wrong value for calculator plugins with version 3.1.5

User 86810cf9fa

23-05-2007 17:19:01

Dear support,

I am using JChem version 3.1.5

I saw a strange thing using two molecules :

- molecule 1:

Code:

Marvin 05230719002D

32 34 0 0 0 0 999 V2000

5.9196 -5.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.9196 -4.6050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.6341 -4.1925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.3485 -4.6050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.6341 -3.3675 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.3485 -2.9550 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

5.9196 -2.9550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.9196 -2.1300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.2051 -1.7175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.2051 -0.8925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.0301 -0.8925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.3801 -0.8925 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

5.2051 -0.0675 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.4906 0.3450 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

4.4906 1.1700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.2051 1.5825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.2051 2.4075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.4906 2.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.4906 3.6450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

3.7762 4.0575 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

3.0226 3.7219 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0

2.4705 4.3350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

1.6500 4.2488 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

2.8830 5.0495 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

3.6900 4.8780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.3030 5.4300 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

3.7762 2.4075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

3.7762 1.5825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.2051 -3.3675 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.4906 -2.9550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.2051 -4.1925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.4906 -4.6050 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

1 2 1 0 0 0 0

2 3 2 0 0 0 0

3 4 1 0 0 0 0

3 5 1 0 0 0 0

5 6 2 0 0 0 0

5 7 1 0 0 0 0

7 8 1 0 0 0 0

8 9 1 0 0 0 0

9 10 1 0 0 0 0

10 11 1 0 0 0 0

10 12 1 0 0 0 0

10 13 1 0 0 0 0

13 14 1 0 0 0 0

14 15 1 0 0 0 0

15 16 2 0 0 0 0

16 17 1 0 0 0 0

17 18 2 0 0 0 0

18 19 1 0 0 0 0

19 20 1 0 0 0 0

20 21 1 0 0 0 0

21 22 1 0 0 0 0

22 23 2 0 0 0 0

22 24 1 0 0 0 0

24 25 1 0 0 0 0

20 25 1 0 0 0 0

25 26 2 0 0 0 0

18 27 1 0 0 0 0

27 28 2 0 0 0 0

15 28 1 0 0 0 0

7 29 2 0 0 0 0

29 30 1 0 0 0 0

29 31 1 0 0 0 0

2 31 1 0 0 0 0

31 32 2 0 0 0 0

M END

and

- molecule 2:

Code:

Marvin 05230719002D

41 44 0 0 1 0 999 V2000

8.5832 10.9907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.9188 10.2370 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

9.7392 10.1507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.4338 9.5695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.6088 9.5695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.1239 10.2370 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.3034 10.1507 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

7.4594 10.9907 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

6.9746 11.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.3101 12.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.8252 13.0792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.0047 12.9930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.6691 12.2393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.1540 11.5719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.3539 8.7849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.5692 8.5300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.9562 9.0820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.1715 8.8271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.0000 8.0201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.6131 7.4680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.3977 7.7230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.0213 8.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.6888 8.7849 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

9.4734 8.5300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

10.0865 9.0820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

10.8712 8.8271 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0

11.0427 8.0201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

11.4842 9.3791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

12.2689 9.1242 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0

12.4404 8.3172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

12.8819 9.6762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

13.6666 9.4212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

13.8381 8.6143 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

14.2797 9.9733 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

8.0213 7.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.3069 7.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.3069 6.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.0213 5.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.0213 5.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0

8.7358 6.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.7358 7.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

1 2 1 0 0 0 0

2 3 1 0 0 0 0

2 4 1 0 0 0 0

4 5 2 0 0 0 0

5 6 1 0 0 0 0

6 7 2 0 0 0 0

6 8 1 0 0 0 0

8 9 1 0 0 0 0

9 10 2 0 0 0 0

10 11 1 0 0 0 0

11 12 2 0 0 0 0

12 13 1 0 0 0 0

13 14 2 0 0 0 0

9 14 1 0 0 0 0

5 15 1 0 0 0 0

15 16 1 0 0 0 0

16 17 2 0 0 0 0

17 18 1 0 0 0 0

18 19 2 0 0 0 0

19 20 1 0 0 0 0

20 21 2 0 0 0 0

16 21 1 0 0 0 0

15 22 2 0 0 0 0

22 23 1 0 0 0 0

4 23 1 0 0 0 0

23 24 1 0 0 0 0

24 25 1 0 0 0 0

25 26 1 0 0 0 0

26 27 1 6 0 0 0

26 28 1 0 0 0 0

28 29 1 0 0 0 0

29 30 1 6 0 0 0

29 31 1 0 0 0 0

31 32 1 0 0 0 0

32 33 1 0 0 0 0

32 34 2 0 0 0 0

22 35 1 0 0 0 0

35 36 2 0 0 0 0

36 37 1 0 0 0 0

37 38 2 0 0 0 0

38 39 1 0 0 0 0

38 40 1 0 0 0 0

40 41 2 0 0 0 0

35 41 1 0 0 0 0

M END

I calculated the pKa using the pKaPlugin for molecule 2 and I obtained 4.33.

