Does MolPrinter.setMol(string) have a error?

Hi!

I want to create EMF by MolPrinter class.

So, I coded it according to the sample of the following sites.

http://www.chemaxon.com/dotNET/examples/marvin/MoleculeImage/MoleculeImage.cs.html

 

I set the following structure(SDF) by MolPrinter.setMol(string) method.

3-dimethylamino-1,1-di-(2-thienyl)-1-butene
  Marvin  05251012162D          

 17 18  0  0  0  0            999 V2000
oB6WMS4W60
9S4WvR3W60
9S4W-Q1W60
oB6WYQ0W60
oB6WeP+V60
4q7WtDzV60
FC7WGJxV60
LB5WGJxV60
VZ4WtDzVG0
Rx7WcV1W60
v88WoV3W60
-6AW-r3W60
S7BWM62W60
Bn9WZc0WG0
Wi2WMS4W70
    0.3896    1.4073    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
    1.1630    2.6448    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
10201
20301
30402
40501
50602
60701
70802
80901
50901
40A01
A0B02
B0C01
C0D02
D0E01
A0E01
20F01
F0G01
F0H01
M  STY  2   1 SUP   2 SUP
M  SAL   1  1  17
M  SBL   1  1  18
M  SMT   1 Alk
M  SAL   2  1  16
M  SBL   2  1  17
M  SMT   2 Alk
M  END

(This structure's group is not expand.)

 

Then, "Alk" was expanded to "R" automatically.

That is bad. Is it bug?

 

When I converted by MolImporter.importMol(string) The above-mentioned structure to Molecule class instance

and set to MolPrinter.setMol(Molecule),

then "Alk" wasn't expanded to "R" automatically.

That is good.

 

When I create PNG,

both MolPrinter.setMol(string) and MolPrinter.setMol(Molecule) are good working.

 

See the attachment Excel file.

 

I hope the same behavior in case createing EMF.

 

I use the Marvin and JChem version 5.3.6 .NET API.

 

Best Regards.

Hi,

 

could you please send us a sample code that compiles and we can check your problem.

 

Thanks,

Viktor

Hi,

Thanks for reply.

Following is sample code.

using System;
using System.Collections.Generic;
using System.ComponentModel;
using System.Data;
using System.Drawing;
using System.Linq;
using System.Text;
using System.Windows.Forms;
using chemaxon.marvin;
using chemaxon.marvin.paint;
using System.Drawing.Imaging;
using System.IO;
using ikvm.awt;
using chemaxon.struc;
using chemaxon.formats;

namespace MolPrinterEmfTest
{
	public partial class MolImageForm : Form
	{
		public MolImageForm()
		{
			InitializeComponent();
		}

		private void MolImageForm_Load(object sender, EventArgs e)
		{
			string molStr = @"
  Marvin  05251012162D          

 17 18  0  0  0  0            999 V2000
oB6WMS4W60
9S4WvR3W60
9S4W-Q1W60
oB6WYQ0W60
oB6WeP+V60
4q7WtDzV60
FC7WGJxV60
LB5WGJxV60
VZ4WtDzVG0
Rx7WcV1W60
v88WoV3W60
-6AW-r3W60
S7BWM62W60
Bn9WZc0WG0
Wi2WMS4W70
    0.3896    1.4073    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
    1.1630    2.6448    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
10201
20301
30402
40501
50602
60701
70802
80901
50901
40A01
A0B02
B0C01
C0D02
D0E01
A0E01
20F01
F0G01
F0H01
M  STY  2   1 SUP   2 SUP
M  SAL   1  1  17
M  SBL   1  1  18
M  SMT   1 Alk
M  SAL   2  1  16
M  SBL   2  1  17
M  SMT   2 Alk
M  END
";

			SetMoleculeImageUsingMolPrinter(molStr, molStrPictureBox);

