MDocument (Marvin API documentation (c) 1998-2014 ChemAxon Ltd.)

java.lang.Object
- chemaxon.struc.MDocument

All Implemented Interfaces:

chemaxon.core.structure.DocumentForBuilder, MTransformable, Serializable

Direct Known Subclasses:

MSelectionDocument
```
public class MDocument
extends Object
implements MTransformable, Serializable, chemaxon.core.structure.DocumentForBuilder
```
Marvin document. Stores molecules and graphics objects. There are two main groups of graphic objects. One of them contains simple objects without chemical meaning, these are stored directly in this document. The other group, called extra objects, has chemical meaning and belongs to a chemical structure. Extra object are:
- reaction arrow
- S-group bracket
Extra objects are stored in the related chemical structure, but they are available from this class.
Since:

Marvin 3.1.4

Version:

5.3, 09/25/2009

Author:

Peter Csizmadia, Eva Hollo, Erika Biro

See Also:
Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`MDocument.CheckerMark` Provides informations for Structure Checker higlight
`class`	`MDocument.Prop` Property that stores an MDocument.

Field Summary

Fields
Modifier and Type	Field and Description
`protected MChemicalStruct`	`mainMChemicalStruct`
`protected chemaxon.struc.graphics.MMoleculeMovie`	`mainMMoleculeMovie`
`protected MObject`	`objectContainingSelection`
`protected ArrayList<MObject>`	`objects`
`static int`	`SETCOLOR_COLORLESS` The atom/bond set is colorless, normal (CPK, Monochrome etc.) colors are used.
`static int`	`SETCOLOR_DEFAULT` Default set colors are used for coloring the atom/bond set.
`static int`	`SETCOLOR_SPECIFIED` The user specified set colors are used for coloring the atom/bond set.

