Do you have an example of an amine and acid you want to make an amino acid
out of?
Regards,
John W May
john.wilkinson...@gmail.com
On 2 May 2016 at 20:36, hanouna nouna <hanounanouna...@yahoo.fr> 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 <john.wilkinson...@gmail.com> 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
> <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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