org.jmol.jvxl.readers
Class Parameters
java.lang.Object
org.jmol.jvxl.readers.Parameters
public class Parameters
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
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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- Constant Field Values
SURFACE_ELLIPSOID3
static final int SURFACE_ELLIPSOID3
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- Constant Field Values
SURFACE_LOBE
static final int SURFACE_LOBE
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- Constant Field Values
SURFACE_LCAOCARTOON
static final int SURFACE_LCAOCARTOON
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- Constant Field Values
SURFACE_LONEPAIR
public static final int SURFACE_LONEPAIR
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- Constant Field Values
SURFACE_RADICAL
public static final int SURFACE_RADICAL
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- Constant Field Values
SURFACE_FUNCTIONXY
static final int SURFACE_FUNCTIONXY
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- Constant Field Values
SURFACE_FUNCTIONXYZ
static final int SURFACE_FUNCTIONXYZ
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- Constant Field Values
SURFACE_SOLVENT
static final int SURFACE_SOLVENT
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- Constant Field Values
SURFACE_SASURFACE
static final int SURFACE_SASURFACE
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- Constant Field Values
SURFACE_MOLECULARORBITAL
static final int SURFACE_MOLECULARORBITAL
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- Constant Field Values
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_MLP
static final int SURFACE_MLP
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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
String calculationType
atomRadiusData
RadiusData atomRadiusData
addHydrogens
boolean addHydrogens
solventRadius
float solventRadius
solventExtendedAtomRadius
float solventExtendedAtomRadius
propertySmoothing
boolean propertySmoothing
envelopeRadius
float envelopeRadius
cavityRadius
float cavityRadius
isCavity
boolean isCavity
pocket
Boolean pocket
minSet
int minSet
cappingObject
public Object cappingObject
slabbingObject
public Object slabbingObject
slabPlaneOffset
float slabPlaneOffset
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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- Constant Field Values
defaultEdgeFractionRange
static final int defaultEdgeFractionRange
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- Constant Field Values
defaultColorFractionBase
static final int defaultColorFractionBase
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- Constant Field Values
defaultColorFractionRange
static final int defaultColorFractionRange
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- Constant Field Values
defaultMappedDataMin
static final float defaultMappedDataMin
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- Constant Field Values
defaultMappedDataMax
static final float defaultMappedDataMax
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- Constant Field Values
defaultCutoff
static final float defaultCutoff
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- Constant Field Values
defaultOrbitalCutoff
static final float defaultOrbitalCutoff
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- Constant Field Values
defaultQMOrbitalCutoff
public static final float defaultQMOrbitalCutoff
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- Constant Field Values
defaultQMElectronDensityCutoff
static final float defaultQMElectronDensityCutoff
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- Constant Field Values
defaultContourCount
static final int defaultContourCount
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- Constant Field Values
nContourMax
static final int nContourMax
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- Constant Field Values
defaultColorNegative
static final int defaultColorNegative
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- Constant Field Values
defaultColorPositive
static final int defaultColorPositive
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- Constant Field Values
defaultColorNegativeLCAO
static final int defaultColorNegativeLCAO
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- Constant Field Values
defaultColorPositiveLCAO
static final int defaultColorPositiveLCAO
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- Constant Field Values
defaultSolventRadius
static final float defaultSolventRadius
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- Constant Field Values
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
colorDensity
public boolean colorDensity
colorEncoder
public ColorEncoder colorEncoder
iAddGridPoints
boolean iAddGridPoints
remappable
boolean remappable
atomIndex
int atomIndex
isAngstroms
boolean isAngstroms
scale
float scale
scale3d
public float scale3d
anisotropy
float[] anisotropy
isAnisotropic
boolean isAnisotropic
eccentricityMatrix
Matrix3f eccentricityMatrix
eccentricityMatrixInverse
Matrix3f eccentricityMatrixInverse
isEccentric
boolean isEccentric
eccentricityScale
float eccentricityScale
eccentricityRatio
float eccentricityRatio
aniosU
float[] aniosU
anisoB
float[] anisoB
lcaoType
String lcaoType
functionXYinfo
public List 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
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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- Constant Field Values
QM_TYPE_SLATER
static final int QM_TYPE_SLATER
- See Also:
- Constant Field Values
moData
Hashtable moData
mo
Hashtable mo
moCoefficients
float[] moCoefficients
dfCoefMaps
int[][] dfCoefMaps
MO_MAX_GRID
public static final int MO_MAX_GRID
- See Also:
- 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
Point3f center
point
Point3f point
distance
float distance
script
String script
bsSelected
BitSet bsSelected
bsIgnore
BitSet bsIgnore
bsSolvent
BitSet bsSolvent
iUseBitSets
boolean iUseBitSets
title
String[] title
blockCubeData
boolean blockCubeData
readAllData
boolean readAllData
fileIndex
int fileIndex
fileName
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
boolean isBicolorMap
isSquared
public boolean isSquared
thePlane
public Point4f thePlane
isContoured
public boolean isContoured
nContours
int nContours
thisContour
int thisContour
contourFromZero
boolean contourFromZero
resolution
float resolution
downsampleFactor
int downsampleFactor
maxSet
int maxSet
contoursDiscrete
public float[] contoursDiscrete
contourColixes
public short[] contourColixes
contourIncrements
Point3f contourIncrements
boundingBox
public Point3f[] boundingBox
mappedDataBox
public Point3f[] mappedDataBox
bsExcluded
public BitSet[] bsExcluded
contourType
public int contourType
colorSchemeTranslucent
public boolean colorSchemeTranslucent
usePropertyForColorRange
public boolean usePropertyForColorRange
propertyDistanceMax
public float propertyDistanceMax
Parameters
public Parameters()
initialize
void initialize()
setAnisotropy
void setAnisotropy(Point3f pt)
setEccentricity
void setEccentricity(Point4f info)
setPlane
void setPlane(Point4f plane)
setSphere
void setSphere(float radius)
setEllipsoid
void setEllipsoid(Point4f v)
setEllipsoid
public void setEllipsoid(float[] bList)
setLobe
void setLobe(Point4f v)
getScriptParams
private String getScriptParams()
setLp
void setLp(Point4f v)
setRadical
void setRadical(Point4f v)
setLcao
void setLcao(String type,
int colorPtr)
setRadius
void setRadius(RadiusData rd)
setSolvent
void setSolvent(String propertyName,
float radius)
setFunctionXY
void setFunctionXY(List value)
setFunctionXYZ
void setFunctionXYZ(List value)
setAtomicOrbital
boolean setAtomicOrbital(float[] nlmZ)
setMep
void setMep(float[] charges,
boolean isRangeDefined,
boolean isMLP)
setMO
void setMO(int iMo,
boolean isRangeDefined)
setMapRanges
void setMapRanges(SurfaceReader surfaceReader,
boolean haveData)