org.jmol.jvxl.readers
Class Parameters

java.lang.Object
  extended by org.jmol.jvxl.readers.Parameters

public class Parameters
extends java.lang.Object


Field Summary
(package private)  boolean addHydrogens
           
 boolean allowVolumeRender
           
(package private) static float ANGSTROMS_PER_BOHR
           
(package private)  float[] aniosU
           
(package private)  float[] anisoB
           
(package private)  float[] anisotropy
           
(package private)  float assocCutoff
           
(package private)  int atomIndex
           
 RadiusData atomRadiusData
           
(package private)  boolean blockCubeData
           
 javax.vecmath.Point3f[] boundingBox
           
 java.util.BitSet[] bsExcluded
           
 java.util.BitSet bsIgnore
           
 java.util.BitSet bsSelected
           
 java.util.BitSet bsSolvent
           
(package private)  java.lang.String calculationType
           
(package private)  float cavityRadius
           
(package private)  javax.vecmath.Point3f center
           
(package private)  boolean colorByPhase
           
(package private)  boolean colorBySets
           
(package private)  boolean colorBySign
           
 boolean colorDensity
           
 ColorEncoder colorEncoder
           
(package private)  int colorNeg
           
(package private)  int colorNegLCAO
           
(package private)  int colorPhase
           
(package private)  int colorPos
           
(package private)  int colorPosLCAO
           
 int colorRgb
           
 boolean colorSchemeTranslucent
           
 ContactPair contactPair
           
 short[] contourColixes
           
(package private)  boolean contourFromZero
           
(package private)  javax.vecmath.Point3f contourIncrements
           
 float[] contoursDiscrete
           
 int contourType
           
 float cutoff
           
(package private)  boolean cutoffAutomatic
           
 int dataType
           
(package private)  boolean dataXYReversed
           
(package private) static int defaultColorFractionBase
           
(package private) static int defaultColorFractionRange
           
(package private) static int defaultColorNegative
           
(package private) static int defaultColorNegativeLCAO
           
(package private) static int defaultColorPositive
           
(package private) static int defaultColorPositiveLCAO
           
(package private) static int defaultContourCount
           
(package private) static float defaultCutoff
           
(package private) static int defaultEdgeFractionBase
           
(package private) static int defaultEdgeFractionRange
           
(package private) static float defaultLobeCutoff
           
(package private) static float defaultMappedDataMax
           
(package private) static float defaultMappedDataMin
           
(package private) static float defaultMepCutoff
           
(package private) static float defaultMepMax
           
(package private) static float defaultMepMin
           
(package private) static float defaultOrbitalCutoff
           
(package private) static float defaultOrbitalCutoffOld
           
(package private) static float defaultQMElectronDensityCutoff
           
static float defaultQMOrbitalCutoff
           
(package private) static float defaultSolventRadius
           
(package private)  float distance
           
 boolean doFullMolecular
           
(package private)  int downsampleFactor
           
(package private)  javax.vecmath.Matrix3f eccentricityMatrix
           
(package private)  javax.vecmath.Matrix3f eccentricityMatrixInverse
           
(package private)  float eccentricityRatio
           
(package private)  float eccentricityScale
           
(package private)  float envelopeRadius
           
(package private)  int fileIndex
           
(package private)  java.lang.String fileName
           
 boolean fullyLit
           
 java.lang.Object func
           
 java.util.List<java.lang.Object> functionInfo
           
(package private) static int HAS_MAXGRID
           
(package private)  boolean iAddGridPoints
           
(package private)  boolean insideOut
           
 java.util.BitSet[] intersection
           
(package private) static int IS_POINTMAPPABLE
           
(package private) static int IS_SILENT
           
(package private) static int IS_SLABBABLE
           
static int IS_SOLVENTTYPE
           
(package private)  boolean isAngstroms
           
(package private)  boolean isAnisotropic
           
 boolean isBicolorMap
           
(package private)  boolean isCavity
           
(package private)  boolean isColorReversed
           
 boolean isContoured
           
 boolean isCutoffAbsolute
           
(package private)  boolean isEccentric
           
 boolean isPeriodic
           
(package private)  boolean isPositiveOnly
           
 boolean isSilent
           
 boolean isSquared
           
 boolean isXLowToHigh
           
(package private)  java.lang.String lcaoType
           
(package private)  boolean logCompression
           
(package private)  boolean logCube
           
(package private)  boolean logMessages
           
(package private)  float mappedDataMax
           
(package private)  float mappedDataMin
           
