Okay,
But there's no COOH in the Lidociane example...? It's certainly possible to
do what you want but you'll need to do it manually by deleting/adding bonds.
Here's a rough idea:
https://gist.github.com/johnmay/9c814049688cc905c806b9738212809b
> import org.openscience.cdk.exception.CDKException;
> import org.openscience.cdk.interfaces.IAtom;
> import org.openscience.cdk.interfaces.IAtomContainer;
> import org.openscience.cdk.interfaces.IBond;
> import org.openscience.cdk.interfaces.IChemObjectBuilder;
> import org.openscience.cdk.isomorphism.Pattern;
> import org.openscience.cdk.silent.SilentChemObjectBuilder;
> import org.openscience.cdk.smiles.SmilesGenerator;
> import org.openscience.cdk.smiles.SmilesParser;
> import org.openscience.cdk.smiles.smarts.SmartsPattern;
> import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
>
> import java.io.IOException;
> import java.util.ArrayList;
> import java.util.Arrays;
> import java.util.List;
>
> public class CreateAminoAcid {
>
> private static final IChemObjectBuilder BLDR =
> SilentChemObjectBuilder.getInstance();
>
> private static final Pattern AMINE_PATTERN;
> private static final Pattern ACID_PATTERN;
>
> static {
> try {
> AMINE_PATTERN = SmartsPattern.create("[NX3v3h2]", null);
> ACID_PATTERN = SmartsPattern.create("[OX2v2H1][CX3v4]=[OX1v2H0]",
> null);
> } catch (IOException ex) {
> throw new InstantiationError("Bad SMARTS!" + ex.getMessage());
> }
> }
>
> private static List<IAtomContainer> fuse(IAtomContainer amine,
> IAtomContainer acid) throws
>
> CloneNotSupportedException {
>
> // optional
> AtomContainerManipulator.suppressHydrogens(amine);
> AtomContainerManipulator.suppressHydrogens(acid);
>
> List<IAtomContainer> result = new ArrayList<>();
>
> int[][] amineHits =
> AMINE_PATTERN.matchAll(amine).uniqueAtoms().toArray();
> int[][] acidHits =
> ACID_PATTERN.matchAll(acid).uniqueAtoms().toArray();
>
>
> for (int[] amineHit : amineHits) {
> for (int[] acidHit : acidHits) {
> IAtomContainer fused = amine.clone();
> fused.add(acid.clone());
>
> IAtom nAtom = fused.getAtom(amineHit[0]);
> IAtom oAtom = fused.getAtom(amine.getAtomCount() +
> acidHit[0]);
> IAtom cAtom = fused.getAtom(amine.getAtomCount() +
> acidHit[1]);
>
> // 1. remove bond and adjust N valence
> // XXX: this can be much faster by moving to the back first
> and then deleting
> fused.removeAtomAndConnectedElectronContainers(oAtom);
>
> nAtom.setImplicitHydrogenCount(nAtom.getImplicitHydrogenCount()-1);
>
> // This looks confusion but is essentially: 'new Bond(nAtom,
> cAtom, SINGLE)' using a factory
> // (or builder as called here)
> fused.addBond(BLDR.newInstance(IBond.class, nAtom, cAtom,
> IBond.Order.SINGLE));
>
> result.add(fused);
> }
> }
>
> return result;
> }
>
> public static void main(String[] args) throws CDKException,
> CloneNotSupportedException {
>
>
> SmilesParser smipar = new SmilesParser(BLDR);
> SmilesGenerator smigen = SmilesGenerator.isomeric();
>
> // input list of amines/acids
> List<String> amines = Arrays.asList("CC1=CC=CC(C)=C1N");
> List<String> acids = Arrays.asList("CC(O)=O");
>
> for (String amine : amines) {
> for (String acid : acids) {
> IAtomContainer amineMol = smipar.parseSmiles(amine);
> IAtomContainer acidMol = smipar.parseSmiles(acid);
>
> for (IAtomContainer fused : fuse(amineMol, acidMol)) {
> System.out.println(smigen.create(fused));
> }
> }
> }
>
> }
> }
>
>
Regards,
John W May
john.wilkinson...@gmail.com
On 2 May 2016 at 22:38, hanouna nouna <hanounanouna...@yahoo.fr> wrote:
> yes somthing like that, i have to break the double bound between C and O
> from the COOH and the H from NH2 to create the novel amino acide similar to
> Lidociane if you can take me wich package i use to break theme in CDK
>
>
> Le Lundi 2 mai 2016 23h18, John M <john.wilkinson...@gmail.com> a écrit :
>
>
> Okay, but what's the input?
>
> For example for Lidocaine, it looks like a two step synthesis, it's not
> simply just combined a random amine and acid:
> [image: Inline images 4][image: Inline images 5]
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 2 May 2016 at 21:09, hanouna nouna <hanounanouna...@yahoo.fr> wrote:
>
> yes, i have to create an amino acide similar to Lidociane or to
> furano-pyrimidine
>
>
> Le Lundi 2 mai 2016 21h48, John M <john.wilkinson...@gmail.com> 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
> 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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