[Biojava-l] modify structure

Fri Dec 2 08:23:04 EST 2005

Just to be more clear:I store the AminoAcides as HashMap<String,Group> where 1 group contains 1AA, and the String is the name of the AA. (I prefer 1 letter code there)
To shift the desired AA in place, I'd match the Cb atomsThen rotate the AA so that the Ca-Cb line would matchThen rotate the AA so that the N-Ca-Cb pane matches (In this case it's equalto the N-Ca line match)
After this, the AA would be roughly in place.
After this there may should be a collision test, but I think that part canbe handeled by the GROMACS package, which I'd ther run anyway to see how themutation effects the structure.
On 12/2/05, Tamas Horvath <hotafin at gmail.com> wrote:>> Thanks for the codes! I've noticed the methods in Calc, but my main> question is the following. Let's say I've got a primitive library of> AminoAcides. They stored as a group, they have all the atoms. When I'm> mutating the chain, I want to keep the backbone atoms in place, so as far as> your mutate method goes it's ok. But now I want to replace the sidechain. In> order to do that, I'd shift and rotate the desired AA in place (Cbs would be> identical and the other backbone atoms as close as possible), and then copy> the sidechain atoms to the mutated AA... (I hope that's clear)>> So do I have to wrap my Group objects to a Chain/Structure object in order> to shift and rotate them?>> I don't really get how the rotation is supposed to work... what is exactly> the matrix it asks for?>> On 12/2/05, Andreas Prlic <ap3 at sanger.ac.uk> wrote:> >> > Hi Tamas!> >> >> > > If I've got a Group , which is an amino acid, and I want to shift it> > > by a 3D vector (or 3 2D vectors), how may I do it?> >> > There is the org.biojava.bio.structure.Calc class that allows to do> > calculations with the structure.> >> > e.g. to shift a structure do:> >> >> >                  double x = 2.0;> >                  double y = 0.2;> >                  double z = 12.3;> >> >                  Atom vector = new AtomImpl();> >                  vector.setX(x);> >                  vector.setY(y);> >                  vector.setZ(z);> >> >                  // shift the structure.> >                  Calc.shift(structure,vector);> >> >> >> > >  Similarly, if i want to rotate the same structure, how may I do it?> >> >               double[][] matrix = new double[3][3];> >> >                  matrix[0][0] = 0.1;> >                  matrix[0][1] = 0.2;> >                  matrix[0][2] = 0.3;> >                  matrix[1][0] = 0.4;> >                  matrix[1][1] = 0.5;> >                  matrix[1][2] = 0.6;> >                  matrix[2][0] = 0.7;> >                  matrix[2][1] = 0.8;> >                  matrix[2][2] = 0.9;> >> >                  Calc.rotate(structure,matrix);> >> >> > And here is an example regarding your questions from yesterday,> > how to do mutations. most of the code actually deals with finding the> > right  chain and residue.> > I will add the "mutator" class to cvs,  so in future doing mutations> > will be a two liner...> >> > Cheers,> > Andreas> >> >> > /*> >   *                  BioJava development code> >   *> >   * This code may be freely distributed and modified under the> >   * terms of the GNU Lesser General Public Licence.  This should> >   * be distributed with the code.  If you do not have a copy,> >   * see:> >   *> >   *      http://www.gnu.org/copyleft/lesser.html> >   *> >   * Copyright for this code is held jointly by the individual> >   * authors.  These should be listed in @author doc comments.> >   *> >   * For more information on the BioJava project and its aims,> >   * or to join the biojava-l mailing list, visit the home page> >   * at:> >   *> >   *      http://www.biojava.org/> >   *> >   * Created on Nov 30, 2005> >   *> >   */> >> > import java.io.FileOutputStream;> > import java.io.PrintStream;> > import java.util.ArrayList;> > import java.util.Iterator;> > import java.util.List;> >> > import org.biojava.bio.structure.AminoAcid;> > import org.biojava.bio.structure.AminoAcidImpl;> > import org.biojava.bio.structure.Atom;> > import org.biojava.bio.structure.AtomIterator;> > import org.biojava.bio.structure.Chain;> > import org.biojava.bio.structure.ChainImpl;> > import org.biojava.bio.structure.Group;> > import org.biojava.bio.structure.Structure ;> > import org.biojava.bio.structure.StructureImpl;> > import org.biojava.bio.structure.io.PDBFileReader;> > import org.biojava.bio.structure.io.PDBParseException;> >> >> > public class structureTest {> >> >      public structureTest() {> >          super();> >> >      }> >> >      public static void main (String[] args){> >          String filename   =  "/Users/ap3/WORK/PDB/5pti.pdb" ;> >          String outputfile =  "/Users/ap3/WORK/PDB/mutated.pdb" ;> >> >          PDBFileReader pdbreader = new PDBFileReader();> >> >          try{> >                  Structure struc = pdbreader.getStructure(filename);> >                  System.out.println(struc);> >> >> >                  String chainId = " ";> >                  String pdbResnum = "2";> >                  String newType = "ARG";> >> >                  // mutate the original structure and create a new one.