Molecule.toFormat("smiles:u") depends on input??

User c4e58ee8b2

27-01-2011 22:10:57

Hi, I have three smiles string:

C[C@H](N

)C(
)=O |$;;;_R1;;_R2;$|

C[C@H](N
)C(
)=O

C[C@H](N*)C(*)=O

and I expect to get the same result if I pass through the Molecule.toFormat("smiles:u") function, but I got different result. What should I do to assure unique result regardless what the input is?

The following is my test code and run results.

Thanks

Tianhong

---------------------------------------

public class UniqueSmilesTest {

   public static void main(String[] args) {

   try {

   String smiles1 = "C[C@H](N
)C(
)=O |$;;;_R1;;_R2;$|";

toUniqueSmiles(smiles1);

String smiles2 = "C[C@H](N
)C(
)=O";

   toUniqueSmiles(smiles2);

   String smiles3 = "C[C@H](N*)C(*)=O";

   toUniqueSmiles(smiles3);

   } catch (Exception e) {

   e.printStackTrace();

   }

   }

   private static void toUniqueSmiles(String smiles) throws IOException {

   System.out.println("Input: " + smiles);

   InputStream is = new ByteArrayInputStream(smiles.getBytes());

   MolImporter importer = new MolImporter(is);

   Molecule molecule = importer.read();

   String smilesU = molecule.toFormat("smiles:u");

   System.out.println("Output: " + smilesU);

   }

}

------------------------------------------

Input: C[C@H](N
)C(
)=O |$;;;_R1;;_R2;$|

Output: C[C@H](N
)C(
)=O

Input: C[C@H](N
)C(
)=O

Output: C[C@H](N*)C(*)=O

Input: C[C@H](N*)C(*)=O

Output: C[C@H](N*)C(*)=O

ChemAxon 25dcd765a3

28-01-2011 11:08:12

Hi,

From these structures:

1) C[C@H](N

)C(
)=O |$;;;_R1;;_R2;$|
2) C[C@H](N
)C(
)=O
3) C[C@H](N*)C(*)=O

Only the first one gives different SMILES string if you export it to unique smiles.

The first molecule differs from the latter two as it has Rgroups defined. So I think it is correct to mark somehow that it is not the same molecule as the latter two, resulting in : C[C@H](N
)C(
)=O.

If you want to avoid the Rgroup information from the first molecule don't read it as cxsmiles (with the Rgroup information), but read as smiles string, in this case the extended part is neglected.

You can define the molecule format in MolImporter:

MolImporter(java.io.InputStream is, java.lang.String opts)

In your case
```
MolImporter importer = new MolImporter(is, "smiles");
```

User c4e58ee8b2

28-01-2011 13:20:16

Volfi, thanks for your response.

What really concerns me is that the second structure is the cannonical form of the first structure, but it can be further cannonicalized to the third structure.

It seems that I need to call the exporting function twice to get the 'true' cannonical form, which is really I am looking for.

Tianhong

ChemAxon 25dcd765a3

28-01-2011 13:31:50

Dear Tianhong,

You are right, the second structure is unique smiles of the first structure. We loose information during unique smiles export, in this case the Rgroup info (which cannot be stored at smiles format). But instead of double export and loose information during the export you may consider not to use the Rgroup information during the import which is the solution I've suggested, but it is you to choose.

Volfi

User c4e58ee8b2

28-01-2011 13:38:05

Even if I specify the file format as 'smiles' in my importer, the first structure still produces the second structure, not the third. I am using MarvinBeans version 5.0.

Tianhong

ChemAxon 25dcd765a3

28-01-2011 13:48:46

Dear Tianhong,

At the first sight I thought you have found a bug, but I have re-checked it again and it works as expected.

I have attached the test code.

java Test
Input: C[C@H](N)C(
)=O |$;;;_R1;;_R2;$|
Output: C[C@H](N*)C(*)=O
Input: C[C@H](N
)C(
)=O
Output: C[C@H](N*)C(*)=O
Input: C[C@H](N*)C(*)=O
Output: C[C@H](N*)C(*)=O

The tree output are equal.

Volfi

User c4e58ee8b2

28-01-2011 14:39:16

This first one still produces smiles with

when I run your test program.

Could this be due to my MarvinBeans version (5.0)?

Tianhong

ChemAxon 25dcd765a3

28-01-2011 15:00:39

Dear Tianhong,

You are right the problem is that 5.0 is already 3 years old and we have fixed plenty of issues since then.

Please update your Marvin.

All the best

Volfi