Package org.jmol.jvxl.readers

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 BS bsSelected

      • bsIgnore

        public BS bsIgnore

      • bsSolvent

        public 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 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 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

      • isModelConnected

        public boolean isModelConnected

      • surfaceAtoms

        public BS surfaceAtoms

    • 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()