Constructor Summary

Constructors
Modifier	Constructor and Description
	`MDocument(MDocument doc)` Copy constructor.
`protected`	`MDocument(MDocument doc, boolean cloneobjs)` Copy constructor.
	`MDocument(Molecule[] mols)` Creates a document for the specified molecule animation.
	`MDocument(MoleculeGraph m)` Creates a document for the specified molecule graph.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addCheckerMark(MDocument.CheckerMark mark)` Adds a checker mark to the document.
`void`	`addObject(MObject o)` Adds an object to the document.
`DPoint3`	`calcCenter()` Calculates the geometrical center.
`DPoint3`	`calcCenter(CTransform3D t)` Calculates the geometrical center.
`void`	`clear()` Clears the document.
`void`	`clearCheckerMarks()` Clears the checker marks
`void`	`clearSets()` Clears the atomSets and the bondSets.
`Object`	`clone()` Creates a clone.
`MDocument`	`cloneDocument()` Creates a clone.
`Molecule`	`cloneMainMolecule()` Creates a clone.
`MoleculeGraph`	`cloneMainMoleculeGraph()` Creates a clone.
`void`	`cloneSets(MDocument doc)` Clones the atom/bond sets from doc.
`protected void`	`cloneTemporraryObjects(MDocument doc)`
`boolean`	`contains(MDocument doc)` Tests whether the document contains all objects of another document.
`boolean`	`contains(MObject o)` Searches an object in the document.
`boolean`	`containsOnlyOne(Class cl)` Tests whether the document contains only one object of the specified class.
`byte[]`	`exportToBinFormat(String fmt)` Deprecated. As of release 5.7, replaced by `MolExporter.exportToBinFormat(MDocument, String)`.
`String`	`exportToFormat(String fmt)` Deprecated. As of release 5.7, replaced by `MolExporter.exportToFormat(MDocument, String)`
`Object`	`exportToObject(String fmt)` Deprecated. As of release 5.7, replaced by `MolExporter.exportToObject(MDocument, String)`
`static void`	`fixElectronContainers(MDocument doc, boolean lonePairsAutoCalc, boolean lonePairsVisible)` Removes unnecesarry MElectronContainers from the give MDocument corresponding to lone pair display options, if an electron of a MEFlow arrow has been removed the arrow is removed as well.
`Molecule[]`	`getAllMolecules()` Gets an array containing all molecule objects.
`Molecule[]`	`getAllNonEmptyMolecules()` Gets an array containing all non-empty molecule objects.
`List<MObject>`	`getAllObjects()` Gets all objects stored in this document and from the chemical structure of the document.
`Color`	`getAtomSetColor(int seq)` Gets an atom set color.
`int`	`getAtomSetColorMode(int seq)` Gets the atom set coloring mode.
`MFont`	`getAtomSetFont(int seq)` Gets an atom set font.
`int`	`getAtomSetRGB(int seq)` Gets an atom set color.
`int`	`getAtomSetSize()` Gets the size of the atom set.
`Color`	`getBondSetColor(int seq)` Gets a bond set color.
`int`	`getBondSetColorMode(int seq)` Gets the bond set coloring mode.
`int`	`getBondSetRGB(int seq)` Gets a bond set color.
`int`	`getBondSetSize()` Gets the bond set size.
`double`	`getBondSetThickness(int seq)` Gets a bond set thickness.
`MDocument.CheckerMark[]`	`getCheckerMarks()` Returns the array of checker marks NOTE: checker marks will be reset on any molecule change
`MObject`	`getConnectedObject(int i)` Gets an object from the document or from the chemical structure of the document.
`int`	`getConnectedObjectCount()` Gets the number of objects in this document and in the chemical structure of this document.
`MObject`	`getDraggedObject()` Gets the dragged object
`long`	`getEndPosition()` Gets the end position of this document in the input file.
`int`	`getExtraLabelSetColorMode(int seq)` Gets the coloring mode of extra label set sequences.
`MFont`	`getExtraLabelSetFont(int seq)`
`long`	`getExtraLabelSetRGBs(int seq)`
`int`	`getExtraLabelSetSize()`
`MObject`	`getFocus()` Gets the focused object
`int`	`getFreeAtomSetIndex()` Returns the first unused atomset index.
`int`	`getFreeBondSetIndex()` Returns the first unused bondset index.
`MPropertyContainer`	`getGUIPropertyContainer()`
`String`	`getInputFormat()` Gets the input file format.
`MoleculeGraph`	`getMainMoleculeGraph()` Gets the main molecule graph.
`MChemicalStruct`	`getMChemicalStruct()`
`chemaxon.struc.graphics.MMoleculeMovie`	`getMoleculeMovie()` Gets the molecule movie.
`MProp`	`getMProp()` Gets the document as a property.
`MObject`	`getObject(int i)` Gets an object from the document.
`MObject`	`getObjectContainingSelection()` Gets the object that contains the selection.
`int`	`getObjectCount()` Gets the number of objects in this document.
`chemaxon.struc.PageSettings`	`getPageSettings()` Gets the page settings of multipage molecular document.
`Molecule`	`getPrimaryMolecule()` Gets the primary molecule object.
`Molecule[]`	`getPrimaryMolecules()` Gets an array containing the primary molecule objects.
`long`	`getStartPosition()` Gets the starting position of this document in the input file.
`void`	`highlight(MObject o)` Highlight an object.
`int`	`indexOf(MObject o)` Searches for an object in the document or in the chemical structure that belongs to the document.
`boolean`	`isAtomSetColorModeSet()` Decides whether the atomset coloring mode is set.
`boolean`	`isEmpty()` Tests whether the document is empty: the main molecule object in the document is empty no graphic object is included (neither simple nor extra)
`boolean`	`isExtraObject(MObject o)` Decides whether a graphic object belongs to the main chemical structure of the document.
`boolean`	`isHighlighted(MObject o)` Is the specified object currently highlighted?
`boolean`	`isSimpleMolecule()` Tests whether the document is equivalent to a simple molecule.
`void`	`moveMainMoleculeGraphToFront()` Move the main molecule graph to the top of stack.
`void`	`moveMoleculeMovieToFront()` Move the molecule movie (if exists) to the top of stack.
`void`	`moveObject(MObject o, int i)` Move an object to another place in the stack.
`static MDocument`	`parseMRV(String sval)` Deprecated. As of release 5.7, replaced by `MolImporter.parseMRV(String)`
`MPropertyContainer`	`properties()` Gets the property container.
`void`	`removeAtom(MolAtom a)` Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
`void`	`removeAtom(MolAtom a, int cleanupFlags)` Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
`void`	`removeAtomFromGraphs(MolAtom node)` Removes the specified node from all molecule graphs.
`void`	`removeColorsFromMolecules()` Removes coloring from all molecular objects in the document.
`void`	`removeElectronsOf(MolAtom targetAtom)` Removes the Electron containers belongs to targetAtom,
`void`	`removeObject(int i)` Removes an object from the document.
`void`	`removeObject(MObject o)` Removes an object from the document or from the chemical structure of the document.
`void`	`selectAllConnectedObjects(boolean s)` Selects or unselects all objects in this document and objects that belong to the chemical structure of this document.
`void`	`selectAllObjects(boolean s)` Selects or unselects all objects.
`void`	`setAtomSetColorMode(int seq, int m)` Sets the atom set coloring mode.
`void`	`setAtomSetFont(int seq, MFont font)` Sets the font of an atom set.
`void`	`setAtomSetRGB(int seq, int rgb)` Sets the color of an atom set.
`void`	`setBondSetColorMode(int seq, int m)` Sets the bond set coloring mode.
`void`	`setBondSetRGB(int seq, int rgb)` Sets the color of a bond set.
`void`	`setBondSetThickness(int seq, double thickness)` Sets the thickness of a bond set.
`void`	`setDraggedObject(MObject o)` Sets the dragged object.
`void`	`setEndPosition(long off)` Sets the end position of this document in the input file.
`void`	`setExtraLabelColorsForDocument(Molecule mol)` Sets the coloring mode sets and colors of extra labels
`void`	`setExtraLabelSetColorMode(int seq, int mode)`
`void`	`setExtraLabelSetRGBs(int seq, int rgb)`
`void`	`setExtraLabelSetRGBs(int seq, int rgb1, int rgb2)`
`void`	`setFocus(MObject o)` Focus to the specified object.
`void`	`setGUIPropertyContainer(MPropertyContainer gpc)` Sets the property container storing MarvinPane settings
`void`	`setGUIProperyContainer(MPropertyContainer gpc)` Deprecated. As of Marvin 6.1, replaced by `setGUIPropertyContainer(MPropertyContainer)`.
`void`	`setInputFormat(String format)` Sets the input file format.
`void`	`setMainMoleculeGraph(MoleculeGraph m)` Sets the main molecule graph.
`void`	`setMoleculeMovie(chemaxon.struc.graphics.MMoleculeMovie mmm)` Sets the molecule movie.
`void`	`setObject(MObject o, int i)` Sets an object
`void`	`setObjectContainingSelection(MObject o)` Sets the object that contains the selection.
`void`	`setPageSettings(chemaxon.struc.PageSettings pageSettings)` Sets the page settings of multipage molecular document.
`void`	`setStartPosition(long off)` Sets the starting position of this document in the input file.
`void`	`simplifyMolecule()` Simplifies the main molecule object if possible.
`String`	`toString()` Overrides Object.toString() to ease debugging.
`void`	`transform(CTransform3D t)` Transforms all object's coordinates.
`void`	`transform(CTransform3D t, int opts)` Transforms all object's coordinates.
`void`	`transform(CTransform3D t, int opts, CTransform3D trot)` Transforms all object's coordinates.
`void`	`unhighlight(MObject o)` Unhighlights an object.
`void`	`unhighlightAll()` Unhighlights all objects.

