MSpaceEasy (Marvin API documentation (c) 1998-2015 ChemAxon Ltd.)

java.lang.Object
- chemaxon.marvin.space.MSpaceEasy

All Implemented Interfaces:

chemaxon.marvin.util.CallbackIface
```
public class MSpaceEasy
extends Object
implements chemaxon.marvin.util.CallbackIface
```
Easy-to-use functions of MarvinSpace, customizable gui for applets and applications. Reaching basic functions, loading molecules from files, setting the draw properties of MarvinSpace.

Since:

Marvin 4.0.2

Version:

Marvin 5.0.2

Author:

Judit Vasko-Szedlar

Field Summary

Fields
Modifier and Type	Field and Description
`protected JFrame`	`containerFrame`
`protected JSplitPane`	`jSplitPane1`
`protected chemaxon.marvin.space.gui.JMSpaceMenuBar`	`menubar`
`protected chemaxon.marvin.space.gui.JMSpaceOptionsDialog`	`optionsDialog`
`protected chemaxon.marvin.space.gui.JMSpacePopupMenu`	`popup`
`protected chemaxon.marvin.space.gui.JMSpaceProgressBar`	`progressBar`
`protected chemaxon.marvin.space.gui.JMSpaceTree`	`selectionBar`
`protected chemaxon.marvin.space.gui.JMSpaceToolBar`	`toolbar`
`protected static boolean`	`verbose`

