chemaxon.struc.graphics

Class MEFlow

java.lang.Object

chemaxon.struc.MObject

chemaxon.struc.graphics.MPolyline

chemaxon.struc.graphics.MEFlow

All Implemented Interfaces:

Serializable, Cloneable

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

Version:

5.5

Author:

Peter Csizmadia, Peter Vadasz

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	E_SINK Electron sink.
static int	E_SOURCE Electron source.
static String	lonePairState
static String	radicalState

Fields inherited from class chemaxon.struc.graphics.MPolyline

ARROW_BACK_FLAG, ARROW_CROSSED_FLAG, ARROW_CURVED_FLAG, ARROW_DASHED_FLAG, ARROW_EQUILIBRIUM_FLAG, ARROW_GROUP1_MASK, ARROW_GROUP2_MASK, ARROW_HALF_LEFT, ARROW_HALF_MASK, ARROW_HALF_RIGHT, ARROW_RETROSYNTHETIC_FLAG, arrowFlags, CLOSED_FLAG, DEFAULT_ARROW_HEAD_LENGTH, DEFAULT_ARROW_HEAD_WIDTH, DEFAULT_EQUILIBRIUM_HEAD_WIDTH, DEFAULT_MAX_CROSS_SIZE, DEFAULT_RETROSYNTHETIC_HEAD_WIDTH, DEFAULT_THICKNESS, HEAD, points, TAIL, THICKNESS_SET_FLAG

Fields inherited from class chemaxon.struc.MObject

PAINT_ANTIALIAS, PAINT_FOCUSED, TRANSFORM_DISTORT

Constructor Summary

Constructors

Modifier	Constructor and Description
	MEFlow() Contructs an empty 2 electron flow arrow.
	MEFlow(int ne) Contructs an empty electron flow arrow.
protected	MEFlow(MEFlow l) Copy constructor.
	MEFlow(MPoint p1, MPoint p2, int ne) Contructs an electron flow arrow with the specified endpoints.