(package private)  int maxSet
           
 int mep_calcType
           
(package private)  int mep_gridMax
           
(package private)  float mep_marginAngstroms
           
static int MEP_MAX_GRID
           
(package private)  float mep_ptsPerAngstrom
           
(package private)  int minSet
           
static int MO_MAX_GRID
           
(package private)  java.util.Map<java.lang.String,java.lang.Object> moData
           
(package private)  int modelIndex
           
(package private) static int nContourMax
           
(package private)  int nContours
           
(package private) static int NO_ANISOTROPY
           
 javax.vecmath.Point3f origin
           
(package private)  float[] parameters
           
(package private)  int plane_gridMax
           
(package private)  float plane_ptsPerAngstrom
           
(package private)  java.lang.Boolean pocket
           
(package private)  javax.vecmath.Point3f point
           
 javax.vecmath.Point3f points
           
 float propertyDistanceMax
           
(package private)  boolean propertySmoothing
           
(package private)  int propertySmoothingPower
           
(package private)  int psi_l
           
(package private)  int psi_m
           
 int psi_monteCarloCount
           
(package private)  int psi_n
           
(package private)  float psi_ptsPerAngstrom
           
(package private)  float psi_Znuc
           
(package private)  int qm_gridMax
           
(package private)  float qm_marginAngstroms
           
(package private)  float[] qm_moLinearCombination
           
(package private)  int qm_moNumber
           
(package private)  int qm_nAtoms
           
(package private)  float qm_ptsPerAngstrom
           
(package private) static int QM_TYPE_GAUSSIAN
           
(package private) static int QM_TYPE_NCI_PRO
           
(package private) static int QM_TYPE_NCI_SCF
           
(package private) static int QM_TYPE_SLATER
           
(package private) static int QM_TYPE_UNKNOWN
           
(package private) static int QM_TYPE_VOLUME_DATA
           
(package private)  int qmOrbitalCount
           
(package private)  int qmOrbitalType
           
 int randomSeed
           
(package private)  boolean rangeAll
           
 boolean rangeDefined
           
(package private)  boolean rangeSelected
           
(package private)  boolean readAllData
           
 float resolution
           
(package private)  float scale
           
 float scale3d
           
(package private)  java.lang.String script
           
 float sigma
           
 java.util.List<java.lang.Object[]> slabInfo
           
(package private)  float slabPlaneOffset
           
(package private)  int solvent_gridMax
           
(package private)  float solvent_ptsPerAngstrom
           
(package private)  float solventExtendedAtomRadius
           
(package private)  float solventRadius
           
(package private)  int state
           
static int STATE_DATA_COLORED
           
static int STATE_DATA_READ
           
static int STATE_INITIALIZED
           
static int STATE_UNINITIALIZED
           
 javax.vecmath.Point3f steps
           
(package private) static int SURFACE_ATOMICORBITAL
           
(package private) static int SURFACE_ELLIPSOID2
           
(package private) static int SURFACE_ELLIPSOID3
           
(package private) static int SURFACE_FUNCTIONXY
           
(package private) static int SURFACE_FUNCTIONXYZ
           
(package private) static int SURFACE_INTERSECT
           
(package private) static int SURFACE_LCAOCARTOON
           
(package private) static int SURFACE_LOBE
           
static int SURFACE_LONEPAIR
           
(package private) static int SURFACE_MEP
           
(package private) static int SURFACE_MLP
           
(package private) static int SURFACE_MOLECULAR
           
(package private) static int SURFACE_MOLECULARORBITAL
           
(package private) static int SURFACE_NCI
           
(package private) static int SURFACE_NOMAP
           
(package private) static int SURFACE_NONE
           
(package private) static int SURFACE_PROPERTY
           
static int SURFACE_RADICAL
           
(package private) static int SURFACE_SASURFACE
           
(package private) static int SURFACE_SOLVENT
           
(package private) static int SURFACE_SPHERE
           
(package private)  int surfaceType
           
 int testFlags
           
 javax.vecmath.Point4f thePlane
           
(package private)  float[] theProperty
           
(package private)  int thisContour
           
(package private)  java.lang.String[] title
           
 boolean usePropertyForColorRange
           
(package private)  float valueMappedToBlue
           
(package private)  float valueMappedToRed
           
 int[] vertexSource
           
 VolumeData volumeData
           
 
Constructor Summary
Parameters()
           
 
Method Summary
 void addSlabInfo(java.lang.Object[] slabObject)
           
private  java.lang.String getScriptParams()
           
(package private)  void initialize()
           
 void resetForMapping(boolean haveSurface)
          reset some parameters at the "MAP" keyword
(package private)  void setAnisotropy(javax.vecmath.Point3f pt)
           
