Drawing a Molecule SurfaceΒΆ

The 2D representation of the molecule surface is calculated by first drawing circles around each atom of the molecule and then identifying the external arc segments that define a continuous surface around the molecule. This process is illustrated in the table Table: Calculation of the 2D representation of a molecule surface

Calculation of the 2D representation of a molecule surface
../_images/Draw2DSurface-Step-01.png ../_images/Draw2DSurface-Step-02.png
../_images/Draw2DSurface-Step-03.png ../_images/Draw2DSurface-Step-04.png
../_images/Draw2DSurface-Step-05.png ../_images/Draw2DSurface-Step-06.png

The following Listing 1 example shows how to the display a molecule surface. After creating an image object and preparing the molecule for 2D depiction, an arc drawing functor is added to each atom of the molecule by using the OESetSurfaceArcFxn function. The surface then can be drawn by calling the OEDraw2DSurface function that calculates the arc segments that form a continuous curve around the molecule. The image created by Listing 1 is shown in Figure: Example of surface drawing.

Listing 1: Example of surface drawing

double scale  = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetTitleLocation(OETitleLocation.Hidden);
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts));

OEPen pen = new OEPen(oechem.getOEGrey(), oechem.getOEGrey());
OEEyelashArcFxn arcfxn = new OEEyelashArcFxn(pen);

for (OEAtomBase atom : mol.GetAtoms()) {
    oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn);
}

OE2DMolDisplay disp = new OE2DMolDisplay(mol, opts);
oegrapheme.OEDraw2DSurface(disp);
../_images/Draw2DSurface.png

Example of surface drawing

The Listing 1 example uses the OESurfaceArcStyle.Eyelash style to draw the molecule surface. The following table lists all surface drawing styles that are available in Grapheme TK.

Supported surface drawing styles
../_images/OESurfaceArc_Small_OEAlphaRainbowArcFxn.png ../_images/OESurfaceArc_Small_OEBrickRoadArcFxn.png ../_images/OESurfaceArc_Small_OECastleArcFxn.png ../_images/OESurfaceArc_Small_OECogArcFxn.png
OEAlphaRainbowArcFxn OEBrickRoadArcFxn OECastleArcFxn OECogArcFxn
../_images/OESurfaceArc_Small_OEDefaultArcFxn.png ../_images/OESurfaceArc_Small_OEEyelashArcFxn.png ../_images/OESurfaceArc_Small_OEFlowerArcFxn.png ../_images/OESurfaceArc_Small_OENecklaceArcFxn.png
OEDefaultArcFxn OEEyelashArcFxn OEFlowerArcFxn OENecklaceArcFxn
../_images/OESurfaceArc_Small_OENullArcFxn.png ../_images/OESurfaceArc_Small_OEOliveBranchArcFxn.png ../_images/OESurfaceArc_Small_OEPearlsArcFxn.png ../_images/OESurfaceArc_Small_OERaceTrackArcFxn.png
OENullArcFxn OEOliveBranchArcFxn OEPearlsArcFxn OERaceTrackArcFxn
../_images/OESurfaceArc_Small_OERailroadTrackArcFxn.png ../_images/OESurfaceArc_Small_OESawArcFxn.png ../_images/OESurfaceArc_Small_OESimpsonArcFxn.png ../_images/OESurfaceArc_Small_OEStitchArcFxn.png
OEStitchArcFxn OESunArcFxn OEWreathArcFxn OERailroadTrackArcFxn
  ../_images/OESurfaceArc_Small_OESunArcFxn.png ../_images/OESurfaceArc_Small_OEWreathArcFxn.png  
  OESawArcFxn OESimpsonArcFxn  

User-defined surface drawing functors can be implemented by deriving from the OESurfaceArcFxnBase abstract base class. In the Listing 2 example, a user defined arc drawing functor is implemented that colors the eyelash arcs according to the atom they belong to. The image created by Listing 2 is shown in Figure: Example of user-defined surface drawing.

Listing 2: Example of user-defined surface drawing

public static class AtomColorArcFxn extends OESurfaceArcFxnBase {
    @Override
    public boolean constCall(OEImageBase image, OESurfaceArc arc) {
        OE2DAtomDisplay adisp = arc.GetAtomDisplay();
        if (adisp == null || !adisp.IsVisible())
            return false;

        OEPen pen = new OEPen();
        OEColor color = adisp.GetLabelFont().GetColor();
        pen.SetForeColor(color);

        OE2DPoint center = arc.GetCenter();
        double radius    = arc.GetRadius();
        double bgnAngle  = arc.GetBgnAngle();
        double endAngle  = arc.GetEndAngle();

        oegrapheme.OEDrawEyelashSurfaceArc(image, center, bgnAngle, endAngle, radius, pen);
        return true;
    }