Method Summary

Methods

Modifier and Type	Method and Description
void	addAttributeKeys(List<String> v) Adds the attribute names to the specified vector.
MEFlow	clone() Creates a clone.
void	copyProperties(MPolyline l) Copies line properties to another line object.
double	distanceFrom(double x, double y, CTransform3D t) Gets the 2D distance from the specified point.
static MolAtom	getAtom(Object terminus) Gets the atom at the terminus of an arrow.
static MolAtom[]	getAtoms(Object terminus) Gets the atom or atoms at the terminus of an arrow.
String	getAttribute(String s) Gets the value of an attribute.
int	getBaseElectronContainerIndex()
int	getBaseElectronIndexInContainer()
static MolBond	getBond(Object terminus) Gets the bond at the terminus of an arrow.
static List<MEFlow>	getEFlowsFromAtom(MolAtom atom) Returns all the EFlow from this atom.
static List<MEFlow>	getEFlowsOfAtom(MolAtom atom) Returns all the EFlows that are started from this atom or pointing to this atom.
static List<MEFlow>	getEFlowsToAtom(MolAtom atom) Returns all the EFlows to this atom.
chemaxon.struc.graphics.MElectron	getMElectron()
chemaxon.struc.graphics.MElectronContainer	getMElectronContainer()
chemaxon.struc.graphics.MElectron	getMElectronRef()
Object	getMolObject(int i) Gets the electron source or sink.
int	getNumElectrons() Gets the number of electrons the arrow represents.
MPoint	getPoint(int i) Gets a point of the line.
int	getPointRefCount() Gets the number of point references.
Object	getSink() Gets the destination of the electron-flow arrow (MolAtom, MolBond, or MolAtom[2] for incipient bond).
MolAtom	getSinkAtom() Gets the atom at the sink of this arrow.
MolAtom[]	getSinkAtoms() Gets the atom or atoms at the arrow sink.
MolBond	getSinkBond() Gets the bond at the sink of this arrow.
Object	getSource() Gets the origin of the electron-flow arrow (MolAtom or MolBond).
MolAtom	getSourceAtom() Gets the atom at the source of this arrow.
MolAtom[]	getSourceAtoms() Gets the atom or atoms at the arrow source.
MolBond	getSourceBond() Gets the bond at the source of this arrow.
static MolAtom[][]	getValidSinkAtomPairsForMolecule(Molecule m, MolAtom source) Deprecated. As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolAtom) .
static MolAtom[][]	getValidSinkAtomPairsForMolecule(Molecule m, MolBond source) Deprecated. As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolBond) .
static MolAtom[]	getValidSinkAtomsForMolecule(Molecule m, MolAtom source) Deprecated. As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolAtom) .
static MolAtom[]	getValidSinkAtomsForMolecule(Molecule m, MolBond source) Deprecated. As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolBond) .
static MolBond[]	getValidSinkBondsForMolecule(Molecule m, MolAtom source) Deprecated. As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkBonds(Molecule, MolAtom) .
static MolBond[]	getValidSinkBondsForMolecule(Molecule m, MolBond source) Deprecated. As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSinkBonds(Molecule, MolBond) .
static MolAtom[][]	getValidSourceAtomPairsForMolecule(Molecule m) Deprecated. As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceAtomPairs(Molecule) .
static MolAtom[]	getValidSourceAtomsForMolecule(Molecule m) Deprecated. As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceAtoms(Molecule) .
static MolBond[]	getValidSourceBondsForMolecule(Molecule m) Deprecated. As of Marvin 6.1, replaced by EFlowPlacementValidators.getValidSourceBonds(Molecule) .
static boolean	isAtom(Object terminus) Gets whether the arrow's terminus is at an atom.
static boolean	isBond(Object terminus) Gets whether the arrow's terminus is at a bond.
static boolean	isIncipBond(Object sink) Gets whether the arrow's sink is at an incipient bond.
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.
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) .
void	releaseBaseMElectrons()
void	removeAtom(MolAtom atom) Removes the atom from the corresponding molecule object.
void	resetBaseElectronContainer(MolAtom atom, MDocument doc)
void	setAttribute(String s, String v) Sets the value of an attribute.
void	setBaseElectronContainer(MolAtom atom, MDocument doc)
void	setBaseElectronContainerIndex(int idx)
void	setBaseElectronIndexInContainer(int idx)
void	setSkipsToEndPoints()
boolean	sinkIsAtom() Gets whether this arrow's sink is an atom.
boolean	sinkIsBond() Gets whether this arrow's sink is a bond.
boolean	sinkIsIncipBond() Gets whether this arrow's sink is an incipient bond.
boolean	sourceIsAtom() Gets whether this arrow's source is an atom.
boolean	sourceIsBond() Gets whether this arrow's source is a bond.

Methods inherited from class chemaxon.struc.graphics.MPolyline

calcCenter, checkValidity, containsAtom, finishCloning, fixClonedPoints, fixMidPointClones, getArcAngle, getArcCenter, getArcRadius, getArcRadius, getArrowFlags, getArrowLength, getArrowWidth, getFlags, getLineMiddlePoint, getMidPointLocation, getMirroredArrowFlags, getPointCount, getPointRef, getPoints, getSkip, getThickness, hasBackground, hasColor, hasFace, hasLineColor, hasOutline, isArrow, isEmpty, isThicknessSet, removeChild, removeNotify, replaceAtom, reverse, rotate, setArcAngle, setArrow, setArrowFlags, setArrowLength, setArrowWidth, setFlags, setPoints, setSkip, setThickness, transform, unselectContents, updateBoundingRect

Methods inherited from class chemaxon.struc.MObject

addCdataAttributeKeys, addNotify, addNotify, connectToSgroupOfAtom, containsPoint, distanceFrom, getBackground, getColor, getLineColor, isChildOf, isInternalSelectable, isReactionArrow, isSelectableNow, isSelected, isTransformable, makeColor, removeNotify, setBackground, setColor, setLineColor, setSelected, toString

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

lonePairState

public static final String lonePairState

See Also:

Constant Field Values

radicalState

public static final String radicalState

See Also:

Constant Field Values

E_SOURCE

public static final int E_SOURCE

Electron source.

See Also:

getMolObject(int), Constant Field Values

E_SINK

public static final int E_SINK

Electron sink.

See Also:

getMolObject(int), Constant Field Values

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