private byte[] RenderHighlightedObject(IndigoObject mol, IndigoObject query)
{
query.aromatize();
IndigoObject matcher = indigo.substructureMatcher(mol);
foreach (IndigoObject match in matcher.iterateMatches(query))
{
foreach (IndigoObject queryAtom in query.iterateAtoms())
{
IndigoObject atom = match.mapAtom(queryAtom);
atom.highlight();
foreach (IndigoObject nei in atom.iterateNeighbors())
{
if (!nei.isPseudoatom() && !nei.isRSite() && nei.atomicNumber() == 1)
{
nei.highlight();
nei.bond().highlight();
}
}
}
foreach (IndigoObject bond in query.iterateBonds())
{
match.mapBond(bond).highlight();
}
}
indigo.setOption("render-coloring", false);
mol.dearomatize();
mol.layout();
return(renderer.renderToBuffer(mol));
}
/// <summary>
/// Returns a depiction of the chemical structure as a bitmap.
/// </summary>
/// <param name="width">The desired width in pixels.</param>
/// <param name="height">The desired height in pixels.</param>
/// <returns>The bitmap depicting the chemical structure.</returns>
public Bitmap ToBitmap(int width, int height)
{
Bitmap bitmap = null;
try
{
using (Indigo indigo = new Indigo())
{
IndigoRenderer indigoRenderer = new IndigoRenderer(indigo);
indigo.setOption("render-coloring", true);
indigo.setOption("render-image-size", width, height);
indigo.setOption("render-label-mode", "hetero");
indigo.setOption("render-margins", 10, 10);
indigo.setOption("render-output-format", "png");
indigo.setOption("render-relative-thickness", 1.6f);
IndigoObject structure = CreateIndigoStructure(indigo);
structure.dearomatize();
structure.layout();
bitmap = indigoRenderer.renderToBitmap(structure);
structure.Dispose();
}
}
catch
{
bitmap = Properties.Resources.Error;
}
return(bitmap);
}
public void WriteImageFile(string fname, IndigoObject mol, string format, string comment, float weight)
{
switch (format)
{
case "png": { indigo.setOption("render-output-format", "png"); break; }
case "svg": { indigo.setOption("render-output-format", "svg"); break; }
case "pdf": { indigo.setOption("render-output-format", "pdf"); break; }
case "emf": { indigo.setOption("render-output-format", "emf"); break; }
default: throw new Exception("format not handled by Indigo: " + format);
}
// http://ggasoftware.com/opensource/indigo/api/options#rendering
//png, svg, pdf are allowed. On Windows, emf is also allowed.
indigo.setOption("render-bond-length", "18");
indigo.setOption("render-relative-thickness", Math.Round(weight, 2).ToString());
indigo.setOption("render-coloring", true);
indigo.setOption("render-margins", 1, 1);
//indigo.setOption("render-atom-ids-visible", true);
indigo.setOption("render-comment", comment);
indigo.setOption("render-implicit-hydrogens-visible", false);
indigo.setOption("render-label-mode", "hetero");
indigo.setOption("render-comment-font-size", "15");
indigo.setOption("render-comment-offset", "6");
mol.layout();
renderer.renderToFile(mol, fname);
//indigo.setOption("render-output-format", "svg");
}
private void renderMolecule(IndigoObject input)
{
IndigoRenderer renderer = new IndigoRenderer(_indigo);
_indigo.setOption("render-output-format", "emf");
_indigo.setOption("render-margins", 10, 10);
if (showBonds == true)
{
_indigo.setOption("render-bond-ids-visible", true);
}
else
{
_indigo.setOption("render-bond-ids-visible", false);
}
if (showAtoms == true)
{
_indigo.setOption("render-atom-ids-visible", true);
}
else
{
_indigo.setOption("render-atom-ids-visible", false);
}
_indigo.setOption("render-label-mode", "hetero");
_indigo.setOption("render-stereo-style", "none");
_indigo.setOption("render-bond-length", 45);
input.layout();
MemoryStream ms = new MemoryStream(renderer.renderToBuffer(input));
pictureBox1.Image = Image.FromStream(ms);
ms.Close();
}