Highlighting¶

Atoms and bonds of a molecule can be highlighted by using the OEAddHighlighting functions. OEDepict TK provides four built-in highlighting styles:

color: This style is associated with the OEHighlightStyle.Color constant. See Figure: Example of highlighting using the ‘color’ style.

Example of highlighting using the ‘color’ style¶
stick: This style is associated with the OEHighlightStyle.Stick constant. See Figure: Example of highlighting using the ‘stick’ style.

Example of highlighting using the ‘stick’ style¶
ball and stick: This style is associated with the OEHighlightStyle.BallAndStick constant. See Figure: Example of highlighting using the ‘ball and stick’ style.

Example of highlighting using the ‘ball and stick’ style¶
cogwheel: This style is associated with the OEHighlightStyle.Cogwheel constant. See Figure: Example of highlighting using the ‘cogwheel’ style.

Example of highlighting using the ‘cogwheel’ style¶
lasso: This style is associated with the OEHighlightStyle.Lasso constant. See Figure: Example of highlighting using the ‘lasso’ style.

Example of highlighting using the ‘lasso’ style¶

Using Highlighting Styles¶

The following example (Listing 1) shows how to use the built-in highlighting styles. The OEAddHighlighting function takes an OEMatchBase object and highlights each of its target atoms and bonds using the given style. In this case, the two pyridine rings in the target structure are highlighted by red color using the stick style. The image created by Listing 1 is shown in Figure: Example of using ‘stick’ highlighting style.

Listing 1: Example of using highlighting style

public class HighlightSimple {
    public static void main(String argv[]) {
        OEGraphMol mol = new OEGraphMol();
        oechem.OESmilesToMol(mol, "c1cncc2c1cc3c(cncc3)c2");
        oedepict.OEPrepareDepiction(mol);

        OESubSearch ss = new OESubSearch("c1ncccc1");

        OE2DMolDisplay disp = new OE2DMolDisplay(mol);

        boolean unique = true;
        for (OEMatchBase match : ss.Match(mol, unique)) {
            oedepict.OEAddHighlighting(disp, oechem.getOERed(), OEHighlightStyle.Stick, match);
        }

        oedepict.OERenderMolecule("HighlightSimple.svg", disp);
    }
}

Example of using ‘stick’ highlighting style¶

See also

OEHighlightStyle namespace
OEAddHighlighting function
Depicting Substructure Search Match example

Using Highlighting Classes¶

OEDepict TK also provides the highlighting classes that correspond to the highlighting styles. Each highlighting style can be customized by using the corresponding class:

The next example (Listing 2) shows how the stick style can be customized by using the corresponding OEHighlightByStick class. The image created by Listing 2 is shown in Figure: Example of customizing the ‘stick’ highlighting style.

Listing 2: Example of using highlighting class

public class HighlightStyle {
    public static void main(String argv[]) {
        OEGraphMol mol = new OEGraphMol();
        oechem.OESmilesToMol(mol, "c1cncc2c1cc3c(cncc3)c2");
        oedepict.OEPrepareDepiction(mol);

        OESubSearch ss =  new OESubSearch("c1ncccc1");

        OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(240.0, 100.0, OEScale.AutoScale);
        opts.SetMargins(10.0);
        OE2DMolDisplay disp = new OE2DMolDisplay(mol, opts);

        double stickWidthScale = 6.0;
        boolean monochrome = true;
        OEHighlightByStick highlight = new OEHighlightByStick(oechem.getOERed(),
                stickWidthScale,
                !monochrome);

        boolean unique = true;
        for (OEMatchBase match : ss.Match(mol, unique)) {
            oedepict.OEAddHighlighting(disp, highlight, match);
        }

        oedepict.OERenderMolecule("HighlightStyle.svg", disp);
    }
}

Example of customizing the ‘stick’ highlighting style¶

See also

OEAddHighlighting function

Highlighting Overlapped Patterns¶

If more than one part of a molecule is highlighted, these highlights can overlap resulting in loss of information. For example, highlighting the matches of the c1cc[c,n]cc1 SMARTS pattern will produce the following image.

Example of highlighting multiple matches in the same image¶

There are two ways how this can be avoided and correctly highlight overlapping parts of a molecule. The first example demonstrates how to depict multiple matches in different image cells one by one. The image created by Listing 3 is shown in Figure: Example of highlighting multiple matches one by one.

Listing 3: Example of highlighting multiple matches one by one

public class HighlightMulti {
    public static void main(String argv[]) {
        OEGraphMol mol = new OEGraphMol();
        oechem.OESmilesToMol(mol, "c1cncc2c1cc3c(cncc3)c2");
        oedepict.OEPrepareDepiction(mol);

        OESubSearch ss = new OESubSearch("c1cc[c,n]cc1");

        double width  = 350;
        double height = 250;
        OEImage image = new OEImage(width, height);

        int rows = 2;
        int cols = 2;
        OEImageGrid grid = new OEImageGrid(image, rows, cols);
        OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(grid.GetCellWidth(),
                grid.GetCellHeight(),
                OEScale.AutoScale);

        boolean unique = true;
        OEImageBaseIter celliter = grid.GetCells();
        for (OEMatchBase match : ss.Match(mol, unique)) {
            OE2DMolDisplay disp = new OE2DMolDisplay(mol, opts);
            oedepict.OEAddHighlighting(disp, oechem.getOEPink(), OEHighlightStyle.Color, match);
            oedepict.OERenderMolecule(celliter.Target(), disp);
            celliter.Increment();
        }
        oedepict.OEWriteImage("HighlightMulti.svg", image);
    }
}

Example of highlighting multiple matches one by one¶

See also

OEImageGrid class
Depicting Molecules in a Grid section

The second example (Listing 4) illustrates how to highlight overlapping matches at once using the OEHighlightOverlayByBallAndStick class. In this example, the OEAddHighlightOverlay function takes all matches being highlighted and colors the overlapped atoms and bonds using the colors by turn. The colors used for highlighting are determined when the OEHighlightOverlayByBallAndStick object is constructed. The image created by Listing 4 is shown in Figure: Example of highlighting overlapping matches at once.

Listing 4: Example of highlighting multiple matches simultaneously

public class HighlightOverlay {
    public static void main(String argv[]) {
        OEGraphMol mol = new OEGraphMol();
        oechem.OESmilesToMol(mol, "c1cncc2c1cc3c(cncc3)c2");
        oedepict.OEPrepareDepiction(mol);

        OESubSearch subs = new OESubSearch("c1cc[c,n]cc1");

        OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(240.0, 100.0, OEScale.AutoScale);
        opts.SetMargins(10.0);
        OE2DMolDisplay disp = new OE2DMolDisplay(mol, opts);

        OEHighlightOverlayByBallAndStick highlight =
            new OEHighlightOverlayByBallAndStick(oechem.OEGetContrastColors());

        boolean unique = true;
        oedepict.OEAddHighlightOverlay(disp, highlight, subs.Match(mol, unique));
        oedepict.OERenderMolecule("HighlightOverlay.png", disp);
    }
}

Example of highlighting overlapping matches at once¶

See also

OEHighlightOverlayBase base class
OEHighlightOverlayByBallAndStick class
OEHighlightOverlayStyle namespace
OEGetColors, OEGetContrastColors, OEGetDeepColors, OEGetLightColors and OEGetVividColors functions