Constructor Summary

Constructors
Constructor and Description
`MSpaceEasy(boolean install)` Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container.
`MSpaceEasy(boolean install, boolean verbose, URL codebase)` Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container.
`MSpaceEasy(int rowCount, int columnCount, boolean install)` Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container.
`MSpaceEasy(int rowCount, int columnCount, boolean install, boolean verboseMsg, URL codebase)` Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addCanvas(Container container)` Adds the basic MarvinSpace viewer to the container.
`void`	`addMenuBar(RootPaneContainer appletOrFrame)` Adds the basic MarvinSpace menubar to the container.
`MoleculeComponent`	`addMolecule(Molecule mol)` Adds a `Molecule` object to the actual cell of the viewer.
`ArrayList<Object>`	`addMolecule(String s)` Reads the molecule file, and adds molecule component(s) to the actual cell of the viewer.
`MoleculeComponent`	`addMoleculeTo(Molecule mol, int cellIndex)` Makes the given cell to be the active cell, and adds the molecule to it.
`MoleculeComponent`	`addMoleculeToEmptyCell(Molecule mol)` Adds the molecule to the next empty cell, or creates a new empty cell if all existing cell contains at least 1 component.
`ArrayList`	`addMoleculeToEmptyCell(String s)` Reads the molecule, and adds molecule(s) to the next empty cell of the viewer, creating new cell if necessary.
`MoleculeComponent`	`addMoleculeWithoutChange(Molecule mol, boolean reset)` Adds a `Molecule` object to the actual cell of the viewer and resets the view only if required.
`void`	`addPDB(String pdbId)` Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)
`void`	`addPopupMenu()` Adds the basic MarvinSpace popup menu to the JPanel.
`void`	`addSelectionPanel(RootPaneContainer appletOrFrame)` Adds the basic MarvinSpace selection panel to the container.
`void`	`addSelectionPanelAndProgressBar(RootPaneContainer appletOrFrame)` Adds the basic MarvinSpace selection panel to the container.
`void`	`addToolBar(RootPaneContainer appletOrFrame)` Adds the basic MarvinSpace toolbar to the container.
`Object`	`callback(String method, Object arg)` Callback function to make avoiding direct calls easier.
`MolecularSurfaceComponent`	`computeSurface(MacroMoleculeComponent.MoleculeVisualizer mv)` Activates the container cell of the `MoleculeVisualizer`, and computes its Connolly surface.
`MolecularSurfaceComponent`	`computeSurface(String type)` Computes the given type of surface in the active cell of the viewer.
`JPanel`	`createSelectionPanel(int maxSize)` Adds the basic MarvinSpace selection panel to the container.
`JPanel`	`createSelectionPanelAndProgressBar()` Adds the basic MarvinSpace selection panel to the container.
`chemaxon.marvin.space.MSpaceEventHandler`	`getEventHandler()` Returns the actual event handler of MarvinSpace.
`GraphicScene`	`getGraphicScene()` Returns the `GraphicScene` of MarvinSpace to be able to explicitly set more advanced features.
`static InputStream`	`getInputStream(String s)` Creates an `InputStream` from the given `String`.
`static MolInputStream`	`getMolInputStream(String s)` Creates a `MolInputStream` from the given `String` to be able to manually add molecules to the event handler.
`static String`	`getRCSBLink(String pdbId)` Returns the URL of the RCSB database
`static String`	`getRCSBLink(String pdbId, boolean compressed)` Returns the URL of the RCSB database
`static boolean`	`isURL(String path)` Tells whether the given path is an URL (Uniform Resource Locator) or not.
`void`	`mapPropertyFile(String filename, float min, float max)` Maps the given property file (Gaussian or Charmm) to a previously read or computed molecular surface and sets minimum and maximum values as visualization setting of the surface coloring.
`ArrayList<Object>`	`openMolecule(String s)` Closes all components from the viewer, and reads the molecule(s).
`void`	`processArguments(int maxMolCount, ArrayList infileName, ArrayList molecules, boolean readStdIn, boolean multicell, boolean singleCell, Properties sceneProperties, String displayQuality)` Processes the command line arguments of MarvinSpace listed below.
`void`	`readPDB(String s)` Reads a protein given as String.
`void`	`readPropertyFile(String filename)`
`void`	`refresh()` Makes all unprocessed event to be processed and makes the graphic canvas redraw.
`void`	`removeAllComponents()` Removes all components from the scene.
`void`	`removeComponent(GraphicComponent gc)` Activates the container cell of the component, removes it from the scene, and also from the selection panel if that exists.
`void`	`resetAll()` Resets view settings of all cells including rotation, zoom and shifting.
`void`	`setCellProperty(String propertyName, String propertyValue)` Sets a draw property of MarvinSpace that will affect the active cell only.
`void`	`setComponentProperty(Object component, String propertyName, String propertyValue)` Sets a draw property of MarvinSpace that will affect only the given component.
`static void`	`setIconImage(JFrame frame)` Sets the MarvinSpace icon to the frame.
`void`	`setLayout(int rowCount, int columnCount)` Sets the number of rows and columns of cells the viewport is sepearted to.
`void`	`setProperty(String propertyName, String propertyValue)` Sets a draw property of MarvinSpace.
`void`	`setSize(int w, int h)` Sets the physical size of the graphic canvas.
`void`	`setVerbose(boolean flag)` Sets whether writing technical details to console is enabled or not.

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

- Field Detail
  - menubar
```
protected chemaxon.marvin.space.gui.JMSpaceMenuBar menubar
```
  - toolbar
```
protected chemaxon.marvin.space.gui.JMSpaceToolBar toolbar
```
  - popup
```
protected chemaxon.marvin.space.gui.JMSpacePopupMenu popup
```
  - selectionBar
```
protected chemaxon.marvin.space.gui.JMSpaceTree selectionBar
```
  - progressBar
```
protected chemaxon.marvin.space.gui.JMSpaceProgressBar progressBar
```
  - jSplitPane1
```
protected JSplitPane jSplitPane1
```
  - optionsDialog
```
protected chemaxon.marvin.space.gui.JMSpaceOptionsDialog optionsDialog
```
  - containerFrame
```
protected JFrame containerFrame
```
  - verbose
```
protected static boolean verbose
```
- Constructor Detail
  - MSpaceEasy
```
public MSpaceEasy(boolean install)
           throws Exception
```
    Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container. See addSelectionPanel(javax.swing.RootPaneContainer), addSelectionPanelAndProgressBar(javax.swing.RootPaneContainer), addCanvas(java.awt.Container).
    
