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

opts = OE2DMolDisplayOptions(imagewidth, imageheight, OEScale_AutoScale)
opts.SetTitleLocation(OETitleLocation_Hidden)
opts.SetScale(OEGetMoleculeSurfaceScale(mol, opts))

arcfxn = OEEyelashArcFxn(OEPen(OEGrey, OEGrey))

for atom in mol.GetAtoms():
    OESetSurfaceArcFxn(mol, atom, arcfxn)

disp = OE2DMolDisplay(mol, opts)
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

class AtomColorArcFxn(OESurfaceArcFxnBase):
    def __call__(self, image, arc):
        adisp = arc.GetAtomDisplay()
        if adisp is None or not adisp.IsVisible():
            return False

        color = adisp.GetLabelFont().GetColor()
        pen = OEPen(color, color, OEFill_Off, 1.0)

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

        OEDrawEyelashSurfaceArc(image, center, bgnAngle, endAngle, radius, pen)
        return True


def Draw2DSurface(image, mol):

    OEPrepareDepiction(mol)

    opts = OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(), OEScale_AutoScale)
    opts.SetTitleLocation(OETitleLocation_Hidden)
    opts.SetScale(OEGetMoleculeSurfaceScale(mol, opts))

    arcfxn = AtomColorArcFxn()
    for atom in mol.GetAtoms():
        OESetSurfaceArcFxn(mol, atom, arcfxn)

    disp = OE2DMolDisplay(mol, opts)
    OEDraw2DSurface(disp)
    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

class AtomPartialChargeArcFxn(OESurfaceArcFxnBase):
    def __init__(self, colorg):
        OESurfaceArcFxnBase.__init__(self)
        self.colorg = colorg

    def __call__(self, image, arc):
        adisp = arc.GetAtomDisplay()
        if adisp is None or not adisp.IsVisible():
            return False

        atom = adisp.GetAtom()
        if atom is None:
            return False

        charge = atom.GetPartialCharge()
        if charge == 0.0:
            return True
        color = self.colorg.GetColorAt(charge)

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

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

        edgeAngle = 5.0
        dir = OEPatternDirection_Outside
        patternAngle = 10.0
        OEDrawBrickRoadSurfaceArc(image, center, bAngle, eAngle, radius, pen,
                                  edgeAngle, dir, patternAngle)
        return True

    def CreateCopy(self):
        return AtomPartialChargeArcFxn(self.colorg).__disown__()


def Draw2DSurfacePartialCharge(image, mol):

    OEPrepareDepiction(mol)

    OEMMFFAtomTypes(mol)
    OEMMFF94PartialCharges(mol)

    opts = OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(), OEScale_AutoScale)
    opts.SetTitleLocation(OETitleLocation_Hidden)
    opts.SetScale(OEGetMoleculeSurfaceScale(mol, opts))

    coloranion = OEColorStop(-1.0, OEColor(OEDarkRed))
    colorcation = OEColorStop(+1.0, OEColor(OEDarkBlue))
    colorg = OELinearColorGradient(coloranion, colorcation)
    colorg.AddStop(OEColorStop(0.0, OEColor(OEWhite)))

    arcfxn = AtomPartialChargeArcFxn(colorg)

    for atom in mol.GetAtoms():
        OESetSurfaceArcFxn(mol, atom, arcfxn)

    disp = OE2DMolDisplay(mol, opts)
    OEDraw2DSurface(disp)
    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

def Draw2DSurface(disp, atompred, radius, color):

    penA = OEPen(color, color, OEFill_Off, 2.0)
    arcfxnA = OEDefaultArcFxn(penA)

    penB = OEPen(OELightGrey, OELightGrey, OEFill_Off, 2.0, OEStipple_ShortDash)
    arcfxnB = OEDefaultArcFxn(penB)

    layer = disp.GetLayer(OELayerPosition_Below)

    for adisp in disp.GetAtomDisplays():
        for arc in OEGet2DSurfaceArcs(disp, adisp, radius):
            if atompred(adisp.GetAtom()):
                arcfxnA(layer, arc)
            else:
                arcfxnB(layer, arc)


def Draw2DSurfaces(image, mol):

    OEPrepareDepiction(mol)

    opts = OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(), OEScale_AutoScale)
    opts.SetTitleLocation(OETitleLocation_Hidden)
    opts.SetScale(OEGetMoleculeSurfaceScale(mol, opts, 1.50))

    disp = OE2DMolDisplay(mol, opts)

    Draw2DSurface(disp, OEHasAtomicNum(OEElemNo_C), 1.00, OEBlack)
    Draw2DSurface(disp, OEHasAtomicNum(OEElemNo_N), 1.25, OEDarkBlue)
    Draw2DSurface(disp, OEHasAtomicNum(OEElemNo_O), 1.50, OEDarkRed)

    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

def DrawSurfaces(image, mol):

    OEAssignCovalentRadii(mol)
    minradius = OEGetCovalentRadius(OEElemNo_H)

    radiusScales = OEDoubleVector(mol.GetMaxAtomIdx(), 0.0)
    maxrscale = float("-inf")

    for atom in mol.GetAtoms():
        rscale = (atom.GetRadius() - minradius) + OESurfaceArcScale_Minimum
        radiusScales[atom.GetIdx()] = rscale
        maxrscale = max(maxrscale, rscale)

    opts = OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(), OEScale_AutoScale)
    opts.SetTitleLocation(OETitleLocation_Hidden)
    opts.SetScale(OEGetMoleculeSurfaceScale(mol, opts, maxrscale))

    disp = OE2DMolDisplay(mol, opts)

    layer = disp.GetLayer(OELayerPosition_Below)

    penA = OEPen(OELightGrey, OELightGrey, OEFill_Off, 2.0, OEStipple_ShortDash)
    arcfxnA = OEDefaultArcFxn(penA)

    for arc in OEGet2DSurfaceArcs(disp, OESurfaceArcScale_Minimum):
        arcfxnA(layer, arc)

    penB = OEPen(OEGrey, OEGrey, OEFill_Off, 2.0)
    arcfxnB = OEDefaultArcFxn(penB)

    for arc in OEGet2DSurfaceArcs(disp, radiusScales):
        arcfxnB(layer, arc)

    OERenderMolecule(image, disp)
../_images/Draw2DSurfaceVariousRadii.png

Example of drawing 2D surface with various radii

See also

OEGetCovalentRadius function in the OEChem TK manual