Package chemaxon.struc.graphics

Class MEFlow

  • All Implemented Interfaces:
    Serializable, Cloneable
    @PublicAPI
public class MEFlow
extends MPolyline
    Electron flow arrow.
    Representing the movement of one or two electrons in a reaction as a curved arrow.
    Electron flow can start from any atom or bond, but not from any atom pairs that has no connection bond.
    The logic of the electron flows:
    • If the source is an Atom, the sink can be:
      • any Atom
      • Bond connected to this Atom
      • an atom pair from this atom and any other atom (incipient bond)
    • If the source is a Bond, the sink can be:
      • one of the Atoms on the end of this Bond
      • a Bond connected to this Bond (has common ending Atom)
      • an atom pair from one of the Atoms on the end of this Bond and any other atom (incipient bond)
    • If only the sink/source is in an sgroup, the sink/source must be the attachment point.
    Since:
    Marvin 3.5, 07/14/2004
    See Also:
    Serialized Form

    • Constructor Detail

      • MEFlow

        public MEFlow()
        Contructs an empty 2 electron flow arrow.

      • MEFlow

        public MEFlow​(int ne)
        Contructs an empty electron flow arrow.
        Parameters:
        ne - one-electron (1) or two-electron (2) transfer

      • MEFlow

        public MEFlow​(MPoint p1,
              MPoint p2,
              int ne)
        Contructs an electron flow arrow with the specified endpoints.
        Parameters:
        p1 - the starting point
        p2 - the endpoint
        ne - one-electron (1) or two-electron (2) transfer
        See Also:
        MAtomSetPoint

      • MEFlow

        protected MEFlow​(MEFlow l)
        Copy constructor.
        Parameters:
        l - the original arrow

    • Method Detail

      • getNumElectrons

        public int getNumElectrons()
        Gets the number of electrons the arrow represents.
        Returns:
        1 or 2

      • getPoint

        public MPoint getPoint​(int i)
        Gets a point of the line.
        Overrides:
        getPoint in class MPolyline
        Parameters:
        i - the point index
        Returns:
        the point's clone

      • clone

        public MEFlow clone()
        Description copied from class: MObject
        Creates a clone.
        Overrides:
        clone in class MPolyline
        Returns:
        the clone

      • getMolObject

        public Object getMolObject​(int i)
        Gets the electron source or sink.
        Parameters:
        i - E_SOURCE or E_SINK
        Returns:
        a MolAtom, MolBond or MolAtom[2] (incipient bond) object

      • getPointRefCount

        public int getPointRefCount()
        Gets the number of point references.
        Overrides:
        getPointRefCount in class MPolyline
        Returns:
        2 because middle point is not needed

      • getSource

        public Object getSource()
        Gets the origin of the electron-flow arrow (MolAtom or MolBond).
        Returns:
        origin of the electron-flow arrow

      • getSink

        public Object getSink()
        Gets the destination of the electron-flow arrow (MolAtom, MolBond, or MolAtom[2] for incipient bond).
        Returns:
        destination of the electron-flow arrow

      • sourceIsAtom

        public boolean sourceIsAtom()
        Gets whether this arrow's source is an atom.
        Returns:
        whether this arrow's source is an atom

      • sinkIsAtom

        public boolean sinkIsAtom()
        Gets whether this arrow's sink is an atom.
        Returns:
        whether this arrow's sink is an atom

      • isAtom

        public static boolean isAtom​(Object terminus)
        Gets whether the arrow's terminus is at an atom.
        Parameters:
        terminus - the arrow terminus
        Returns:
        whether the arrow's terminus is at an atom

      • sourceIsBond

        public boolean sourceIsBond()
        Gets whether this arrow's source is a bond.
        Returns:
        whether this arrow's source is a bond

      • sinkIsBond

        public boolean sinkIsBond()
        Gets whether this arrow's sink is a bond.
        Returns:
        whether this arrow's sink is a bond

      • isBond

        public static boolean isBond​(Object terminus)
        Gets whether the arrow's terminus is at a bond.
        Parameters:
        terminus - the arrow terminus
        Returns:
        whether the arrow's terminus is at a bond

      • sinkIsIncipBond

        public boolean sinkIsIncipBond()
        Gets whether this arrow's sink is an incipient bond.
        Returns:
        whether this arrow's sink is an incipient bond

