Package chemaxon.struc

Class MDocument

java.lang.Object
chemaxon.struc.MDocument
All Implemented Interfaces:
chemaxon.core.structure.DocumentForBuilder, MTransformable, Serializable
Direct Known Subclasses:
MSelectionDocument
@PublicApi 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
See Also:

  • Field Details

  • Constructor Details

    • 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 Details

    • 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(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static MDocument parseMRV(String sval) throws IOException
      Deprecated, for removal: This API element is subject to removal in a future version.
      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 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(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

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public boolean containsOnlyOne(Class<?> cl)
      Deprecated, for removal: This API element is subject to removal in a future version.
      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:

    • 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:

    • 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:

    • transform

      public void transform(CTransform3D t, CTransform3D textBoxT, int opts, CTransform3D trot)
      Transforms all object's coordinates.
      Parameters:
      t - the transformation matrix
      textBoxT - the object transformation matrix
      opts - the transformation options
      trot - the viewing transformation
      Since:
      Marvin 4.1, 04/28/2006
      See Also:

    • 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(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public final String exportToFormat(String fmt) throws IOException
      Deprecated, for removal: This API element is subject to removal in a future version.
      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
      Since:
      Marvin 4.0, 07/01/2005

    • exportToBinFormat

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public final byte[] exportToBinFormat(String fmt) throws IOException
      Deprecated, for removal: This API element is subject to removal in a future version.
      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
      Since:
      Marvin 4.0, 07/01/2005

    • exportToObject

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public Object exportToObject(String fmt) throws IOException
      Deprecated, for removal: This API element is subject to removal in a future version.
      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
      Since:
      Marvin 4.0, 07/01/2005

    • 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)
      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:

    • 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:

    • 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:

    • 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)
      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:

    • 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:

    • 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:

    • 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:

    • 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 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(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
      Since:
      5.2.2 11/05/2009

    • setGUIProperyContainer

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void setGUIProperyContainer(MPropertyContainer gpc)
      Deprecated, for removal: This API element is subject to removal in a future version.
      As of Marvin 6.1, replaced by setGUIPropertyContainer(MPropertyContainer).
      Sets the property container storing MarvinPane settings
      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,

    • 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.

    • hasExplicitLonePairs

      public boolean hasExplicitLonePairs()
      Returns true if the MDocument has any electrons drawn by the user.
      Returns:
      true if any electrons if set by the user.
      Since:
      Marvin 15.9.21

    • getExplicitLonePairCount

      public int getExplicitLonePairCount()
      Returns the number of Lone Pair electrons set by the user.
      Returns:
      number of user drawn lone pairs.
      Since:
      Marvin 15.9.21

    • getLonePairCount

      public int getLonePairCount()
      Returns the number of Lone Pair electrons.
      Returns:
      number of user lone pairs.
      Since:
      Marvin 15.9.21

    • hasRadicals

      public boolean hasRadicals()
      Returns true if the MDocument has any Radical Electrons.
      Returns:
      true if MDocument has any radical electrons.
      Since:
      Marvin 15.9.21

    • getRadicalCount

      public int getRadicalCount()
      Returns the number of Radical electrons.
      Returns:
      number of Radical electrons.
      Since:
      Marvin 15.9.21

    • hasElectrons

      public boolean hasElectrons()
      Returns whether MDocument contains any electrons.
      Returns:
      true if the MDocument contains any electrons.
      Since:
      Marvin 15.9.21

    • getElectronCount

      public int getElectronCount()
      Returns the number of electrons.
      Returns:
      number of electrons.
      Since:
      Marvin 15.9.21