    Parameters:
    install - should Jogl libraries be loaded or they are already loaded
    
    Throws:
    
    Exception - on installation failure
  - MSpaceEasy
```
public MSpaceEasy(int rowCount,
          int columnCount,
          boolean install)
           throws Exception
```
    Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container. See addSelectionPanel(javax.swing.RootPaneContainer), addSelectionPanelAndProgressBar(javax.swing.RootPaneContainer), addCanvas(java.awt.Container).
    
    Parameters:
    rowCount - number of cells of the viewer in vertical direction
    columnCount - number of cells of the viewer in horizontal direction
    install - should Jogl libraries be loaded or they are already loaded
    
    Throws:
    
    Exception - on installation failure
  - MSpaceEasy
```
public MSpaceEasy(boolean install,
          boolean verbose,
          URL codebase)
           throws Exception
```
    Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container. See addSelectionPanel(javax.swing.RootPaneContainer), addSelectionPanelAndProgressBar(javax.swing.RootPaneContainer), addCanvas(java.awt.Container).
    
    Parameters:
    install - should Jogl libraries be loaded or they are already loaded
    verbose - should technical details be writed to the console or not
    codebase - in case of applets codebase is required for installing
    
    Throws:
    
    Exception - on installation failure
  - MSpaceEasy
```
public MSpaceEasy(int rowCount,
          int columnCount,
          boolean install,
          boolean verboseMsg,
          URL codebase)
           throws Exception
```
    Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container. See addSelectionPanel(javax.swing.RootPaneContainer), addSelectionPanelAndProgressBar(javax.swing.RootPaneContainer), addCanvas(java.awt.Container).
    
    Parameters:
    rowCount - number of cells of the viewer in vertical direction
    columnCount - number of cells of the viewer in horizontal direction
    install - should Jogl libraries be loaded or they are already loaded
    verboseMsg - should technical details be written to the console or not
    codebase - in case of applets codebase is required for installing
    
    Throws:
    
    Exception - on installation failure
- Method Detail
  - isURL
```
public static boolean isURL(String path)
```
    Tells whether the given path is an URL (Uniform Resource Locator) or not.
    
    Parameters:
    path - String to be recognized as an URL expression
    
    Returns:
    true if the given string starts with a specific expression
  - setIconImage
```
public static void setIconImage(JFrame frame)
```
    Sets the MarvinSpace icon to the frame.
    
    Parameters:
    frame - a JFrame to set mspace icon to
  - setLayout
```
public void setLayout(int rowCount,
             int columnCount)
               throws Exception
```
    Sets the number of rows and columns of cells the viewport is sepearted to.
    
    Parameters:
    rowCount - number of cells of the viewer in vertical direction
    columnCount - number of cells of the viewer in horizontal direction
    
    Throws:
    
    Exception - if the graphic canvas couldn't be initialized
  - setVerbose
```
public void setVerbose(boolean flag)
```
    Sets whether writing technical details to console is enabled or not.
    
    Parameters:
    flag - verbosing is enabled or not
  - setSize
```
public void setSize(int w,
           int h)
```
    Sets the physical size of the graphic canvas.
    
    Parameters:
    w - width of the panel in pixels
    h - height of the panel in pixels
  - addMenuBar
```
public void addMenuBar(RootPaneContainer appletOrFrame)
```
    Adds the basic MarvinSpace menubar to the container. Note that the menubar itself is not customizable yet.
    
    Parameters:
    appletOrFrame - the container swing component of the JPanel
  - addToolBar
```
public void addToolBar(RootPaneContainer appletOrFrame)
```
    Adds the basic MarvinSpace toolbar to the container. Note that the toolbar itself is not customizable yet.
    
    Parameters:
    appletOrFrame - the container swing component of the JPanel
  - addPopupMenu
```
public void addPopupMenu()
```
    Adds the basic MarvinSpace popup menu to the JPanel. Note that the popup menu itself is not customizable yet.
  - addSelectionPanel
```
public void addSelectionPanel(RootPaneContainer appletOrFrame)
```
    Adds the basic MarvinSpace selection panel to the container. The viewer itself is a JPanel with the OpenGL2 canvas. The viewer and the selection panel will be embedded in a JSplitPane. // * Note that for technical reasons the selection panel is essential to add now.
    
