org.jmol.jvxl.readers

Class Parameters

public class Parameters extends Object

Field Summary
static floatANGSTROMS_PER_BOHR
booleanaddHydrogens
float[]aniosU
float[]anisoB
float[]anisotropy
floatassocCutoff
intatomIndex
booleanblockCubeData
BitSetbsIgnore
BitSetbsSelected
BitSetbsSolvent
StringcalculationType
Point4fcappingPlane
floatcavityRadius
Point3fcenter
booleancolorByPhase
booleancolorBySets
booleancolorBySign
intcolorNeg
intcolorNegLCAO
intcolorPhase
intcolorPos
intcolorPosLCAO
booleancontourFromZero
floatcutoff
static intCAN_CONTOUR
intdataType
static intdefaultColorFractionBase
static intdefaultColorFractionRange
static intdefaultColorNegative
static intdefaultColorNegativeLCAO
static intdefaultColorPositive
static intdefaultColorPositiveLCAO
static intdefaultContourCount
static floatdefaultCutoff
static intdefaultEdgeFractionBase
static intdefaultEdgeFractionRange
static floatdefaultMappedDataMax
static floatdefaultMappedDataMin
static floatdefaultMepCutoff
static floatdefaultMepMax
static floatdefaultMepMin
static floatdefaultOrbitalCutoff
static floatdefaultQMOrbitalCutoff
static floatdefaultSolventRadius
floatdistance
booleandoCapIsosurface
intdownsampleFactor
Matrix3feccentricityMatrix
Matrix3feccentricityMatrixInverse
floateccentricityRatio
floateccentricityScale
floatenvelopeRadius
intfileIndex
StringfileName
VectorfunctionXYinfo
static intHAS_MAXGRID
booleaniAddGridPoints
booleaninsideOut
booleanisAngstroms
booleanisAnisotropic
booleanisBicolorMap
booleanisCavity
booleanisColorReversed
booleanisContoured
booleanisCutoffAbsolute
booleanisEccentric
booleanisPositiveOnly
booleanisSilent
booleanisSquared
booleanisXLowToHigh
booleaniUseBitSets
static intIS_SILENT
static intIS_SOLVENTTYPE
StringlcaoType
booleanlogCompression
booleanlogCube
booleanlogMessages
floatmappedDataMax
floatmappedDataMin
intmaxSet
intmep_gridMax
floatmep_marginAngstroms
floatmep_ptsPerAngstrom
intminSet
Hashtablemo
float[]moCoefficients
intmodelIndex
HashtablemoData
static intMEP_MAX_GRID
static intMO_MAX_GRID
static intnContourMax
intnContours
static intNO_ANISOTROPY
Booleanpocket
Point3fpoint
booleanpropertySmoothing
intpsi_l
intpsi_m
intpsi_n
floatpsi_ptsPerAngstrom
floatpsi_Znuc
intqmOrbitalCount
intqmOrbitalType
intqm_gridMax
floatqm_marginAngstroms
intqm_moNumber
intqm_nAtoms
floatqm_ptsPerAngstrom
static intQM_TYPE_GAUSSIAN
static intQM_TYPE_SLATER
static intQM_TYPE_UNKNOWN
booleanrangeAll
booleanrangeDefined
booleanremappable
floatresolution
floatscale
Stringscript
floatsolventAtomRadiusAbsolute
floatsolventAtomRadiusFactor
floatsolventAtomRadiusOffset
floatsolventExtendedAtomRadius
floatsolventRadius
intsolvent_gridMax
floatsolvent_ptsPerAngstrom
intstate
intsurfaceType
static intSTATE_DATA_COLORED
static intSTATE_DATA_READ
static intSTATE_INITIALIZED
static intSTATE_UNINITIALIZED
static intSURFACE_ATOMICORBITAL
static intSURFACE_ELLIPSOID2
static intSURFACE_ELLIPSOID3
static intSURFACE_FILE
static intSURFACE_FUNCTIONXY
static intSURFACE_INFO
static intSURFACE_LCAOCARTOON
static intSURFACE_LOBE
static intSURFACE_MEP
static intSURFACE_MOLECULAR
static intSURFACE_MOLECULARORBITAL
static intSURFACE_NOMAP
static intSURFACE_NONE
static intSURFACE_PROPERTY
static intSURFACE_SASURFACE
static intSURFACE_SOLVENT
static intSURFACE_SPHERE
Point4fthePlane
float[]theProperty
intthisContour
String[]title
booleanuseIonic
floatvalueMappedToBlue
floatvalueMappedToRed
Method Summary
voidinitialize()
voidsetAnisotropy(Point3f pt)
booleansetAtomicOrbital(float[] nlmZ)
voidsetEccentricity(Point4f info)
voidsetEllipsoid(Point4f v)
voidsetEllipsoid(float[] bList)
voidsetFunctionXY(Vector value)
voidsetLcao(String type, int colorPtr)
voidsetLobe(Point4f v)
voidsetMapRanges(VoxelReader voxelReader)
voidsetMep(float[] charges, boolean isRangeDefined)
voidsetMO(int iMo)
voidsetPlane(Point4f plane)
voidsetRadius(boolean useIonic, float radius)
voidsetSolvent(String propertyName, float radius)
voidsetSphere(float radius)