But when I calculated molecule 1 and then molecule 2, I obtain -1.28 for molecule 2.

Thus, I tested using version 3.2.6 and I have the correct value 4.33 for molecule 2.

I have the same thing with other plugins.

Can you please tell me from which version of JChem this issue has been fixed?

Best regards,

Severine

ChemAxon e08c317633

24-05-2007 10:28:59

severine wrote:

I calculated the pKa using the pKaPlugin for molecule 2 and I obtained 4.33.

But when I calculated molecule 1 and then molecule 2, I obtain -1.28 for molecule 2.

Thus, I tested using version 3.2.6 and I have the correct value 4.33 for molecule 2.

I have the same thing with other plugins.

Can you please tell me from which version of JChem this issue has been fixed?

Hi,

How did you get these values?

Did you use pKaPlugin through

- MarvinSketch/MarvinView: Tools->pKa

- cxcalc batch mode, the 2 molecules were in the same SDfile

- Chemical Terms pKa() function

- Java API

Best regards,

Zsolt

User 86810cf9fa

24-05-2007 11:23:03

I am using the API

ChemAxon e08c317633

24-05-2007 11:33:28

severine wrote:

I am using the API

Could you post/attach the part of you code that produces this error?

Regards,

Zsolt

User 86810cf9fa

24-05-2007 12:43:15

Hi Zsolt,

This is my code:

Code:

pKaPlugin pka = new pKaPlugin();

while (rs.next()){

pka.validate(licencePKaPlugin);

pka.setpH(7.4);

pka.setMolecule(mol);

pka.run();

acidic_pka = new double[1];

acidic_indices = new int[1];

basic_indices = new int[1];

pka.getSortedValues(pKaPlugin.ACIDIC, acidic_pka, acidic_indices);

if (!Double.isNaN(acidic_pka[0])) {

return acidic_pka[0];

}

pka.getSortedValues(pKaPlugin.BASIC, basic_pka, basic_indices);

result = basic_pka[0];

}

rs is my resultSet with a diffrent molecule each time I loop on it.

I hope this will help you

Best regards,

Severine

ChemAxon e08c317633

24-05-2007 15:10:21

Hi,

I tried to reproduce the error with the following code:

Code:

import java.io.*;

import chemaxon.struc.*;

import chemaxon.formats.MolImporter;

import chemaxon.marvin.calculations.pKaPlugin;

import chemaxon.marvin.plugin.PluginException;

public class pKaPluginTest {

public static void main(String[] args) {

   try {

      pKaPlugin pka = new pKaPlugin();

      MolImporter importer = new MolImporter(args[0]);

      Molecule mol = null;

      while ((mol = importer.read()) != null) {

         //pka.validate(licencePKaPlugin);

         pka.setpH(7.4);

         pka.setMolecule(mol);

         pka.run();

         double[] acidic_pka = new double[1];

         int[] acidic_indices = new int[1];

         double[] basic_pka = new double[1];

         int[] basic_indices = new int[1];

         pka.getSortedValues(pKaPlugin.ACIDIC, acidic_pka, acidic_indices);

         if (!Double.isNaN(acidic_pka[0])) {

            System.out.println(acidic_pka[0]);

         }

         pka.getSortedValues(pKaPlugin.BASIC, basic_pka, basic_indices);

         double result = basic_pka[0];

      }

      importer.close();

   } catch (IOException e) {

      e.printStackTrace();

   } catch (PluginException e) {

      e.printStackTrace();

   }

}

}

After I have compiled this code using JChem library version 3.1.5 I got these results:

Code:

$ java pKaPluginTest mols.sdf

6.0135863919185235

4.328072908505882

These results are good => I can not reproduce the error.

Are you sure the code you have posted is responsible for the error?

I have attached mols.sdf (contains the molcules you have posted) and pKaPluginTest.java (contains the above code).

Best regards,

Zsolt

User 86810cf9fa

25-05-2007 07:22:57

Hi Zsolt,

I reduced my code for you but I am calculating other properties in the same code. I find that it is the PolarizabilityPlugin which gives me the error.

I attached the code which gives me the error with JChem 3.1.5 and not which JChem 3.2.5

Best regards,

Severine

ChemAxon e08c317633

26-05-2007 09:44:18

Hi Severine,

Thanks for the code, I was able to reproduce the error using it.

The error occurred when PolarizabilityPlugin or ChargePlugin was run between two other plugin.run() method calls.

This error was fixed in JChem 3.2 version, so JChem 3.2 or later versions return the correct result.

Best regards,

Zsolt

User 86810cf9fa

26-05-2007 10:29:07

Thank you very much Zsolt for your help and patience.

Kind regards,

Severine