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - SETCOLOR_DEFAULT
```
public static final int SETCOLOR_DEFAULT
```
    Default set colors are used for coloring the atom/bond set.
    
    Since:
    
    Marvin 4.1, 05/31/2006
    
    See Also:
    getAtomSetColorMode(int), getBondSetColorMode(int), Constant Field Values
  - SETCOLOR_SPECIFIED
```
public static final int SETCOLOR_SPECIFIED
```
    The user specified set colors are used for coloring the atom/bond set.
    
    Since:
    
    Marvin 4.1, 05/31/2006
    
    See Also:
    getAtomSetColorMode(int), getBondSetColorMode(int), Constant Field Values
  - SETCOLOR_COLORLESS
```
public static final int SETCOLOR_COLORLESS
```
    The atom/bond set is colorless, normal (CPK, Monochrome etc.) colors are used.
    
    Since:
    
    Marvin 4.1, 05/31/2006
    
    See Also:
    getAtomSetColorMode(int), getBondSetColorMode(int), Constant Field Values
  - objects
```
protected transient ArrayList<MObject> objects
```
  - mainMChemicalStruct
```
protected transient MChemicalStruct mainMChemicalStruct
```
  - mainMMoleculeMovie
```
protected transient chemaxon.struc.graphics.MMoleculeMovie mainMMoleculeMovie
```
  - objectContainingSelection
```
protected transient MObject objectContainingSelection
```
- Constructor Detail
  - MDocument
```
public MDocument(MoleculeGraph m)
```
    Creates a document for the specified molecule graph.
    
    Parameters:
    m - the main molecule graph
    
    Throws:
    
    IllegalArgumentException - if the given molecule has a parent (root, rgroup, component)
  - MDocument
```
public MDocument(Molecule[] mols)
```
    Creates a document for the specified molecule animation.
    
    Parameters:
    mols - the molecule animation
    Since:
    
    Marvin 4.0, 06/30/2005
  - MDocument
```
public MDocument(MDocument doc)
```
    Copy constructor.
    
    Parameters:
    doc - the source
  - MDocument
```
protected MDocument(MDocument doc,
         boolean cloneobjs)
```
    Copy constructor.
    
    Parameters:
    doc - the source
    cloneobjs - whether to clone objects
    Since:
    
    Marvin 3.5, 11/06/2004
- Method Detail
  - getMChemicalStruct
```
public MChemicalStruct getMChemicalStruct()
```
  - cloneTemporraryObjects
```
protected void cloneTemporraryObjects(MDocument doc)
```
  - cloneSets
```
public void cloneSets(MDocument doc)
```
    Clones the atom/bond sets from doc.
    
    Parameters:
    doc - the document to clone from.
  - parseMRV
```
@Deprecated
public static MDocument parseMRV(String sval)
                          throws IOException
```
    Deprecated. As of release 5.7, replaced by MolImporter.parseMRV(String)
    
    Parses a document from a string in Marvin Document (MRV) format.
    
    Parameters:
    sval - the string
    
    Returns:
    The document
    
    Throws:
    
    IOException - if an exception occurs during parsing
    Since:
    
    Marvin 4.1, 11/20/2005
  - cloneDocument
```
public MDocument cloneDocument()
```
    Creates a clone.
    
    Returns:
    the clone
    Since:
    
    Marvin 3.5.1, 11/20/2004
  - cloneMainMolecule
```
public final Molecule cloneMainMolecule()
```
    Creates a clone.
    
    Returns:
    the main molecule of the clone
    
    Throws:
    
    ClassCastException - if the main molecule graph is not a Molecule instance
    Since:
    
    Marvin 3.5.1, 11/20/2004
  - cloneMainMoleculeGraph
```
public final MoleculeGraph cloneMainMoleculeGraph()
```
    Creates a clone.
    
    Returns:
    the main molecule graph of the clone
    Since:
    
    Marvin 3.5.1, 11/20/2004
  - clone
```
public final Object clone()
```
    Creates a clone.
    
    Overrides:
    
    clone in class Object
    
    Returns:
    the clone
  - removeAtomFromGraphs
```
public void removeAtomFromGraphs(MolAtom node)
```
    Removes the specified node from all molecule graphs.
    