> >                  Mutator m = new Mutator();> >                  Structure newstruc => > m.mutate(struc,chainId,pdbResnum,newType);> >> >                  FileOutputStream out= new FileOutputStream(outputfile);> >                  PrintStream p =  new PrintStream( out );> >> >                  p.println (newstruc.toPDB());> >> >                  p.close();> >> >> >          } catch (Exception e) {> >              e.printStackTrace();> >          }> >      }> > }> >> > class Mutator{> >      List supportedAtoms;> >> >      public Mutator(){> >          supportedAtoms = new ArrayList();> >          supportedAtoms.add("N");> >          supportedAtoms.add("CA");> >          supportedAtoms.add ("C");> >          supportedAtoms.add("O");> >          supportedAtoms.add("CB");> >      }> >> >      /** creates a new structure which is identical with the original> > one.> >       * only one amino acid will be different.> >       *> >       * @param struc> >       * @param chainId> >       * @param pdbResnum> >       * @param newType> >       * @return> >       * @throws PDBParseException> >       */> >      public Structure  mutate(Structure struc, String chainId, String> > pdbResnum, String newType)> >      throws PDBParseException{> >> >> >          // create a  container for the new structure> >          Structure newstruc = new StructureImpl();> >> >          // first we need to find our corresponding chain> >> >          // get the chains for model nr. 0> >          // if structure is xray there will be only one "model".> >          List chains = struc.getChains(0);> >> >          // iterate over all chains.> >          Iterator iter = chains.iterator();> >          while (iter.hasNext()){> >              Chain c = (Chain)iter.next();> >              if (c.getName().equals(chainId)) {> >                  // here is our chain!> >> >                  Chain newchain = new ChainImpl();> >                  newchain.setName(c.getName());> >> >                   List groups = c.getGroups();> >> >                  // now iterate over all groups in this chain.> >                  // in order to find the amino acid that has this> > pdbRenum.> >> >                  Iterator giter = groups.iterator();> >                  while (giter.hasNext()){> >                      Group g = (Group) giter.next();> >                      String rnum = g.getPDBCode();> >> >                      // we only mutate amino acids> >                      // and ignore hetatoms and nucleotides in this case> >                      if ( rnum.equals(pdbResnum) &&> > (g.getType().equals("amino"))){> >> >                          // create the mutated amino acid and add it to> > our new chain> >                          AminoAcid newgroup => > mutateResidue((AminoAcid)g,newType);> >                          newchain.addGroup(newgroup);> >                      }> >                      else {> >                          // add the group  to the new chain unmodified.> >                          newchain.addGroup(g);> >                      }> >                  }> >> >                  // add the newly constructed chain to the structure;> >                  newstruc.addChain(newchain);> >              } else {> >                  // this chain is not requested, add it to the new> > structure unmodified.> >                  newstruc.addChain(c);> >              }> >> >          }> >          return newstruc;> >      }> >> >      /** create a new residue which is of the new type.> >       * Only the atoms N, Ca, C, O, Cb will be considered.> >       * prolines are not mutated...> >       * @param oldAmino> >       * @param newType> >       * @return> >       */> >      public AminoAcid mutateResidue(AminoAcid oldAmino, String newType)> >      throws PDBParseException {> >> >          AminoAcid newgroup = new AminoAcidImpl();> >> >          newgroup.setPDBCode (oldAmino.getPDBCode());> >          newgroup.setPDBName(newType);> >> >> >          AtomIterator aiter =new AtomIterator(oldAmino);> >          while (aiter.hasNext()){> >              Atom a = (Atom)aiter.next();> >              if ( supportedAtoms.contains(a.getName())){> >                  newgroup.addAtom(a);> >              }> >          }> >> >          return newgroup;> >> >      }> >> > }> >> > -----------------------------------------------------------------------> >> > Andreas Prlic      Wellcome Trust Sanger Institute> >                                Hinxton, Cambridge CB10 1SA, UK> >                          +44 (0) 1223 49 6891> >> > _______________________________________________> > Biojava-l mailing list  -  Biojava-l at biojava.org> > http://biojava.org/mailman/listinfo/biojava-l> >>>