Re: [Cdk-user] create amino acide

[hanouna n. <han...@ya...>]

yes, i have to create an amino acide similar to Lidociane or to furano-pyrimidine 

    Le Lundi 2 mai 2016 21h48, John M <joh...@gm...> a écrit :
 

 Do you have an example of an amine and acid you want to make an amino acid out of?
Regards,
John W May 
joh...@gm...
On 2 May 2016 at 20:36, hanouna nouna <han...@ya...> wrote:

thanks for answering, about your first question i download the acides and the amines from ChemSpider database in mol format, and i wont to make a novel amino acid from this two fragments , and i will use the first way (using SMARTS) to create it .
 

    Le Lundi 2 mai 2016 21h21, John M <joh...@gm...> a écrit :
 

 What do the amines look like and what to the acids look like? It sounds like you're not simply building a polypeptide but want to make novel amino acids from an amine and an acid? In bonding these to things together any algorithm can't simply know which atoms you want to bond and you must tell it. 
There are two ways this is typically done but depends on your use case: a) Use a SMARTS pattern/reaction transformation (e.g. SMIRKS) this is okay but handling unwanted bonds may be a problem if you're patterns aren't strict enough. b) Use attachment points/leaving groups to specify where monomers can be bound. This requires rewriting your monomer set but is more robust and efficient if you building polymers. This is the approach taken by HELM.
Unfortunately both of these are rather involved.
- John
Regards,
John W May 
joh...@gm...
On 1 May 2016 at 19:23, hanouna nouna <han...@ya...> wrote:

hello i have  a set of fragment acides.mol and a set of fragments amine.mol in my disc  and i wont to read an acide and an amin and to create an amino acide i try with this code but i have an errorimport java.io.FileNotFoundException;
import java.io.InputStream;

import org.openscience.cdk.BioPolymer;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.tools.ProteinBuilderTool;

public class AA {
    public static void main(String[] args) throws CDKException, FileNotFoundException{
        String filename1 = "C:/amine/amine_59.mol";
        
        InputStream ins =InputStream.class.getClass().getClassLoader().getResourceAsStream(filename1);
        MDLReader reader = new MDLReader(ins);
    String filename2 = "C:/acide/acide_1.mol";
        InputStream in =InputStream.class.getClass().getClassLoader().getResourceAsStream(filename2);
        MDLReader read = new MDLReader(in);
        BioPolymer crambin = ProteinBuilderTool.createProtein( filename1+filename2 );
        System.out.println("Crambin has " + crambin.getAtomCount() +" atoms.");
}
}the error is java.lang.NullPointerExceptioni wate your answer please 
thanks
 

    Le Vendredi 29 avril 2016 17h06, John M <joh...@gm...> a écrit :
 

 Hi Hanouna,
Sorry I didn't see your other messages, they were marked as spam due the writing style and yahoo.fr authentication failures.
If you're still having trouble building/using the CDK in an IDE (e.g. Eclipse) I put together a guide here: https://github.com/cdk/cdk/wiki/Building-CDK
I've you're new CDK you should use the least release 1.5.14. Also there are more relevant pages/updates on the GitHub wiki.
John 
Regards,
John W May 
joh...@gm...
On 27 April 2016 at 19:39, hanouna nouna <han...@ya...> wrote:

hello 
i have to create an amino acide from a library of fragment acide and a library of fragments amine if you can help me with packages of CDK that i have to use that will be a big pleasur to me 
and thank you so mutch