chemaxon.marvin.space
Class MSpaceEasy

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

All Implemented Interfaces:

chemaxon.marvin.util.CallbackIface

public class MSpaceEasy
extends java.lang.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

protected javax.swing.JFrame	containerFrame
protected javax.swing.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

MSpaceEasy(boolean install)
Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container.

MSpaceEasy(boolean install, boolean verbose, java.net.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, java.net.URL codebase)
Creates the JPanel with the OpenGL2 canvas, but does not embed it in any swing container.

Method Summary

void	addCanvas(java.awt.Container container) Adds the basic MarvinSpace viewer to the container.
void	addMenuBar(javax.swing.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.
java.util.ArrayList<java.lang.Object>	addMolecule(java.lang.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.
java.util.ArrayList	addMoleculeToEmptyCell(java.lang.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(java.lang.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(javax.swing.RootPaneContainer appletOrFrame) Adds the basic MarvinSpace selection panel to the container.
void	addSelectionPanelAndProgressBar(javax.swing.RootPaneContainer appletOrFrame) Adds the basic MarvinSpace selection panel to the container.
void	addToolBar(javax.swing.RootPaneContainer appletOrFrame) Adds the basic MarvinSpace toolbar to the container.
java.lang.Object	callback(java.lang.String method, java.lang.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(java.lang.String type) Computes the given type of surface in the active cell of the viewer.
javax.swing.JPanel	createSelectionPanel(int maxSize) Adds the basic MarvinSpace selection panel to the container.
javax.swing.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 java.io.InputStream	getInputStream(java.lang.String s) Creates an InputStream from the given String.
static MolInputStream	getMolInputStream(java.lang.String s) Creates a MolInputStream from the given String to be able to manually add molecules to the event handler.
static java.lang.String	getRCSBLink(java.lang.String pdbId) Returns the URL of the RCSB database
static java.lang.String	getRCSBLink(java.lang.String pdbId, boolean compressed) Returns the URL of the RCSB database
static boolean	isURL(java.lang.String path) Tells whether the given path is an URL (Uniform Resource Locator) or not.
void	mapPropertyFile(java.lang.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.
java.util.ArrayList<java.lang.Object>	openMolecule(java.lang.String s) Closes all components from the viewer, and reads the molecule(s).
void	processArguments(int maxMolCount, java.util.ArrayList infileName, java.util.ArrayList molecules, boolean readStdIn, boolean multicell, boolean singleCell, java.util.Properties sceneProperties, java.lang.String displayQuality) Processes the command line arguments of MarvinSpace listed below.
void	readPDB(java.lang.String s) Reads a protein given as String.
void	readPropertyFile(java.lang.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(java.lang.String propertyName, java.lang.String propertyValue) Sets a draw property of MarvinSpace that will affect the active cell only.
void	setComponentProperty(java.lang.Object component, java.lang.String propertyName, java.lang.String propertyValue) Sets a draw property of MarvinSpace that will affect only the given component.
static void	setIconImage(javax.swing.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(java.lang.String propertyName, java.lang.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 javax.swing.JSplitPane jSplitPane1

optionsDialog

protected chemaxon.marvin.space.gui.JMSpaceOptionsDialog optionsDialog

containerFrame

protected javax.swing.JFrame containerFrame

verbose

protected static boolean verbose

Constructor Detail

MSpaceEasy

public MSpaceEasy(boolean install)
           throws java.lang.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:

java.lang.Exception - on installation failure

MSpaceEasy

public MSpaceEasy(int rowCount,
                  int columnCount,
                  boolean install)
           throws java.lang.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:

java.lang.Exception - on installation failure

MSpaceEasy

public MSpaceEasy(boolean install,
                  boolean verbose,
                  java.net.URL codebase)
           throws java.lang.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:

java.lang.Exception - on installation failure

MSpaceEasy

public MSpaceEasy(int rowCount,
                  int columnCount,
                  boolean install,
                  boolean verboseMsg,
                  java.net.URL codebase)
           throws java.lang.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:

java.lang.Exception - on installation failure

Method Detail

isURL

public static boolean isURL(java.lang.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(javax.swing.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 java.lang.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:

java.lang.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(javax.swing.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(javax.swing.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(javax.swing.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(javax.swing.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 javax.swing.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 javax.swing.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(java.awt.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(java.lang.String propertyName,
                        java.lang.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(java.lang.String propertyName,
                            java.lang.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(java.lang.Object component,
                                 java.lang.String propertyName,
                                 java.lang.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(java.lang.String pdbId)
            throws java.lang.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:

java.io.IOException - if connecting RCSB fails

java.lang.Exception

readPDB

public void readPDB(java.lang.String s)
             throws java.lang.Exception

Reads a protein given as String.

Parameters:

s - String content of a PDB file

Throws:

java.lang.Exception - when reading or adding component fails

getRCSBLink

public static java.lang.String getRCSBLink(java.lang.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 java.lang.String getRCSBLink(java.lang.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 java.util.ArrayList<java.lang.Object> addMolecule(java.lang.String s)
                                                  throws java.lang.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:

java.lang.Exception - when reading file or adding component fails

addMoleculeToEmptyCell

public java.util.ArrayList addMoleculeToEmptyCell(java.lang.String s)
                                           throws java.lang.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:

java.lang.Exception - when reading adding component fails

openMolecule

public java.util.ArrayList<java.lang.Object> openMolecule(java.lang.String s)
                                                   throws java.lang.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:

java.lang.Exception - when reading or adding component fails

addMolecule

public MoleculeComponent addMolecule(Molecule mol)
                              throws java.lang.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:

java.lang.Exception - if adding component fails

addMoleculeWithoutChange

public MoleculeComponent addMoleculeWithoutChange(Molecule mol,
                                                  boolean reset)
                                           throws java.lang.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:

java.lang.Exception - if adding component fails

addMoleculeToEmptyCell

public MoleculeComponent addMoleculeToEmptyCell(Molecule mol)
                                         throws java.lang.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:

java.lang.Exception - if adding component fails

addMoleculeTo

public MoleculeComponent addMoleculeTo(Molecule mol,
                                       int cellIndex)
                                throws java.lang.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:

java.lang.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(java.lang.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(java.lang.String filename)

mapPropertyFile

public void mapPropertyFile(java.lang.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,
                             java.util.ArrayList infileName,
                             java.util.ArrayList molecules,
                             boolean readStdIn,
                             boolean multicell,
                             boolean singleCell,
                             java.util.Properties sceneProperties,
                             java.lang.String displayQuality)
                      throws java.lang.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:

java.lang.Exception - if processing an argument fails

getMolInputStream

public static MolInputStream getMolInputStream(java.lang.String s)
                                        throws java.io.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:

java.io.IOException - if an I/O exception occurs

Since:

Marvin 4.0.3

getInputStream

public static java.io.InputStream getInputStream(java.lang.String s)
                                          throws java.io.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:

java.io.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 java.lang.Object callback(java.lang.String method,
                                 java.lang.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