org.biojava.bio.structure
Class StructureTools

java.lang.Object
  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 The names of the Atoms that form the backbone.
static String	caAtomName The Atom name of C-alpha atoms.
static Logger	logger
static Character	UNKNOWN_GROUP_LABEL

Constructor Summary

StructureTools()

Method Summary

static Character	convert_3code_1code(String code3) convert three character amino acid codes into single character e.g.
static Character	get1LetterCode(String groupCode3) convert a three letter code into single character.
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.
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(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 String caAtomName

The Atom name of C-alpha atoms.

See Also:

Constant Field Values

backboneAtomNames

public static final String[] backboneAtomNames

The names of the Atoms that form the backbone.

UNKNOWN_GROUP_LABEL

public static final Character UNKNOWN_GROUP_LABEL

logger

public static 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,
                                  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 Character convert_3code_1code(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 Character get1LetterCode(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(String groupCode3)