(package private)  boolean setAtomicOrbital(float[] nlmZprs)
           
(package private)  void setEccentricity(javax.vecmath.Point4f info)
           
 void setEllipsoid(float[] bList)
           
(package private)  void setEllipsoid(javax.vecmath.Point4f v)
           
(package private)  void setFunctionXY(java.util.List<java.lang.Object> value)
           
(package private)  void setFunctionXYZ(java.util.List<java.lang.Object> value)
           
(package private)  void setLcao(java.lang.String type, int colorPtr)
           
(package private)  void setLobe(javax.vecmath.Point4f v)
           
(package private)  void setLp(javax.vecmath.Point4f v)
           
(package private)  void setMapRanges(SurfaceReader surfaceReader, boolean haveData)
           
(package private)  void setMep(float[] charges, boolean isMLP)
           
(package private)  void setMO(int iMo, float[] linearCombination)
           
(package private)  void setNci(boolean isPromolecular)
           
(package private)  void setPlane(javax.vecmath.Point4f plane)
           
(package private)  void setRadical(javax.vecmath.Point4f v)
           
(package private)  void setSolvent(java.lang.String propertyName, float radius)
           
(package private)  void setSphere(float radius)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

STATE_UNINITIALIZED

public static final int STATE_UNINITIALIZED
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Constant Field Values

STATE_INITIALIZED

public static final int STATE_INITIALIZED
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Constant Field Values

STATE_DATA_READ

public static final int STATE_DATA_READ
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Constant Field Values

STATE_DATA_COLORED

public static final int STATE_DATA_COLORED
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Constant Field Values

state

int state

testFlags

public int testFlags

logMessages

boolean logMessages

logCompression

boolean logCompression

logCube

boolean logCube

isSilent

public boolean isSilent

assocCutoff

float assocCutoff

NO_ANISOTROPY

static final int NO_ANISOTROPY
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Constant Field Values

IS_SILENT

static final int IS_SILENT
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Constant Field Values

IS_SOLVENTTYPE

public static final int IS_SOLVENTTYPE
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Constant Field Values

HAS_MAXGRID

static final int HAS_MAXGRID
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IS_POINTMAPPABLE

static final int IS_POINTMAPPABLE
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IS_SLABBABLE

static final int IS_SLABBABLE
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dataType

public int dataType

surfaceType

int surfaceType

SURFACE_NONE

static final int SURFACE_NONE
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SURFACE_SPHERE

static final int SURFACE_SPHERE
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SURFACE_ELLIPSOID2

static final int SURFACE_ELLIPSOID2
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SURFACE_ELLIPSOID3

static final int SURFACE_ELLIPSOID3
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SURFACE_LOBE

static final int SURFACE_LOBE
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SURFACE_LCAOCARTOON

static final int SURFACE_LCAOCARTOON
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SURFACE_LONEPAIR

public static final int SURFACE_LONEPAIR
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SURFACE_RADICAL

public static final int SURFACE_RADICAL
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SURFACE_FUNCTIONXY

static final int SURFACE_FUNCTIONXY
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SURFACE_FUNCTIONXYZ

static final int SURFACE_FUNCTIONXYZ
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SURFACE_SOLVENT

static final int SURFACE_SOLVENT
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SURFACE_SASURFACE

static final int SURFACE_SASURFACE
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SURFACE_MOLECULARORBITAL

static final int SURFACE_MOLECULARORBITAL
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SURFACE_ATOMICORBITAL

static final int SURFACE_ATOMICORBITAL
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SURFACE_MEP

static final int SURFACE_MEP
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SURFACE_MLP

static final int SURFACE_MLP
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SURFACE_MOLECULAR

static final int SURFACE_MOLECULAR
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SURFACE_NCI

static final int SURFACE_NCI
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SURFACE_INTERSECT

static final int SURFACE_INTERSECT
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SURFACE_NOMAP

static final int SURFACE_NOMAP
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SURFACE_PROPERTY

static final int SURFACE_PROPERTY
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Constant Field Values

calculationType

java.lang.String calculationType

atomRadiusData

public RadiusData atomRadiusData

addHydrogens

boolean addHydrogens

solventRadius

float solventRadius

solventExtendedAtomRadius

float solventExtendedAtomRadius

propertySmoothing

boolean propertySmoothing

propertySmoothingPower

int propertySmoothingPower

envelopeRadius

float envelopeRadius

cavityRadius

float cavityRadius

isCavity

boolean isCavity

pocket

java.lang.Boolean pocket

minSet

int minSet

slabInfo

public java.util.List<java.lang.Object[]> slabInfo

slabPlaneOffset

float slabPlaneOffset

theProperty

float[] theProperty

solvent_ptsPerAngstrom

float solvent_ptsPerAngstrom

solvent_gridMax

int solvent_gridMax

plane_ptsPerAngstrom

float plane_ptsPerAngstrom

plane_gridMax

int plane_gridMax

ANGSTROMS_PER_BOHR

static final float ANGSTROMS_PER_BOHR
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Constant Field Values