    Parameters:
    appletOrFrame - the container swing component of the JPanel
  - addSelectionPanelAndProgressBar
```
public void addSelectionPanelAndProgressBar(RootPaneContainer appletOrFrame)
```
    Adds the basic MarvinSpace selection panel to the container. The viewer itself is a JPanel with the OpenGL2 canvas. The viewer and the selection panel will be embedded in a JSplitPane. // * Note that for technical reasons the selection panel is essential to add now.
    
    Parameters:
    appletOrFrame - the container swing component of the JPanel
  - createSelectionPanel
```
public JPanel createSelectionPanel(int maxSize)
```
    Adds the basic MarvinSpace selection panel to the container. The viewer itself is a JPanel with the OpenGL2 canvas. The viewer and the selection panel will be added directly on graphicScene.
    
    Returns:
    JPanel containing the canvas and the selection panel
  - createSelectionPanelAndProgressBar
```
public JPanel createSelectionPanelAndProgressBar()
```
    Adds the basic MarvinSpace selection panel to the container. The viewer itself is a JPanel with the OpenGL2 canvas. The viewer and the selection panel will be embedded in a JSplitPane.
    
    Returns:
    JPanel containing the canvas and the selection panel in a JSplitPane
  - addCanvas
```
public void addCanvas(Container container)
```
    Adds the basic MarvinSpace viewer to the container. The viewer itself is a JPanel with the OpenGL2 canvas.
    
    Parameters:
    container - the container swing component of the JPanel
  - setProperty
```
public void setProperty(String propertyName,
               String propertyValue)
```
    Sets a draw property of MarvinSpace. To see available properties, value ranges and default values, please visit this page.
    
    Parameters:
    propertyName - identifier of a draw property
    propertyValue - value of the property to be set given as a String
  - setCellProperty
```
public void setCellProperty(String propertyName,
                   String propertyValue)
```
    Sets a draw property of MarvinSpace that will affect the active cell only. To see available properties, value ranges and default values, please visit this page.
    
    Parameters:
    propertyName - identifier of a draw property
    propertyValue - value of the property to be set given as a String
  - setComponentProperty
```
public void setComponentProperty(Object component,
                        String propertyName,
                        String propertyValue)
```
    Sets a draw property of MarvinSpace that will affect only the given component. To see available properties, value ranges and default values, please visit this page.
    
    Parameters:
    component - this must be a UsableObject
    propertyName - identifier of a draw property
    propertyValue - value of the property to be set given as a String
  - addPDB
```
public void addPDB(String pdbId)
            throws Exception
```
    Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)
    
    Parameters:
    pdbId - PDB ID used by the RSCB PDB
    
    Throws:
    
    IOException - if connecting RCSB fails
    
    Exception
  - readPDB
```
public void readPDB(String s)
             throws Exception
```
    Reads a protein given as String.
    
    Parameters:
    s - String content of a PDB file
    
    Throws:
    
    Exception - when reading or adding component fails
  - getRCSBLink
```
public static String getRCSBLink(String pdbId)
```
    Returns the URL of the RCSB database
    
    Parameters:
    pdbId - the 4 letter id of a protein, e.g. 1AID
    
    Returns:
    the full URL to the required protein
  - getRCSBLink
```
public static String getRCSBLink(String pdbId,
                 boolean compressed)
```
    Returns the URL of the RCSB database
    
    Parameters:
    pdbId - the 4 letter id of a protein, e.g. 1AID
    compressed - whether the protein is required in gzipped format
    
    Returns:
    the full URL to the required protein
  - addMolecule
```
public ArrayList<Object> addMolecule(String s)
                              throws Exception
```
    Reads the molecule file, and adds molecule component(s) to the actual cell of the viewer.
    
    Parameters:
    s - url or filename or molecule as String
    
    Returns:
    list of read molecules
    
    Throws:
    
    Exception - when reading file or adding component fails
  - addMoleculeToEmptyCell
```
public ArrayList addMoleculeToEmptyCell(String s)
                                 throws Exception
```
    Reads the molecule, and adds molecule(s) to the next empty cell of the viewer, creating new cell if necessary.
    
