[Biojava-l] modify structure
Andreas Prlic
ap3 at sanger.ac.uk
Fri Dec 2 05:17:49 EST 2005
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
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*
* 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
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