    Parameters:
    node - the node to remove
  - selectAllObjects
```
public void selectAllObjects(boolean s)
```
    Selects or unselects all objects.
  - selectAllConnectedObjects
```
public void selectAllConnectedObjects(boolean s)
```
    Selects or unselects all objects in this document and objects that belong to the chemical structure of this document.
  - getObjectContainingSelection
```
public MObject getObjectContainingSelection()
```
    Gets the object that contains the selection.
    
    Returns:
    the object or null
  - setObjectContainingSelection
```
public void setObjectContainingSelection(MObject o)
```
    Sets the object that contains the selection. All other objects's contents are unselected.
    
    Parameters:
    o - the object or null
  - isHighlighted
```
public boolean isHighlighted(MObject o)
```
    Is the specified object currently highlighted?
    
    Returns:
    true if it is highlighted, false otherwise
  - highlight
```
public void highlight(MObject o)
```
    Highlight an object.
    
    Parameters:
    o - the object to highlight
  - unhighlight
```
public void unhighlight(MObject o)
```
    Unhighlights an object.
    
    Parameters:
    o - the object to unhighlight
  - unhighlightAll
```
public void unhighlightAll()
```
    Unhighlights all objects.
  - getDraggedObject
```
public MObject getDraggedObject()
```
    Gets the dragged object
    
    Returns:
    the dragged object or null
  - setDraggedObject
```
public void setDraggedObject(MObject o)
```
    Sets the dragged object.
    
    Parameters:
    o - the object
  - getFocus
```
public MObject getFocus()
```
    Gets the focused object
    
    Returns:
    the focused object or null
  - setFocus
```
public void setFocus(MObject o)
```
    Focus to the specified object.
    
    Parameters:
    o - the object
  - getMainMoleculeGraph
```
public MoleculeGraph getMainMoleculeGraph()
```
    Gets the main molecule graph.
    
    Returns:
    the molecule graph
  - setMainMoleculeGraph
```
public void setMainMoleculeGraph(MoleculeGraph m)
```
    Sets the main molecule graph.
    
    Parameters:
    m - the molecule graph
  - getMoleculeMovie
```
public chemaxon.struc.graphics.MMoleculeMovie getMoleculeMovie()
```
    Gets the molecule movie.
    
    Returns:
    the molecule movie or null
    Since:
    
    Marvin 4.0, 06/30/2005
  - getPrimaryMolecule
```
public Molecule getPrimaryMolecule()
```
    Gets the primary molecule object. The main molecule graph is returned if it is a molecule, unless it is empty and a molecule movie is also present. In that case, the current molecule of the movie is returned. WARNING! Do not change the returned molecule object! The document may become corrupted.
    
    Returns:
    the array of molecules
    Since:
    
    Marvin 4.0, 06/30/2005
  - getPrimaryMolecules
```
public Molecule[] getPrimaryMolecules()
```
    Gets an array containing the primary molecule objects. The main molecule graph is returned if it is a molecule, unless it is empty and a molecule movie is also present. In that case, the molecules of the movie are returned. WARNING! Do not change the returned molecule objects! The document may become corrupted.
    
    Returns:
    the array of molecules
    Since:
    
    Marvin 4.0, 06/30/2005
  - getAllMolecules
```
public Molecule[] getAllMolecules()
```
    Gets an array containing all molecule objects. WARNING! Do not change the returned molecule objects! The document may become corrupted.
    
    Returns:
    the array of molecules
    Since:
    
    Marvin 4.0, 06/30/2005
  - getAllNonEmptyMolecules
```
public Molecule[] getAllNonEmptyMolecules()
```
    Gets an array containing all non-empty molecule objects. WARNING! Do not change the returned molecule objects! The document may become corrupted.
    
    Returns:
    the array of molecules
    Since:
    
    Marvin 4.0, 06/30/2005
  - setMoleculeMovie
```
public void setMoleculeMovie(chemaxon.struc.graphics.MMoleculeMovie mmm)
```
    Sets the molecule movie.
    
    Parameters:
    mmm - the molecule movie
    Since:
    
    Marvin 4.0, 06/30/2005
  - indexOf
```
public int indexOf(MObject o)
```
    Searches for an object in the document or in the chemical structure that belongs to the document.
    
    Parameters:
    o - the object
    
    Returns:
    the object's index if found, -1 otherwise
  - moveObject
```
public void moveObject(MObject o,
              int i)
```
    Move an object to another place in the stack.
    
    Parameters:
    o - the object
    i - the new position
  - moveMainMoleculeGraphToFront
```
public void moveMainMoleculeGraphToFront()
```
    Move the main molecule graph to the top of stack.
  - moveMoleculeMovieToFront
```
public void moveMoleculeMovieToFront()
```
    Move the molecule movie (if exists) to the top of stack.
    
    Since:
    
    Marvin 4.0, 06/30/2005
  - contains
```
public boolean contains(MObject o)
```
    Searches an object in the document.
    
    Parameters:
    o - the object
    
    Returns:
    true if the document contains the object, false otherwise
  - contains
```
public boolean contains(MDocument doc)
```
    Tests whether the document contains all objects of another document.
    
    Parameters:
    doc - the other document
    
    Returns:
    true if the document contains the objects of the other document, false otherwise
    Since:
    
    Marvin 3.4
  - containsOnlyOne
```
public boolean containsOnlyOne(Class cl)
```
    Tests whether the document contains only one object of the specified class.
    
