org.biojava.bio.structure

Interface Group

All Known Subinterfaces:

AminoAcid

All Known Implementing Classes:

AminoAcidImpl, HetatomImpl, NucleotideImpl, SecStrucGroup

public interface Group

This is the data structure for a single Group of atoms. A protein sequence (Chain in PDB file) is represented as a list of Groups. There are 3 types of Groups:

• AminoAcid
• Hetatom
• Nucleotide

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic, Horvath Tamas

See Also:

HetatomImpl, AminoAcidImpl, NucleotideImpl

Method Summary

Methods

Modifier and Type	Method and Description
void	addAltLoc(Group g) Add a group that is an alternate location for this group.
void	addAtom(Atom atom) add an atom to this group.
void	clearAtoms() Remove all atoms from this group.
java.lang.Object	clone() returns and identical copy of this Group object .
Group	getAltLocGroup(java.lang.Character altLoc) Gets the alternate location group to this group that has the alt-loc character code passed.
java.util.List<Group>	getAltLocs() Get the list of alternate locations.
Atom	getAtom(int position) Get at atom by position.
Atom	getAtom(java.lang.String name) Get an atom.
Atom	getAtomByPDBname(java.lang.String pdbName) Get an atom by the full PDB name e.g.
java.util.List<Atom>	getAtoms() Get list of atoms.
Chain	getChain() Returns the parent Chain of the Group.
java.lang.String	getChainId() Utility method for returning the chainId of the Group or null if no Chain has been set.
ChemComp	getChemComp() Get the chemical component that closer describes this group.
Chain	getParent() Deprecated. replaced by getChain()
java.lang.String	getPDBCode() Deprecated. replaced by getResidueNumber()
java.lang.String	getPDBName() Get the PDB 3 character name for this group.
java.util.Map<java.lang.String,java.lang.Object>	getProperties() return properties.
java.lang.Object	getProperty(java.lang.String key) get a single property .
ResidueNumber	getResidueNumber() returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
java.lang.String	getType() get Type of group, e.g.
boolean	has3D() returns true or false, depending if this group has 3D coordinates or not.
boolean	hasAltLoc() Test if this group has alternate locations.
boolean	hasAminoAtoms() calculate if a groups has all atoms required for an amino acid.
boolean	hasAtom(java.lang.String name) Teturns flag whether a particular atom is existing within this group .
boolean	isWater() Determines if this group is water.
java.util.Iterator<Atom>	iterator() get an Atom Iterator.
void	setAtoms(java.util.List<Atom> atoms) Set the atoms of this group.
void	setChain(Chain chain) Sets the back-reference to its parent Chain.
void	setChemComp(ChemComp cc) Set the Chemical Component that closer describes this group.
void	setParent(Chain parent) Deprecated.
void	setPDBCode(java.lang.String pdbcode) Deprecated. replaced by setResidueNumber(ResidueNumber)
void	setPDBFlag(boolean flag) flag if group has 3D data .
void	setPDBName(java.lang.String s) Set the PDB 3 letter name for this group.
void	setProperties(java.util.Map<java.lang.String,java.lang.Object> properties) properties of this amino acid.
void	setProperty(java.lang.String key, java.lang.Object value) set a single property .
void	setResidueNumber(ResidueNumber residueNumber) sets the ResidueNumber for this Group
void	setResidueNumber(java.lang.String chainId, java.lang.Integer residueNumber, java.lang.Character iCode) Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet.
int	size() getnumber of atoms.
void	trimToSize() attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.

Method Detail

getPDBCode

@Deprecated
java.lang.String getPDBCode()

Deprecated. replaced by getResidueNumber()

Return the PDBcode (residue number + insertion code ) of this group. The residue number is treated as a String for the following reasons: Every amino acid in a PDB file is identified uniquely by 3 things: The chain ID, the residue number and the insertion code. To make sure one does not forget about the insertion code, in BioJava it is appended to the residue number. To add to this, residue numbers can be negative, non-consecutive and also non-sequential. As such it is often easiest, to treat them as public identifiers and within your own code work with the internal atom or group positions...

