Class MAtomSetPoint

  • All Implemented Interfaces:
    Serializable, Cloneable

    @PublicAPI
    public class MAtomSetPoint
    extends MPoint
    Point fixed to the location of one or more atoms. The point's location is the weighted average of the atom locations. Useful for creating bond or atom pair type electron source/sink points for MEFlow.
    Since:
    Marvin 3.5, 07/05/2004
    See Also:
    Serialized Form
    • Constructor Detail

      • MAtomSetPoint

        public MAtomSetPoint()
        Contructs an empty point object.
      • MAtomSetPoint

        public MAtomSetPoint​(MolAtom[] a)
        Contructs a point object.
        Parameters:
        a - array of atoms
      • MAtomSetPoint

        public MAtomSetPoint​(MAtomSetPoint p)
        Copy constructor.
        Parameters:
        p - the point
    • Method Detail

      • equals

        public boolean equals​(Object o)
        Two points equal if their atoms equal.
        Overrides:
        equals in class MPoint
        Parameters:
        o - the other point
        Returns:
        true if they equal, false otherwise
      • setAtoms

        public void setAtoms​(MolAtom[] a)
        Sets the atoms.
        Parameters:
        a - the atoms
      • getAtoms

        public MolAtom[] getAtoms()
        Gets the atoms.
        Returns:
        the atoms
      • containsAtom

        public boolean containsAtom​(MolAtom a)
        Checks if the atom set contains the specified atom object.
        Overrides:
        containsAtom in class MObject
        Returns:
        true if the atom set contains the specified object, false otherwise
        Since:
        Marvin 3.5, 07/04/2004
      • replaceAtom

        public void replaceAtom​(MolAtom orig,
                                MolAtom a)
        Replaces a contained atom with another one.
        Overrides:
        replaceAtom in class MObject
        Parameters:
        orig - the original atom
        a - the new atom
        Since:
        Marvin 3.5, 07/04/2004
      • getLocation

        public void getLocation​(DPoint3 q,
                                CTransform3D trot)
        Gets the location. The atom set's location is the weighted average of the atom locations.
        Overrides:
        getLocation in class MPoint
        Parameters:
        q - the output point object
        trot - the viewing transformation or null
        Since:
        Marvin 4.1, 04/28/2006
      • setLocation

        public void setLocation​(DPoint3 p,
                                CTransform3D trot)
        Sets the atom coordinates. The atom set's location is the weighted average of the atom locations.
        Overrides:
        setLocation in class MPoint
        Parameters:
        p - the new location
        trot - the viewing transformation or null
      • getPoint

        public MPoint getPoint​(int i)
        Gets the point.
        Overrides:
        getPoint in class MPoint
        Parameters:
        i - the point index (must be 0)
        Returns:
        the point's clone
      • getWeights

        public double[] getWeights()
        Gets the atom weights used in average location calculation.
        Returns:
        the weights or null
        Since:
        Marvin 4.1, 04/21/2006
      • setWeights

        public void setWeights​(double[] w)
        Sets the atom weights for location calculation.
        Parameters:
        w - the atom weights or null
        Since:
        Marvin 4.1, 04/21/2006
      • transform

        public void transform​(CTransform3D t,
                              int opts,
                              CTransform3D trot)
        Does not perform any operation. An atom set point's location is fixed to the atoms.
        Overrides:
        transform in class MPoint
        Parameters:
        t - the transformation matrix
        opts - transform options or 0
        trot - the viewing transformation or null
        See Also:
        MObject.TRANSFORM_DISTORT
      • isTransformable

        public boolean isTransformable()
        Is it a transformable object?
        Overrides:
        isTransformable in class MObject
        Returns:
        true if the object can be transformed, false otherwise
        Since:
        Marvin 3.5, 07/06/2004
      • checkValidity

        public boolean checkValidity​(MDocument doc,
                                     Collection<MolAtom> invec)
        Is it a valid object in the document?
        Overrides:
        checkValidity in class MObject
        Parameters:
        doc - the document
        invec - collection of invalid atoms or null
        Returns:
        true if the object is valid, false if it contains an unknown atom
        Since:
        Marvin 3.5, 07/06/2004
      • finishCloning

        public void finishCloning​(MDocument olddoc,
                                  MDocument newdoc)
        Finish cloning a document. Called by the copy constructor.
        Overrides:
        finishCloning in class MObject
        Since:
        Marvin 3.5, 07/02/2004
      • getAtomArray

        protected MolAtom[] getAtomArray()
      • toString

        public String toString()
        Description copied from class: MObject
        Overrides Object.toString() to ease debugging. Returns a string consisting of the classname (without the package name!), the at-sign character `@', and the unsigned hexadecimal representation of the hash code of the object.
        Overrides:
        toString in class MPoint
        Returns:
        a string representation of the object