Package org.jmol.jvxl.readers
Class Parameters
java.lang.Object
org.jmol.jvxl.readers.Parameters
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Field Summary
FieldsModifier and TypeFieldDescription(package private) boolean
boolean
(package private) static final float
(package private) float[]
(package private) float[]
(package private) float[]
(package private) float
(package private) int
(package private) boolean
javajs.util.P3[]
javajs.util.BS[]
javajs.util.BS
javajs.util.BS
javajs.util.BS
(package private) String
(package private) float
(package private) javajs.util.P3
(package private) boolean
(package private) boolean
(package private) boolean
boolean
int
(package private) int
(package private) int
int
(package private) int
int
boolean
short[]
(package private) boolean
(package private) javajs.util.P3
float[]
int
float
(package private) boolean
float[]
int
(package private) boolean
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final float
(package private) static final int
(package private) static final int
(package private) static final float
(package private) static final float
(package private) static final float
(package private) static final float
(package private) static final float
(package private) static final float
(package private) static final float
(package private) static final float
(package private) static final float
static final float
(package private) static final float
(package private) float
boolean
(package private) int
(package private) javajs.util.M3
(package private) javajs.util.M3
(package private) float
(package private) float
(package private) float
float
(package private) int
Object[]
boolean
javajs.util.Lst
<Object> (package private) static final int
boolean
(package private) boolean
javajs.util.BS[]
(package private) static final int
(package private) static final int
(package private) static final int
static final int
(package private) boolean
(package private) boolean
boolean
(package private) boolean
(package private) boolean
boolean
boolean
(package private) boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
(package private) String
(package private) boolean
(package private) boolean
(package private) boolean
javajs.util.P3
(package private) float
(package private) float
(package private) int
int
(package private) int
(package private) float
static final int
(package private) float
(package private) int
static final int
int
javajs.util.M4
(package private) static final int
(package private) int
(package private) static final int
javajs.util.P3
(package private) float[]
(package private) int
(package private) float
(package private) Boolean
(package private) javajs.util.P3
javajs.util.P3
float
javajs.util.P3[]
float[]
float
(package private) boolean
(package private) int
(package private) int
(package private) int
int
(package private) int
(package private) float
(package private) float
(package private) int
(package private) float
(package private) float[]
(package private) int
(package private) int
(package private) float
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) int
(package private) int
int
(package private) boolean
boolean
(package private) boolean
(package private) boolean
float
javajs.util.SB
(package private) float
float
boolean
float
javajs.util.Lst
<Object[]> (package private) float
(package private) int
(package private) float
(package private) float
(package private) float
int
static final int
static final int
static final int
static final int
javajs.util.P3
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
static final int
(package private) static final int
(package private) static final int
(package private) static final int
javajs.util.BS
(package private) int
int
javajs.util.P4
(package private) float[]
(package private) int
String[]
boolean
(package private) float
(package private) float
int[]
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addSlabInfo
(Object[] slabObject) private String
(package private) void
boolean
boolean
void
resetForMapping
(boolean haveSurface) reset some parameters at the "MAP" keyword or initially(package private) void
setAnisotropy
(javajs.util.P3 pt) (package private) boolean
setAtomicOrbital
(float[] nlmZprs) (package private) void
setEccentricity
(javajs.util.P4 info) void
setEllipsoidAF
(float[] bList) (package private) void
setEllipsoidP4
(javajs.util.P4 v) (package private) void
setFunctionXY
(javajs.util.Lst<Object> value) (package private) void
setFunctionXYZ
(javajs.util.Lst<Object> value) (package private) void
(package private) void
setLobe
(javajs.util.P4 v) (package private) void
setLp
(javajs.util.P4 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
(javajs.util.P4 plane) (package private) void
setRadical
(javajs.util.P4 v) (package private) void
setSolvent
(String propertyName, float radius) (package private) void
setSphere
(float radius, boolean isGeodesic)
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Field Details
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STATE_UNINITIALIZED
public static final int STATE_UNINITIALIZED- See Also:
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STATE_INITIALIZED
public static final int STATE_INITIALIZED- See Also:
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STATE_DATA_READ
public static final int STATE_DATA_READ- See Also:
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STATE_DATA_COLORED
public static final int STATE_DATA_COLORED- See Also:
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state
public 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- See Also:
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IS_SILENT
static final int IS_SILENT- See Also:
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IS_SOLVENTTYPE
public static final int IS_SOLVENTTYPE- See Also:
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HAS_MAXGRID
static final int HAS_MAXGRID- See Also:
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IS_POINTMAPPABLE
