A C D E G H I J M P R S U V

A

AbstractMarvinApplet - Class in chemaxon.marvin.applet

Abstract applet implementation, for common applet functionalities.

AbstractMarvinApplet() - Constructor for class chemaxon.marvin.applet.AbstractMarvinApplet

addMol(String) - Method in class chemaxon.marvin.applet.JMView

Starts loading molecules in a separate thread.

addMol(String, String) - Method in class chemaxon.marvin.applet.JMView

Starts loading molecules in a separate thread.

addMolecule(String) - Method in class chemaxon.marvin.applet.MSpaceApplet

Adds a molecule to the active cell without removing components from it.

addMolecules(String, String) - Method in class chemaxon.marvin.applet.MSpaceApplet

Adds molecules to display without removing existing components from the viewer.

addMoleculeString(String) - Method in class chemaxon.marvin.applet.MSpaceApplet

Adds a molecule to the active cell without removing components from it.

addPDB(String) - Method in class chemaxon.marvin.applet.MSpaceApplet

Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)

animate(String) - Method in class chemaxon.marvin.applet.JMView

Starts or stops animation.

C

chemaxon.marvin.applet - package chemaxon.marvin.applet

clean2D() - Method in class chemaxon.marvin.applet.JMSketch

Invokes the Clean2D command.

clean3D() - Method in class chemaxon.marvin.applet.JMSketch

Invokes the Clean3D command.

createGUI() - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

createGUI() - Method in class chemaxon.marvin.applet.JMSketch

createGUI() - Method in class chemaxon.marvin.applet.JMView

createSlabComponent() - Method in class chemaxon.marvin.applet.MSpaceApplet

Creates a SlabComponent, that can be initailized by SlabComponent.beginSlab(), vertices can be set by the SlabComponent.addVertex(float, float, float) method, and finally SlabComponent.endSlab() should be invoked.

createSlabComponent(String) - Method in class chemaxon.marvin.applet.MSpaceApplet

Creates a SlabComponent, that can be initailized by SlabComponent.beginSlab(), vertices can be set by the SlabComponent.addVertex(float, float, float) method, and finally SlabComponent.endSlab() should be invoked.

createSlabComponent(String, int, int, int) - Method in class chemaxon.marvin.applet.MSpaceApplet

Creates a SlabComponent, that can be initailized by SlabComponent.beginSlab(), vertices can be set by the SlabComponent.addVertex(float, float, float) method, and finally SlabComponent.endSlab() should be invoked.

createSlabComponent(float[][]) - Method in class chemaxon.marvin.applet.MSpaceApplet

Creates a SlabComponent with the given vertices.

createSlabComponent(float[]) - Method in class chemaxon.marvin.applet.MSpaceApplet

Creates a SlabComponent with the given vertices.

D

debug - Variable in class chemaxon.marvin.applet.AbstractMarvinApplet

destroy() - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

E

enqueueForPrivilegedProcessing(String, Object, T, Object...) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

evaluateChemicalTerms(String) - Method in class chemaxon.marvin.applet.JMSketch

Evaluates a Chemical Terms expression on the molecule in MarvinSketch, and returns the result in string format.

evaluateChemicalTerms(String, int) - Method in class chemaxon.marvin.applet.JMView

Evaluates a Chemical Terms expression on the molecule in given cell, and returns the result in string format.

evaluateChemicalTerms0(String, Molecule) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

evaluateChemicalTerms0(String, Molecule) - Method in class chemaxon.marvin.applet.JMSketch

evaluateChemicalTerms0(String, Molecule) - Method in class chemaxon.marvin.applet.JMView

G

getAppletInBrowser() - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

getAppletInfo() - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

getAtomAlias(int) - Method in class chemaxon.marvin.applet.JMSketch

Gets atom alias.

getAtomAlias(int, int) - Method in class chemaxon.marvin.applet.JMView

Gets atom alias.

getAtomCharge(int) - Method in class chemaxon.marvin.applet.JMSketch

Gets the charge of the specified atom, from the molecule currently used.

getAtomCount() - Method in class chemaxon.marvin.applet.JMSketch

Returns the number of atoms.

getAtomCount(int) - Method in class chemaxon.marvin.applet.JMView

Gets the number of atoms in the specified molecule cell.

getAtomExtraLabel(int) - Method in class chemaxon.marvin.applet.JMSketch

Gets extra atom label.

getAtomExtraLabel(int, int) - Method in class chemaxon.marvin.applet.JMView

Gets extra atom label.

getAtomRadicalState(int) - Method in class chemaxon.marvin.applet.JMSketch

Gets the radical state of the specified atom, from the molecule currently used.

