How you can Protein Data Bank PDB Structure Mutation Model Tool Java code Script Biojava you can mutate file using following code
package pdb;
import java.io.FileOutputStream;
import java.io.PrintStream;
import org.biojava.bio.structure.Mutator;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.io.PDBFileReader;
/**
*
* @author Usman
*/
public class Mutate {
public static void main(String[] args) {
String ProjectPath= System.getProperties().getProperty("user.dir");
String filename = ProjectPath+"/SamplePDB/12E8.pdb" ;
String outputfile = ProjectPath+"/SamplePDB/mutated.pdb" ;
PDBFileReader pdbreader = new PDBFileReader();
try{
Structure struc = pdbreader.getStructure(filename);
System.out.println(struc);
String chainId = " ";
String pdbResnum = "3";
String newType = "ARG";
// mutate the original structure and create a new one.
// lets side chain point into the same direction, but only uses Cb atom
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();
}
}
}
package pdb;
import java.io.FileOutputStream;
import java.io.PrintStream;
import org.biojava.bio.structure.Mutator;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.io.PDBFileReader;
/**
*
* @author Usman
*/
public class Mutate {
public static void main(String[] args) {
String ProjectPath= System.getProperties().getProperty("user.dir");
String filename = ProjectPath+"/SamplePDB/12E8.pdb" ;
String outputfile = ProjectPath+"/SamplePDB/mutated.pdb" ;
PDBFileReader pdbreader = new PDBFileReader();
try{
Structure struc = pdbreader.getStructure(filename);
System.out.println(struc);
String chainId = " ";
String pdbResnum = "3";
String newType = "ARG";
// mutate the original structure and create a new one.
// lets side chain point into the same direction, but only uses Cb atom
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();
}
}
}
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