Field Detail

ANGSTROMS_PER_BOHR

static final float ANGSTROMS_PER_BOHR

addHydrogens

boolean addHydrogens

aniosU

float[] aniosU

anisoB

float[] anisoB

anisotropy

float[] anisotropy

assocCutoff

float assocCutoff

atomIndex

int atomIndex

blockCubeData

boolean blockCubeData

bsIgnore

BitSet bsIgnore

bsSelected

BitSet bsSelected

bsSolvent

BitSet bsSolvent

calculationType

String calculationType

cappingPlane

Point4f cappingPlane

cavityRadius

float cavityRadius

center

Point3f center

colorByPhase

boolean colorByPhase

colorBySets

boolean colorBySets

colorBySign

boolean colorBySign

colorNeg

int colorNeg

colorNegLCAO

int colorNegLCAO

colorPhase

int colorPhase

colorPos

int colorPos

colorPosLCAO

int colorPosLCAO

contourFromZero

boolean contourFromZero

cutoff

float cutoff

CAN_CONTOUR

static final int CAN_CONTOUR

dataType

int dataType

defaultColorFractionBase

static final int defaultColorFractionBase

defaultColorFractionRange

static final int defaultColorFractionRange

defaultColorNegative

static final int defaultColorNegative

defaultColorNegativeLCAO

static final int defaultColorNegativeLCAO

defaultColorPositive

static final int defaultColorPositive

defaultColorPositiveLCAO

static final int defaultColorPositiveLCAO

defaultContourCount

static final int defaultContourCount

defaultCutoff

static final float defaultCutoff

defaultEdgeFractionBase

static final int defaultEdgeFractionBase

defaultEdgeFractionRange

static final int defaultEdgeFractionRange

defaultMappedDataMax

static final float defaultMappedDataMax

defaultMappedDataMin

static final float defaultMappedDataMin

defaultMepCutoff

static final float defaultMepCutoff

defaultMepMax

static final float defaultMepMax

defaultMepMin

static final float defaultMepMin

defaultOrbitalCutoff

static final float defaultOrbitalCutoff

defaultQMOrbitalCutoff

public static final float defaultQMOrbitalCutoff

defaultSolventRadius

static final float defaultSolventRadius

distance

float distance

doCapIsosurface

boolean doCapIsosurface

downsampleFactor

int downsampleFactor

eccentricityMatrix

Matrix3f eccentricityMatrix

eccentricityMatrixInverse

Matrix3f eccentricityMatrixInverse

eccentricityRatio

float eccentricityRatio

eccentricityScale

float eccentricityScale

envelopeRadius

float envelopeRadius

fileIndex

int fileIndex

fileName

String fileName

functionXYinfo

Vector functionXYinfo

HAS_MAXGRID

static final int HAS_MAXGRID

iAddGridPoints

boolean iAddGridPoints

insideOut

boolean insideOut

isAngstroms

boolean isAngstroms

isAnisotropic

boolean isAnisotropic

isBicolorMap

boolean isBicolorMap

isCavity

boolean isCavity

isColorReversed

boolean isColorReversed

isContoured

boolean isContoured

isCutoffAbsolute

boolean isCutoffAbsolute

isEccentric

boolean isEccentric

isPositiveOnly

boolean isPositiveOnly

isSilent

boolean isSilent

isSquared

boolean isSquared

isXLowToHigh

boolean isXLowToHigh

iUseBitSets

boolean iUseBitSets

IS_SILENT

static final int IS_SILENT

IS_SOLVENTTYPE

static final int IS_SOLVENTTYPE

lcaoType

String lcaoType

logCompression

boolean logCompression

logCube

boolean logCube

logMessages

boolean logMessages

mappedDataMax

float mappedDataMax

mappedDataMin

float mappedDataMin

maxSet

int maxSet

mep_gridMax

int mep_gridMax

mep_marginAngstroms

float mep_marginAngstroms

mep_ptsPerAngstrom

float mep_ptsPerAngstrom

minSet

int minSet

mo

Hashtable mo

moCoefficients

float[] moCoefficients

modelIndex

int modelIndex

moData

Hashtable moData

