/// <summary>
/// Get the SVG for a molecule within a specified size rectangle (units important, eg. px, mm
/// </summary>
/// <param name="width"></param>
/// <param name="height"></param>
/// <param name="units"></param>
/// <param name="dp"></param>
/// <returns></returns>
public string GetMoleculeSvg(
int width = -1,
int height = -1,
string units = Depiction.UnitsPixel,
DisplayPreferences dp = null)
{
string svg = null;
UpdateNativeMolecule();
if (NativeMol == null || NativeMol.Atoms.Count == 0)
{
return(null);
}
//width = height = -1; // debug
//units = null;
//NativeMol.setProperty(CDKConstants.TITLE, "caffeine"); // title already set from input!
// Use size and units if specified. If not defined then a mm size box just containing the structure will be defined in generated svg
DepictionGenerator dptgen = new DepictionGenerator();
if (width > 0 && height > 0)
{
dptgen.Size = new System.Windows.Size(width, height);
dptgen.FillToFit = true;
}
Depiction d = dptgen.Depict(NativeMol);
if (Lex.IsDefined(units))
{
if (units != Depiction.UnitsPixel && units != Depiction.UnitsMM)
{
throw new Exception("Invalid Depiction units: " + units);
}
svg = d.ToSvgString(units); // get SVG setting desired units in the XML
}
else
{
svg = d.ToSvgString();
}
return(svg);
}
/// <summary>
/// Render molecule into bitmap of specified size.
/// </summary>
/// <param name="bitmapWidth"></param>
/// <param name="bitmapHeight"></param>
/// <param name="dp"></param>
/// <returns></returns>
public Bitmap GetMoleculeBitmap(
int bitmapWidth,
int bitmapHeight,
DisplayPreferences dp = null)
{
byte[] ba;
FileStream fs;
float top, bottom, left, right, height, width, strBottom, hCenter, drop, stdBndLen, scale, fontSize, bondThickness;
int txtLen;
Bitmap bm;
UpdateNativeMolecule();
if (NativeMol == null || NativeMol.Atoms.Count == 0)
{
return(null);
}
//NativeMol.setProperty(CDKConstants.TITLE, "caffeine"); // title already set from input!
DepictionGenerator dptgen = new DepictionGenerator();
dptgen.Size = new System.Windows.Size(bitmapWidth, bitmapHeight);
Depiction d = dptgen.Depict(NativeMol);
dptgen.Size = new System.Windows.Size(bitmapWidth, bitmapHeight);
dptgen.FillToFit = true;
//string svg = d.ToSvgString();
//bm = SvgUtil.GetBitmapFromSvgXml(svg, bitmapWidth);
//System.Windows.Media.Imaging.RenderTargetBitmap rtBm = d.ToBitmap();
string path = TempFile.GetTempFileName(ClientDirs.TempDir, "jpg", true);
d.WriteTo("jpg", path);
bm = new Bitmap(path);
return(bm);
}
/// <summary>
/// https://github.com/cdk/cdk/wiki/Toolkit-Rosetta
/// </summary>
/// <returns>Full path to created .png file</returns>
public static string DepictMolecule(this NCDK.IAtomContainer mol, string folder = null, int width = 300, int height = 350)
{
folder = folder ?? Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.ApplicationData),
@"NCDK\Images");
width = width < 100 ? 300 : width;
height = height < 100 ? 350 : height;
if (!Directory.Exists(folder))
{
Directory.CreateDirectory(folder);
}
var dptgen = new DepictionGenerator {
Size = new Size(width, height), ShowMoleculeTitle = true
};
dptgen.SymbolVisibility = SymbolVisibility.All;
var depiction = dptgen.Depict(mol);
var canonicalSmiles = mol.GetProperty <string>(NCDK.CDKPropertyName.Title) ?? Path.GetRandomFileName();
var filterName = new StringBuilder();
foreach (var c in canonicalSmiles.ToCharArray())
{
if (Path.GetInvalidPathChars().Contains(c) ||
Path.GetInvalidFileNameChars().Contains(c))
{
continue;
}
filterName.Append(c);
}
filterName.Append(".png");
var filename = Path.Combine(folder, filterName.ToString());
depiction.WriteTo(filename);
return(filename);
}
/// <summary>
/// Render molecule into bitmap of specified size.
/// </summary>
/// <param name="bitmapWidth"></param>
/// <param name="bitmapHeight"></param>
/// <param name="dp"></param>
/// <returns></returns>
public Bitmap GetMoleculeBitmap(
int bitmapWidth,
int bitmapHeight,
DisplayPreferences dp = null)
{
byte[] ba;
FileStream fs;
float top, bottom, left, right, height, width, strBottom, hCenter, drop, stdBndLen, scale, fontSize, bondThickness;
int txtLen;
Bitmap bm;
UpdateNativeMolecule();
if (NativeMol == null || NativeMol.getAtomCount() == 0)
{
return(null);
}
//NativeMol.setProperty(CDKConstants.TITLE, "caffeine"); // title already set from input!
sun.awt.Win32FontManager w32Font = new sun.awt.Win32FontManager(); // need this for class to be found
Environment.SetEnvironmentVariable("CLASSPATH", ".", EnvironmentVariableTarget.Process);
Environment.SetEnvironmentVariable("JAVA_HOME", @"C:\Mobius_OpenSource\MobiusCommon\CdkMx\bin\Debug", EnvironmentVariableTarget.Process);
Environment.SetEnvironmentVariable("Path", @"%JAVA_HOME%", EnvironmentVariableTarget.Process);
/* Need following?
* CLASSPATH=.; / JAVA_HOME=C:\Program Files\Java\jdk1.6.0_21 / Path=%JAVA_HOME%\bin;
*/
//DecimalFormatSymbols.getInstance(Local.ENGLISH);
//Locale.forLanguageTag("en-US")
DepictionGenerator dptgen = new DepictionGenerator();
dptgen.withSize(bitmapWidth, bitmapHeight); // px (raster) or mm (vector)
//dptgen.withMolTitle();
//dptgen.withTitleColor(Color.DarkGray); // annotations are red by default
Depiction d = dptgen.depict(NativeMol);
/*
*
* public const string SVG_FMT = "svg";
* public const string PS_FMT = "ps";
* public const string EPS_FMT = "eps";
* public const string PDF_FMT = "pdf";
* public const string JPG_FMT = "jpg";
* public const string PNG_FMT = "png";
* public const string GIF_FMT = "gif";
*
* public const string UNITS_MM = "mm";
* public const string UNITS_PX = "px";
*/
java.util.List formats = d.listFormats();
java.io.File file = new java.io.File(@"c:\downloads\test.jpg");
bool b = file.canWrite();
string s = d.toSvgStr();
d.writeTo("jpg", file);
//d.writeTo("svg", @"c:\downloads\test.svg");
//string svg = d.toSvgStr();
//bm = SvgUtil.GetBitmapFromSvgXml(svg, bitmapWidth);
bm = new Bitmap(@"c:\downloads\test.jpg");
return(bm);
}
public ChemObjectBox()
{
Generator = new DepictionGenerator();
}
