Package org.jmol.symmetry

Class UnitCell

  • class UnitCell
extends SimpleUnitCell
    a class private to the org.jmol.symmetry package to be accessed only through the SymmetryInterface API adds vertices and offsets orientation, and a variety of additional calculations that in principle could be put in SimpleUnitCell if desired, but for now are in this optional package.

    • Field Detail

      • vertices

        private javajs.util.P3[] vertices

      • fractionalOffset

        private javajs.util.P3 fractionalOffset

      • allFractionalRelative

        private boolean allFractionalRelative

      • cartesianOffset

        protected final javajs.util.P3 cartesianOffset

      • unitCellMultiplier

        protected javajs.util.P3 unitCellMultiplier

      • moreInfo

        public javajs.util.Lst<java.lang.String> moreInfo

      • name

        public java.lang.String name

      • unitVectors

        private static final javajs.util.V3[] unitVectors

    • Constructor Detail

      • UnitCell

        private UnitCell()

    • Method Detail

      • newP

        static UnitCell newP​(javajs.util.T3[] points,
                     boolean setRelative)
        A special constructor for spacially defined unit cells. Not used by readers.
        Parameters:
        points - [origin, a, b, c]
        setRelative -
        Returns:
        new unit cell

      • newA

        public static UnitCell newA​(float[] params,
                            boolean setRelative)

      • initOrientation

        void initOrientation​(javajs.util.M3 mat)

      • toUnitCell

        final void toUnitCell​(javajs.util.T3 pt,
                      javajs.util.T3 offset)
        when offset is null, use the current cell, otherwise use the original unit cell
        Parameters:
        pt -
        offset -

      • unitize

        public void unitize​(javajs.util.T3 pt)

      • reset

        public void reset()

      • setOffset

        void setOffset​(javajs.util.T3 pt)

      • setCartesianOffset

        private void setCartesianOffset​(javajs.util.T3 origin)

      • setMinMaxLatticeParameters

        void setMinMaxLatticeParameters​(javajs.util.P3i minXYZ,
                                javajs.util.P3i maxXYZ)

      • dumpInfo

        final java.lang.String dumpInfo​(boolean isFull)

      • getVertices

        javajs.util.P3[] getVertices()

      • getCartesianOffset

        javajs.util.P3 getCartesianOffset()

      • getFractionalOffset

        javajs.util.P3 getFractionalOffset()

      • getTensor

        Tensor getTensor​(Viewer vwr,
                 float[] parBorU)

      • getCanonicalCopy

        javajs.util.P3[] getCanonicalCopy​(float scale,
                                  boolean withOffset)

      • toFractionalX

        private static float toFractionalX​(float x)

      • initUnitcellVertices

        private void initUnitcellVertices()

      • checkDistance

        public boolean checkDistance​(javajs.util.P3 f1,
                             javajs.util.P3 f2,
                             float distance,
                             float dx,
                             int iRange,
                             int jRange,
                             int kRange,
                             javajs.util.P3 ptOffset)
        Parameters:
        f1 -
        f2 -
        distance -
        dx -
        iRange -
        jRange -
        kRange -
        ptOffset - TODO
        Returns:
        TRUE if pt has been set.

      • getUnitCellMultiplier

        public javajs.util.P3 getUnitCellMultiplier()

      • getUnitCellVectors

        public javajs.util.P3[] getUnitCellVectors()

      • fix

        private float fix​(float x)

      • isSameAs

        public boolean isSameAs​(UnitCell uc)

      • hasOffset

        public boolean hasOffset()

      • getState

        public java.lang.String getState()

      • getQuaternionRotation

        public javajs.util.Quat getQuaternionRotation​(java.lang.String abc)
        Returns a quaternion that will take the standard frame to a view down a particular axis, expressed as its counterparts.
        Parameters:
        abc - ab bc ca
        Returns:
        quaternion

      • getV0abc

        public javajs.util.T3[] getV0abc​(java.lang.Object def)

      • toFromPrimitive

        public boolean toFromPrimitive​(boolean toPrimitive,
                               char type,
                               javajs.util.T3[] uc)
        Parameters:
        toPrimitive - or assumed conventional
        type - P, R, A, B, C, I(BCC), or F(FCC)
        uc - either [origin, va, vb, vc] or just [va, vb, vc]
        Returns:
        true if successful