Binary Data Issue

I am successfully able to retrieve String data of the structure from the Database ( SQl Server ).

But when I try to retrieve Binary data , it returns null. Not sure what the issue is.

JChem.NET 15.6.2200

below is the Code 

returns Null data

JChemDBMolecule.Representations.Represent(MoleculeFormat.MRV).BinaryData; 

 

returns string representation

JChemDBMolecule.Representations.Represent(MoleculeFormat.MRV).StringData

Thanks

 Hi,

 

MRV is a string-based (XML) molecule format so you can get the string representation of the structure only. When you try to get the binary representation the result is null (exception doesn't occur).

Binary molecule formats are e.g. SKC, CDX. It should work:

byte[] molData = JChemDBMolecule.Representations.Represent(MoleculeFormat.SKC).BinaryData;

molData won't be null.

 

You can get the string molecule data like this:

JChemDBMolecule.MoleculeData.StringData

In this case you can get the original molecule representation. E.g. if you store SMILES strings in your database then the result will be the SMILES string. You don't need to convert the structures to MRV format.

 

What is your workflow? What would you like to do with the binary data? Which format do you use in your DB?

 

Regards,

Gergely

I have started to use the MRV format to store in the DB.  I need the BinaryData for a different project and data was null. It is very confusing as I do not see any documentation outlining what you indicated below.

So your suggestion is , instead of retrieving the MRV format from DB retrieve the SKC format to get the binary representation. Let me know if i am wrong?

 

Workflow I have is I need to retrieve the structure Image in the byte[] in order to display them on the ASP page ( not a MVC project ).

Thanks

 Hi,

 

Do not convert MRV data to SKC! SKC is a standard of the MDL Inc.:

https://en.wikipedia.org/wiki/ISIS/Draw

That was just an example for the binary stored data. SKC is a binary data itself (not a readable, string-based format). But if you use ChemAxon platform and work with MRV data that is a bad practice to convert MRV to SKC. You can loss data and it can be a slow process. Do not do that! (CDX is the same.)

If I understand correctly you need the binary representation of the MRV string. It is only a string -> binary "conversion". Like these:

System.Text.Encoding.UTF8.GetBytes(mrvString)

System.Text.Encoding.Unicode.GetBytes(mrvString)

System.Text.Encoding.ASCII.GetBytes(mrvString)

You have to specify the encoding.

 

What kind of data does the "different project" need? Can you give me some details about that? It can help. Maybe the MRV -> binary "conversion" won't be enough. What is the required input of that application? Does that know MRV format?

 

Anyway, I'm not familiar with molecule storing in databases but I can imagine you can choose better format than MRV. As I mentioned MRV is an XML what can be ineffective using RDBMS. Structure formats SMILES, SMARTS or CXSMILES, CXSMARTS can be more effective. If you have questions related this topic JChem Base Team can help you.

 

Regards,

Gergely

 

I'm really sorry I did not notice the essential part of your response:

"Workflow I have is I need to retrieve the structure Image in the byte[] in order to display them on the ASP page"

 

You can render a JChemDBMolecule easily:

JChemDBMolecule.Renderer.RenderToBinary(ImageFormat.Emf)   // PNG, BMP, JPEG, etc.

 

You can use the following methods as well:

- RenderToImage

- RenderToStream

- RenderToFile

 

You can find some examples here:

https://www.chemaxon.com/dotNET/6.3/examples.html#rendering

 

Regards,

Gergely

Hi,

Thanks for a quick response and being clear of the issue. 

Since you have brought the question of ineffective using RDBMS, I would like to educated as I would like to do right thing / job. Chemist draws the chemical structure and save those in the SQL Server. 

Below is the workflow to save. Please correct me if I am wrong any where

1. First step, Create molecule using MRV format.  IJChemMolecule savemolecule = MainFactory.Chemistry.CreateMolecule(savemodel.Structure, MoleculeFormat.MRV);


2. Make a SQL DB Connection  IJChemDatabaseHandler database = MainFactory.Database.OpenJChem(connection);


3. Insert or Update the Data  Table.Insert(molecule);

May i request to please suggest which format (SMILES, SMARTS or CXSMILES, CXSMARTS ) should I have to use for more effectives in SQL Server DB

Please suggest?

Thanks

gkovacs wrote:

I'm really sorry I did not notice the essential part of your response: "Workflow I have is I need to retrieve the structure Image in the byte[] in order to display them on the ASP page"   You can render a JChemDBMolecule easily: JChemDBMolecule.Renderer.RenderToBinary(ImageFormat.Emf)   // PNG, BMP, JPEG, etc.   You can use the following methods as well: - RenderToImage - RenderToStream - RenderToFile   You can find some examples here: https://www.chemaxon.com/dotNET/6.3/examples.html#rendering   Regards, Gergely

Thank you for your response. I did resolve the issue but wanted a confirmation.

Below is what i am doing

• Get the Molecule from the Database  JChemDBMolecule dbmolecule = db.GetMolecule(primarykey, keypassed);


• I type cast the JChemDBMolecule  to IJchemmolecule  IJChemMolecule molecule = dbmolecule.ToIJChemMolecule();


• byte[] structure = molecule.Renderer.RenderToBinary(ImageFormat.Emf);

This solve the issue. But please reply back to my other question on effectiveness of storing...

1.) Rendering:

You don't need to cast JChemDBMolecule to IJChemMolecule for rendering. You can call function RenderToBinary() on JChemDBMolecule directly. It should work. But the steps are OK what you described, your code snippet has to work correctly.

 

2.) Molecule data storing in databases:

For these kind of questions please contant JChem Base Team: jcb-support _at_ chemaxon.com

 

Regards,

Gergely

I talked to JCemBase Team about the data storing issue. If you used JChem tools, especially JChem Manager for creating structure table in your DB you don't need to change anything. In this case MRV is a good (best) choice.

So as I can see now your DB configuration is correct and the code what you use is also perfect.

Sorry for the misunderstanding.

Regards,

Gergely

gkovacs wrote:

I talked to JCemBase Team about the data storing issue. If you used JChem tools, especially JChem Manager for creating structure table in your DB you don't need to change anything. In this case MRV is a good (best) choice. So as I can see now your DB configuration is correct and the code what you use is also perfect. Sorry for the misunderstanding. Regards, Gergely

Hi Gergely,

Thanks for your quick response and clarifying. Structure table was created by JChemManager. 

I am happy that I have not written something bad and please do not sorry.

This helped me to re validate that legacy code I have replaced is in right direction.

Thanks