Returns:

a String representing the PDBCode value

See Also:

setPDBCode(java.lang.String)

setPDBCode

@Deprecated
void setPDBCode(java.lang.String pdbcode)

Deprecated. replaced by setResidueNumber(ResidueNumber)

Specifies the PDBCode (residue number + insertion code) value.

Parameters:

pdbcode - a String specifying the PDBCode value

See Also:

getPDBCode()

size

int size()

getnumber of atoms.

Returns:

number of atoms of this Group

has3D

boolean has3D()

returns true or false, depending if this group has 3D coordinates or not.

Returns:

true if Group has 3D coordinates

setPDBFlag

void setPDBFlag(boolean flag)

flag if group has 3D data .

Parameters:

flag - true to set flag that this Group has 3D coordinates

getType

java.lang.String getType()

get Type of group, e.g. amino, hetatom, nucleotide.

Returns:

a String representing the type value

addAtom

void addAtom(Atom atom)

add an atom to this group.

Parameters:

atom - an Atom object

getAtoms

java.util.List<Atom> getAtoms()

Get list of atoms.

Returns:

an List object representing the atoms

See Also:

setAtoms(List)

setAtoms

void setAtoms(java.util.List<Atom> atoms)

Set the atoms of this group.

Parameters:

atoms - a list of atoms

See Also:

Atom

clearAtoms

void clearAtoms()

Remove all atoms from this group.

getAtom

Atom getAtom(java.lang.String name)
             throws StructureException

Get an atom. Throws StructureException if atom not found.

Parameters:

name - a String

Returns:

an Atom object

Throws:

StructureException - if atom not found.

getAtomByPDBname

Atom getAtomByPDBname(java.lang.String pdbName)
                      throws StructureException

Get an atom by the full PDB name e.g. " N " for N. Throws StructureException if atom not found.

Parameters:

pdbName - a String

Returns:

an Atom object

Throws:

StructureException - ...

getAtom

Atom getAtom(int position)
             throws StructureException

Get at atom by position.

Parameters:

position - an int

Returns:

an Atom object

Throws:

StructureException - if not atom at this position

hasAtom

boolean hasAtom(java.lang.String name)

Teturns flag whether a particular atom is existing within this group .

Parameters:

name - a String ...

Returns:

true if Atom with name is existing within this group

getPDBName

java.lang.String getPDBName()

Get the PDB 3 character name for this group. (e.g. ALA)

Returns:

a String representing the PDBName value

See Also:

setPDBName(java.lang.String)

setPDBName

void setPDBName(java.lang.String s)
                throws PDBParseException

Set the PDB 3 letter name for this group. (e.g. ALA)

Parameters:

s - a String specifying the PDBName value

Throws:

PDBParseException - ...

See Also:

getPDBName()

hasAminoAtoms

boolean hasAminoAtoms()

calculate if a groups has all atoms required for an amino acid. this allows to include chemically modified amino acids that are labeled hetatoms into some computations ... the usual way to identify if a group is an amino acid is getType() !

amino atoms are : N, CA, C, O, CB GLY does not have CB (unless we would calculate some artificially

Example: 1DW9 chain A first group is a Selenomethionine, provided as HETATM, but here returns true.

     HETATM    1  N   MSE A   1      11.720  20.973   1.584  0.00  0.00           N
     HETATM    2  CA  MSE A   1      10.381  20.548   1.139  0.00  0.00           C
     HETATM    3  C   MSE A   1       9.637  20.037   2.398  0.00  0.00           C
     HETATM    4  O   MSE A   1      10.198  19.156   2.985  0.00  0.00           O
     HETATM    5  CB  MSE A   1      10.407  19.441   0.088  0.00  0.00           C
     

Returns:

true if all Atoms required for an AminoAcid are available (N, CA, C, O, CB)

See Also:

getType()

setProperties

void setProperties(java.util.Map<java.lang.String,java.lang.Object> properties)

properties of this amino acid. currerntly available properties. are: phi psi

Parameters:

properties - a Map object specifying the properties value

See Also:

getProperties()

getProperties

java.util.Map<java.lang.String,java.lang.Object> getProperties()

return properties.