    Parameters:
    cl - MObject.class or a derived class
    
    Returns:
    true if no more and not less than one non-empty object is instance of the specified class
    Since:
    
    Marvin 3.5, 07/12/2004
  - addObject
```
public void addObject(MObject o)
```
    Adds an object to the document.
    
    Parameters:
    o - the object
  - isExtraObject
```
public boolean isExtraObject(MObject o)
```
    Decides whether a graphic object belongs to the main chemical structure of the document.
    
    Parameters:
    o - the graphic object
    
    Returns:
    true if the graphic object belongs to the main chemical structure, false otherwise.
  - removeObject
```
public void removeObject(MObject o)
```
    Removes an object from the document or from the chemical structure of the document.
    
    Parameters:
    o - the object
  - removeObject
```
public void removeObject(int i)
```
    Removes an object from the document.
    
    Parameters:
    i - the object index
  - getObjectCount
```
public int getObjectCount()
```
    Gets the number of objects in this document.
    
    Returns:
    the number of objects
  - getConnectedObjectCount
```
public int getConnectedObjectCount()
```
    Gets the number of objects in this document and in the chemical structure of this document.
    
    Returns:
    the number of objects
  - getObject
```
public MObject getObject(int i)
```
    Gets an object from the document.
    
    Parameters:
    i - the index of the object
    
    Returns:
    the object at the specified index.
  - getConnectedObject
```
public MObject getConnectedObject(int i)
```
    Gets an object from the document or from the chemical structure of the document.
    
    Parameters:
    i - the index of the object
    
    Returns:
    the object at the specified index.
  - getAllObjects
```
public List<MObject> getAllObjects()
```
    Gets all objects stored in this document and from the chemical structure of the document.
    
    Returns:
    the list of objects
  - setObject
```
public void setObject(MObject o,
             int i)
```
    Sets an object
    
    Parameters:
    o - the object
    i - the index
  - removeAtom
```
public void removeAtom(MolAtom a)
```
    Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
    
    Parameters:
    a - the atom to remove
    Since:
    
    Marvin 3.5, 07/05/2004
  - removeAtom
```
public void removeAtom(MolAtom a,
              int cleanupFlags)
```
    Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
    
    Parameters:
    a - the atom to remove
    cleanupFlags - cleanup options
    Since:
    
    Marvin 4.1, 03/07/2006
  - clear
```
public void clear()
```
    Clears the document. Removes all objects except the main molecule graph, from which all atoms, bonds and other objects are removed.
  - clearSets
```
public void clearSets()
```
    Clears the atomSets and the bondSets.
  - isEmpty
```
public boolean isEmpty()
```
    Tests whether the document is empty:
    - the main molecule object in the document is empty
    - no graphic object is included (neither simple nor extra)
    Returns:
    true if the document is empty, false otherwise
  - isSimpleMolecule
```
public boolean isSimpleMolecule()
```
    Tests whether the document is equivalent to a simple molecule.
    
    Returns:
    true if the document does not have extra properties, false otherwise
    Since:
    
    Marvin 4.1, 11/19/2005
  - simplifyMolecule
```
public void simplifyMolecule()
```
    Simplifies the main molecule object if possible. Note that it makes the original molecule object invalid.
    
    Since:
    
    Marvin 4.1.13, 09/20/2007
    
    See Also:
    Molecule.getSimplifiedMolecule()
  - transform
```
public void transform(CTransform3D t)
```
    Transforms all object's coordinates.
    
    Specified by:
    
    transform in interface MTransformable
    
    Parameters:
    t - the transformation matrix
  - transform
```
public void transform(CTransform3D t,
             int opts)
```
    Transforms all object's coordinates.
    
    Parameters:
    t - the transformation matrix
    opts - the transformation options
    See Also:
    MObject.transform(CTransform3D, int, CTransform3D)
  - transform
```
public void transform(CTransform3D t,
             int opts,
             CTransform3D trot)
```
    Transforms all object's coordinates.
    
    Parameters:
    t - the transformation matrix
    opts - the transformation options
    trot - the viewing transformation
    Since:
    
    Marvin 4.1, 04/28/2006
    
    See Also:
    MObject.transform(CTransform3D, int, CTransform3D)
  - calcCenter
```
public DPoint3 calcCenter()
```
    Calculates the geometrical center.
    
    Returns:
    the center in `absolute' coordinates
  - calcCenter
```
public DPoint3 calcCenter(CTransform3D t)
```
    Calculates the geometrical center.
    
    Parameters:
    t - the viewing transformation or null
    
    Returns:
    the center in transformed coordinates
    Since:
    
    Marvin 4.1, 04/28/2006
  - getStartPosition
```
public long getStartPosition()
```
    Gets the starting position of this document in the input file.
    
    Returns:
    the starting position
  - setStartPosition
```
public void setStartPosition(long off)
```
    Sets the starting position of this document in the input file.
    
    Parameters:
    off - the starting position
  - getEndPosition
```
public long getEndPosition()
```
    Gets the end position of this document in the input file.
    
    Returns:
    the end position
  - setEndPosition
```
public void setEndPosition(long off)
```
    Sets the end position of this document in the input file.
    
