org.biojava.bio.structure
Class StructureTools

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

public class StructureTools
extends java.lang.Object

A class that provides some tool methods.

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

Field Summary
static java.lang.String[] backboneAtomNames
          The names of the Atoms that form the backbone.
static java.lang.String caAtomName
          The Atom name of C-alpha atoms.
static java.util.logging.Logger logger
           
static java.lang.Character UNKNOWN_GROUP_LABEL
           
 
Constructor Summary
StructureTools()
           
 
Method Summary
static java.lang.Character convert_3code_1code(java.lang.String code3)
          convert three character amino acid codes into single character e.g.
static java.lang.Character get1LetterCode(java.lang.String groupCode3)
          convert a three letter code into single character.
static Atom[] getAtomArray(Structure s, java.lang.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.
static int getNrAtoms(Structure s)
          Count how many number of Atoms are contained within a Structure object.
static int getNrGroups(Structure s)
          Count how many groups are contained within a structure object.
static boolean isNucleotide(java.lang.String groupCode3)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

caAtomName

public static final java.lang.String caAtomName
The Atom name of C-alpha atoms.

See Also:
Constant Field Values

backboneAtomNames

public static final java.lang.String[] backboneAtomNames
The names of the Atoms that form the backbone.


UNKNOWN_GROUP_LABEL

public static final java.lang.Character UNKNOWN_GROUP_LABEL

logger

public static java.util.logging.Logger logger
Constructor Detail

StructureTools

public StructureTools()
Method Detail

getNrAtoms

public static int getNrAtoms(Structure s)
Count how many number of Atoms are contained within a Structure object.

Parameters:
s - the structure object
Returns:
the number of Atoms in this Structure

getNrGroups

public static int getNrGroups(Structure s)
Count how many groups are contained within a structure object.

Parameters:
s - the structure object
Returns:
the number of groups in the structure

getAtomArray

public static Atom[] getAtomArray(Structure s,
                                  java.lang.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 - the structure object
Returns:
an Atom[] array

getBackboneAtomArray

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

Parameters:
s - the structure object
Returns:
an Atom[] array

convert_3code_1code

public static java.lang.Character convert_3code_1code(java.lang.String code3)
                                               throws IllegalSymbolException
convert three character amino acid codes into single character e.g. convert CYS to C

Parameters:
code3 - a three character amino acid representation String
Returns:
a character
Throws:
IllegalSymbolException

get1LetterCode

public static java.lang.Character get1LetterCode(java.lang.String groupCode3)
convert a three letter code into single character. catches for unusual characters

Parameters:
groupCode3 - three letter representation
Returns:
null if group is a nucleotide code

isNucleotide

public static boolean isNucleotide(java.lang.String groupCode3)