Questions about showing Bounding Box through MarvinSpace

Hi,

I would like to view the bounding box of  an moleule,

but i am not sure if it is possible to show (and how to show) the bounding box of the molecule through MarvineSpace? Thank you very much!

Best, 

Flora

Hi Flora,

The visualisation of the bounding box is not available in the MarvinSpace application GUI. However, this feature is supported on the API level - are you interested in such programmatic approach, or your scope is the GUI exclusively.

Miklos

Thank you Miklos!

    I have used the BoundingBox feature on the API level, but I would like to show the "Box" for a ligand only to explain and demonstrate clearly. 

I don't really understand how the bounding box for a ligand is defined(such as the length of x, y, z of the box for a ligand.) Are there any documents or references that I can refer to ?

Thank you very much!

Best,

Flora

Hi Flora,

Apologies for the long silence.. I was on holiday and forgot to reassign the topic to my colleagues. My bad...

I'll reply to your question soon.

BR
Miklos 

Hi,

I created a lightweight graphic component:

  class BoundingBoxComponent extends GraphicComponent
        {
            BoundingBox _boundingBox;
            public BoundingBoxComponent(BoundingBox b)
            {
                super();
                _boundingBox = b;
            }
            public void draw(){
                _boundingBox.draw(gl);
            }
        }

that helps visualizing the bounding box of a molecule.

It can be used the following way (for example):

  // get the first component. mspace is an instance of the MSpaceEasy class
GraphicComponent graphicComponent = mspace.getGraphicScene().getGraphicComponent(0);
 // retrieve the bounding box of the component
 BoundingBox boundingBox = graphicComponent.getBoundingBox();
 // Create the component that draws the bounding box
 BoundingBoxComponent boundingBoxComponent = new BoundingBoxComponent(boundingBox);
 // add it to the components
mspace.getGraphicScene().addComponent(boundingBoxComponent);

Please let me know, if this answers your question.

Regards,

András

akovacs wrote:

Hi, I created a lightweight graphic component:   class BoundingBoxComponent extends GraphicComponent         {             BoundingBox _boundingBox;             public BoundingBoxComponent(BoundingBox b)             {                 super();                 _boundingBox = b;             }             public void draw(){                 _boundingBox.draw(gl);             }         } that helps visualizing the bounding box of a molecule. It can be used the following way (for example):   // get the first component. mspace is an instance of the MSpaceEasy class GraphicComponent graphicComponent = mspace.getGraphicScene().getGraphicComponent(0);  // retrieve the bounding box of the component  BoundingBox boundingBox = graphicComponent.getBoundingBox();  // Create the component that draws the bounding box  BoundingBoxComponent boundingBoxComponent = new BoundingBoxComponent(boundingBox);  // add it to the components mspace.getGraphicScene().addComponent(boundingBoxComponent); Please let me know, if this answers your question. Regards, András

Hi András,

The script really does help a lot ~!!  I will also find out more.  

Thank you for your reply and explanation in detail.  

Regards,

Flora