org.biojava.bio.structure

Class StructureTools

java.lang.Object

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, Jules Jacobsen

Field Summary

Fields

Modifier and Type	Field and Description
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.lang.String	cbAtomName
static java.util.logging.Logger	logger
static java.lang.String	nAtomName
static java.lang.String	oAtomName
static java.util.regex.Pattern	pdbNumRangeRegex Pattern to describe subranges.
static java.lang.Character	UNKNOWN_GROUP_LABEL

Constructor Summary

Constructors

Constructor and Description
StructureTools()

Method Summary

Methods

Modifier and Type	Method and Description
static Atom[]	cloneCAArray(Atom[] ca) Provides an equivalent copy of Atoms in a new array.
static Group[]	cloneGroups(Atom[] ca) Clone a set of CA Atoms, but returns the parent groups
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.String	convertAtomsToSeq(Atom[] atoms)
static Atom[]	duplicateCA2(Atom[] ca2) Utility method for working with circular permutations.
static java.util.List<Bond>	findBonds(Group group, java.util.List<Group> groups)
static java.lang.Character	get1LetterCode(java.lang.String groupCode3) convert a three letter code into single character.
static Atom[]	getAllAtomArray(Structure s) Convert all atoms of the structure (first model) into an Atom array
static Atom[]	getAtomArray(Chain c, java.lang.String[] atomNames) Returns an array of the requested Atoms from the Structure object.
static Atom[]	getAtomArray(Structure s, java.lang.String[] atomNames) Returns an array of the requested Atoms from the Structure object.
static Atom[]	getAtomArrayAllModels(Structure s, java.lang.String[] atomNames) Returns an array of the requested Atoms from the Structure object.
static Atom[]	getAtomCAArray(Chain c) Returns an Atom array of the CA atoms.
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 Group	getGroupByPDBResidueNumber(Structure struc, ResidueNumber pdbResNum) Get a group represented by a ResidueNumber.
static java.util.List<Group>	getGroupsWithinShell(Structure structure, Group group, double distance, boolean includeWater)
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 ResidueNumber	getPDBResidueNumber(Group g) Deprecated. replaced by Group.getResidueNumber()
static Structure	getReducedStructure(Structure s, int chainNr) Reduce a structure to provide a smaller representation.
static Structure	getReducedStructure(Structure s, java.lang.String chainId) Reduce a structure to provide a smaller representation .
static Structure	getSubRanges(Structure s, java.lang.String ranges) In addition to the functionality provided by getReducedStructure also provides a way to specify sub-regions of a structure with the following specification: ranges can be surrounded by ( and ).
static boolean	isNucleotide(java.lang.String groupCode3)
static Structure	removeModels(Structure s) Remove all models from a Structure and keep only the first

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

nAtomName

public static final java.lang.String nAtomName

See Also:

Constant Field Values

oAtomName

public static final java.lang.String oAtomName

See Also:

Constant Field Values

cbAtomName

public static final java.lang.String cbAtomName

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

pdbNumRangeRegex

public static final java.util.regex.Pattern pdbNumRangeRegex

Pattern to describe subranges. Matches "A", "A:", "A:7-53","A_7-53", etc.

See Also:

getSubRanges(Structure, String)

Constructor Detail

StructureTools

public StructureTools()

Method Detail

getNrAtoms

public static final 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 final 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 final 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 HetatomImpl group. For structures with more than one model, only model 0 will be used.

Parameters:

s - the structure to get the atoms from

atomNames - contains the atom names to be used.

Returns:

an Atom[] array

getAtomArrayAllModels

public static final Atom[] getAtomArrayAllModels(Structure s,
                           java.lang.String[] atomNames)

Returns an array of the requested Atoms from the Structure object. In contrast to getAtomArray(Structure, String[]) this method iterates over all chains. Iterates over all chains and groups and checks if the requested atoms are in this group, no matter if this is a AminoAcid or HetatomImpl group. For structures with more than one model, only model 0 will be used.

Parameters:

s - the structure to get the atoms from

atomNames - contains the atom names to be used.

