Package org.jmol.quantum
Class NciCalculation
java.lang.Object
org.jmol.quantum.QuantumCalculation
org.jmol.quantum.QuantumPlaneCalculation
org.jmol.quantum.NciCalculation
-
Field Summary
Fields inherited from class org.jmol.quantum.QuantumCalculation
atomIndex, bohr_per_angstrom, bsExcluded, countsXYZ, doDebug, firstAtomOffset, integration, nX, nY, nZ, originBohr, points, qmAtoms, rangeBohrOrAngstroms, stepBohr, thisAtom, unitFactor, volume, voxelData, voxelDataTemp, X, X2, xBohr, xMax, xMin, Y, Y2, yBohr, yMax, yMin, Z, Z2, zBohr, zMax, zMin
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
calcPlane
(int x, float[] plane) For reduced density only; coloring is done point by point.void
float
Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.void
getPlane
(int ix, float[] yzPlane) protected void
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.void
setPlanes
(float[][] planes) Raw file data planes are passed to us here from VolumeFileReaderboolean
setupCalculation
(VolumeData volumeData, BS bsSelected, BS bsExcluded, BS[] bsMolecules, T3[] atomCoordAngstroms, int firstAtomOffset, boolean isReducedDensity, T3[] points, float[] parameters, int testFlags) Methods inherited from class org.jmol.quantum.QuantumCalculation
getIntegration, initialize, initialize0, initializeOnePointQC, processPoints, processPt, setMinMax, setupCoordinates, setXYZBohr
-
Constructor Details
-
NciCalculation
public NciCalculation()
-
-
Method Details
-
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 classQuantumPlaneCalculation
- Returns:
- NO_VALUE
-
setupCalculation
-
createCube
public void createCube()- Specified by:
createCube
in classQuantumCalculation
-
initializeOnePoint
protected void initializeOnePoint()- Overrides:
initializeOnePoint
in classQuantumCalculation
-
getPlane
public void getPlane(int ix, float[] yzPlane) - Specified by:
getPlane
in classQuantumPlaneCalculation
-
process
protected void process()- Specified by:
process
in classQuantumCalculation
-
setPlanes
public void setPlanes(float[][] planes) Raw file data planes are passed to us here from VolumeFileReader- Specified by:
setPlanes
in classQuantumPlaneCalculation
- Parameters:
planes
-
-
calcPlane
public void calcPlane(int x, float[] plane) For reduced density only; coloring is done point by point.- Specified by:
calcPlane
in classQuantumPlaneCalculation
- 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 classQuantumPlaneCalculation
- Parameters:
vA
-vB
-f
-- Returns:
- value at point f-way between vA and vB
-