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
<http://www.pistoiaalliance.org/projects/hierarchical-editing-language-for-macromolecules-helm/>
.
Unfortunately both of these are rather involved.
- John
Regards,
John W May
john.wilkinson...@gmail.com
On 1 May 2016 at 19:23, hanouna nouna <hanounanouna...@yahoo.fr> 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 error
> import 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.NullPointerException
> i wate your answer please
> thanks
>
>
> Le Vendredi 29 avril 2016 17h06, John M <john.wilkinson...@gmail.com> 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
> john.wilkinson...@gmail.com
>
> On 27 April 2016 at 19:39, hanouna nouna <hanounanouna...@yahoo.fr> 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
>
>
>
>
>
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