belka.parser
Class PDBParser

java.lang.Object
  extended by belka.parser.PDBParser

public class PDBParser
extends Object

Object of this class parses PDB-file either from file or from URL and creates a molecule. Filename is used as a name for new molecule.

Author:
Alexej Abyzov

Constructor Summary
PDBParser()
           
 
Method Summary
 Molecule[] parseFile(File file)
          Parses PDB-file and creates a molecule.
 Molecule[] parseFile(URL urlFileName)
          Parses PDB-file from URL and creates molecules.
 StringBuffer print(Molecule[] molsToSave)
          Prints PDB-file to a string buffer.
 int saveToFile(Molecule[] molsToSave, File file)
          Saves molecules into a PDB-file.
 int saveToFile(Molecule[] molsToSave, URL urlFileName)
          Saves moleculs into a PDB-file.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PDBParser

public PDBParser()
Method Detail

saveToFile

public int saveToFile(Molecule[] molsToSave,
                      URL urlFileName)
Saves moleculs into a PDB-file.

Parameters:
molsToSave - array of molecules to be save.
urlFileName - name of file on the web to save.
Returns:
number of atoms saved. Negative if error happend.

saveToFile

public int saveToFile(Molecule[] molsToSave,
                      File file)
Saves molecules into a PDB-file.

Parameters:
molsToSave - array of molecules to be save.
file - name of file to save.
Returns:
number of atoms saved. Negative if error happend.

print

public StringBuffer print(Molecule[] molsToSave)
Prints PDB-file to a string buffer.

Returns:
string buffer with PDB-file.

parseFile

public Molecule[] parseFile(File file)
Parses PDB-file and creates a molecule.

Parameters:
file - file to parse
Returns:
new molecules.

parseFile

public Molecule[] parseFile(URL urlFileName)
Parses PDB-file from URL and creates molecules.

Parameters:
urlFileName - name of file on URL;
Returns:
new molecules.