Drawing a Molecule Surface¶

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**¶

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

OE2DMolDisplayOptions opts(width, height, OEScale::AutoScale);
opts.SetTitleLocation(OETitleLocation::Hidden);
opts.SetScale(OEGetMoleculeSurfaceScale(mol, opts));

OEEyelashArcFxn arcfxn(OEPen(OEGrey, OEGrey));

for (OEIter<OEAtomBase> atom = mol.GetAtoms(); atom; ++atom)
  OESetSurfaceArcFxn(mol, atom, arcfxn);

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

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**¶

OEAlphaRainbowArcFxn	OEBrickRoadArcFxn	OECastleArcFxn	OECogArcFxn

OEDefaultArcFxn	OEEyelashArcFxn	OEFlowerArcFxn	OENecklaceArcFxn

OENullArcFxn	OEOliveBranchArcFxn	OEPearlsArcFxn	OERaceTrackArcFxn

OEStitchArcFxn	OESunArcFxn	OEWreathArcFxn	OERailroadTrackArcFxn

	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 : public OESurfaceArcFxnBase
{
public:
  AtomColorArcFxn() {}
  bool operator()(OEImageBase &image, const OESurfaceArc &arc) const
  {
    const OE2DAtomDisplay* adisp = arc.GetAtomDisplay();
    if (adisp == nullptr || !adisp->IsVisible())
      return false;

    const OEColor color = adisp->GetLabelFont().GetColor();
    const OEPen pen(color, color, OEFill::Off, 1.0);

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

    OEDrawEyelashSurfaceArc(image, center, bgnAngle, endAngle, radius, pen);
    return true;
  }
  OESurfaceArcFxnBase *CreateCopy() const
  {
    return new AtomColorArcFxn();
  }
};

void Draw2DSurface(OEImageBase& image, OEMolBase& mol)
{
  OEPrepareDepiction(mol);

  OE2DMolDisplayOptions opts(image.GetWidth(), image.GetHeight(), OEScale::AutoScale);
  opts.SetTitleLocation(OETitleLocation::Hidden);
  opts.SetScale(OEGetMoleculeSurfaceScale(mol, opts));

  AtomColorArcFxn arcfxn;
  for (OEIter<OEAtomBase> atom = mol.GetAtoms(); atom; ++atom)
    OESetSurfaceArcFxn(mol, atom, arcfxn);

  OE2DMolDisplay disp(mol, opts);
  OEDraw2DSurface(disp);
  OERenderMolecule(image, disp);
}

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 : public OESurfaceArcFxnBase
{
public:
  AtomPartialChargeArcFxn(const OELinearColorGradient cg)
  : m_colorg(cg)
  { }

  bool operator()(OEImageBase &image, const OESurfaceArc &arc) const
  {
    const OE2DAtomDisplay* adisp = arc.GetAtomDisplay();
    if (adisp == nullptr || !adisp->IsVisible())
      return false;

    const OEAtomBase* atom = adisp->GetAtom();
    if (atom == nullptr)
      return false;

    const double charge = atom->GetPartialCharge();
    if (charge == 0.0)
      return true;
    const OEColor color = m_colorg.GetColorAt(charge);

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

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

    const double edgeAngle = 5.0;
    const unsigned dir = OEPatternDirection::Outside;
    const double patternAngle = 10.0;
    OEDrawBrickRoadSurfaceArc(image, center, bAngle, eAngle, radius, pen,
                              edgeAngle, dir, patternAngle);
    return true;
  }
  OESurfaceArcFxnBase *CreateCopy() const
  {
    return new AtomPartialChargeArcFxn(m_colorg);
  }
private :
  OELinearColorGradient m_colorg;
};

void Draw2DSurfacePartialCharge(OEImageBase& image, OEMolBase& mol)
{
  OEPrepareDepiction(mol);

  OEMMFFAtomTypes(mol);
  OEMMFF94PartialCharges(mol);

  OE2DMolDisplayOptions opts(image.GetWidth(), image.GetHeight(), OEScale::AutoScale);
  opts.SetTitleLocation(OETitleLocation::Hidden);
  opts.SetScale(OEGetMoleculeSurfaceScale(mol, opts));

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

  AtomPartialChargeArcFxn arcfxn(colorg);

  for (OEIter<OEAtomBase> atom = mol.GetAtoms(); atom; ++atom)
    OESetSurfaceArcFxn(mol, atom, arcfxn);

  OE2DMolDisplay disp(mol, opts);
  OEDraw2DSurface(disp);
  OERenderMolecule(image, disp);
}

../_images/Draw2DSurfacePartialCharge.png

Example of depicting atom properties¶

See also

OELinearColorGradient class in the OEDepict TK manual

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

void Draw2DSurface(OE2DMolDisplay& disp, const OEUnaryPredicate<OEAtomBase>& atompred,
                                         double radius, const OEColor& color)
{
  OEPen penA(color, color, OEFill::Off, 2.0);
  OEDefaultArcFxn arcfxnA(penA);

  OEPen penB(OELightGrey, OELightGrey, OEFill::Off, 2.0, OEStipple::ShortDash);
  OEDefaultArcFxn arcfxnB(penB);

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

  for (OEIter<OE2DAtomDisplay> ai = disp.GetAtomDisplays(); ai; ++ai)
  {
    const OE2DAtomDisplay& adisp = (*ai);
    for (OEIter<const OESurfaceArc> arc = OEGet2DSurfaceArcs(disp, adisp, radius); arc; ++arc)
    {
      if (atompred(*adisp.GetAtom()))
        arcfxnA(layer, arc);
      else
        arcfxnB(layer, arc);
    }
  }
}

void Draw2DSurfaces(OEImageBase& image, OEMolBase& mol)
{
  OEPrepareDepiction(mol);

  OE2DMolDisplayOptions opts(image.GetWidth(), image.GetHeight(), OEScale::AutoScale);
  opts.SetTitleLocation(OETitleLocation::Hidden);
  opts.SetScale(OEGetMoleculeSurfaceScale(mol, opts, 1.50));

  OE2DMolDisplay disp(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);
}

Example of drawing multiple 2D surfaces¶