Returns:

an Atom[] array

getAllAtomArray

public static final Atom[] getAllAtomArray(Structure s)

Convert all atoms of the structure (first model) into an Atom array

Parameters:

s - input structure

Returns:

all atom array

getAtomArray

public static final Atom[] getAtomArray(Chain c,
                  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:

c - the Chain to get the atoms from

atomNames - contains the atom names to be used.

Returns:

an Atom[] array

getAtomCAArray

public static final Atom[] getAtomCAArray(Chain c)

Returns an Atom array of the CA atoms.

Parameters:

c - the structure object

Returns:

an Atom[] array

cloneCAArray

public static final Atom[] cloneCAArray(Atom[] ca)
                                 throws StructureException

Provides an equivalent copy of Atoms in a new array. Clones everything, starting with parent groups and chains. The chain will only contain groups that are part of the CA array.

Parameters:

ca - array of CA atoms

Returns:

Atom array

Throws:

StructureException

cloneGroups

public static Group[] cloneGroups(Atom[] ca)

Clone a set of CA Atoms, but returns the parent groups

Parameters:

ca - Atom array

Returns:

Group array

duplicateCA2

public static Atom[] duplicateCA2(Atom[] ca2)
                           throws StructureException

Utility method for working with circular permutations. Creates a duplicated and cloned set of Calpha atoms from the input array.

Parameters:

ca2 - atom array

Returns:

cloned and duplicated set of input array

Throws:

StructureException

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 final java.lang.Character convert_3code_1code(java.lang.String code3)
                                                     throws UnknownPdbAminoAcidException

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

UnknownPdbAminoAcidException

get1LetterCode

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

getReducedStructure

public static final Structure getReducedStructure(Structure s,
                            java.lang.String chainId)
                                           throws StructureException

Reduce a structure to provide a smaller representation . Only takes the first model of the structure. If chainId is provided only return a structure containing that Chain ID. Converts lower case chain IDs to upper case if structure does not contain a chain with that ID.

Parameters:

s -

chainId -

Returns:

Structure

Throws:

StructureException

Since:

3.0

getReducedStructure

public static final Structure getReducedStructure(Structure s,
                            int chainNr)
                                           throws StructureException

Reduce a structure to provide a smaller representation. Only takes the first model of the structure. If chainNr >=0 only takes the chain at that position into account.

Parameters:

s -

chainNr - can be -1 to request all chains of model 0, otherwise will only add chain at this position

Returns:

Structure object

Throws:

StructureException

Since:

3.0

getSubRanges

public static final Structure getSubRanges(Structure s,
                     java.lang.String ranges)
                                    throws StructureException

In addition to the functionality provided by getReducedStructure also provides a way to specify sub-regions of a structure with the following specification: ranges can be surrounded by ( and ). (but will be removed). ranges are specified as PDBresnum1 : PDBresnum2 a list of ranges is separated by , Example 4GCR (A:1-83) 1CDG (A:407-495,A:582-686) 1CDG (A_407-495,A_582-686)

Parameters:

s - The full structure

ranges - A comma-seperated list of ranges, optionally surrounded by parentheses

Returns:

Substructure of s specified by ranges

Throws:

StructureException

convertAtomsToSeq

public static final java.lang.String convertAtomsToSeq(Atom[] atoms)

getPDBResidueNumber

public static final ResidueNumber getPDBResidueNumber(Group g)

Deprecated. replaced by Group.getResidueNumber()

get a PDB residue number object for this group

Parameters:

g - Group object

Returns:

a ResidueNumber object

getGroupByPDBResidueNumber

public static final Group getGroupByPDBResidueNumber(Structure struc,
                               ResidueNumber pdbResNum)
                                              throws StructureException

Get a group represented by a ResidueNumber.

Parameters:

struc - a Structure

pdbResNum - a ResidueNumber

Returns:

a group in the structure that is represented by the pdbResNum.

Throws:

StructureException - if the group cannot be found.

getGroupsWithinShell

public static java.util.List<Group> getGroupsWithinShell(Structure structure,
                                         Group group,
                                         double distance,
                                         boolean includeWater)

findBonds

public static java.util.List<Bond> findBonds(Group group,
                             java.util.List<Group> groups)

removeModels

public static Structure removeModels(Structure s)

Remove all models from a Structure and keep only the first

Parameters:

s - original Structure

Returns:

a structure that contains only the first model

Since:

3.0.5