MEP_MAX_GRID

public static final int MEP_MAX_GRID

MO_MAX_GRID

public static final int MO_MAX_GRID

nContourMax

static final int nContourMax

nContours

int nContours

NO_ANISOTROPY

static final int NO_ANISOTROPY

pocket

Boolean pocket

point

Point3f point

propertySmoothing

boolean propertySmoothing

psi_l

int psi_l

psi_m

int psi_m

psi_n

int psi_n

psi_ptsPerAngstrom

float psi_ptsPerAngstrom

psi_Znuc

float psi_Znuc

qmOrbitalCount

int qmOrbitalCount

qmOrbitalType

int qmOrbitalType

qm_gridMax

int qm_gridMax

qm_marginAngstroms

float qm_marginAngstroms

qm_moNumber

int qm_moNumber

qm_nAtoms

int qm_nAtoms

qm_ptsPerAngstrom

float qm_ptsPerAngstrom

QM_TYPE_GAUSSIAN

static final int QM_TYPE_GAUSSIAN

QM_TYPE_SLATER

static final int QM_TYPE_SLATER

QM_TYPE_UNKNOWN

static final int QM_TYPE_UNKNOWN

rangeAll

boolean rangeAll

rangeDefined

boolean rangeDefined

remappable

boolean remappable

resolution

float resolution

scale

float scale

script

String script

solventAtomRadiusAbsolute

float solventAtomRadiusAbsolute

solventAtomRadiusFactor

float solventAtomRadiusFactor

solventAtomRadiusOffset

float solventAtomRadiusOffset

solventExtendedAtomRadius

float solventExtendedAtomRadius

solventRadius

float solventRadius

solvent_gridMax

int solvent_gridMax

solvent_ptsPerAngstrom

float solvent_ptsPerAngstrom

state

int state

surfaceType

int surfaceType

STATE_DATA_COLORED

public static final int STATE_DATA_COLORED

STATE_DATA_READ

public static final int STATE_DATA_READ

STATE_INITIALIZED

public static final int STATE_INITIALIZED

STATE_UNINITIALIZED

public static final int STATE_UNINITIALIZED

SURFACE_ATOMICORBITAL

static final int SURFACE_ATOMICORBITAL

SURFACE_ELLIPSOID2

static final int SURFACE_ELLIPSOID2

SURFACE_ELLIPSOID3

static final int SURFACE_ELLIPSOID3

SURFACE_FILE

static final int SURFACE_FILE

SURFACE_FUNCTIONXY

static final int SURFACE_FUNCTIONXY

SURFACE_INFO

static final int SURFACE_INFO

SURFACE_LCAOCARTOON

static final int SURFACE_LCAOCARTOON

SURFACE_LOBE

static final int SURFACE_LOBE

SURFACE_MEP

static final int SURFACE_MEP

SURFACE_MOLECULAR

static final int SURFACE_MOLECULAR

SURFACE_MOLECULARORBITAL

static final int SURFACE_MOLECULARORBITAL

SURFACE_NOMAP

static final int SURFACE_NOMAP

SURFACE_NONE

static final int SURFACE_NONE

SURFACE_PROPERTY

static final int SURFACE_PROPERTY

SURFACE_SASURFACE

static final int SURFACE_SASURFACE

SURFACE_SOLVENT

static final int SURFACE_SOLVENT

SURFACE_SPHERE

static final int SURFACE_SPHERE

thePlane

Point4f thePlane

theProperty

float[] theProperty

thisContour

int thisContour

title

String[] title

useIonic

boolean useIonic

valueMappedToBlue

float valueMappedToBlue

valueMappedToRed

float valueMappedToRed

Method Detail

initialize

void initialize()

setAnisotropy

void setAnisotropy(Point3f pt)

setAtomicOrbital

boolean setAtomicOrbital(float[] nlmZ)

setEccentricity

void setEccentricity(Point4f info)

setEllipsoid

void setEllipsoid(Point4f v)

setEllipsoid

public void setEllipsoid(float[] bList)

setFunctionXY

void setFunctionXY(Vector value)

setLcao

void setLcao(String type, int colorPtr)

setLobe

void setLobe(Point4f v)

setMapRanges

void setMapRanges(VoxelReader voxelReader)

setMep

void setMep(float[] charges, boolean isRangeDefined)

setMO

void setMO(int iMo)

setPlane

void setPlane(Point4f plane)

setRadius

void setRadius(boolean useIonic, float radius)

setSolvent

void setSolvent(String propertyName, float radius)

setSphere

void setSphere(float radius)