parameters, int testFlags)`

Methods inherited from class org.jmol.quantum.QuantumCalculation
initialize, initialize0, initializeOnePointQC, processPoints, processPt, setMinMax, setupCoordinates, setXYZBohr

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

havePoints
```
private boolean havePoints
```

isReducedDensity
```
private boolean isReducedDensity
```

DEFAULT_RHOPLOT_SCF
```
private double DEFAULT_RHOPLOT_SCF
```

DEFAULT_RHOPLOT_PRO
```
private double DEFAULT_RHOPLOT_PRO
```

DEFAULT_RHOPARAM
```
private double DEFAULT_RHOPARAM
```

rhoMin
```
private double rhoMin
```

rhoPlot
```
private double rhoPlot
```

rhoParam
```
private double rhoParam
```

TYPE_ALL
```
private static final int TYPE_ALL
```
See Also:

Constant Field Values

TYPE_INTRA
```
private static final int TYPE_INTRA
```
See Also:

Constant Field Values

TYPE_INTER
```
private static final int TYPE_INTER
```
See Also:

Constant Field Values

TYPE_LIGAND
```
private static final int TYPE_LIGAND
```
See Also:

Constant Field Values

NO_VALUE
```
private static final double NO_VALUE
```
See Also:

Constant Field Values

dataScaling
```
private float dataScaling
```

dataIsReducedDensity
```
private boolean dataIsReducedDensity
```

eigen
```
private javajs.util.Eigen eigen
```

rhoMolecules
```
private double[] rhoMolecules
```

type
```
private int type
```

nMolecules
```
private int nMolecules
```

isPromolecular
```
private boolean isPromolecular
```

bsOK
```
private BS bsOK
```

noValuesAtAll
```
private boolean noValuesAtAll
```

useAbsolute
```
private boolean useAbsolute
```

c
```
private static double c
```

rpower
```
private static double rpower
```

hess
```
private double[][] hess
```

grad
```
private double grad
```

gxTemp
```
private double gxTemp
```

gyTemp
```
private double gyTemp
```

gzTemp
```
private double gzTemp
```

gxxTemp
```
private double gxxTemp
```

gyyTemp
```
private double gyyTemp
```

gzzTemp
```
private double gzzTemp
```

gxyTemp
```
private double gxyTemp
```

gyzTemp
```
private double gyzTemp
```

gxzTemp
```
private double gxzTemp
```

eigenValues
```
private float[] eigenValues
```

test1
```
double test1
```

yzPlanesRaw
```
private float[][] yzPlanesRaw
```

yzCount
```
private int yzCount
```

yzPlanesRho
```
private float[][] yzPlanesRho
```

p0
```
private float[] p0
```

p1
```
private float[] p1
```

p2
```
private float[] p2
```

coef1
```
private static double[] coef1
```

coef2
```
private static double[] coef2
```

coef3
```
private static double[] coef3
```

zeta1
```
private static double[] zeta1
```

zeta2
```
private static double[] zeta2
```

zeta3
```
private static double[] zeta3
```

dMax
```
private static double[] dMax
```

Constructor Detail
- NciCalculation
```
public NciCalculation()
```

Method Detail
- getNoValue
```
public float getNoValue()
```
  Description copied from class: QuantumPlaneCalculation
  
  Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.
  
  Specified by:
  
  getNoValue in class QuantumPlaneCalculation
  
  Returns:
  
  NO_VALUE
- setupCalculation
```
public boolean setupCalculation(VolumeData volumeData,
                                BS bsSelected,
                                BS bsExcluded,
                                BS[] bsMolecules,
                                javajs.util.T3[] atomCoordAngstroms,
                                int firstAtomOffset,
                                boolean isReducedDensity,
                                javajs.util.T3[] points,
                                float[] parameters,
                                int testFlags)
```
- getParameter
```
private static double getParameter(float[] parameters,
                                   int i,
                                   double def,
                                   java.lang.String name)
```
- getBsOK
```
private void getBsOK()
```
  grid-based discrete SCF calculation needs to know which atoms to consider inter and which intramolecular
- createCube
```
public void createCube()
```
  Specified by:
  
