public static string MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse = null,
Str_Vect atomSymbols = null, Str_Vect bondSymbols = null,
bool isomericSmiles = true, bool kekuleSmiles = false, int rootedAtAtom = -1, bool canonical = true,
bool allBondsExplicit = false, bool allHsExplicit = false)
{
return(RDKFuncs.MolFragmentToSmiles(mol, atomsToUse, bondsToUse, atomSymbols, bondSymbols, isomericSmiles, kekuleSmiles, rootedAtAtom, canonical));
}
public static string MolToSVG(ROMol mol, int width = 300, int height = 300,
Int_Vect highlightAtoms = null, bool kekulize = true, int lineWidthMult = 1, int fontSize = 12,
bool includeAtomCircles = true, int confId = -1)
{
// See Code\GraphMol\Wrap\MolOps.cpp
var drawer = new MolDraw2DSVG(width, height);
drawer.setFontSize(fontSize / 24.0);
drawer.setLineWidth(drawer.lineWidth() * lineWidthMult);
drawer.drawOptions().circleAtoms = includeAtomCircles;
drawer.drawMolecule(mol, highlightAtoms, null, null, confId);
drawer.finishDrawing();
return(drawer.getDrawingText());
}
public static string MolFragmentToSmarts(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse = null, bool isomericSmiles = true)
{
return(RDKFuncs.MolFragmentToSmarts(mol, atomsToUse, bondsToUse, isomericSmiles));
}
public static ROMol PathToSubmol(ROMol mol, Int_Vect path, bool useQuery = false, Int_Int_Map atomIdxMap = null)
{
return(RDKFuncs.pathToSubmol(mol, path, useQuery, atomIdxMap));
}
public static ROMol_Vect GetMolFrags(ROMol mol,
bool sanitizeFrags = false, Int_Vect frags = null, Int_Vect_Vect fragsMolAtomMapping = null)
{
return(RDKFuncs.getMolFrags(mol, sanitizeFrags, frags, fragsMolAtomMapping));
}
/// <summary>
/// Generates a drawing of a molecule and writes it to a file.
/// </summary>
/// <seealso href="https://github.com/rdkit/rdkit/blob/1649029367a8e517cf1913a5b80b91813874e002/rdkit/Chem/Draw/__init__.py#L265-L300"/>
public static void MolToFile(
RWMol mol,
string filename,
Tuple <int, int> size = null,
bool kekulize = true,
bool wedgeBonds = true,
string imageType = null,
bool fitImage = false,
string legend = "",
Int_Vect highlight_atoms = null,
Int_Vect highlight_bonds = null,
DrawColour highlightColor = null
)
{
if (size == null)
{
size = new Tuple <int, int>(300, 300);
}
if (imageType == null)
{
imageType = Path.GetExtension(filename).Substring(1).ToLowerInvariant();
}
try
{
RdMolDraw2D.PrepareMolForDrawing(mol, kekulize: kekulize, wedgeBonds: wedgeBonds);
}
catch (Exception)
{
RdMolDraw2D.PrepareMolForDrawing(mol, kekulize: false, wedgeBonds: wedgeBonds);
}
MolDraw2D d2d;
switch (imageType)
{
case "png":
d2d = new MolDraw2DCairo(size.Item1, size.Item2);
break;
case "svg":
d2d = new MolDraw2DSVG(size.Item1, size.Item2);
break;
default:
throw new Exception($"{imageType} is not supported.");
}
if (highlightColor != null)
{
d2d.DrawOptions().highlightColour = highlightColor;
}
d2d.DrawOptions().prepareMolsBeforeDrawing = false;
d2d.DrawMolecule(mol, legend, highlight_atoms, highlight_bonds);
d2d.FinishDrawing();
switch (d2d)
{
case MolDraw2DCairo d:
d.WriteDrawingText(filename);
break;
case MolDraw2DSVG d:
using (var w = new StreamWriter(filename))
{
w.Write(d.GetDrawingText());
}
break;
}
}
public static void GetOnBits(this BitVect bv, Int_Vect v) => bv.getOnBits(v);
public static void DrawMolecule(this MolDraw2D view, ROMol mol, string legend = "", Int_Vect highlight_atoms = null, Int_Vect highlight_bonds = null) => view.drawMolecule(mol, legend, highlight_atoms, highlight_bonds);
public static void PrepareAndDrawMolecule(MolDraw2D drawer, ROMol mol, string legend = "", Int_Vect highlight_atoms = null, Int_Vect highlight_bonds = null)
{
RDKFuncs.prepareAndDrawMolecule(drawer, mol, legend, highlight_atoms, highlight_bonds);
}
