org.biojava.nbio.structure

Interface Group

All Superinterfaces:

Serializable

All Known Subinterfaces:

AminoAcid

All Known Implementing Classes:

AminoAcidImpl, HetatomImpl, NucleotideImpl

public interface Group
extends Serializable

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

Field Summary

Fields

Modifier and Type	Field and Description
static String	SEC_STRUC Group property key for secondary structure annotation

Method Summary

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.
Object	clone() Returns and identical copy of this Group object .
Group	getAltLocGroup(Character altLoc) Gets the alternate location group to this group that has the alt-loc character code passed.
List<Group>	getAltLocs() Get the list of other alternate location groups.
Atom	getAtom(int position) Get at atom by position.
Atom	getAtom(String name) Get an atom given its PDB name.
List<Atom>	getAtoms() Get list of atoms.
Chain	getChain() Returns the parent Chain of the Group.
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.
String	getPDBName() Get the PDB 3-letter name for this group.
Map<String,Object>	getProperties() Return properties.
Object	getProperty(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.
GroupType	getType() Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE
boolean	has3D() Return true or false, depending if this group has 3D coordinates or not.
boolean	hasAltLoc() Check if this group has alternate location groups.
boolean	hasAminoAtoms() Calculate if this group has all atoms required for an amino acid backbone.
boolean	hasAtom(String name) Tell whether a particular atom exists within this group.
boolean	isAminoAcid() Check if this group is an aminoacid group, from the definition in Chemical Component Dictionary
boolean	isHetAtomInFile() Tells whether the group is annotated as HETATM in the file.
boolean	isNucleotide() Check if this group is a nucleotide group, from the definition in Chemical Component Dictionary
boolean	isPolymeric() Check if this group is a polymeric group, from the definition in Chemical Component Dictionary
boolean	isWater() Determines if this group is water.
Iterator<Atom>	iterator() Get an Atom Iterator.
void	setAtoms(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	setHetAtomInFile(boolean isHetAtomInFile) Sets the field isHetAtomInFile which is intented only for helping in infering if a polymeric group is in a ligand chain or in a polymeric chain.
void	setPDBFlag(boolean flag) Flag if group has 3D data .
void	setPDBName(String s) Set the PDB 3-letter name for this group.
void	setProperties(Map<String,Object> properties) Properties of this amino acid.
void	setProperty(String key, Object value) Set a single property .
void	setResidueNumber(ResidueNumber residueNumber) Sets the ResidueNumber for this Group
void	setResidueNumber(String chainId, Integer residueNumber, Character iCode) Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet.
int	size() Get number of atoms.
String	toSDF() Function to get the Group as an MDL molblock
void	trimToSize() Attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.

Field Detail

SEC_STRUC

static final String SEC_STRUC

Group property key for secondary structure annotation

See Also:

Constant Field Values

Method Detail

size

int size()

Get number of atoms.

Returns:

number of atoms of this Group

has3D

boolean has3D()

Return 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

GroupType getType()

Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.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

List<Atom> getAtoms()

Get list of atoms.

Returns:

a List object representing the atoms

See Also:

setAtoms(List)

setAtoms

void setAtoms(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(String name)

Get an atom given its PDB name. Beware that some PDB atom names are ambiguous (e.g. CA, which means C-alpha or Calcium), ambiguities should not occur within the same group though. To solve these ambiguities one would need to check the atom returned for the required element with Atom.getElement()

Parameters:

name - a trimmed String representing the atom's PDB name, e.g. "CA"

Returns:

an Atom object or null if no such atom exists within this group

getAtom

Atom getAtom(int position)

Get at atom by position.

Parameters:

position - an int

Returns:

an Atom object or null if no Atom exists for given position

hasAtom

boolean hasAtom(String name)

Tell whether a particular atom exists within this group. Beware that some PDB atom names are ambiguous (e.g. CA, which means C-alpha or Calcium), ambiguities should not occur within the same group though.

Parameters:

name - a trimmed String representing the atom's PDB name, e.g. "CA"

Returns:

true if Atom with name exists within this group

getPDBName

String getPDBName()

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

Returns:

a String representing the PDBName value

See Also:

setPDBName(java.lang.String)

setPDBName

void setPDBName(String s)

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

Parameters:

s - a String specifying the PDBName value

See Also:

getPDBName()

hasAminoAtoms

boolean hasAminoAtoms()

Calculate if this group has all atoms required for an amino acid backbone. 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

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)

See Also:

getType()

isPolymeric

boolean isPolymeric()

Check if this group is a polymeric group, from the definition in Chemical Component Dictionary

Returns:

true if a polymeric group

isAminoAcid

boolean isAminoAcid()

Check if this group is an aminoacid group, from the definition in Chemical Component Dictionary

Returns:

true if an amino acid

isNucleotide

boolean isNucleotide()

Check if this group is a nucleotide group, from the definition in Chemical Component Dictionary

Returns:

true if a nucleotide

setProperties

void setProperties(Map<String,Object> properties)

Properties of this amino acid. Currently available properties are: phi psi secstruc

Parameters:

properties - a Map object specifying the properties value

See Also:

getProperties()

getProperties

Map<String,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(String key,
                 Object value)

Set a single property .

Parameters:

key - a String

value - an Object

See Also:

getProperty(java.lang.String)

getProperty

Object getProperty(String key)

Get a single property .

Parameters:

key - a String

Returns:

an Object

See Also:

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

iterator

Iterator<Atom> iterator()

Get an Atom Iterator.

Returns:

an Iterator object

clone

Object clone()

Returns and identical copy of this Group object .

Returns:

and identical copy of this Group object

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(String chainId,
                      Integer residueNumber,
                      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

String getChainId()

Utility method for returning the chainId of the Group or null if no Chain has been set. This is equivalent to calling getChain().getId() Prior to version 5.0 this method returned the chain name.

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()

Check if this group has alternate location groups.

Returns:

boolean flag if there are alternate locations.

See Also:

getAltLocs()

getAltLocs

List<Group> getAltLocs()

Get the list of other alternate location groups.

The main group (this group) will contain the first altloc (be it the default '.' or 'A' or a mix of '.' and 'A').

This method will return the altloc groups that are not the main group, e.g.:

if '.' (default), 'A' and 'B' altlocs are present in file, the main group will contain the default '.' and this method will return 2 altloc groups if 'A' and 'B' are present in file without a default '.' group, then the main group will contain the 'A' location whilst this method will return only 1 altloc group with the 'B' location

Note that atoms with the default altloc (.) are included in all groups. Atoms with other altlocs (typically A, B, etc) will be sorted into groups by altloc.

Thus it can happen that an altloc group duplicate the contents of the main group.

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.

Parameters:

g - the altloc group to add

isWater

boolean isWater()

Determines if this group is water.

Returns:

true if it's water, false otherwise.

See Also:

GroupType.WATERNAMES

getAltLocGroup

Group getAltLocGroup(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.

toSDF

String toSDF()

Function to get the Group as an MDL molblock

Returns:

the string of the MDL molblock

isHetAtomInFile

boolean isHetAtomInFile()

Tells whether the group is annotated as HETATM in the file. To be used only at parsing time to be able to infer that a polymeric group is in a ligand chain or not.

Returns:

setHetAtomInFile

void setHetAtomInFile(boolean isHetAtomInFile)

Sets the field isHetAtomInFile which is intented only for helping in infering if a polymeric group is in a ligand chain or in a polymeric chain.

Parameters:

isHetAtomInFile -