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

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

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

C

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ParentPanelIface.getProgName() for details.

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

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

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

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

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

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

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

See ParentPanelIface.getVersion() for details.

H

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

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

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

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

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

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

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

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

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

M

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

P

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

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

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.

R

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

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

Quick refresh of the graphic canvas.

S

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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