      • isIncipBond

        public static boolean isIncipBond​(Object sink)
        Gets whether the arrow's sink is at an incipient bond.
        Parameters:
        sink - the arrow sink
        Returns:
        whether the arrow's sink is at an incipient bond

      • getSourceAtom

        public MolAtom getSourceAtom()
        Gets the atom at the source of this arrow. Use only after sourceIsAtom().
        Returns:
        the atom at the source of this arrow

      • getSinkAtom

        public MolAtom getSinkAtom()
        Gets the atom at the sink of this arrow. Use only after sinkIsAtom().
        Returns:
        the atom at the sink of this arrow

      • getAtom

        public static MolAtom getAtom​(Object terminus)
        Gets the atom at the terminus of an arrow.
        Parameters:
        terminus - the arrow terminus
        Returns:
        the atom at the terminus of an arrow or null if it is not a MolAtom.

      • getBond

        public static MolBond getBond​(Object terminus)
        Gets the bond at the terminus of an arrow.
        Parameters:
        terminus - the arrow terminus
        Returns:
        the bond at the terminus of an arrow or null if the terminus is not a MolBond.

      • getSourceBond

        public MolBond getSourceBond()
        Gets the bond at the source of this arrow. Use only after sourceIsBond().
        Returns:
        the bond at the source of this arrow

      • getSinkBond

        public MolBond getSinkBond()
        Gets the bond at the sink of this arrow. Use only after sinkIsBond().
        Returns:
        the bond at the sink of this arrow

      • getSourceAtoms

        public MolAtom[] getSourceAtoms()
        Gets the atom or atoms at the arrow source.
        Returns:
        the atom or atoms at the arrow source

      • getSinkAtoms

        public MolAtom[] getSinkAtoms()
        Gets the atom or atoms at the arrow sink.
        Returns:
        the atom or atoms at the arrow sink

      • getAtoms

        public static MolAtom[] getAtoms​(Object terminus)
        Gets the atom or atoms at the terminus of an arrow.
        Parameters:
        terminus - the arrow terminus
        Returns:
        the atom or atoms at the terminus of an arrow

      • getEFlowsOfAtom

        public static List<MEFlow> getEFlowsOfAtom​(MolAtom atom)
        Returns all the EFlows that are started from this atom or pointing to this atom.
        Parameters:
        atom - the sink or source atom
        Returns:
        List of EFlows, empty if no EFlow starts from this atom and no EFlow ends to this atom.

      • getEFlowsFromAtom

        public static List<MEFlow> getEFlowsFromAtom​(MolAtom atom)
        Returns all the EFlow from this atom. See getEFlowsOfAtom(MolAtom).
        Parameters:
        atom -
        Returns:
        List of MEFlows, empty if no electron flow arrow is connected to the atom.

      • getEFlowsToAtom

        public static List<MEFlow> getEFlowsToAtom​(MolAtom atom)
        Returns all the EFlows to this atom. See getEFlowsOfAtom(MolAtom).
        Parameters:
        atom -
        Returns:
        List of MEFlows, empty if no electron flow arrow is connected to the atom.

      • setSkipsToEndPoints

        public void setSkipsToEndPoints()

      • setBaseElectronContainer

        public void setBaseElectronContainer​(MolAtom atom,
                                     MDocument doc)

      • resetBaseElectronContainer

        public void resetBaseElectronContainer​(MolAtom atom,
                                       MDocument doc)

      • getBaseElectronContainerIndex

        public int getBaseElectronContainerIndex()

      • setBaseElectronContainerIndex

        public void setBaseElectronContainerIndex​(int idx)

      • getBaseElectronIndexInContainer

        public int getBaseElectronIndexInContainer()

      • setBaseElectronIndexInContainer

        public void setBaseElectronIndexInContainer​(int idx)

      • getValidSourceAtomsForMolecule

        @Deprecated
public static MolAtom[] getValidSourceAtomsForMolecule​(Molecule m)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceAtoms(Molecule) .

      • getValidSourceBondsForMolecule

        @Deprecated
public static MolBond[] getValidSourceBondsForMolecule​(Molecule m)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceBonds(Molecule) .