    Parameters:
    s - url or filename or molecule as String
    
    Returns:
    list of read molecules
    
    Throws:
    
    Exception - when reading adding component fails
  - openMolecule
```
public ArrayList<Object> openMolecule(String s)
                               throws Exception
```
    Closes all components from the viewer, and reads the molecule(s).
    
    Parameters:
    s - url or filename or molecule as String
    
    Returns:
    list of read molecules
    
    Throws:
    
    Exception - when reading or adding component fails
  - addMolecule
```
public MoleculeComponent addMolecule(Molecule mol)
                              throws Exception
```
    Adds a Molecule object to the actual cell of the viewer.
    
    Parameters:
    mol - Molecule object that will be cleaned and hydrogenized if necessary.
    
    Returns:
    MoleculeComponent that is the visualizer component of the molecule.
    
    Throws:
    
    Exception - if adding component fails
  - addMoleculeWithoutChange
```
public MoleculeComponent addMoleculeWithoutChange(Molecule mol,
                                         boolean reset)
                                           throws Exception
```
    Adds a Molecule object to the actual cell of the viewer and resets the view only if required.
    
    Parameters:
    mol - Molecule object that won't be cleaned, hydrogenized or aromatized.
    reset - whether resetting the view is required, see resetAll().
    
    Returns:
    MoleculeComponent that is the visualizer component of the molecule
    
    Throws:
    
    Exception - if adding component fails
  - addMoleculeToEmptyCell
```
public MoleculeComponent addMoleculeToEmptyCell(Molecule mol)
                                         throws Exception
```
    Adds the molecule to the next empty cell, or creates a new empty cell if all existing cell contains at least 1 component.
    
    Parameters:
    mol - Molecule object that will be cleaned and hydrogenized if it is necessary.
    
    Returns:
    MoleculeComponent that is the visualizer component of the molecule
    
    Throws:
    
    Exception - if adding component fails
  - addMoleculeTo
```
public MoleculeComponent addMoleculeTo(Molecule mol,
                              int cellIndex)
                                throws Exception
```
    Makes the given cell to be the active cell, and adds the molecule to it.
    
    Parameters:
    mol - Molecule object that will be cleaned and hydrogenized if it is necessary.
    cellIndex - internal index of the cell
    
    Returns:
    MoleculeComponent that is the visualizer component of the molecule
    
    Throws:
    
    Exception - if adding component fails
  - removeComponent
```
public void removeComponent(GraphicComponent gc)
```
    Activates the container cell of the component, removes it from the scene, and also from the selection panel if that exists.
    
    Parameters:
    gc - component to remove
  - removeAllComponents
```
public void removeAllComponents()
```
    Removes all components from the scene.
  - computeSurface
```
public MolecularSurfaceComponent computeSurface(MacroMoleculeComponent.MoleculeVisualizer mv)
```
    Activates the container cell of the MoleculeVisualizer, and computes its Connolly surface.
    
    Parameters:
    mv - see MacroMoleculeComponent.MoleculeVisualizer
    
    Returns:
    MolecularSurfaceComponent that is the visualizer component of molecular surface.
  - computeSurface
```
public MolecularSurfaceComponent computeSurface(String type)
```
    Computes the given type of surface in the active cell of the viewer. Note that spaces and other delimiters are allowed in the parameter.
    
    Parameters:
    type - "van der Waals", "Solvent-accessible", "Connolly", "Blobby"
    
    Returns:
    the computed surface
  - readPropertyFile
```
public void readPropertyFile(String filename)
```
  - mapPropertyFile
```
public void mapPropertyFile(String filename,
                   float min,
                   float max)
```
    Maps the given property file (Gaussian or Charmm) to a previously read or computed molecular surface and sets minimum and maximum values as visualization setting of the surface coloring. This function is equivalent of the following:
```
      eventHandler.readPropertyFile( filename );
      graphicScene.processEvent("Palette.Minimum", ""+min);
      graphicScene.processEvent("Palette.Maximum", ""+max);
      eventHandler.refresh();
 
```
    Parameters:
    filename - url of the property file to be mapped
    min - values less than the minimum will be colored by the color of the minimum value
    max - values greater than the maximum will be colored by the color of the maximum value
  - refresh
```
public void refresh()
```
    Makes all unprocessed event to be processed and makes the graphic canvas redraw.
    