  createCube in class QuantumCalculation
- initializeOnePoint
```
protected void initializeOnePoint()
```
  Overrides:
  
  initializeOnePoint in class QuantumCalculation
- initializeEigen
```
private void initializeEigen()
```
- getPlane
```
public void getPlane(int ix,
                     float[] yzPlane)
```
  Specified by:
  
  getPlane in class QuantumPlaneCalculation
- process
```
protected void process()
```
  Specified by:
  
  process in class QuantumCalculation
- getValue
```
private float getValue(double rho,
                       boolean isReducedDensity)
```
- processAtoms
```
private double processAtoms(int ix,
                            int iy,
                            int iz,
                            int index)
```
  At each grid point we need to calculate the sum of the atom-based promolecular data. We partition this calculation into molecular subsets if necessary, and we check for atoms that are too far away to make a difference before we waste time doing exponentiation. If index >= 0, then this is just a check for intra- vs. inter- molecularity based on promolecular density. This is needed for applying intra- and inter-molecular filters to SCF CUBE data.
  
  Parameters:
  
  ix -
  
  iy -
  
  iz -
  
  index -
  
  Returns:
  
  rho value or NO_VALUE
- setPlanes
```
public void setPlanes(float[][] planes)
```
  Raw file data planes are passed to us here from VolumeFileReader
  
  Specified by:
  
  setPlanes in class QuantumPlaneCalculation
  
  Parameters:
  
  planes -
- calcPlane
```
public void calcPlane(int x,
                      float[] plane)
```
  For reduced density only; coloring is done point by point.
  
  Specified by:
  
  calcPlane in class QuantumPlaneCalculation
  
  Parameters:
  
  x -
  
  plane - an OUTPUT plane, to be filled here and used by MarchingCubes
- process
```
public float process(int vA,
                     int vB,
                     float f)
```
  Passing the grid points of the two ends of an edge and a fraction to this method returns the value at a triangle point. This way we do not need to calculate this for EVERY point on the grid, only the ones that are part of the surface.
  
  Specified by:
  
  process in class QuantumPlaneCalculation
  
  Parameters:
  
  vA -
  
  vB -
  
  f -
  
  Returns:
  
  value at point f-way between vA and vB
- getPlaneValue
```
private double getPlaneValue(int vA)
```
  We always have four raw planes in hand; we just need to know which three to use in any particular case.
  
  Parameters:
  
  vA -
  
  Returns:
  
  value of sign(lambda2)*rho at this grid point

Class NciCalculation

Field Summary

Fields inherited from class org.jmol.quantum.QuantumCalculation

Constructor Summary

Method Summary

Methods inherited from class org.jmol.quantum.QuantumCalculation

Methods inherited from class java.lang.Object

Field Detail

havePoints

isReducedDensity

DEFAULT_RHOPLOT_SCF

DEFAULT_RHOPLOT_PRO

DEFAULT_RHOPARAM

rhoMin

rhoPlot

rhoParam

TYPE_ALL

TYPE_INTRA

TYPE_INTER

TYPE_LIGAND

NO_VALUE

dataScaling

dataIsReducedDensity

eigen

rhoMolecules

type

nMolecules

isPromolecular

bsOK

noValuesAtAll

useAbsolute

c

rpower

hess

grad

gxTemp

gyTemp

gzTemp

gxxTemp

gyyTemp

gzzTemp

gxyTemp

gyzTemp

gxzTemp

eigenValues

test1

yzPlanesRaw

yzCount

yzPlanesRho

p0

p1

p2

coef1

coef2

coef3

zeta1

zeta2

zeta3

dMax

Constructor Detail

NciCalculation

Method Detail

getNoValue

setupCalculation

getParameter

getBsOK

createCube

initializeOnePoint

initializeEigen

getPlane

process

getValue

processAtoms

setPlanes

calcPlane

process

getPlaneValue