Class Parameters


  • public class Parameters
    extends java.lang.Object
    • Field Detail

      • state

        public int state
      • testFlags

        public int testFlags
      • logMessages

        boolean logMessages
      • logCompression

        boolean logCompression
      • logCube

        boolean logCube
      • isSilent

        public boolean isSilent
      • assocCutoff

        float assocCutoff
      • dataType

        public int dataType
      • surfaceType

        int surfaceType
      • calculationType

        java.lang.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

        java.lang.Boolean pocket
      • minSet

        int minSet
      • slabInfo

        public javajs.util.Lst<java.lang.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
      • defaultQMOrbitalCutoff

        public static final float defaultQMOrbitalCutoff
        See Also:
        Constant Field Values
      • defaultQMElectronDensityCutoff

        static final float defaultQMElectronDensityCutoff
        See Also:
        Constant Field Values
      • 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

        java.lang.String lcaoType
      • functionInfo

        public javajs.util.Lst<java.lang.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_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
      • moData

        public java.util.Map<java.lang.String,​java.lang.Object> moData
      • 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 java.lang.String script
      • bsSelected

        public javajs.util.BS bsSelected
      • bsIgnore

        public javajs.util.BS bsIgnore
      • bsSolvent

        public javajs.util.BS bsSolvent
      • func

        public java.lang.Object func
      • title

        public java.lang.String[] title
      • blockCubeData

        boolean blockCubeData
      • readAllData

        boolean readAllData
      • fileIndex

        int fileIndex
      • fileName

        public java.lang.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
      • 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
      • 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
      • 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 java.lang.Object[] filesData
      • probeValues

        public float[] probeValues
      • sbOut

        public javajs.util.SB sbOut
    • Constructor Detail

      • Parameters

        public Parameters()
    • Method Detail

      • 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 java.lang.String getScriptParams()
      • setLp

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

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

        void setLcao​(java.lang.String type,
                     int colorPtr)
      • setSolvent

        void setSolvent​(java.lang.String propertyName,
                        float radius)
      • setFunctionXY

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

        void setFunctionXYZ​(javajs.util.Lst<java.lang.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​(java.lang.Object[] slabObject)
      • isInsideOut

        public boolean isInsideOut()
      • isFullyLit

        public boolean isFullyLit()