Chemical Validation Plugin

To whom it concerns,





Is there any plugin/code for Chemical validation? My programme has 'created' the following molecule





Cc7ccccc7Cc1(c7ccccc7)nnnc2cc(C(=O))c21





I would like to be able to pass this molecule to a piece of code which would tell me if this molecule is Chemically Valid or not( the above molecule is not valid because the 'c1' is trying to form FIVE bounds which is wrong).








Thanks,


Miriam

Hi,





The valenceCheck() and the hasValenceError() methods are available in the MolAtom class http://www.chemaxon.com/jchem/doc/api/index.html








The valence-error of atoms will be checked with the next simple example code.

Code:

MolAtom a; for (int i=0; i<mol.getAtomCount(); i++){       a=mol.getAtom(i);       a.valenceCheck();            if (a.hasValenceError()){              System.err.println("atom index= "+i+" has valence problem");                 }  }

// "mol" is your molecule to be checked








Jozsi

We will develop a specialized tool for structure checking soon, which will make the validation progress easier.

Thanks for your help. It will be great to have the validation tool.





Kind regards,


Miriam

Hi Jozsi,





I have a piece of code that I use to extract properties from my SMILES molecule(e.g., mass, logP etc). I added your code for valency checking to this code but, when I compiled the code





javac -d ./ My_MolCalculator_Two.java








I got the following error message:


Note: My_MolCalculator_Two.java uses or overrides a deprecated API.


Note: Recompile with -Xlint:deprecation for details.





Then, I recompiled my code as follows;





javac -Xlint My_MolCalculator_Two.java





and I got the following error.





My_MolCalculator_Two.java:103: warning: [deprecation] getTPSA() in chemaxon.marvin.calculations.TPSAPlugin has been deprecated


double nTPSA = nTP.getTPSA();


^


1 warning





I would be grateful if you could explain this error to me and how I can correct it.





Thanks again,


Miriam

Hi,





I sorted out the problem. I replaced getTPSA() with getSurfaceArea() in my code and it compiled fine.





Thanks,


Miriam

Hi,

Quote:

I would be grateful if you could explain this error to me and how I can correct it.

This deprecation warning is only an information for you (not an error!). It means that we are going to rename or delete the getTPSA() method in the TPSAplugin in the future.








The method summary (see the attached picture) part of the TPSA plugin inform you about the new name:

Quote:

getTPSA() Deprecated. as of Marvin 4.1, replaced by getSurfaceArea()

I see you accepted the getSurfaceArea() name.








Jozsi

Gyuri wrote:

We will develop a specialized tool for structure checking soon, which will make the validation progress easier.

Hi,

sorry for digging up such an old topic. I wonder if the validation tool is still in your pipeline or already available?

 

Regards,

Ingo

Hi Ingo,

YESSSS, we will release it in Marvin 5.3. Very close now. :)

Cheers,

Gyorgy