getAtomSymbol(int) - Method in class chemaxon.marvin.applet.JMSketch

Gets the atom symbol of the specified atom, from the molecule currently used.

getAtomValenceProperty(int) - Method in class chemaxon.marvin.applet.JMSketch

Gets the valence property of the specified atom, from the molecule currently used.

getAutoScale() - Method in class chemaxon.marvin.applet.JMSketch

Returns the autoscale property.

getBestTabScale(int) - Method in class chemaxon.marvin.applet.JMView

Gets the best scale value for a molecule cell.

getBestTabScale() - Method in class chemaxon.marvin.applet.JMView

Gets the smallest best scale value in the molecule table.

getC(int) - Method in class chemaxon.marvin.applet.JMView

Gets the state of a checkbox.

getCellCount() - Method in class chemaxon.marvin.applet.JMView

Gets the number of cells in the table.

getCodeBase() - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

getDocInPanel() - Method in class chemaxon.marvin.applet.JMSketch

getImageShowURL() - Method in class chemaxon.marvin.applet.JMSketch

Gets the show image URL.

getL(int) - Method in class chemaxon.marvin.applet.JMView

Gets a label.

getM(int, String) - Method in class chemaxon.marvin.applet.JMView

Gets the nth molecule in a text format.

getMol(String) - Method in class chemaxon.marvin.applet.JMSketch

Gets the molecule in a text format.

getMolExactMass() - Method in class chemaxon.marvin.applet.JMSketch

Gets the exact molecule weight.

getMolExactMass(int) - Method in class chemaxon.marvin.applet.JMView

Gets the exact molecule weight.

getMolFormula() - Method in class chemaxon.marvin.applet.JMSketch

Gets the molecule formula.

getMolFormula(int) - Method in class chemaxon.marvin.applet.JMView

Gets the molecule formula.

getMolInPanel() - Method in class chemaxon.marvin.applet.JMSketch

getMolMass() - Method in class chemaxon.marvin.applet.JMSketch

Gets the molecule weight.

getMolMass(int) - Method in class chemaxon.marvin.applet.JMView

Gets the molecule weight.

getMolProperty(String) - Method in class chemaxon.marvin.applet.JMSketch

Gets an RDfile/SDfile property.

getMolPropertyCount() - Method in class chemaxon.marvin.applet.JMSketch

Gets the number of RDfile/SDfile properties.

getMolPropertyKey(int) - Method in class chemaxon.marvin.applet.JMSketch

Gets an RDfile/SDfile property key.

getMProperty(int, String) - Method in class chemaxon.marvin.applet.JMView

Gets an RDfile/SDfile property.

getMPropertyCount(int) - Method in class chemaxon.marvin.applet.JMView

Gets the number of RDfile/SDfile properties.

getMPropertyKey(int, int) - Method in class chemaxon.marvin.applet.JMView

Gets an RDfile/SDfile property key.

getMSpaceEasy() - Method in class chemaxon.marvin.applet.MSpaceApplet

Returns MSpaceEasy which offers some more API calls.

getPanel() - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

getPanel() - Method in class chemaxon.marvin.applet.JMSketch

getPanel() - Method in class chemaxon.marvin.applet.JMView

getParameter(String) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

getPiece(String) - Method in class chemaxon.marvin.applet.JMSketch

Gets the current molecule piece in the specified format.

getProgName() - Method in class chemaxon.marvin.applet.MSpaceApplet

See ParentPanelIface.getProgName() for details.

getScale() - Method in class chemaxon.marvin.applet.JMSketch

Gets the magnification.

getSelectedIndex() - Method in class chemaxon.marvin.applet.JMView

Gets the index of the molecule that is selected by the user.

getSelectedMol(String) - Method in class chemaxon.marvin.applet.JMSketch

Gets the selected molecule part in a text format.

getT(int) - Method in class chemaxon.marvin.applet.JMView

Gets the value of a text field.

getTabScale(int) - Method in class chemaxon.marvin.applet.JMView

Gets the magnification for a molecule cell.

getVersion() - Method in class chemaxon.marvin.applet.MSpaceApplet

See ParentPanelIface.getVersion() for details.

H

hasValenceError() - Method in class chemaxon.marvin.applet.JMSketch

Determines if this molecule has a valence error on any of its atoms.

hasValenceError(int) - Method in class chemaxon.marvin.applet.JMView

Determines if the molecule in the specified cell has a valence error on any of its atoms.

hideWindow(Window) - Method in class chemaxon.marvin.applet.MSpaceApplet

See ParentPanelIface.hideWindow(java.awt.Window) for details.

