org.jmol.jvxl.readers
public class Parameters extends Object
Modifier and Type | Field and Description |
---|---|
(package private) boolean |
addHydrogens |
boolean |
allowVolumeRender |
(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 |
RadiusData |
atomRadiusData |
(package private) boolean |
blockCubeData |
Point3f[] |
boundingBox |
BitSet[] |
bsExcluded |
BitSet |
bsIgnore |
BitSet |
bsSelected |
BitSet |
bsSolvent |
(package private) String |
calculationType |
(package private) float |
cavityRadius |
(package private) 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 |
int |
colorRgb |
boolean |
colorSchemeTranslucent |
ContactPair |
contactPair |
short[] |
contourColixes |
(package private) boolean |
contourFromZero |
(package private) 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 |
defaultLobeCutoff |
(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 |
defaultOrbitalCutoffOld |
(package private) static float |
defaultQMElectronDensityCutoff |
static float |
defaultQMOrbitalCutoff |
(package private) static float |
defaultSolventRadius |
(package private) float |
distance |
boolean |
doFullMolecular |
(package private) int |
downsampleFactor |
(package private) Matrix3f |
eccentricityMatrix |
(package private) Matrix3f |
eccentricityMatrixInverse |
(package private) float |
eccentricityRatio |
(package private) float |
eccentricityScale |
(package private) float |
envelopeRadius |
(package private) int |
fileIndex |
(package private) String |
fileName |
boolean |
fullyLit |
Object |
func |
List<Object> |
functionInfo |
(package private) static int |
HAS_MAXGRID |
(package private) boolean |
iAddGridPoints |
(package private) boolean |
insideOut |
BitSet[] |
intersection |
(package private) static int |
IS_POINTMAPPABLE |
(package private) static int |
IS_SILENT |
(package private) static int |
IS_SLABBABLE |
static int |
IS_SOLVENTTYPE |
(package private) boolean |
isAngstroms |
(package private) boolean |
isAnisotropic |
boolean |
isBicolorMap |
(package private) boolean |
isCavity |
(package private) boolean |
isColorReversed |
boolean |
isContoured |
boolean |
isCutoffAbsolute |
(package private) boolean |
isEccentric |
boolean |
isPeriodic |
(package private) boolean |
isPositiveOnly |
boolean |
isSilent |
boolean |
isSquared |
boolean |
isXLowToHigh |
(package private) 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 |
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 |
static int |
MO_MAX_GRID |
(package private) Map<String,Object> |
moData |
(package private) int |
modelIndex |
(package private) static int |
nContourMax |
(package private) int |
nContours |
(package private) static int |
NO_ANISOTROPY |
Point3f |
origin |
(package private) float[] |
parameters |
(package private) int |
plane_gridMax |
(package private) float |
plane_ptsPerAngstrom |
(package private) Boolean |
pocket |
(package private) Point3f |
point |
Point3f |
points |
float |
propertyDistanceMax |
(package private) boolean |
propertySmoothing |
(package private) int |
propertySmoothingPower |
(package private) int |
psi_l |
(package private) int |
psi_m |
int |
psi_monteCarloCount |
(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) float[] |
qm_moLinearCombination |
(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_NCI_PRO |
(package private) static int |
QM_TYPE_NCI_SCF |
(package private) static int |
QM_TYPE_SLATER |
(package private) static int |
QM_TYPE_UNKNOWN |
(package private) static int |
QM_TYPE_VOLUME_DATA |
(package private) int |
qmOrbitalCount |
(package private) int |
qmOrbitalType |
int |
randomSeed |
(package private) boolean |
rangeAll |
boolean |
rangeDefined |
(package private) boolean |
rangeSelected |
(package private) boolean |
readAllData |
float |
resolution |
(package private) float |
scale |
float |
scale3d |
(package private) String |
script |
float |
sigma |
List<Object[]> |
slabInfo |
(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 |
Point3f |
steps |
(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_INTERSECT |
(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_NCI |
(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 |
int |
testFlags |
Point4f |
thePlane |
(package private) float[] |
theProperty |
(package private) int |
thisContour |
(package private) String[] |
title |
boolean |
usePropertyForColorRange |
(package private) float |
valueMappedToBlue |
(package private) float |
valueMappedToRed |
int[] |
vertexSource |
VolumeData |
volumeData |
Constructor and Description |
---|
Parameters() |
Modifier and Type | Method and Description |
---|---|
void |