defaultEdgeFractionBase

static final int defaultEdgeFractionBase
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defaultEdgeFractionRange

static final int defaultEdgeFractionRange
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defaultColorFractionBase

static final int defaultColorFractionBase
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defaultColorFractionRange

static final int defaultColorFractionRange
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defaultMappedDataMin

static final float defaultMappedDataMin
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defaultMappedDataMax

static final float defaultMappedDataMax
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defaultCutoff

static final float defaultCutoff
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defaultOrbitalCutoff

static final float defaultOrbitalCutoff
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defaultLobeCutoff

static final float defaultLobeCutoff
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Constant Field Values

defaultOrbitalCutoffOld

static final float defaultOrbitalCutoffOld
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Constant Field Values

defaultQMOrbitalCutoff

public static final float defaultQMOrbitalCutoff
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defaultQMElectronDensityCutoff

static final float defaultQMElectronDensityCutoff
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defaultContourCount

static final int defaultContourCount
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nContourMax

static final int nContourMax
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defaultColorNegative

static final int defaultColorNegative
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defaultColorPositive

static final int defaultColorPositive
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defaultColorNegativeLCAO

static final int defaultColorNegativeLCAO
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defaultColorPositiveLCAO

static final int defaultColorPositiveLCAO
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Constant Field Values

defaultSolventRadius

static final float defaultSolventRadius
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defaultMepCutoff

static final float defaultMepCutoff
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defaultMepMin

static final float defaultMepMin
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defaultMepMax

static final float defaultMepMax
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Constant Field Values

colorBySign

boolean colorBySign

colorByPhase

boolean colorByPhase

colorBySets

boolean colorBySets

colorRgb

public int colorRgb

colorNeg

int colorNeg

colorPos

int colorPos

colorPosLCAO

int colorPosLCAO

colorNegLCAO

int colorNegLCAO

colorPhase

int colorPhase

colorDensity

public boolean colorDensity

iAddGridPoints

boolean iAddGridPoints

atomIndex

int atomIndex

isAngstroms

boolean isAngstroms

scale

float scale

scale3d

public float scale3d

anisotropy

float[] anisotropy

isAnisotropic

boolean isAnisotropic

eccentricityMatrix

javax.vecmath.Matrix3f eccentricityMatrix

eccentricityMatrixInverse

javax.vecmath.Matrix3f eccentricityMatrixInverse

isEccentric

boolean isEccentric

eccentricityScale

float eccentricityScale

eccentricityRatio

float eccentricityRatio

aniosU

float[] aniosU

anisoB

float[] anisoB

lcaoType

java.lang.String lcaoType

functionInfo

public java.util.List<java.lang.Object> functionInfo

psi_n

int psi_n

psi_l

int psi_l

psi_m

int psi_m

psi_Znuc

float psi_Znuc

psi_ptsPerAngstrom

float psi_ptsPerAngstrom

psi_monteCarloCount

public int psi_monteCarloCount

MEP_MAX_GRID

public static final int MEP_MAX_GRID
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Constant Field Values

mep_gridMax

int mep_gridMax

mep_ptsPerAngstrom

float mep_ptsPerAngstrom

mep_marginAngstroms

float mep_marginAngstroms

mep_calcType

public int mep_calcType

qmOrbitalType

int qmOrbitalType

qmOrbitalCount

int qmOrbitalCount

QM_TYPE_UNKNOWN

static final int QM_TYPE_UNKNOWN
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Constant Field Values

QM_TYPE_GAUSSIAN

static final int QM_TYPE_GAUSSIAN
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QM_TYPE_SLATER

static final int QM_TYPE_SLATER
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QM_TYPE_NCI_PRO

static final int QM_TYPE_NCI_PRO
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QM_TYPE_NCI_SCF

static final int QM_TYPE_NCI_SCF
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QM_TYPE_VOLUME_DATA

static final int QM_TYPE_VOLUME_DATA
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Constant Field Values

moData

java.util.Map<java.lang.String,java.lang.Object> moData

MO_MAX_GRID

public static final int MO_MAX_GRID
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Constant Field Values