    Since:
    
    Marvin 4.1
  - resetAll
```
public void resetAll()
```
    Resets view settings of all cells including rotation, zoom and shifting. Takes effect at the next redraw because of threading issues.
    
    Since:
    
    Marvin 4.1
  - processArguments
```
public void processArguments(int maxMolCount,
                    ArrayList infileName,
                    ArrayList molecules,
                    boolean readStdIn,
                    boolean multicell,
                    boolean singleCell,
                    Properties sceneProperties,
                    String displayQuality)
                      throws Exception
```
    Processes the command line arguments of MarvinSpace listed below.
    
    Parameters:
    maxMolCount - maximum number of molecules that can be displayed at a time
    infileName - list of molecule files that should be read
    molecules - molecule objects to be read
    readStdIn - if input molecules should be read from the standard input
    multicell - whether the read molecules should be put in different cells or ask
    singleCell - whether the read molecules should be put in one cells or ask
    sceneProperties - a set of drawing properties
    displayQuality - requires display quality, can be "High", "Medium" or "Low"
    
    Throws:
    
    Exception - if processing an argument fails
  - getMolInputStream
```
public static MolInputStream getMolInputStream(String s)
                                        throws IOException
```
    Creates a MolInputStream from the given String to be able to manually add molecules to the event handler.
    
    Parameters:
    s - url or absolute filename or a molecule as String
    
    Returns:
    MolInputStream to read the molecules from
    
    Throws:
    
    IOException - if an I/O exception occurs
    Since:
    
    Marvin 4.0.3
  - getInputStream
```
public static InputStream getInputStream(String s)
                                  throws IOException
```
    Creates an InputStream from the given String. The InputStream is either a MonitorableInputStream or FileInputStream or ByteArrayInputStream.
    
    Parameters:
    s - url or absolute filename or String
    
    Returns:
    InputStream
    
    Throws:
    
    IOException - if an I/O exception occurs
  - getEventHandler
```
public chemaxon.marvin.space.MSpaceEventHandler getEventHandler()
```
    Returns the actual event handler of MarvinSpace.
    
    Returns:
    handler of advanced events
    Since:
    
    Marvin 4.1
  - getGraphicScene
```
public GraphicScene getGraphicScene()
```
    Returns the GraphicScene of MarvinSpace to be able to explicitly set more advanced features. It is necessary if features given by MSpaceEasy is not enough for the required action.
    
    Returns:
    the top level visualizer class
    Since:
    
    Marvin 4.1
  - callback
```
public Object callback(String method,
              Object arg)
```
    Callback function to make avoiding direct calls easier.
    
    Specified by:
    
    callback in interface chemaxon.marvin.util.CallbackIface
    
    Parameters:
    method - name of MSpaceEasy method
    arg - Object[] or Object or null
    
    Returns:
    the return object of the function or the Exception if there is any

Class MSpaceEasy

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

menubar

toolbar

popup

selectionBar

progressBar

jSplitPane1

optionsDialog

containerFrame

verbose

Constructor Detail

MSpaceEasy

MSpaceEasy

MSpaceEasy

MSpaceEasy

Method Detail

isURL

setIconImage

setLayout

setVerbose

setSize

addMenuBar

addToolBar

addPopupMenu

addSelectionPanel

addSelectionPanelAndProgressBar

createSelectionPanel

createSelectionPanelAndProgressBar

addCanvas

setProperty

setCellProperty

setComponentProperty

addPDB

readPDB

getRCSBLink

getRCSBLink

addMolecule

addMoleculeToEmptyCell

openMolecule

addMolecule

addMoleculeWithoutChange

addMoleculeToEmptyCell

addMoleculeTo

removeComponent

removeAllComponents

computeSurface

computeSurface

readPropertyFile

mapPropertyFile

refresh

resetAll

processArguments

getMolInputStream

getInputStream

getEventHandler

getGraphicScene

callback