static final int IS_POINTMAPPABLE- See Also:
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IS_SLABBABLE
static final int IS_SLABBABLE- See Also:
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dataType
public int dataType -
surfaceType
int surfaceType -
SURFACE_NONE
static final int SURFACE_NONE- See Also:
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SURFACE_SPHERE
static final int SURFACE_SPHERE- See Also:
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SURFACE_ELLIPSOID2
static final int SURFACE_ELLIPSOID2- See Also:
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SURFACE_ELLIPSOID3
static final int SURFACE_ELLIPSOID3- See Also:
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SURFACE_LOBE
static final int SURFACE_LOBE- See Also:
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SURFACE_LCAOCARTOON
static final int SURFACE_LCAOCARTOON- See Also:
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SURFACE_LONEPAIR
public static final int SURFACE_LONEPAIR- See Also:
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SURFACE_RADICAL
public static final int SURFACE_RADICAL- See Also:
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SURFACE_FUNCTIONXY
static final int SURFACE_FUNCTIONXY- See Also:
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SURFACE_FUNCTIONXYZ
static final int SURFACE_FUNCTIONXYZ- See Also:
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SURFACE_GEODESIC
static final int SURFACE_GEODESIC- See Also:
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SURFACE_SOLVENT
static final int SURFACE_SOLVENT- See Also:
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SURFACE_SASURFACE
static final int SURFACE_SASURFACE- See Also:
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SURFACE_MOLECULARORBITAL
static final int SURFACE_MOLECULARORBITAL- See Also:
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SURFACE_ATOMICORBITAL
static final int SURFACE_ATOMICORBITAL- See Also:
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SURFACE_MEP
static final int SURFACE_MEP- See Also:
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SURFACE_MLP
static final int SURFACE_MLP- See Also:
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SURFACE_MOLECULAR
static final int SURFACE_MOLECULAR- See Also:
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SURFACE_NCI
static final int SURFACE_NCI- See Also:
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SURFACE_INTERSECT_ATOM
static final int SURFACE_INTERSECT_ATOM- See Also:
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SURFACE_INTERSECT_FILE
static final int SURFACE_INTERSECT_FILE- See Also:
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SURFACE_NOMAP
static final int SURFACE_NOMAP- See Also:
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SURFACE_PROPERTY
static final int SURFACE_PROPERTY- See Also:
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calculationType
String calculationType -
atomRadiusData
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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
Boolean pocket -
minSet
int minSet -
slabInfo
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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- See Also:
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defaultEdgeFractionBase
static final int defaultEdgeFractionBase- See Also:
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defaultEdgeFractionRange
static final int defaultEdgeFractionRange- See Also:
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defaultColorFractionBase
static final int defaultColorFractionBase- See Also:
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defaultColorFractionRange
static final int defaultColorFractionRange- See Also:
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defaultMappedDataMin
static final float defaultMappedDataMin- See Also:
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defaultMappedDataMax
static final float defaultMappedDataMax- See Also:
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defaultCutoff
static final float defaultCutoff- See Also:
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defaultOrbitalCutoff
static final float defaultOrbitalCutoff- See Also:
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defaultLobeCutoff
static final float defaultLobeCutoff- See Also:
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defaultOrbitalCutoffOld
static final float defaultOrbitalCutoffOld- See Also:
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defaultQMOrbitalCutoff
public static final float defaultQMOrbitalCutoff- See Also:
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defaultQMElectronDensityCutoff
static final float defaultQMElectronDensityCutoff- See Also:
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defaultContourCount
static final int defaultContourCount- See Also:
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nContourMax
static final int nContourMax- See Also:
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defaultColorNegative
static final int defaultColorNegative- See Also:
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defaultColorPositive
static final int defaultColorPositive- See Also:
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defaultColorNegativeLCAO
static final int defaultColorNegativeLCAO- See Also:
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defaultColorPositiveLCAO
static final int defaultColorPositiveLCAO- See Also:
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defaultSolventRadius
static final float defaultSolventRadius- See Also:
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defaultMepCutoff
static final float defaultMepCutoff- See Also:
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defaultMepMin
static final float defaultMepMin- See Also:
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defaultMepMax