qm_gridMax

int qm_gridMax

qm_ptsPerAngstrom

float qm_ptsPerAngstrom

qm_marginAngstroms

float qm_marginAngstroms

qm_nAtoms

int qm_nAtoms

qm_moNumber

int qm_moNumber

qm_moLinearCombination

float[] qm_moLinearCombination

center

javax.vecmath.Point3f center

point

javax.vecmath.Point3f point

distance

float distance

allowVolumeRender

public boolean allowVolumeRender

script

java.lang.String script

bsSelected

public java.util.BitSet bsSelected

bsIgnore

public java.util.BitSet bsIgnore

bsSolvent

public java.util.BitSet bsSolvent

func

public java.lang.Object func

title

java.lang.String[] title

blockCubeData

boolean blockCubeData

readAllData

boolean readAllData

fileIndex

int fileIndex

fileName

java.lang.String fileName

modelIndex

int modelIndex

isXLowToHigh

public boolean isXLowToHigh

insideOut

boolean insideOut

dataXYReversed

boolean dataXYReversed

cutoff

public float cutoff

sigma

public float sigma

cutoffAutomatic

boolean cutoffAutomatic

isCutoffAbsolute

public boolean isCutoffAbsolute

isPositiveOnly

boolean isPositiveOnly

rangeAll

boolean rangeAll

rangeSelected

boolean rangeSelected

rangeDefined

public boolean rangeDefined

valueMappedToRed

float valueMappedToRed

valueMappedToBlue

float valueMappedToBlue

mappedDataMin

float mappedDataMin

mappedDataMax

float mappedDataMax

isColorReversed

boolean isColorReversed

isBicolorMap

public boolean isBicolorMap

isSquared

public boolean isSquared

thePlane

public javax.vecmath.Point4f thePlane

isContoured

public boolean isContoured

nContours

int nContours

thisContour

int thisContour

contourFromZero

boolean contourFromZero

parameters

float[] parameters

resolution

public float resolution

downsampleFactor

int downsampleFactor

maxSet

int maxSet

contoursDiscrete

public float[] contoursDiscrete

contourColixes

public short[] contourColixes

contourIncrements

javax.vecmath.Point3f contourIncrements

boundingBox

public javax.vecmath.Point3f[] boundingBox

bsExcluded

public java.util.BitSet[] bsExcluded

contourType

public int contourType

colorSchemeTranslucent

public boolean colorSchemeTranslucent

colorEncoder

public ColorEncoder colorEncoder

usePropertyForColorRange

public boolean usePropertyForColorRange

isPeriodic

public boolean isPeriodic

doFullMolecular

public boolean doFullMolecular

propertyDistanceMax

public float propertyDistanceMax

randomSeed

public int randomSeed

fullyLit

public boolean fullyLit

vertexSource

public int[] vertexSource

intersection

public java.util.BitSet[] intersection

origin

public javax.vecmath.Point3f origin

steps

public javax.vecmath.Point3f steps

points

public javax.vecmath.Point3f points

volumeData

public VolumeData volumeData

contactPair

public ContactPair contactPair
Constructor Detail

Parameters

public Parameters()
Method Detail

initialize

void initialize()

setAnisotropy

void setAnisotropy(javax.vecmath.Point3f pt)

setEccentricity

void setEccentricity(javax.vecmath.Point4f info)

setPlane

void setPlane(javax.vecmath.Point4f plane)

setSphere

void setSphere(float radius)

setEllipsoid

void setEllipsoid(javax.vecmath.Point4f v)

setEllipsoid

public void setEllipsoid(float[] bList)

setLobe

void setLobe(javax.vecmath.Point4f v)

getScriptParams

private java.lang.String getScriptParams()

setLp

void setLp(javax.vecmath.Point4f v)

setRadical

void setRadical(javax.vecmath.Point4f v)

setLcao

void setLcao(java.lang.String type,
             int colorPtr)

setSolvent

void setSolvent(java.lang.String propertyName,
                float radius)

setFunctionXY

void setFunctionXY(java.util.List<java.lang.Object> value)

setFunctionXYZ

void setFunctionXYZ(java.util.List<java.lang.Object> value)

setAtomicOrbital

boolean setAtomicOrbital(float[] nlmZprs)

setMep

void setMep(float[] charges,
            boolean isMLP)

setNci

void setNci(boolean isPromolecular)

setMO

void setMO(int iMo,
           float[] linearCombination)

setMapRanges

void setMapRanges(SurfaceReader surfaceReader,
                  boolean haveData)

resetForMapping

public void resetForMapping(boolean haveSurface)
reset some parameters at the "MAP" keyword

Parameters:
haveSurface -

addSlabInfo

public void addSlabInfo(java.lang.Object[] slabObject)