public class Parameters
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
(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) RadiusData |
atomRadiusData |
(package private) boolean |
blockCubeData |
javax.vecmath.Point3f[] |
boundingBox |
java.util.BitSet[] |
bsExcluded |
(package private) java.util.BitSet |
bsIgnore |
(package private) java.util.BitSet |
bsSelected |
(package private) java.util.BitSet |
bsSolvent |
(package private) java.lang.String |
calculationType |
java.lang.Object |
cappingObject |
(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 |
boolean |
colorSchemeTranslucent |
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 |
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) int[][] |
dfCoefMaps |
(package private) float |
distance |
(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.List |
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 |
boolean |
isContoured |
boolean |
isCutoffAbsolute |
(package private) boolean |
isEccentric |
(package private) boolean |
isPositiveOnly |
(package private) boolean |
isSilent |
boolean |
isSquared |
boolean |
isXLowToHigh |
(package private) boolean |
iUseBitSets |
(package private) java.lang.String |
lcaoType |
(package private) boolean |
logCompression |
(package private) boolean |
logCube |
(package private) boolean |
logMessages |
javax.vecmath.Point3f[] |
mappedDataBox |
(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 |
(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 |
float |
propertyDistanceMax |
(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 |
rangeSelected |
(package private) boolean |
readAllData |
(package private) boolean |
remappable |
(package private) float |
resolution |
(package private) float |
scale |
float |
scale3d |
(package private) java.lang.String |
script |
float |
sigma |
java.lang.Object |
slabbingObject |
(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 |
(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_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_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 |
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 |
Constructor and Description |
---|
Parameters() |
Modifier and Type | Method and Description |
---|---|
private java.lang.String |
getScriptParams() |
(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.List value) |
(package private) void |
setFunctionXYZ(java.util.List 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 isRangeDefined,
boolean isMLP) |
(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(RadiusData rd) |
(package private) void |
setSolvent(java.lang.String propertyName,
float radius) |
(package private) void |
setSphere(float radius) |
public static final int STATE_UNINITIALIZED
public static final int STATE_INITIALIZED
public static final int STATE_DATA_READ
public static final int STATE_DATA_COLORED
int state
boolean logMessages
boolean logCompression
boolean logCube
boolean isSilent
float assocCutoff
static final int NO_ANISOTROPY
static final int IS_SILENT
public static final int IS_SOLVENTTYPE
static final int HAS_MAXGRID
public int dataType
int surfaceType
static final int SURFACE_NONE
static final int SURFACE_SPHERE
static final int SURFACE_ELLIPSOID2
static final int SURFACE_ELLIPSOID3
static final int SURFACE_LOBE
static final int SURFACE_LCAOCARTOON
public static final int SURFACE_LONEPAIR
public static final int SURFACE_RADICAL
static final int SURFACE_FUNCTIONXY
static final int SURFACE_FUNCTIONXYZ
static final int SURFACE_SOLVENT
static final int SURFACE_SASURFACE
static final int SURFACE_MOLECULARORBITAL
static final int SURFACE_ATOMICORBITAL
static final int SURFACE_MEP
static final int SURFACE_MLP
static final int SURFACE_MOLECULAR
static final int SURFACE_NOMAP
static final int SURFACE_PROPERTY
java.lang.String calculationType
RadiusData atomRadiusData
boolean addHydrogens
float solventRadius
float solventExtendedAtomRadius
boolean propertySmoothing
float envelopeRadius
float cavityRadius
boolean isCavity
java.lang.Boolean pocket
int minSet
public java.lang.Object cappingObject
public java.lang.Object slabbingObject
float slabPlaneOffset