    @Override
    public OESurfaceArcFxnBase CreateCopy() {
        AtomColorArcFxn copy = new AtomColorArcFxn();
        copy.swigReleaseOwnership();
        return copy;
    }
}
static void draw2DSurface(OEImageBase image, OEMolBase mol) {

    oedepict.OEPrepareDepiction(mol);

    double scale =  OEScale.AutoScale;
    OE2DMolDisplayOptions opts =  new OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(), scale);
    opts.SetTitleLocation(OETitleLocation.Hidden);
    opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts));

    AtomColorArcFxn arcfxn = new AtomColorArcFxn();
    for (OEAtomBase atom : mol.GetAtoms()) {
        oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn);
    }

    OE2DMolDisplay disp = new OE2DMolDisplay(mol, opts);
    oegrapheme.OEDraw2DSurface(disp);
    oedepict.OERenderMolecule(image, disp);
}
../_images/Draw2DSurfaceUserDefined.png

Example of user-defined surface drawing

The Listing 3 example shows how to project atom properties, such as partial charges into the molecule surface. The image created by Listing 3 is shown in Figure: Example of depicting atom properties.

Listing 3: Example of depicting atom properties on the molecule surface

private static class AtomPartialChargeArcFxn extends OESurfaceArcFxnBase {
    private OELinearColorGradient colorg;
    private AtomPartialChargeArcFxn() {}
    public AtomPartialChargeArcFxn(OELinearColorGradient cg) {
        colorg = new OELinearColorGradient(cg);
    }

    @Override
    public boolean constCall(OEImageBase image, OESurfaceArc arc) {
        OE2DAtomDisplay adisp = arc.GetAtomDisplay();
        if (adisp == null || !adisp.IsVisible())
            return false;

        OEAtomBase atom = adisp.GetAtom();
        if (atom == null)
            return false;

        double charge = atom.GetPartialCharge();
        if (charge == 0.0)
            return true;
        OEColor color = colorg.GetColorAt(charge);

        OEPen pen = new OEPen();
        pen.SetForeColor(color);
        pen.SetLineWidth(2.0);

        OE2DPoint center = arc.GetCenter();
        double bAngle = arc.GetBgnAngle();
        double eAngle = arc.GetEndAngle();
        double radius = arc.GetRadius();

        double edgeAngle = 5.0;
        int dir = OEPatternDirection.Outside;
        double patternAngle = 10.0;
        oegrapheme.OEDrawBrickRoadSurfaceArc(image, center, bAngle, eAngle, radius,
                pen, edgeAngle, dir, patternAngle);
        return true;
    }

    @Override
    public OESurfaceArcFxnBase CreateCopy() {
        AtomPartialChargeArcFxn copy = new AtomPartialChargeArcFxn(colorg);
        copy.swigReleaseOwnership();
        return copy;
    }
}
static void draw2DSurfacePartialCharge(OEImageBase image, OEMolBase mol) {

    oedepict.OEPrepareDepiction(mol);

    oechem.OEMMFFAtomTypes(mol);
    oechem.OEMMFF94PartialCharges(mol);

    double scale  = OEScale.AutoScale;
    OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(), scale);
    opts.SetTitleLocation(OETitleLocation.Hidden);
    opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts));

    OEColorStop coloranion = new OEColorStop(-1.0, oechem.getOEDarkRed());
    OEColorStop colorcation = new OEColorStop(+1.0, oechem.getOEDarkBlue());
    OELinearColorGradient colorg = new OELinearColorGradient(coloranion, colorcation);
    colorg.AddStop(new OEColorStop(0.0, oechem.getOEWhite()));

    AtomPartialChargeArcFxn arcfxn = new AtomPartialChargeArcFxn(colorg);

    for (OEAtomBase atom : mol.GetAtoms()) {
        oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn);
    }

    OE2DMolDisplay disp = new OE2DMolDisplay(mol, opts);
    oegrapheme.OEDraw2DSurface(disp);

    oedepict.OERenderMolecule(image, disp);
}
../_images/Draw2DSurfacePartialCharge.png

Example of depicting atom properties

See also

It is also possible to draw multiple 2D surfaces arc-by-arc. In the Listing 4 example below the arcs returned by the OEGet2DSurfaceArcs function for the given atom display and radius are directly rendered below the molecule diagram. In this case it is important to call the OEGetMoleculeSurfaceScale function with the largest radius scale of the 2D surfaces drawn. This reduces the scaling of the molecule in order to able to fit the molecule diagram and all of the arcs of the 2D surfaces into the image. The image created by Listing 4 is shown in Figure: Example of drawing multiple 2D surfaces.

