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
           
(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
           
(package private)  boolean blockCubeData
           
(package private)  java.util.BitSet bsIgnore
           
(package private)  java.util.BitSet bsSelected
           
(package private)  java.util.BitSet bsSolvent
           
(package private)  java.lang.String calculationType
           
(package private) static int CAN_CONTOUR
           
(package private)  javax.vecmath.Point4f cappingPlane
           
(package private)  float cavityRadius
           
(package private)  javax.vecmath.Point3f center
           
(package private)  boolean colorByPhase
           
(package private)  boolean colorBySets
           
(package private)  boolean colorBySign
           
(package private)  int colorNeg
           
(package private)  int colorNegLCAO
           
(package private)  int colorPhase
           
(package private)  int colorPos
           
(package private)  int colorPosLCAO
           
(package private)  boolean contourFromZero
           
(package private)  float cutoff
           
 int dataType
           
(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 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 defaultQMElectronDensityCutoff
           
static float defaultQMOrbitalCutoff
           
(package private) static float defaultSolventRadius
           
(package private)  float distance
           
(package private)  boolean doCapIsosurface
           
(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
           
 java.util.Vector functionXYinfo
           
(package private) static int HAS_MAXGRID
           
(package private)  boolean iAddGridPoints
           
(package private)  boolean insideOut
           
(package private) static int IS_SILENT
           
static int IS_SOLVENTTYPE
           
(package private)  boolean isAngstroms
           
(package private)  boolean isAnisotropic
           
(package private)  boolean isBicolorMap
           
(package private)  boolean isCavity
           
(package private)  boolean isColorReversed
           
(package private)  boolean isContoured
           
(package private)  boolean isCutoffAbsolute
           
(package private)  boolean isEccentric
           
(package private)  boolean isPositiveOnly
           
(package private)  boolean isSilent
           
(package private)  boolean isSquared
           
(package private)  boolean isXLowToHigh
           
(package private)  boolean iUseBitSets
           
(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
           
(package private)  int mep_gridMax
           
(package private)  float mep_marginAngstroms
           
static int MEP_MAX_GRID
           
(package private)  float mep_ptsPerAngstrom
           
(package private)  int minSet
           
(package private)  java.util.Hashtable mo
           
static int MO_MAX_GRID
           
(package private)  float[] moCoefficients
           
(package private)  java.util.Hashtable moData
           
(package private)  int modelIndex
           
(package private) static int nContourMax
           
(package private)  int nContours
           
(package private) static int NO_ANISOTROPY
           
(package private)  java.lang.Boolean pocket
           
(package private)  javax.vecmath.Point3f point
           
(package private)  boolean propertySmoothing
           
(package private)  int psi_l
           
(package private)  int psi_m
           
(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)  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_SLATER
           
(package private) static int QM_TYPE_UNKNOWN
           
(package private)  int qmOrbitalCount
           
(package private)  int qmOrbitalType
           
(package private)  boolean rangeAll
           
 boolean rangeDefined
           
(package private)  boolean readAllData
           
(package private)  boolean remappable
           
(package private)  float resolution
           
(package private)  float scale
           
(package private)  java.lang.String script
           
(package private)  int solvent_gridMax
           
(package private)  float solvent_ptsPerAngstrom
           
(package private)  float solventAtomRadiusAbsolute
           
(package private)  float solventAtomRadiusFactor
           
(package private)  float solventAtomRadiusOffset
           
(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
           
(package private) static int SURFACE_ATOMICORBITAL
           
(package private) static int SURFACE_ELLIPSOID2
           
(package private) static int SURFACE_ELLIPSOID3
           
(package private) static int SURFACE_FILE
           
(package private) static int SURFACE_FUNCTIONXY
           
(package private) static int SURFACE_FUNCTIONXYZ
           
(package private) static int SURFACE_INFO
           
(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_MOLECULAR
           
(package private) static int SURFACE_MOLECULARORBITAL
           
(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
           
(package private)  javax.vecmath.Point4f thePlane
           
(package private)  float[] theProperty
           
(package private)  int thisContour
           
(package private)  java.lang.String[] title
           
(package private)  boolean useIonic
           
(package private)  float valueMappedToBlue
           
(package private)  float valueMappedToRed
           
 
Constructor Summary
Parameters()
           
 
Method Summary
(package private)  void initialize()
           
(package private)  void setAnisotropy(javax.vecmath.Point3f pt)
           
(package private)  boolean setAtomicOrbital(float[] nlmZ)
           
(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.Vector value)
           
(package private)  void setFunctionXYZ(java.util.Vector 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)
           
(package private)  void setMep(float[] charges, boolean isRangeDefined)
           
(package private)  void setMO(int iMo, boolean isRangeDefined)
           
(package private)  void setPlane(javax.vecmath.Point4f plane)
           
(package private)  void setRadical(javax.vecmath.Point4f v)
           
(package private)  void setRadius(boolean useIonic, float radius)
           
(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

logMessages

boolean logMessages

logCompression

boolean logCompression

logCube

boolean logCube

isSilent

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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Constant Field Values