			Molecule mol = MolImporter.importMol(molStr);
			SetMoleculeImageUsingMolPrinter(mol, molculePictureBox);
		}

		private void SetMoleculeImageUsingMolPrinter(object mol, PictureBox targetPictureBox)
		{
			Bitmap bmp;
			Graphics graphicsMf = null;
			Graphics graphics = null;
			Metafile mf = null;

			try
			{
				MolPrinter molPrinter = new MolPrinter();
				if (mol is Molecule)
					molPrinter.setMol((Molecule)mol);
				else if (mol is String || mol is string)
					molPrinter.setMol((string)mol);
				else
					return;

				bmp = new Bitmap(300, 300, PixelFormat.Format32bppArgb);
				graphicsMf = Graphics.FromImage(bmp);

				IntPtr hdc = graphicsMf.GetHdc();

				//Creating double size rectangle fixes some drawing issues.
				mf = new Metafile(new MemoryStream(), hdc, new RectangleF(0, 0, 600, 600), MetafileFrameUnit.Pixel);

				graphics = Graphics.FromImage(mf);

				NetGraphics g = new NetGraphics(graphics);

				molPrinter.setDispopts(molPrinter.getDispopts() | DispOptConsts.__Fields.RGROUPS_FLAG);
				java.awt.Rectangle r = new java.awt.Rectangle(300, 300);
				molPrinter.setScale(molPrinter.maxScale(r));

				molPrinter.paint(g, r);

				targetPictureBox.Image = mf;
				graphics.Dispose();
				bmp.Dispose();


				graphicsMf.Dispose();
				g.dispose();
				g = null;
				graphics = null;
				graphicsMf = null;
			}
			finally
			{
				if (graphics != null)
				{
					graphics.Dispose();
				}
			}
		}
	}
}

 

 

I attached project file.

Thanks.

Cunjing

I am checking your code and it does not work for any reason, I am back to you asap.

Viktor

Hi,

Thank you for your working.

I am looking forward to be solved.

 

Best regards.

cunjing

Dear Cunjing,

you should call

   Molecule mol = MolImporter.importMol(molStr);
              
         mol.expandSgroups();
   SetMoleculeImageUsingMolPrinter(mol, molculePictureBox);

otherwise the molecule leave it as is. It seems that that is the default behaviour. WHen it is passed as string,

the painter makes a "clean" on it before rendering.

 

 Viktor

Dear Viktor.

 

No. No. No.

I don't want expand S-Group automatically by using MolPrinter.setMol(String).

I hope setMol(String)  behave same as setMol(Molecule).

 

Thanks.

Dear Cunjing,

in the meantime  I passed this issue over to Erika, she is involved more in R/S-Groups,

I think this issue is not reallt related to the .NET solution but to the basic java api.

Thanks,

Viktor

Dear Cunjing,

We need some more time to find the cause. We will get back with the solution shortly.

Thanks for your patience.

Regards,

Erika.

Dear Erika.

Hi,

Thanks for your reply soon.

Regards.

 

Cunjing

Dear Cunjing,

 

on java side Erika did not manage to reproduce the issue. I try to use her code to reproduce the issue with dotnet or find the difference between her code and our tests.

 

For the time being you can use the workaround I sent to you.

Viktor

Erika,

please try out with the molPrinter and with the string directly not by passing the imported Molecule object.

molPrinter.setMol(string); The mol string can be found in the forum (code snippet).

Viktor

 

Dear Viktor,

 

Thank you for your support.

 

Regards,

 

Cunjing

Dear Cunjing,

it seems what you reported is an inconsistent work, lets say a kind of bug,

For the time being we highly recommend with Erika you should use MolImporter and with the returned molecule object you should initialize the MolpRinter with, in setMol. In this way the object will give you the desired behaviour.
If you even want to expand the Alk to R explicitly please call the mol.expandSgroups();

The bug has been registered in issue tracking system.

Viktor

 

Dear Viktor and Erika

 

 Thank you for your working.

 

Regards.

 

Cunjing

Dear Cunjing,

The correction will be available in Marvin 5.4.
Can you please confirm if it is working for you?

Best Regards,
Erika

Dear Erika,

Thank you for your woking.

Best Regards,
Cunjing