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
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    • STATE_INITIALIZED

      public static final int STATE_INITIALIZED
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    • STATE_DATA_READ

      public static final int STATE_DATA_READ
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    • STATE_DATA_COLORED

      public static final int STATE_DATA_COLORED
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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
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    • IS_SILENT

      static final int IS_SILENT
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    • IS_SOLVENTTYPE

      public static final int IS_SOLVENTTYPE
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    • HAS_MAXGRID

      static final int HAS_MAXGRID
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    • IS_POINTMAPPABLE

      static final int IS_POINTMAPPABLE
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    • IS_SLABBABLE

      static final int IS_SLABBABLE
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    • dataType

      public int dataType
    • surfaceType

      int surfaceType
    • SURFACE_NONE

      static final int SURFACE_NONE
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    • SURFACE_SPHERE

      static final int SURFACE_SPHERE
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    • SURFACE_ELLIPSOID2

      static final int SURFACE_ELLIPSOID2
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    • SURFACE_ELLIPSOID3

      static final int SURFACE_ELLIPSOID3
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    • SURFACE_LOBE

      static final int SURFACE_LOBE
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    • SURFACE_LCAOCARTOON

      static final int SURFACE_LCAOCARTOON
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    • SURFACE_LONEPAIR

      public static final int SURFACE_LONEPAIR
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    • SURFACE_RADICAL

      public static final int SURFACE_RADICAL
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    • SURFACE_FUNCTIONXY

      static final int SURFACE_FUNCTIONXY
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    • SURFACE_FUNCTIONXYZ

      static final int SURFACE_FUNCTIONXYZ
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    • SURFACE_GEODESIC

      static final int SURFACE_GEODESIC
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    • SURFACE_SOLVENT

      static final int SURFACE_SOLVENT
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    • SURFACE_SASURFACE

      static final int SURFACE_SASURFACE
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    • SURFACE_MOLECULARORBITAL

      static final int SURFACE_MOLECULARORBITAL
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    • SURFACE_ATOMICORBITAL

      static final int SURFACE_ATOMICORBITAL
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    • SURFACE_MEP

      static final int SURFACE_MEP
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    • SURFACE_MLP

      static final int SURFACE_MLP
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    • SURFACE_MOLECULAR

      static final int SURFACE_MOLECULAR
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    • SURFACE_NCI

      static final int SURFACE_NCI
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    • SURFACE_INTERSECT_ATOM

      static final int SURFACE_INTERSECT_ATOM
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    • SURFACE_INTERSECT_FILE

      static final int SURFACE_INTERSECT_FILE
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    • SURFACE_NOMAP

      static final int SURFACE_NOMAP
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    • SURFACE_PROPERTY

      static final int SURFACE_PROPERTY
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    • calculationType

      String calculationType
    • atomRadiusData

      public RadiusData atomRadiusData
    • 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

      public javajs.util.Lst<Object[]> slabInfo
    • 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
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    • defaultEdgeFractionBase

      static final int defaultEdgeFractionBase
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    • defaultEdgeFractionRange

      static final int defaultEdgeFractionRange
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    • defaultColorFractionBase

      static final int defaultColorFractionBase
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    • defaultColorFractionRange

      static final int defaultColorFractionRange
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    • defaultMappedDataMin

      static final float defaultMappedDataMin
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    • defaultMappedDataMax

      static final float defaultMappedDataMax
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    • defaultCutoff

      static final float defaultCutoff
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    • defaultOrbitalCutoff

      static final float defaultOrbitalCutoff
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    • defaultLobeCutoff

      static final float defaultLobeCutoff
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    • defaultOrbitalCutoffOld

      static final float defaultOrbitalCutoffOld
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    • defaultQMOrbitalCutoff

      public static final float defaultQMOrbitalCutoff
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    • defaultQMElectronDensityCutoff

      static final float defaultQMElectronDensityCutoff
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    • defaultContourCount

      static final int defaultContourCount
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    • nContourMax

      static final int nContourMax
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    • defaultColorNegative

      static final int defaultColorNegative
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    • defaultColorPositive

      static final int defaultColorPositive
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    • defaultColorNegativeLCAO

      static final int defaultColorNegativeLCAO
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    • defaultColorPositiveLCAO

      static final int defaultColorPositiveLCAO
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    • defaultSolventRadius

      static final float defaultSolventRadius
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    • defaultMepCutoff

      static final float defaultMepCutoff
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    • defaultMepMin

      static final float defaultMepMin
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    • defaultMepMax

      static final float defaultMepMax
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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

      public javajs.util.Lst<Object> functionInfo
    • 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
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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
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    • QM_TYPE_GAUSSIAN

      static final int QM_TYPE_GAUSSIAN
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    • QM_TYPE_SLATER

      static final int QM_TYPE_SLATER
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    • QM_TYPE_NCI_PRO

      static final int QM_TYPE_NCI_PRO
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    • QM_TYPE_NCI_SCF

      static final int QM_TYPE_NCI_SCF
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    • QM_TYPE_VOLUME_DATA

      static final int QM_TYPE_VOLUME_DATA
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    • moData

      public Map<String,Object> moData
    • MO_MAX_GRID

      public static final int MO_MAX_GRID
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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

      public String script
    • bsSelected

      public javajs.util.BS bsSelected
    • bsIgnore

      public javajs.util.BS bsIgnore
    • bsSolvent

      public javajs.util.BS bsSolvent
    • func

      public Object func
    • title

      public String[] title
    • blockCubeData

      boolean blockCubeData
    • readAllData

      boolean readAllData
    • fileIndex

      int fileIndex
    • fileName

      public String fileName
    • 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

      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 javajs.util.BS[] intersection
    • origin

      public javajs.util.P3 origin
    • steps

      public javajs.util.P3 steps
    • points

      public javajs.util.P3 points
    • volumeData

      public VolumeData volumeData
    • contactPair

      public ContactPair contactPair
    • 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

      public Object[] filesData
    • probeValues

      public float[] probeValues
    • sbOut

      public javajs.util.SB sbOut
  • Constructor Details

    • Parameters

      public Parameters()
  • Method Details

    • initialize

      void initialize()
    • resetForMapping

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

      private String getScriptParams()
    • setLp

      void setLp(javajs.util.P4 v)
    • setRadical

      void setRadical(javajs.util.P4 v)
    • setLcao

      void setLcao(String type, int colorPtr)
    • setSolvent

      void setSolvent(String propertyName, float radius)
    • setFunctionXY

      void setFunctionXY(javajs.util.Lst<Object> value)
    • setFunctionXYZ

      void setFunctionXYZ(javajs.util.Lst<Object> value)
    • 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

      void setMapRanges(SurfaceReader surfaceReader, boolean haveData)
    • addSlabInfo

      public void addSlabInfo(Object[] slabObject)
    • isInsideOut

      public boolean isInsideOut()
    • isFullyLit

      public boolean isFullyLit()