Atom and bond-set handling

Format styles (journal styles)

You can get more advanced display format for the molecule by applying journal styles. Format styles in Marvin include the setting of the following attributes:

type of atom font,
scale of atom font,
color of atoms and atom labels,
thickness of bonds,
color of bonds.

Maximum 64 atom sets can be defined in a molecule. Indexing of atom sets starts from zero. The atom set having the zero index is the default atom set. When loading a molecule all the atoms belong to the default atom set by default. After selecting an atom set and applying a style for it, the selected atoms are removed from the default atom set and a new set is created from the atoms with new style. All the atoms, whose style were not yet modified by applying a style on them, still belong to the default atom set.

You can create an atom- or bond-set in Marvin to specify an atom-font/atom-color and bond-thickness/bond-color. The colors, fonts, thickness values are stored in a lookup table of MDocument.

The following code example will change the format of some atoms and bonds in a 11 atom - long chain:

		//import a simple chain
		Molecule mol = MolImporter.importMol("CCNCCCCCNCC");
		//create a document to register color, font, size in the lookup table
		MDocument mdoc = new MDocument(mol);
		//define two colors
		Color green = new Color(0, 255, 0);
		Color blue = new Color(0, 0, 255);
		MFont font = new MFont("Helvetica", MFont.BOLD, 20 );

To create a new color/font setting for a set of atom you have to register the color and font in the lookup table the following way:

		//specify a new atom-style by setting color and font of the 1. atom set
		//set the coloring mode
		mdoc.setAtomSetColorMode(1, MDocument.SETCOLOR_SPECIFIED);
		//set the color of the 1. atom-set
		mdoc.setAtomSetRGB(1, green.getRGB());
		//set the font of the 1. atom-set
		mdoc.setAtomSetFont(1, font);

To create a new color/thickness setting for a set of bonds you have to register the color and the thickness in the lookup table the following way:

		//specify a new bond-style by setting color and thickness of the 2. atom set
		//set the coloring mode
		mdoc.setBondSetColorMode(2, MDocument.SETCOLOR_SPECIFIED);
		//set the color of the 2. bond-set
		mdoc.setBondSetRGB(2, blue.getRGB());
		//set the thickness of the 2. bond-set
		mdoc.setBondSetThickness(2, 0.2);

You can create an atom-set in Marvin the following way:

		//set the color and font of the 2. and 8. atoms in the molecule
		//by adding these atoms to the 1. atom set.
		mol.getAtom(2).setSetSeq(1);
		mol.getAtom(8).setSetSeq(1);

You can create a bond-set in Marvin the following way:

		//set the color and thickness of 4. bond in the molecule
		//by adding this bond to the 2. atom set.
                mol.getBond(4).setSetSeq(2);

The result of atom and bond set coloring example is shown on the picture:

The atom- and bond-set coloring is available using the atomSetColor, bondSetColor applet and beans parameters.

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