    Parameters:
    off - the end position
  - getInputFormat
```
public final String getInputFormat()
```
    Gets the input file format. Set by the import module if the molecule is from a file.
    
    Returns:
    the input file format for the document
  - setInputFormat
```
public void setInputFormat(String format)
```
    Sets the input file format.
    
    Parameters:
    format - the input format
  - exportToFormat
```
@Deprecated
public final String exportToFormat(String fmt)
                            throws IOException
```
    Deprecated. As of release 5.7, replaced by MolExporter.exportToFormat(MDocument, String)
    Creates a string representation of the document. The format descriptor string can also contain export options. Format and options are separated by a colon, multiple options can be separated by commas. See the text formats and their options on the File Formats in Marvin page. Examples:
```
 s1 = doc.exportToFormat("mol");
 s2 = doc.exportToFormat("smiles:a-H"); // aromatize and remove Hydrogens
 
```
    Parameters:
    fmt - the format descriptor string
    
    Returns:
    string representation of the document in the specified format
    
    Throws:
    
    MolExportException - Export error
    
    IllegalArgumentException - Invalid format string.
    
    SecurityException - Export module cannot be loaded because of security reasons (firewall).
    
    IOException
    Since:
    
    Marvin 4.0, 07/01/2005
    
    See Also:
    exportToBinFormat(java.lang.String), exportToObject(java.lang.String), Molecule.exportToFormat(java.lang.String)
  - exportToBinFormat
```
@Deprecated
public final byte[] exportToBinFormat(String fmt)
                               throws IOException
```
    Deprecated. As of release 5.7, replaced by MolExporter.exportToBinFormat(MDocument, String).
    Creates a binary representation of the document. Works with all the text formats that are supported by the exportToFormat method, and also with the binary image formats (jpeg, msbmp, png). When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples:
```
 byte[] d1 = doc.exportToBinFormat("mrv");
 byte[] d2 = doc.exportToBinFormat("smiles:a-H"); // aromatize and remove H
 byte[] d3 = doc.exportToBinFormat("png:w300,h300,b32,#00ffff00");
 byte[] d4 = doc.exportToBinFormat("jpeg:w300,h300,Q95,#ffff00,spacefill");
 
```
    Parameters:
    fmt - the format descriptor string
    
    Returns:
    a binary representation of the document in the specified format
    
    Throws:
    
    MolExportException - Export error.
    
    IllegalArgumentException - Invalid format string.
    
    SecurityException - Export module cannot be loaded because of security reasons (firewall).
    
    IOException
    Since:
    
    Marvin 4.0, 07/01/2005
    
    See Also:
    exportToFormat(java.lang.String), exportToObject(java.lang.String), Molecule.exportToBinFormat(java.lang.String)
  - exportToObject
```
@Deprecated
public Object exportToObject(String fmt)
                      throws IOException
```
    Deprecated. As of release 5.7, replaced by MolExporter.exportToObject(MDocument, String)
    Creates a String, byte[] array or Image representation of the molecule. When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples:
```
 import java.awt.Image;
 ...
 String s1 = (String)doc.exportToObject("mol");
 String s2 = (String)doc.exportToObject("smiles:a-H"); // aromatize, remove H
 Image img = (Image)doc.exportToObject("image:w300,h300,#ffff00");
 byte[] d3 = (byte[])doc.exportToObject("png:w300,h300,b32,#00ffff00");
 byte[] d4 = (byte[])doc.exportToObject("jpeg:w300,h300,Q95,#ffff00,spacefill");
 
```
    Parameters:
    fmt - the format descriptor string
    
    Returns:
    a String, a byte[] array or an Image
    
    Throws:
    
    MolExportException - Export error.
    
    IllegalArgumentException - Invalid format string.
    
    SecurityException - Export module cannot be loaded because of security reasons (firewall).
    
    IOException
    Since:
    
    Marvin 4.0, 07/01/2005
    
    See Also:
    exportToFormat(java.lang.String), exportToBinFormat(java.lang.String), Molecule.exportToObject(java.lang.String)
  - getMProp
```
public MProp getMProp()
```
    Gets the document as a property.
    
    Since:
    
    Marvin 4.1, 08/01/2006
  - properties
```
public MPropertyContainer properties()
```
    Gets the property container.
    
    Since:
    
    Marvin 4.0, 06/18/2005
  - getAtomSetFont
```
public MFont getAtomSetFont(int seq)
```
    Gets an atom set font.
    
    Parameters:
    seq - the atom set sequence number
    
    Returns:
    the font
    Since:
    
    Marvin 4.0.3, 06/10/2005
  - setAtomSetFont
```
public void setAtomSetFont(int seq,
                  MFont font)
```
    Sets the font of an atom set.
    
    Parameters:
    seq - atom set sequence number (0, ..., MolAtom.SETSEQ_MAX)
    font -
    Since:
    
    Marvin 4.0.3, 06/10/2005
  - getAtomSetColorMode
```
public int getAtomSetColorMode(int seq)
```
    Gets the atom set coloring mode.
    
    Parameters:
    seq - the atom set sequence number
    
    Returns:
    the mode
    Since:
    
    Marvin 4.1, 05/31/2006
    
    See Also:
    SETCOLOR_DEFAULT, SETCOLOR_SPECIFIED, SETCOLOR_COLORLESS
  - setAtomSetColorMode
```
public void setAtomSetColorMode(int seq,
                       int m)
```
    Sets the atom set coloring mode.
    
