Class PyMOLMolecularRenderer

java.lang.Object

org.episteme.natural.ui.viewers.chemistry.backends.PyMOLMolecularRenderer

All Implemented Interfaces:

MolecularRenderer

public class PyMOLMolecularRenderer
extends Object
implements MolecularRenderer

PyMOL-based molecular renderer backend.

Generates PyMOL scripts (.pml) and controls an external PyMOL process. PyMOL must be installed and accessible in the system PATH.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Constructor Summary

Constructors

Constructor	Description
PyMOLMolecularRenderer()

Method Summary

Modifier and Type	Method	Description
void	clear()	Clears the current view.
void	drawAtom(Atom atom)	Draw a single atom.
void	drawBond(Bond bond)	Draw a bond between two atoms.
MolecularBackend	getBackend()	Returns the backend type of this renderer.
Object	getViewComponent()	Retrieves the native component (e.g.
void	launchPyMOL()	Generates and launches PyMOL with the current scene.
void	setBackgroundColor(javafx.scene.paint.Color color)	Set background color of the viewer.
void	setStyle(RenderStyle style)	Set global rendering style.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

PyMOLMolecularRenderer

public PyMOLMolecularRenderer()

Method Details

clear

public void clear()

Description copied from interface: MolecularRenderer

Clears the current view.

Specified by:

clear in interface MolecularRenderer

setStyle

public void setStyle(RenderStyle style)

Description copied from interface: MolecularRenderer

Set global rendering style.

Specified by:

setStyle in interface MolecularRenderer

Parameters:

style - The style to apply.

drawAtom

public void drawAtom(Atom atom)

Description copied from interface: MolecularRenderer

Draw a single atom.

Specified by:

drawAtom in interface MolecularRenderer

Parameters:

atom - The atom data model.

drawBond

public void drawBond(Bond bond)

Description copied from interface: MolecularRenderer

Draw a bond between two atoms.

Specified by:

drawBond in interface MolecularRenderer

Parameters:

bond - The bond data model.

setBackgroundColor

public void setBackgroundColor(javafx.scene.paint.Color color)

Description copied from interface: MolecularRenderer

Set background color of the viewer.

Specified by:

setBackgroundColor in interface MolecularRenderer

Parameters:

color - JavaFX Color (Implementations may convert this).

getViewComponent

public Object getViewComponent()

Description copied from interface: MolecularRenderer

Retrieves the native component (e.g. SubScene for JavaFX, JPanel for Swing/Jmol).

Specified by:

getViewComponent in interface MolecularRenderer

Returns:

The UI component.

getBackend

public MolecularBackend getBackend()

Description copied from interface: MolecularRenderer

Returns the backend type of this renderer.

Specified by:

getBackend in interface MolecularRenderer

Returns:

The backend enum.

launchPyMOL

public void launchPyMOL()

Generates and launches PyMOL with the current scene.