float[] theProperty
float solvent_ptsPerAngstrom
int solvent_gridMax
static final float ANGSTROMS_PER_BOHR
static final int defaultEdgeFractionBase
static final int defaultEdgeFractionRange
static final int defaultColorFractionBase
static final int defaultColorFractionRange
static final float defaultMappedDataMin
static final float defaultMappedDataMax
static final float defaultCutoff
static final float defaultOrbitalCutoff
public static final float defaultQMOrbitalCutoff
static final float defaultQMElectronDensityCutoff
static final int defaultContourCount
static final int nContourMax
static final int defaultColorNegative
static final int defaultColorPositive
static final int defaultColorNegativeLCAO
static final int defaultColorPositiveLCAO
static final float defaultSolventRadius
static final float defaultMepCutoff
static final float defaultMepMin
static final float defaultMepMax
boolean colorBySign
boolean colorByPhase
boolean colorBySets
int colorNeg
int colorPos
int colorPosLCAO
int colorNegLCAO
int colorPhase
public boolean colorDensity
public ColorEncoder colorEncoder
boolean iAddGridPoints
boolean remappable
int atomIndex
boolean isAngstroms
float scale
public float scale3d
float[] anisotropy
boolean isAnisotropic
javax.vecmath.Matrix3f eccentricityMatrix
javax.vecmath.Matrix3f eccentricityMatrixInverse
boolean isEccentric
float eccentricityScale
float eccentricityRatio
float[] aniosU
float[] anisoB
java.lang.String lcaoType
public java.util.List functionXYinfo
int psi_n
int psi_l
int psi_m
float psi_Znuc
float psi_ptsPerAngstrom
public static final int MEP_MAX_GRID
int mep_gridMax
float mep_ptsPerAngstrom
float mep_marginAngstroms
public int mep_calcType
int qmOrbitalType
int qmOrbitalCount
static final int QM_TYPE_UNKNOWN
static final int QM_TYPE_GAUSSIAN
static final int QM_TYPE_SLATER
java.util.Hashtable moData
java.util.Hashtable mo
float[] moCoefficients
int[][] dfCoefMaps
public static final int MO_MAX_GRID
int qm_gridMax
float qm_ptsPerAngstrom
float qm_marginAngstroms
int qm_nAtoms
int qm_moNumber
javax.vecmath.Point3f center
javax.vecmath.Point3f point
float distance
java.lang.String script
java.util.BitSet bsSelected
java.util.BitSet bsIgnore
java.util.BitSet bsSolvent
boolean iUseBitSets
java.lang.String[] title
boolean blockCubeData
boolean readAllData
int fileIndex
java.lang.String fileName
int modelIndex
public boolean isXLowToHigh
boolean insideOut
boolean dataXYReversed
public float cutoff
public float sigma
boolean cutoffAutomatic
public boolean isCutoffAbsolute
boolean isPositiveOnly
boolean rangeAll
boolean rangeSelected
public boolean rangeDefined
float valueMappedToRed
float valueMappedToBlue
float mappedDataMin
float mappedDataMax
boolean isColorReversed
boolean isBicolorMap
public boolean isSquared
public javax.vecmath.Point4f thePlane
public boolean isContoured
int nContours
int thisContour
boolean contourFromZero
float resolution
int downsampleFactor
int maxSet
public float[] contoursDiscrete
public short[] contourColixes
javax.vecmath.Point3f contourIncrements
public javax.vecmath.Point3f[] boundingBox
public javax.vecmath.Point3f[] mappedDataBox
public java.util.BitSet[] bsExcluded
public int contourType
public boolean colorSchemeTranslucent
public boolean usePropertyForColorRange
public float propertyDistanceMax
void initialize()
void setAnisotropy(javax.vecmath.Point3f pt)
void setEccentricity(javax.vecmath.Point4f info)
void setPlane(javax.vecmath.Point4f plane)
void setSphere(float radius)
void setEllipsoid(javax.vecmath.Point4f v)
public void setEllipsoid(float[] bList)
void setLobe(javax.vecmath.Point4f v)
private java.lang.String getScriptParams()
void setLp(javax.vecmath.Point4f v)
void setRadical(javax.vecmath.Point4f v)
void setLcao(java.lang.String type, int colorPtr)
void setRadius(RadiusData rd)
void setSolvent(java.lang.String propertyName, float radius)
void setFunctionXY(java.util.List value)
void setFunctionXYZ(java.util.List value)
boolean setAtomicOrbital(float[] nlmZ)
void setMep(float[] charges, boolean isRangeDefined, boolean isMLP)
void setMO(int iMo, boolean isRangeDefined)
void setMapRanges(SurfaceReader surfaceReader, boolean haveData)