org.jmol.jvxl.readers
Class Parameters
public
class
Parameters
extends Object
static final float ANGSTROMS_PER_BOHR
boolean addHydrogens
float[] aniosU
float[] anisoB
float[] anisotropy
float assocCutoff
int atomIndex
boolean blockCubeData
BitSet bsIgnore
BitSet bsSelected
BitSet bsSolvent
String calculationType
Point4f cappingPlane
float cavityRadius
Point3f center
boolean colorByPhase
boolean colorBySets
boolean colorBySign
int colorNeg
int colorNegLCAO
int colorPhase
int colorPos
int colorPosLCAO
boolean contourFromZero
float cutoff
static final int CAN_CONTOUR
int dataType
static final int defaultColorFractionBase
static final int defaultColorFractionRange
static final int defaultColorNegative
static final int defaultColorNegativeLCAO
static final int defaultColorPositive
static final int defaultColorPositiveLCAO
static final int defaultContourCount
static final float defaultCutoff
static final int defaultEdgeFractionBase
static final int defaultEdgeFractionRange
static final float defaultMappedDataMax
static final float defaultMappedDataMin
static final float defaultMepCutoff
static final float defaultMepMax
static final float defaultMepMin
static final float defaultOrbitalCutoff
public static final float defaultQMOrbitalCutoff
static final float defaultSolventRadius
float distance
boolean doCapIsosurface
int downsampleFactor
Matrix3f eccentricityMatrix
Matrix3f eccentricityMatrixInverse
float eccentricityRatio
float eccentricityScale
float envelopeRadius
int fileIndex
String fileName
Vector functionXYinfo
static final int HAS_MAXGRID
boolean iAddGridPoints
boolean insideOut
boolean isAngstroms
boolean isAnisotropic
boolean isBicolorMap
boolean isCavity
boolean isColorReversed
boolean isContoured
boolean isCutoffAbsolute
boolean isEccentric
boolean isPositiveOnly
boolean isSilent
boolean isSquared
boolean isXLowToHigh
boolean iUseBitSets
static final int IS_SILENT
static final int IS_SOLVENTTYPE
String lcaoType
boolean logCompression
boolean logCube
boolean logMessages
float mappedDataMax
float mappedDataMin
int maxSet
int mep_gridMax
float mep_marginAngstroms
float mep_ptsPerAngstrom
int minSet
Hashtable mo
float[] moCoefficients
int modelIndex
Hashtable moData
public static final int MEP_MAX_GRID
public static final int MO_MAX_GRID
static final int nContourMax
int nContours
static final int NO_ANISOTROPY
Boolean pocket
Point3f point
boolean propertySmoothing
int psi_l
int psi_m
int psi_n
float psi_ptsPerAngstrom
float psi_Znuc
int qmOrbitalCount
int qmOrbitalType
int qm_gridMax
float qm_marginAngstroms
int qm_moNumber
int qm_nAtoms
float qm_ptsPerAngstrom
static final int QM_TYPE_GAUSSIAN
static final int QM_TYPE_SLATER
static final int QM_TYPE_UNKNOWN
boolean rangeAll
boolean rangeDefined
boolean remappable
float resolution
float scale
String script
float solventAtomRadiusAbsolute
float solventAtomRadiusFactor
float solventAtomRadiusOffset
float solventExtendedAtomRadius
float solventRadius
int solvent_gridMax
float solvent_ptsPerAngstrom
int state
int surfaceType
public static final int STATE_DATA_COLORED
public static final int STATE_DATA_READ
public static final int STATE_INITIALIZED
public static final int STATE_UNINITIALIZED
static final int SURFACE_ATOMICORBITAL
static final int SURFACE_ELLIPSOID2
static final int SURFACE_ELLIPSOID3
static final int SURFACE_FILE
static final int SURFACE_FUNCTIONXY
static final int SURFACE_INFO
static final int SURFACE_LCAOCARTOON
static final int SURFACE_LOBE
static final int SURFACE_MEP
static final int SURFACE_MOLECULAR
static final int SURFACE_MOLECULARORBITAL
static final int SURFACE_NOMAP
static final int SURFACE_NONE
static final int SURFACE_PROPERTY
static final int SURFACE_SASURFACE
static final int SURFACE_SOLVENT
static final int SURFACE_SPHERE
Point4f thePlane
float[] theProperty
int thisContour
String[] title
boolean useIonic
float valueMappedToBlue
float valueMappedToRed
void initialize()
void setAnisotropy(Point3f pt)
boolean setAtomicOrbital(float[] nlmZ)
void setEccentricity(Point4f info)
void setEllipsoid(Point4f v)
public void setEllipsoid(float[] bList)
void setFunctionXY(Vector value)
void setLcao(String type, int colorPtr)
void setLobe(Point4f v)
void setMep(float[] charges, boolean isRangeDefined)
void setMO(int iMo)
void setPlane(Point4f plane)
void setRadius(boolean useIonic, float radius)
void setSolvent(String propertyName, float radius)
void setSphere(float radius)