Returns:

a HashMap object representing the properties value

See Also:

setProperties(java.util.Map<java.lang.String, java.lang.Object>)

setProperty

void setProperty(java.lang.String key,
               java.lang.Object value)

set a single property .

Parameters:

key - a String

value - an Object

See Also:

getProperty(java.lang.String)

getProperty

java.lang.Object getProperty(java.lang.String key)

get a single property .

Parameters:

key - a String

Returns:

an Object

See Also:

setProperty(java.lang.String, java.lang.Object)

iterator

java.util.Iterator<Atom> iterator()

get an Atom Iterator.

Returns:

an Iterator object

clone

java.lang.Object clone()

returns and identical copy of this Group object .

Returns:

and identical copy of this Group object

setParent

@Deprecated
void setParent(Chain parent)

Deprecated.

Set the back-reference (to its parent Chain).

Parameters:

parent - the parent Chain

See Also:

setChain(Chain), getChain()

getParent

@Deprecated
Chain getParent()

Deprecated. replaced by getChain()

Returns the parent Chain of the Group.

Returns:

Chain the Chain object that contains the Group

See Also:

setChain(Chain)

setChain

void setChain(Chain chain)

Sets the back-reference to its parent Chain.

Parameters:

chain - the parent Chain

Since:

3.0

See Also:

getChain()

getChain

Chain getChain()

Returns the parent Chain of the Group.

Returns:

Chain the Chain object that contains the Group

Since:

3.0

See Also:

setChain(Chain)

getResidueNumber

ResidueNumber getResidueNumber()

returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.

Returns:

ResidueNumber for the group.

Since:

3.0

See Also:

ResidueNumber

setResidueNumber

void setResidueNumber(ResidueNumber residueNumber)

sets the ResidueNumber for this Group

Parameters:

residueNumber - the PDB residueNumber

setResidueNumber

void setResidueNumber(java.lang.String chainId,
                    java.lang.Integer residueNumber,
                    java.lang.Character iCode)

Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet. Not recommended for general use other than parsing.

Parameters:

chainId -

residueNumber -

iCode -

getChainId

java.lang.String getChainId()

Utility method for returning the chainId of the Group or null if no Chain has been set. This replaces the need to use the expression group.getChain().getId()

Returns:

the ID of the chain

Since:

3.0

setChemComp

void setChemComp(ChemComp cc)

Set the Chemical Component that closer describes this group.

Parameters:

cc - the chemical component

getChemComp

ChemComp getChemComp()

Get the chemical component that closer describes this group. If the information does not exist yet, fetches the information from PDB web site.

Returns:

the Chemical Component definition for this Group.

hasAltLoc

boolean hasAltLoc()

Test if this group has alternate locations.

Returns:

boolean flag if there are alternate locations.

getAltLocs

java.util.List<Group> getAltLocs()

Get the list of alternate locations.

Returns:

List of other groups that are on alternate locations

addAltLoc

void addAltLoc(Group g)

Add a group that is an alternate location for this group.

isWater

boolean isWater()

Determines if this group is water.

Returns:

true if it's water, false otherwise.

See Also:

GroupType#WATERNAMES}

getAltLocGroup

Group getAltLocGroup(java.lang.Character altLoc)

Gets the alternate location group to this group that has the alt-loc character code passed.

Parameters:

altLoc - the alternate location code of the group desired

Returns:

the alternate location group if found, or null otherwise

trimToSize

void trimToSize()

attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.