      • getValidSourceAtomPairsForMolecule

        @Deprecated
public static MolAtom[][] getValidSourceAtomPairsForMolecule​(Molecule m)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceAtomPairs(Molecule) .

      • getValidSinkAtomsForMolecule

        @Deprecated
public static MolAtom[] getValidSinkAtomsForMolecule​(Molecule m,
                                                     MolAtom source)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolAtom) .

      • getValidSinkAtomsForMolecule

        @Deprecated
public static MolAtom[] getValidSinkAtomsForMolecule​(Molecule m,
                                                     MolBond source)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolBond) .

      • getValidSinkBondsForMolecule

        @Deprecated
public static MolBond[] getValidSinkBondsForMolecule​(Molecule m,
                                                     MolAtom source)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkBonds(Molecule, MolAtom) .

      • getValidSinkBondsForMolecule

        @Deprecated
public static MolBond[] getValidSinkBondsForMolecule​(Molecule m,
                                                     MolBond source)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkBonds(Molecule, MolBond) .

      • getValidSinkAtomPairsForMolecule

        @Deprecated
public static MolAtom[][] getValidSinkAtomPairsForMolecule​(Molecule m,
                                                           MolAtom source)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolAtom) .

      • getValidSinkAtomPairsForMolecule

        @Deprecated
public static MolAtom[][] getValidSinkAtomPairsForMolecule​(Molecule m,
                                                           MolBond source)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolBond) .

      • isValidSourceForMolecule

        @Deprecated
public static boolean isValidSourceForMolecule​(Object source,
                                               Molecule m)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.isValidSource(MolAtom, Molecule) or EFlowPlacementValidators.isValidSource(MolAtom[], Molecule) or EFlowPlacementValidators.isValidSource(MolBond, Molecule) .

      • isValidSourceAndSinkForMolecule

        @Deprecated
public static boolean isValidSourceAndSinkForMolecule​(Object source,
                                                      Object sink,
                                                      Molecule m)
        Deprecated.
        As of Marvin 6.1, replaced by EFlowPlacementValidators.isValidFlow(MolAtom, MolAtom, Molecule) or one of the other implementations instead.

      • distanceFrom

        public double distanceFrom​(double x,
                           double y,
                           CTransform3D t)
        Description copied from class: MPolyline
        Gets the 2D distance from the specified point.
        Overrides:
        distanceFrom in class MPolyline
        Parameters:
        x - the x coordinate
        y - the y coordinate
        t - transformation or null

      • copyProperties

        public void copyProperties​(MPolyline l)
        Description copied from class: MPolyline
        Copies line properties to another line object.
        Overrides:
        copyProperties in class MPolyline
        Parameters:
        l - the other line

      • getAttribute

        public String getAttribute​(String s)
        Description copied from class: MPolyline
        Gets the value of an attribute.
        Overrides:
        getAttribute in class MPolyline
        Parameters:
        s - the attribute name
        Returns:
        the value or null

      • addAttributeKeys

        public void addAttributeKeys​(List<String> v)
        Description copied from class: MPolyline
        Adds the attribute names to the specified vector.
        Overrides:
        addAttributeKeys in class MPolyline
        Parameters:
        v - the vector

      • setAttribute

        public void setAttribute​(String s,
                         String v)
        Description copied from class: MPolyline
        Sets the value of an attribute.
        Overrides:
        setAttribute in class MPolyline
        Parameters:
        s - the attribute name
        v - the attribute value

      • getMElectron

        public chemaxon.struc.graphics.MElectron getMElectron()

      • getMElectronRef

        public chemaxon.struc.graphics.MElectron getMElectronRef()

      • getMElectronContainer

        public chemaxon.struc.graphics.MElectronContainer getMElectronContainer()

      • releaseBaseMElectrons

        public void releaseBaseMElectrons()

      • removeAtom

        public void removeAtom​(MolAtom atom)
        Description copied from class: MObject
        Removes the atom from the corresponding molecule object.
        Overrides:
        removeAtom in class MObject
        Parameters:
        atom - the atom to remove

      • removeNotify

        public void removeNotify​(MDocument doc)
        Description copied from class: MObject
        Called when the object is removed from a document.
        Overrides:
        removeNotify in class MPolyline
        Parameters:
        doc - The document from which the object is removed.