I

init() - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Initializes the applet.

init() - Method in class chemaxon.marvin.applet.MSpaceApplet

Initializes the applet by loading necessary natives and processing parameters.

isAtomSelected(int) - Method in class chemaxon.marvin.applet.JMSketch

Returns true if atom is selected.

isAtomSetVisible(int) - Method in class chemaxon.marvin.applet.JMView

Is the specified atom set visible?

isChemicalTermsExpressionSyntaxError() - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Returns true, if the last Chemical Terms expression evaluated by the evaluateChemicalTerms(String, int) applet method is a syntactically not correct expression.

isEmpty() - Method in class chemaxon.marvin.applet.JMSketch

Returns true sketcher canvas is empty.

isEmpty(int) - Method in class chemaxon.marvin.applet.JMView

Returns true if molecule cell is empty.

isSelected(int, int) - Method in class chemaxon.marvin.applet.JMView

Is the specified atom selected?

J

JMSketch - Class in chemaxon.marvin.applet

Swing version of the MarvinSketch Applet.

JMSketch() - Constructor for class chemaxon.marvin.applet.JMSketch

JMView - Class in chemaxon.marvin.applet

Swing version of the MarvinView Applet.

JMView() - Constructor for class chemaxon.marvin.applet.JMView

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mapPropertyFile(String, String, float, float) - Method in class chemaxon.marvin.applet.MSpaceApplet

Computes an arbitrary type molecular surface, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.

mapPropertyFile(String, String, float, float, float) - Method in class chemaxon.marvin.applet.MSpaceApplet

Computes a Connolly molecular surfaces by the given precision, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.

mapPropertyFile(String, float, float) - Method in class chemaxon.marvin.applet.MSpaceApplet

Computes a Connolly molecular surface, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.

mapPropertyFile(String, float, float, float) - Method in class chemaxon.marvin.applet.MSpaceApplet

Computes a Connolly molecular surface by the given precision, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.

mouseClicked(MouseEvent) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Does nothing.

mouseClicked(MouseEvent) - Method in class chemaxon.marvin.applet.JMView

Does nothing.

mouseEntered(MouseEvent) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Does nothing.

mouseExited(MouseEvent) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Does nothing.

mousePressed(MouseEvent) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Does nothing.

mouseReleased(MouseEvent) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Does nothing.

mouseReleased(MouseEvent) - Method in class chemaxon.marvin.applet.JMSketch

Handles the viewer button press events.

MSpaceApplet - Class in chemaxon.marvin.applet

MarvinSpace applet support.

MSpaceApplet() - Constructor for class chemaxon.marvin.applet.MSpaceApplet

Creates a new instance of MSpaceApplet

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panel - Variable in class chemaxon.marvin.applet.AbstractMarvinApplet

postImage(String, String) - Method in class chemaxon.marvin.applet.JMSketch

Posts image to CGI script.

processLog(String) - Method in class chemaxon.marvin.applet.MSpaceApplet

Processes the given log file.

propertyChange(PropertyChangeEvent) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Invoke propertyChange(prop) JavaScript method on applet's page.

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readPropertyFile(String, float) - Method in class chemaxon.marvin.applet.MSpaceApplet

Reads a property file (Charmm format), and creates isocontour surfaces.

redo() - Method in class chemaxon.marvin.applet.JMSketch

Invokes the Redo command.

refresh() - Method in class chemaxon.marvin.applet.MSpaceApplet

Quick refresh of the graphic canvas.

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selectAllAtoms(boolean) - Method in class chemaxon.marvin.applet.JMSketch

Select or unselect all atoms in the specified molecule.

selectAllAtoms(int, boolean) - Method in class chemaxon.marvin.applet.JMView

Select or unselect all atoms in the specified molecule.

selectAtom(int, boolean) - Method in class chemaxon.marvin.applet.JMSketch

Select or unselect an atom in the specified molecule.

selectAtom(int, int, boolean) - Method in class chemaxon.marvin.applet.JMView

Select or unselect an atom in the specified molecule.

setAbsoluteStereoFlag(boolean) - Method in class chemaxon.marvin.applet.JMSketch

setAbsoluteStereoFlag0(Boolean) - Method in class chemaxon.marvin.applet.JMSketch

setActionB(int, String) - Method in class chemaxon.marvin.applet.JMView

Sets the action string (URL or JavaScript expression) of a button.

setActionC(int, boolean, String) - Method in class chemaxon.marvin.applet.JMView

Sets one of the two action strings (JavaScript expressions) of a checkbox.

setAtomAlias(int, String) - Method in class chemaxon.marvin.applet.JMSketch

Sets atom alias.

setAtomAlias(int, int, String) - Method in class chemaxon.marvin.applet.JMView

Sets atom alias.

setAtomCharge(int, int) - Method in class chemaxon.marvin.applet.JMSketch

Sets the charge of the specified atom, from the molecule currently used.