Listing 4: Example of drawing multiple 2D surfaces

static void draw2DSurface(OE2DMolDisplay disp,  OEUnaryAtomPred atompred,
                          double radius,  OEColor color) {

    OEPen penA = new OEPen(color, color, OEFill.Off, 2.0);
    OEDefaultArcFxn arcfxnA = new OEDefaultArcFxn(penA);

    OEColor grey = new OEColor(oechem.getOELightGrey());
    OEPen penB = new OEPen(grey, grey, OEFill.Off, 2.0, OEStipple.ShortDash);
    OEDefaultArcFxn arcfxnB = new OEDefaultArcFxn(penB);

    OEImage layer = disp.GetLayer(OELayerPosition.Below);

    for (OE2DAtomDisplay adisp : disp.GetAtomDisplays()) {
        for (OESurfaceArc arc : oegrapheme.OEGet2DSurfaceArcs(disp, adisp, radius)) {
            if (atompred.constCall(adisp.GetAtom()))
                arcfxnA.constCall(layer, arc);
            else
                arcfxnB.constCall(layer, arc);
        }
    }
}

static void draw2DSurfaces(OEImageBase image, OEMolBase mol) {

    oedepict.OEPrepareDepiction(mol);

    double scale =  OEScale.AutoScale;
    OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(), scale);
    opts.SetTitleLocation(OETitleLocation.Hidden);
    opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts, 1.50));

    OE2DMolDisplay disp = new OE2DMolDisplay(mol, opts);

    draw2DSurface(disp, new OEHasAtomicNum(OEElemNo.C), 1.00, oechem.getOEBlack());
    draw2DSurface(disp, new OEHasAtomicNum(OEElemNo.N), 1.25, oechem.getOEDarkBlue());
    draw2DSurface(disp, new OEHasAtomicNum(OEElemNo.O), 1.50, oechem.getOEDarkRed());

    oedepict.OERenderMolecule(image, disp);

}
../_images/DrawMultiple2DSurfaces.png

Example of drawing multiple 2D surfaces

See also

OESurfaceArcScale namespace

The last Listing 5 example shows how to draw a 2D surface with various radii. It draws two surfaces one with a minimum radius scale and one with various radius depending on the covalent radius of the atoms. The OEGetMoleculeSurfaceScale function has to be called in this example too with the largest radius scale in order to able to fit the molecule diagram and all of the arcs of the 2D surfaces into the image. The image created by Listing 5 is shown in Figure: Example of drawing 2D surface with various radii.

Listing 5: Example of drawing 2D surface with various radii

    public static void drawSurfaces (OEImageBase image, OEMolBase mol) {    
	oechem.OEAssignCovalentRadii(mol);
	double minradius = oechem.OEGetCovalentRadius(OEElemNo.H);

        ArrayList<Double> radiusScales = new ArrayList<Double>(mol.GetMaxAtomIdx());

        double maxrscale = Double.MIN_VALUE;

        for (OEAtomBase atom : mol.GetAtoms()) {
	    double rscale = (atom.GetRadius() - minradius) + OESurfaceArcScale.Minimum;
            radiusScales.add(atom.GetIdx(), rscale);
	    maxrscale = Math.max(maxrscale, rscale);
	}

        OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(image.GetWidth(), 
                                                               image.GetHeight(), OEScale.AutoScale);
        opts.SetTitleLocation(OETitleLocation.Hidden);
        opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts, maxrscale));

        OE2DMolDisplay disp = new OE2DMolDisplay(mol, opts);

        OEImage layer = disp.GetLayer(OELayerPosition.Below);

        OEPen penA = new OEPen(oechem.getOELightGrey(), oechem.getOELightGrey(), OEFill.Off, 2.0, OEStipple.ShortDash);
        OEDefaultArcFxn arcfxnA = new OEDefaultArcFxn(penA);

        for (OESurfaceArc arc : oegrapheme.OEGet2DSurfaceArcs(disp, OESurfaceArcScale.Minimum)) {
	    arcfxnA.constCall(layer, arc);
	}

        OEPen penB = new OEPen(oechem.getOEGrey(), oechem.getOEGrey(), OEFill.Off, 2.0);
	OEDefaultArcFxn arcfxnB = new OEDefaultArcFxn(penB);

        for (OESurfaceArc arc : oegrapheme.OEGet2DSurfaceArcs(disp, radiusScales)) { 
	    arcfxnB.constCall(layer, arc);
	}

	oedepict.OERenderMolecule(image, disp);
    }    
../_images/Draw2DSurfaceVariousRadii.png

Example of drawing 2D surface with various radii

See also

OEGetCovalentRadius function in the OEChem TK manual