CAN_CONTOUR

static final int CAN_CONTOUR
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dataType

public int dataType

surfaceType

int surfaceType

SURFACE_NONE

static final int SURFACE_NONE
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Constant Field Values

SURFACE_SPHERE

static final int SURFACE_SPHERE
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Constant Field Values

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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Constant Field Values

SURFACE_MEP

static final int SURFACE_MEP
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Constant Field Values

SURFACE_FILE

static final int SURFACE_FILE
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SURFACE_INFO

static final int SURFACE_INFO
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Constant Field Values

SURFACE_MOLECULAR

static final int SURFACE_MOLECULAR
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Constant Field Values

SURFACE_NOMAP

static final int SURFACE_NOMAP
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Constant Field Values

SURFACE_PROPERTY

static final int SURFACE_PROPERTY
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Constant Field Values

calculationType

java.lang.String calculationType

addHydrogens

boolean addHydrogens

solventRadius

float solventRadius

solventExtendedAtomRadius

float solventExtendedAtomRadius

solventAtomRadiusFactor

float solventAtomRadiusFactor

solventAtomRadiusAbsolute

float solventAtomRadiusAbsolute

solventAtomRadiusOffset

float solventAtomRadiusOffset

propertySmoothing

boolean propertySmoothing

useIonic

boolean useIonic

envelopeRadius

float envelopeRadius

cavityRadius

float cavityRadius

isCavity

boolean isCavity

pocket

java.lang.Boolean pocket

minSet

int minSet

cappingPlane

javax.vecmath.Point4f cappingPlane

doCapIsosurface

boolean doCapIsosurface

theProperty

float[] theProperty

solvent_ptsPerAngstrom

float solvent_ptsPerAngstrom

solvent_gridMax

int solvent_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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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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Constant Field Values

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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defaultSolventRadius

static final float defaultSolventRadius
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defaultMepCutoff

static final float defaultMepCutoff
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Constant Field Values

defaultMepMin

static final float defaultMepMin
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Constant Field Values

defaultMepMax

static final float defaultMepMax
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Constant Field Values

colorBySign

boolean colorBySign

colorByPhase

boolean colorByPhase

colorBySets

boolean colorBySets

colorNeg

int colorNeg

colorPos

int colorPos

colorPosLCAO

int colorPosLCAO

colorNegLCAO

int colorNegLCAO

colorPhase

int colorPhase

iAddGridPoints

boolean iAddGridPoints

remappable

boolean remappable

atomIndex

int atomIndex

isAngstroms

boolean isAngstroms

scale

float scale

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

functionXYinfo

public java.util.Vector functionXYinfo

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

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

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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Constant Field Values

QM_TYPE_SLATER

static final int QM_TYPE_SLATER
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Constant Field Values

moData

java.util.Hashtable moData

mo

java.util.Hashtable mo

moCoefficients

float[] moCoefficients

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

center

javax.vecmath.Point3f center

point

javax.vecmath.Point3f point

distance

float distance

script

java.lang.String script

bsSelected

java.util.BitSet bsSelected

bsIgnore

java.util.BitSet bsIgnore

bsSolvent

java.util.BitSet bsSolvent

iUseBitSets

boolean iUseBitSets

title

java.lang.String[] title

blockCubeData

boolean blockCubeData

readAllData

boolean readAllData

fileIndex

int fileIndex

fileName

java.lang.String fileName

modelIndex

int modelIndex

isXLowToHigh

boolean isXLowToHigh

insideOut

boolean insideOut

cutoff

float cutoff

isCutoffAbsolute

boolean isCutoffAbsolute

isPositiveOnly

boolean isPositiveOnly

rangeAll

boolean rangeAll

rangeDefined

public boolean rangeDefined

valueMappedToRed

float valueMappedToRed

valueMappedToBlue

float valueMappedToBlue

mappedDataMin

float mappedDataMin

mappedDataMax

float mappedDataMax

isColorReversed

boolean isColorReversed

isBicolorMap

boolean isBicolorMap

isSquared

boolean isSquared

thePlane

javax.vecmath.Point4f thePlane

isContoured

boolean isContoured

nContours

int nContours

thisContour

int thisContour

contourFromZero

boolean contourFromZero

resolution

float resolution

downsampleFactor

int downsampleFactor

maxSet

int maxSet
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)

setLp

void setLp(javax.vecmath.Point4f v)

setRadical

void setRadical(javax.vecmath.Point4f v)

setLcao

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

setRadius

void setRadius(boolean useIonic,
               float radius)

setSolvent

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

setFunctionXY

void setFunctionXY(java.util.Vector value)

setFunctionXYZ

void setFunctionXYZ(java.util.Vector value)

setAtomicOrbital

boolean setAtomicOrbital(float[] nlmZ)

setMep

void setMep(float[] charges,
            boolean isRangeDefined)

setMO

void setMO(int iMo,
           boolean isRangeDefined)

setMapRanges

void setMapRanges(SurfaceReader surfaceReader)