setAtomExtraLabel(int, String) - Method in class chemaxon.marvin.applet.JMSketch

Sets extra atom label.

setAtomExtraLabel(int, int, String) - Method in class chemaxon.marvin.applet.JMView

Sets extra atom label.

setAtomRadicalState(int, int) - Method in class chemaxon.marvin.applet.JMSketch

Sets the radical state of the specified atom, from the molecule currently used.

setAtomSetColor(int, int) - Method in class chemaxon.marvin.applet.JMView

Sets the color of an atom set.

setAtomSetSeq(int, int, int) - Method in class chemaxon.marvin.applet.JMView

Sets the set sequence number of the atom.

setAtomSetVisible(int, boolean) - Method in class chemaxon.marvin.applet.JMView

Set the visibility of the specified atom set.

setAtomValenceProperty(int, int) - Method in class chemaxon.marvin.applet.JMSketch

Sets the valence property of the specified atom, from the molecule currently used.

setAutoScale(boolean) - Method in class chemaxon.marvin.applet.JMSketch

Sets the autoscale property.

setBondSetColor(int, int) - Method in class chemaxon.marvin.applet.JMView

Sets the color of a bond set.

setBondSetSeq(int, int, int, int) - Method in class chemaxon.marvin.applet.JMView

Sets the set sequence number of a bond.

setBondSetSeqAll(int, int) - Method in class chemaxon.marvin.applet.JMView

Sets the set sequence number for each bond.

setC(int, boolean) - Method in class chemaxon.marvin.applet.JMView

Sets the state of a checkbox.

setL(int, String) - Method in class chemaxon.marvin.applet.JMView

Sets a label.

setM(int, String) - Method in class chemaxon.marvin.applet.JMView

Starts loading a molecule into the nth cell in a separate thread.

setM(int, String, String) - Method in class chemaxon.marvin.applet.JMView

Starts loading a molecule into the nth cell in a separate thread.

setMol(String) - Method in class chemaxon.marvin.applet.JMSketch

Starts loading a molecule into the sketcher in a separate thread.

setMol(String, String) - Method in class chemaxon.marvin.applet.JMSketch

Starts loading a molecule into the sketcher in a separate thread.

setMol(String) - Method in class chemaxon.marvin.applet.JMView

Starts loading molecules in a separate thread.

setMol(String, String) - Method in class chemaxon.marvin.applet.JMView

Starts loading molecules in a separate thread.

setMolecule(String) - Method in class chemaxon.marvin.applet.MSpaceApplet

Removes all components from the active cell and adds a molecule.

setMoleculeString(String) - Method in class chemaxon.marvin.applet.MSpaceApplet

Removes all components from the active cell and adds a molecule.

setMolProperty(String, String) - Method in class chemaxon.marvin.applet.JMSketch

Sets an RDfile/SDfile property.

setMProperty(int, String, String) - Method in class chemaxon.marvin.applet.JMView

Sets an RDfile/SDfile property.

setPanel(MolPanel) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

setParentApplet(JApplet) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

setPDB(String) - Method in class chemaxon.marvin.applet.MSpaceApplet

Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)

setPiece(String) - Method in class chemaxon.marvin.applet.JMSketch

Sets the current piece.

setProperty(String, String) - Method in class chemaxon.marvin.applet.MSpaceApplet

Sets a draw property of MarvinSpace.

setScale(double) - Method in class chemaxon.marvin.applet.JMSketch

Sets the magnification.

setSelectedIndex(int) - Method in class chemaxon.marvin.applet.JMView

Selects a molecule.

setT(int, String) - Method in class chemaxon.marvin.applet.JMView

Gets the value of a text field.

showWindow(Window) - Method in class chemaxon.marvin.applet.MSpaceApplet

See ParentPanelIface.showWindow(java.awt.Window) for details.

start() - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Starts the applet.

start() - Method in class chemaxon.marvin.applet.JMSketch

start() - Method in class chemaxon.marvin.applet.JMView

stop() - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

stop() - Method in class chemaxon.marvin.applet.JMView

Stops the applet.

U

undo() - Method in class chemaxon.marvin.applet.JMSketch

Invokes the Undo command.

unregWindow(Window) - Method in class chemaxon.marvin.applet.MSpaceApplet

See ParentPanelIface.unregWindow(java.awt.Window) for details.

V

validateMoleculeStr(String) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Evaluates the given string and determine if Marvin is able to import it as a Molecule or not.

validateMoleculeStr(String, String) - Method in class chemaxon.marvin.applet.AbstractMarvinApplet

Evaluates the given string and determine if Marvin is able to import it as a Molecule or not.

A C D E G H I J M P R S U V