addSlabInfo(Object[] slabObject) |
private String |
getScriptParams() |
(package private) void |
initialize() |
void |
resetForMapping(boolean haveSurface)
reset some parameters at the "MAP" keyword
|
(package private) void |
setAnisotropy(Point3f pt) |
(package private) boolean |
setAtomicOrbital(float[] nlmZprs) |
(package private) void |
setEccentricity(Point4f info) |
void |
setEllipsoid(float[] bList) |
(package private) void |
setEllipsoid(Point4f v) |
(package private) void |
setFunctionXY(List<Object> value) |
(package private) void |
setFunctionXYZ(List<Object> value) |
(package private) void |
setLcao(String type,
int colorPtr) |
(package private) void |
setLobe(Point4f v) |
(package private) void |
setLp(Point4f 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(Point4f plane) |
(package private) void |
setRadical(Point4f v) |
(package private) void |
setSolvent(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
public int testFlags
boolean logMessages
boolean logCompression
boolean logCube
public 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
static final int IS_POINTMAPPABLE
static final int IS_SLABBABLE
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_NCI
static final int SURFACE_INTERSECT
static final int SURFACE_NOMAP
static final int SURFACE_PROPERTY
String calculationType
public RadiusData atomRadiusData
boolean addHydrogens
float solventRadius
float solventExtendedAtomRadius
boolean propertySmoothing
int propertySmoothingPower
float envelopeRadius
float cavityRadius
boolean isCavity
Boolean pocket
int minSet
float slabPlaneOffset
float[] theProperty
float solvent_ptsPerAngstrom
int solvent_gridMax
float plane_ptsPerAngstrom
int plane_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
static final float defaultLobeCutoff
static final float defaultOrbitalCutoffOld
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
public int colorRgb
int colorNeg
int colorPos
int colorPosLCAO
int colorNegLCAO
int colorPhase
public boolean colorDensity
boolean iAddGridPoints
int atomIndex
boolean isAngstroms
float scale
public float scale3d
float[] anisotropy
boolean isAnisotropic
Matrix3f eccentricityMatrix
Matrix3f eccentricityMatrixInverse
boolean isEccentric
float eccentricityScale
float eccentricityRatio
float[] aniosU
float[] anisoB
String lcaoType
int psi_n
int psi_l
int psi_m
float psi_Znuc
float psi_ptsPerAngstrom
public int psi_monteCarloCount
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
static final int QM_TYPE_NCI_PRO
static final int QM_TYPE_NCI_SCF
static final int QM_TYPE_VOLUME_DATA
public static final int MO_MAX_GRID
int qm_gridMax
float qm_ptsPerAngstrom
float qm_marginAngstroms
int qm_nAtoms
int qm_moNumber
float[] qm_moLinearCombination
Point3f center
Point3f point
float distance
public boolean allowVolumeRender
String script
public BitSet bsSelected
public BitSet bsIgnore
public BitSet bsSolvent
public Object func
String[] title
boolean blockCubeData
boolean readAllData
int fileIndex
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
public boolean isBicolorMap
public boolean isSquared
public Point4f thePlane
public boolean isContoured
int nContours
int thisContour
boolean contourFromZero
float[] parameters
public float resolution
int downsampleFactor
int maxSet
public float[] contoursDiscrete
public short[] contourColixes
Point3f contourIncrements
public Point3f[] boundingBox
public BitSet[] bsExcluded
public int contourType
public boolean colorSchemeTranslucent
public ColorEncoder colorEncoder
public boolean usePropertyForColorRange
public boolean isPeriodic
public boolean doFullMolecular
public float propertyDistanceMax
public int randomSeed
public boolean fullyLit
public int[] vertexSource
public BitSet[] intersection
public Point3f origin
public Point3f steps
public Point3f points
public VolumeData volumeData
public ContactPair contactPair
void initialize()
void setAnisotropy(Point3f pt)
void setEccentricity(Point4f info)
void setPlane(Point4f plane)
void setSphere(float radius)
void setEllipsoid(Point4f v)
public void setEllipsoid(float[] bList)
void setLobe(Point4f v)
private String getScriptParams()
void setLp(Point4f v)
void setRadical(Point4f v)
void setLcao(String type, int colorPtr)
void setSolvent(String propertyName, float radius)
boolean setAtomicOrbital(float[] nlmZprs)
void setMep(float[] charges, boolean isMLP)
void setNci(boolean isPromolecular)
void setMO(int iMo, float[] linearCombination)
void setMapRanges(SurfaceReader surfaceReader, boolean haveData)
public void resetForMapping(boolean haveSurface)
haveSurface
- public void addSlabInfo(Object[] slabObject)