    Parameters:
    seq - the atom set sequence number
    m - the mode
    Since:
    
    Marvin 4.1, 05/31/2006
    
    See Also:
    SETCOLOR_DEFAULT, SETCOLOR_SPECIFIED, SETCOLOR_COLORLESS
  - isAtomSetColorModeSet
```
public boolean isAtomSetColorModeSet()
```
    Decides whether the atomset coloring mode is set.
    
    Returns:
    true if the coloring mode is set for at lease one atomset false otherwise.
  - setExtraLabelSetColorMode
```
public void setExtraLabelSetColorMode(int seq,
                             int mode)
```
  - getAtomSetSize
```
public int getAtomSetSize()
```
    Gets the size of the atom set.
    
    Returns:
    the atom set size
  - getExtraLabelSetSize
```
public int getExtraLabelSetSize()
```
  - getAtomSetRGB
```
public int getAtomSetRGB(int seq)
```
    Gets an atom set color.
    
    Parameters:
    seq - the atom set sequence number
    
    Returns:
    the RGB values or -1 if unset or default atom coloring is used
    Since:
    
    Marvin 4.0, 03/02/2005
  - getExtraLabelSetRGBs
```
public long getExtraLabelSetRGBs(int seq)
```
  - getExtraLabelSetColorMode
```
public int getExtraLabelSetColorMode(int seq)
```
    Gets the coloring mode of extra label set sequences.
    
    Parameters:
    seq - the atom sequence number
    
    Returns:
    the coloring mode
    Since:
    
    Marvin 4.1, 07/06/2006
    
    See Also:
    SETCOLOR_DEFAULT, SETCOLOR_SPECIFIED, SETCOLOR_COLORLESS
  - getExtraLabelSetFont
```
public MFont getExtraLabelSetFont(int seq)
```
  - setExtraLabelColorsForDocument
```
public void setExtraLabelColorsForDocument(Molecule mol)
```
    Sets the coloring mode sets and colors of extra labels
    
    Parameters:
    mol - the graph union in the document
  - setAtomSetRGB
```
public void setAtomSetRGB(int seq,
                 int rgb)
```
    Sets the color of an atom set. It also sets the color mode of the set to SETCOLOR_SPECIFIED.
    
    Parameters:
    seq - atom set sequence number (0, ..., MolAtom.SETSEQ_MAX)
    rgb - the RGB values
    Since:
    
    Marvin 4.0, 03/02/2005
  - setExtraLabelSetRGBs
```
public void setExtraLabelSetRGBs(int seq,
                        int rgb)
```
  - setExtraLabelSetRGBs
```
public void setExtraLabelSetRGBs(int seq,
                        int rgb1,
                        int rgb2)
```
  - getAtomSetColor
```
public Color getAtomSetColor(int seq)
```
    Gets an atom set color.
    
    Parameters:
    seq - the atom set sequence number
    
    Returns:
    the color or null if unset or default bond coloring is used
    Since:
    
    Marvin 4.0, 03/02/2005
  - getBondSetSize
```
public int getBondSetSize()
```
    Gets the bond set size.
    
    Returns:
    the bond set size
  - getBondSetThickness
```
public double getBondSetThickness(int seq)
```
    Gets a bond set thickness.
    
    Parameters:
    seq - the atom set sequence number
    
    Returns:
    the thickness
    Since:
    
    Marvin 4.0.3, 10/14/2005
  - setBondSetThickness
```
public void setBondSetThickness(int seq,
                       double thickness)
```
    Sets the thickness of a bond set.
    
    Parameters:
    seq - bond set sequence number (0, ..., MolAtom.SETSEQ_MAX)
    thickness -
    Since:
    
    Marvin 4.0.3, 10/14/2005
  - getBondSetColorMode
```
public int getBondSetColorMode(int seq)
```
    Gets the bond set coloring mode.
    
    Parameters:
    seq - the bond set sequence number
    
    Returns:
    the mode
    Since:
    
    Marvin 4.1, 05/31/2006
    
    See Also:
    SETCOLOR_DEFAULT, SETCOLOR_SPECIFIED, SETCOLOR_COLORLESS
  - setBondSetColorMode
```
public void setBondSetColorMode(int seq,
                       int m)
```
    Sets the bond set coloring mode.
    
    Parameters:
    seq - the bond set sequence number
    m - the mode
    Since:
    
    Marvin 4.1, 05/31/2006
    
    See Also:
    SETCOLOR_DEFAULT, SETCOLOR_SPECIFIED, SETCOLOR_COLORLESS
  - getBondSetRGB
```
public int getBondSetRGB(int seq)
```
    Gets a bond set color.
    
    Parameters:
    seq - the bond set sequence number
    
    Returns:
    the RGB values or -1 if unset or default coloring is used
    Since:
    
    Marvin 4.0, 03/02/2005
  - setBondSetRGB
```
public void setBondSetRGB(int seq,
                 int rgb)
```
    Sets the color of a bond set. It also sets the color mode of the set to SETCOLOR_SPECIFIED.
    
    Parameters:
    seq - bond set sequence number (1, ..., MolBond.SETSEQ_MAX)
    rgb - the RGB values
    Since:
    
    Marvin 4.0, 03/02/2005
  - getBondSetColor
```
public Color getBondSetColor(int seq)
```
    Gets a bond set color.
    
