org.biojava.bio.structure
Class StructureTools

java.lang.Object
  extended by org.biojava.bio.structure.StructureTools

public class StructureTools
extends Object

a class that provides some tool methods

Since:
1.0
Version:
%I% %G%
Author:
Andreas Prlic

Field Summary
static String[] backboneAtomNames
           
static String caAtomName
           
 
Constructor Summary
StructureTools()
           
 
Method Summary
static Atom[] getAtomArray(Structure s, String[] atomNames)
          returns an array of the requested Atoms from the Structure object.
static Atom[] getAtomCAArray(Structure s)
          returns an Atom array of the CA atoms
static Atom[] getBackboneAtomArray(Structure s)
          returns an Atom array of the MainChain atoms
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

caAtomName

public static final String caAtomName
See Also:
Constant Field Values

backboneAtomNames

public static final String[] backboneAtomNames
Constructor Detail

StructureTools

public StructureTools()
Method Detail

getAtomArray

public static Atom[] getAtomArray(Structure s,
                                  String[] atomNames)
returns an array of the requested Atoms from the Structure object. Iterates over all groups and checks if the requested atoms are in this group, no matter if this is a AminoAcid or Hetatom group.

Parameters:
s - the structure to get the atoms from
atomNames - contains the atom names to be used.
Returns:
an Atom[] array

getAtomCAArray

public static Atom[] getAtomCAArray(Structure s)
returns an Atom array of the CA atoms

Parameters:
s -
Returns:
an Atom[] array

getBackboneAtomArray

public static Atom[] getBackboneAtomArray(Structure s)
returns an Atom array of the MainChain atoms

Parameters:
s -
Returns:
an Atom[] array