Class Parameters

java.lang.Object
org.jmol.jvxl.readers.Parameters

public class Parameters extends Object
  • Field Details

    • STATE_UNINITIALIZED

      public static final int STATE_UNINITIALIZED
      See Also:
    • STATE_INITIALIZED

      public static final int STATE_INITIALIZED
      See Also:
    • STATE_DATA_READ

      public static final int STATE_DATA_READ
      See Also:
    • STATE_DATA_COLORED

      public static final int STATE_DATA_COLORED
      See Also:
    • state

      public int state
    • testFlags

      public int testFlags
    • isSilent

      public boolean isSilent
    • IS_SOLVENTTYPE

      public static final int IS_SOLVENTTYPE
      See Also:
    • dataType

      public int dataType
    • SURFACE_LONEPAIR

      public static final int SURFACE_LONEPAIR
      See Also:
    • SURFACE_RADICAL

      public static final int SURFACE_RADICAL
      See Also:
    • atomRadiusData

      public RadiusData atomRadiusData
    • slabInfo

      public Lst<Object[]> slabInfo
    • defaultQMOrbitalCutoff

      public static final float defaultQMOrbitalCutoff
      See Also:
    • colorRgb

      public int colorRgb
    • colorNeg

      public int colorNeg
    • colorPos

      public int colorPos
    • colorDensity

      public boolean colorDensity
    • iAddGridPoints

      public boolean iAddGridPoints
    • scale3d

      public float scale3d
    • functionInfo

      public Lst<Object> functionInfo
    • psi_monteCarloCount

      public int psi_monteCarloCount
    • MEP_MAX_GRID

      public static final int MEP_MAX_GRID
      See Also:
    • mep_calcType

      public int mep_calcType
    • moData

      public Map<String,Object> moData
    • MO_MAX_GRID

      public static final int MO_MAX_GRID
      See Also:
    • allowVolumeRender

      public boolean allowVolumeRender
    • script

      public String script
    • bsSelected

      public BS bsSelected
    • bsIgnore

      public BS bsIgnore
    • bsSolvent

      public BS bsSolvent
    • func

      public Object func
    • title

      public String[] title
    • fileName

      public String fileName
    • modelIndex

      public int modelIndex
    • modelInvRotation

      public M4 modelInvRotation
    • isXLowToHigh

      public boolean isXLowToHigh
    • cutoff

      public float cutoff
    • cutoffRange

      public float[] cutoffRange
    • sigma

      public float sigma
    • isCutoffAbsolute

      public boolean isCutoffAbsolute
    • isPositiveOnly

      public boolean isPositiveOnly
    • rangeDefined

      public boolean rangeDefined
    • isBicolorMap

      public boolean isBicolorMap
    • isSquared

      public boolean isSquared
    • isSquaredLinear

      public boolean isSquaredLinear
    • thePlane

      public P4 thePlane
    • isContoured

      public boolean isContoured
    • resolution

      public float resolution
    • contoursDiscrete

      public float[] contoursDiscrete
    • contourColixes

      public short[] contourColixes
    • boundingBox

      public P3[] boundingBox
    • bsExcluded

      public BS[] bsExcluded
    • contourType

      public int contourType
    • colorSchemeTranslucent

      public boolean colorSchemeTranslucent
    • colorEncoder

      public ColorEncoder colorEncoder
    • 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 BS[] intersection
    • origin

      public P3 origin
    • steps

      public P3 steps
    • points

      public P3 points
    • volumeData

      public VolumeData volumeData
    • contactPair

      public ContactPair contactPair
    • mapLattice

      public P3 mapLattice
    • extendGrid

      public float extendGrid
    • isMapped

      public boolean isMapped
    • showTiming

      public boolean showTiming
    • pointSize

      public float pointSize
    • probes

      public P3[] probes
    • isModelConnected

      public boolean isModelConnected
    • surfaceAtoms

      public BS surfaceAtoms
    • filesData

      public Object[] filesData
    • probeValues

      public float[] probeValues
    • sbOut

      public SB sbOut
  • Constructor Details

    • Parameters

      public Parameters()
  • Method Details

    • resetForMapping

      public void resetForMapping(boolean haveSurface)
      reset some parameters at the "MAP" keyword or initially
      Parameters:
      haveSurface -
    • setEllipsoidAF

      public void setEllipsoidAF(float[] bList)
    • addSlabInfo

      public void addSlabInfo(Object[] slabObject)
    • isInsideOut

      public boolean isInsideOut()
    • isFullyLit

      public boolean isFullyLit()