static final float defaultMepMax- See Also:
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colorBySign
boolean colorBySign -
colorByPhase
boolean colorByPhase -
colorBySets
boolean colorBySets -
colorRgb
public int colorRgb -
colorNeg
public int colorNeg -
colorPos
public int colorPos -
colorPosLCAO
int colorPosLCAO -
colorNegLCAO
int colorNegLCAO -
colorPhase
int colorPhase -
colorDensity
public boolean colorDensity -
iAddGridPoints
public boolean iAddGridPoints -
atomIndex
int atomIndex -
isAngstroms
boolean isAngstroms -
scale
float scale -
scale3d
public float scale3d -
anisotropy
float[] anisotropy -
isAnisotropic
boolean isAnisotropic -
eccentricityMatrix
javajs.util.M3 eccentricityMatrix -
eccentricityMatrixInverse
javajs.util.M3 eccentricityMatrixInverse -
isEccentric
boolean isEccentric -
eccentricityScale
float eccentricityScale -
eccentricityRatio
float eccentricityRatio -
aniosU
float[] aniosU -
anisoB
float[] anisoB -
lcaoType
String lcaoType -
functionInfo
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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- See Also:
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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- See Also:
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QM_TYPE_GAUSSIAN
static final int QM_TYPE_GAUSSIAN- See Also:
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QM_TYPE_SLATER
static final int QM_TYPE_SLATER- See Also:
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QM_TYPE_NCI_PRO
static final int QM_TYPE_NCI_PRO- See Also:
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QM_TYPE_NCI_SCF
static final int QM_TYPE_NCI_SCF- See Also:
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QM_TYPE_VOLUME_DATA
static final int QM_TYPE_VOLUME_DATA- See Also:
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moData
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MO_MAX_GRID
public static final int MO_MAX_GRID- See Also:
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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
javajs.util.P3 center -
point
javajs.util.P3 point -
distance
float distance -
allowVolumeRender
public boolean allowVolumeRender -
script
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bsSelected
public javajs.util.BS bsSelected -
bsIgnore
public javajs.util.BS bsIgnore -
bsSolvent
public javajs.util.BS bsSolvent -
func
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title
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blockCubeData
boolean blockCubeData -
readAllData
boolean readAllData -
fileIndex
int fileIndex -
fileName
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modelIndex
public int modelIndex -
modelInvRotation
public javajs.util.M4 modelInvRotation -
isXLowToHigh
public boolean isXLowToHigh -
insideOut
boolean insideOut -
dataXYReversed
boolean dataXYReversed -
cutoff
public float cutoff -
cutoffRange
public float[] cutoffRange -
sigma
public float sigma -
cutoffAutomatic
boolean cutoffAutomatic -
isCutoffAbsolute
public boolean isCutoffAbsolute -
isPositiveOnly
public 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 -
isSquaredLinear
public boolean isSquaredLinear -
thePlane
public javajs.util.P4 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
javajs.util.P3 contourIncrements -
boundingBox
public javajs.util.P3[] boundingBox -
bsExcluded
public javajs.util.BS[] bsExcluded -
contourType
public int contourType -
colorSchemeTranslucent
public boolean colorSchemeTranslucent -
colorEncoder
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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 javajs.util.BS[] intersection -
origin
public javajs.util.P3 origin -
steps
public javajs.util.P3 steps -
points
public javajs.util.P3 points -
volumeData
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contactPair
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mapLattice
public javajs.util.P3 mapLattice -
extendGrid
public float extendGrid -
isMapped
public boolean isMapped -
showTiming
public boolean showTiming -
pointSize
public float pointSize -
probes
public javajs.util.P3[] probes -
isModelConnected
public boolean isModelConnected -
surfaceAtoms
public javajs.util.BS surfaceAtoms -
filesData
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probeValues
public float[] probeValues -
sbOut
public javajs.util.SB sbOut
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Constructor Details
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Parameters
public Parameters()
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Method Details
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initialize
void initialize() -
resetForMapping
public void resetForMapping(boolean haveSurface) reset some parameters at the "MAP" keyword or initially- Parameters:
haveSurface
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setAnisotropy
void setAnisotropy(javajs.util.P3 pt) -
setEccentricity
void setEccentricity(javajs.util.P4 info) -
setPlane
void setPlane(javajs.util.P4 plane) -
setSphere
void setSphere(float radius, boolean isGeodesic) -
setEllipsoidP4
void setEllipsoidP4(javajs.util.P4 v) -
setEllipsoidAF
public void setEllipsoidAF(float[] bList) -
setLobe
void setLobe(javajs.util.P4 v) -
getScriptParams
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setLp
void setLp(javajs.util.P4 v) -
setRadical
void setRadical(javajs.util.P4 v) -
setLcao
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setSolvent
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setFunctionXY
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setFunctionXYZ
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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
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addSlabInfo
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isInsideOut
public boolean isInsideOut() -
isFullyLit
public boolean isFullyLit()
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