# 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

#!/usr/bin/env python
from openeye.oechem import *
from openeye.oedepict import *

mol = OEGraphMol()
OESmilesToMol(mol, "c1cncc2c1cc3c(cncc3)c2")
OEPrepareDepiction(mol)

subs = OESubSearch("c1ncccc1")
disp = OE2DMolDisplay(mol)

unique = True
for match in subs.Match(mol, unique):

OERenderMolecule("HighlightSimple.png", disp)
OERenderMolecule("HighlightSimple.pdf", disp)


Example of using ‘stick’ highlighting style

## 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

#!/usr/bin/env python
from openeye.oechem import *
from openeye.oedepict import *

mol = OEGraphMol()
OESmilesToMol(mol, "c1cncc2c1cc3c(cncc3)c2")
OEPrepareDepiction(mol)

subs = OESubSearch("c1ncccc1")

opts = OE2DMolDisplayOptions(240.0, 100.0, OEScale_AutoScale)
opts.SetMargins(10.0)
disp = OE2DMolDisplay(mol, opts)

stickWidthScale = 6.0
monochrome = True
highlight = OEHighlightByStick(OEColor(OERed), stickWidthScale, not monochrome)

unique = True
for match in subs.Match(mol, unique):

OERenderMolecule("HighlightStyle.png", disp)
OERenderMolecule("HighlightStyle.pdf", disp)


Example of customizing the ‘stick’ highlighting style

## 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

#!/usr/bin/env python
from openeye.oechem import *
from openeye.oedepict import *

mol = OEGraphMol()
OESmilesToMol(mol, "c1cncc2c1cc3c(cncc3)c2")
OEPrepareDepiction(mol)

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

width, height = 350, 250
image = OEImage(width, height)

rows, cols = 2, 2
grid = OEImageGrid(image, rows, cols)
opts = OE2DMolDisplayOptions(grid.GetCellWidth(), grid.GetCellHeight(), OEScale_AutoScale)

unique = True
for match, cell in zip(subs.Match(mol, unique), grid.GetCells()):
disp = OE2DMolDisplay(mol, opts)
OERenderMolecule(cell, disp)

OEWriteImage("HighlightMulti.png", image)
OEWriteImage("HighlightMulti.pdf", image)


Example of highlighting multiple matches one by one

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

#!/usr/bin/env python
from openeye.oechem import *
from openeye.oedepict import *

mol = OEGraphMol()
OESmilesToMol(mol, "c1cncc2c1cc3c(cncc3)c2")
OEPrepareDepiction(mol)

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

opts = OE2DMolDisplayOptions(240.0, 100.0, OEScale_AutoScale)
opts.SetMargins(10.0)
disp = OE2DMolDisplay(mol, opts)

highlight = OEHighlightOverlayByBallAndStick(OEGetContrastColors())

unique = True