    Parameters:
    seq - the bond set sequence number
    
    Returns:
    the color or null if unset or default bond coloring is used
    Since:
    
    Marvin 4.0, 03/02/2005
  - addCheckerMark
```
public void addCheckerMark(MDocument.CheckerMark mark)
```
    Adds a checker mark to the document. The checker mark containts atom indexes, bond indexes, and a color NOTE: checker marks will be reset on any molecule change
    
    Parameters:
    mark - is the checker mark information
    Since:
    
    Marvin 5.3
  - clearCheckerMarks
```
public void clearCheckerMarks()
```
    Clears the checker marks
    
    Since:
    
    Marvin 5.3
    
    See Also:
    addCheckerMark(CheckerMark)
  - getCheckerMarks
```
public MDocument.CheckerMark[] getCheckerMarks()
```
    Returns the array of checker marks NOTE: checker marks will be reset on any molecule change
    
    Returns:
    atom indexes or null
    Since:
    
    Marvin 5.3
    
    See Also:
    addCheckerMark(CheckerMark)
  - toString
```
public String toString()
```
    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. If the main molecule graph is not empty, then the string also contains the number of nodes and edges in "[Na,Mb]" form.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    a string representation of the object
    Since:
    
    Marvin 4.1, 04/18/2006
  - getPageSettings
```
public chemaxon.struc.PageSettings getPageSettings()
```
    Gets the page settings of multipage molecular document.
    
    Returns:
    the page settings
    Since:
    
    Marvin 4.1, 01/09/2006
  - setPageSettings
```
public void setPageSettings(chemaxon.struc.PageSettings pageSettings)
```
    Sets the page settings of multipage molecular document.
    
    Parameters:
    pageSettings - the page settings
    Since:
    
    Marvin 4.1, 01/09/2006
  - setGUIPropertyContainer
```
public void setGUIPropertyContainer(MPropertyContainer gpc)
```
    Sets the property container storing MarvinPane settings
    
    Parameters:
    gpc -
    Since:
    
    5.2.2 11/05/2009
  - setGUIProperyContainer
```
@Deprecated
public void setGUIProperyContainer(MPropertyContainer gpc)
```
    Deprecated. As of Marvin 6.1, replaced by setGUIPropertyContainer(MPropertyContainer).
    
    Sets the property container storing MarvinPane settings
    
    Parameters:
    gpc -
    Since:
    
    4.1 11/04/2006
  - getGUIPropertyContainer
```
public MPropertyContainer getGUIPropertyContainer()
```
    Returns:
    the property container storing GUI settings or null
    Since:
    
    4.1 11/04/2006
  - getFreeAtomSetIndex
```
public int getFreeAtomSetIndex()
```
    Returns the first unused atomset index.
    
    Returns:
    the atomset index
  - getFreeBondSetIndex
```
public int getFreeBondSetIndex()
```
    Returns the first unused bondset index.
    
    Returns:
    the bondset index
  - removeColorsFromMolecules
```
public void removeColorsFromMolecules()
```
    Removes coloring from all molecular objects in the document. Removes coloring of atoms, bonds and extra labels. Removes all color sets from the document.
  - removeElectronsOf
```
public void removeElectronsOf(MolAtom targetAtom)
```
    Removes the Electron containers belongs to targetAtom,
    
    Parameters:
    targetAtom -
  - fixElectronContainers
```
public static void fixElectronContainers(MDocument doc,
                         boolean lonePairsAutoCalc,
                         boolean lonePairsVisible)
```
    Removes unnecesarry MElectronContainers from the give MDocument corresponding to lone pair display options, if an electron of a MEFlow arrow has been removed the arrow is removed as well.
    
    Parameters:
    doc -
    lonePairsAutoCalc -
    lonePairsVisible -

Class MDocument

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SETCOLOR_DEFAULT

SETCOLOR_SPECIFIED

SETCOLOR_COLORLESS

objects

mainMChemicalStruct

mainMMoleculeMovie

objectContainingSelection

Constructor Detail

MDocument

MDocument

MDocument

MDocument

Method Detail

getMChemicalStruct

cloneTemporraryObjects

cloneSets

parseMRV

cloneDocument

cloneMainMolecule

cloneMainMoleculeGraph

clone

removeAtomFromGraphs

selectAllObjects

selectAllConnectedObjects

getObjectContainingSelection

setObjectContainingSelection

isHighlighted

highlight

unhighlight

unhighlightAll

getDraggedObject

setDraggedObject

getFocus

setFocus

getMainMoleculeGraph

setMainMoleculeGraph

getMoleculeMovie

getPrimaryMolecule

getPrimaryMolecules

getAllMolecules

getAllNonEmptyMolecules

setMoleculeMovie

indexOf

moveObject

moveMainMoleculeGraphToFront

moveMoleculeMovieToFront

contains

contains

containsOnlyOne

addObject

isExtraObject

removeObject

removeObject

getObjectCount

getConnectedObjectCount

getObject

getConnectedObject

getAllObjects

setObject

removeAtom

removeAtom

clear

clearSets

isEmpty

isSimpleMolecule

simplifyMolecule

transform

transform

transform

calcCenter

calcCenter

getStartPosition

setStartPosition