org.biojava.nbio.structure

Class HetatomImpl

java.lang.Object

org.biojava.nbio.structure.HetatomImpl

All Implemented Interfaces:

Serializable, Group

Direct Known Subclasses:

AminoAcidImpl, NucleotideImpl

public class HetatomImpl
extends Object
implements Group

Generic Implementation of a Group interface. AminoAcidImpl and NucleotideImpl are closely related classes.

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic, Horvath Tamas

See Also:

AminoAcidImpl, NucleotideImpl, Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	HetatomImpl.PerformanceBehavior Behaviors for how to balance memory vs. performance.

Field Summary

Fields

Modifier and Type	Field and Description
protected List<Atom>	atoms
protected ChemComp	chemComp
protected boolean	pdb_flag stores if 3d coordinates are available.
protected String	pdb_name 3 letter name of amino acid in pdb file.
static HetatomImpl.PerformanceBehavior	performanceBehavior
protected ResidueNumber	residueNumber
static GroupType	type The GroupType is HETATM

Fields inherited from interface org.biojava.nbio.structure.Group

SEC_STRUC

Constructor Summary

Constructors

Constructor and Description
HetatomImpl() Construct a Hetatom instance.

Method Summary

Modifier and Type	Method and Description
void	addAltLoc(Group group) 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
Object	clone() returns and identical copy of this Group object .
protected void	cloneAtomsAndBonds(Group newGroup)
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.
long	getId() the Hibernate database ID
String	getPDBName() Returns the PDBName.
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() returns 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 fullName) 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() return an AtomIterator.
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	setId(long id) the Hibernate database ID
void	setPDBFlag(boolean flag) flag if group has 3D data.
void	setPDBName(String s) Set three character name of Group .
void	setProperties(Map<String,Object> props) 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 resNum, 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
String	toString()
void	trimToSize() attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

type

public static final GroupType type

The GroupType is HETATM

pdb_flag

protected boolean pdb_flag

stores if 3d coordinates are available.

pdb_name

protected String pdb_name

3 letter name of amino acid in pdb file.

residueNumber

protected ResidueNumber residueNumber

atoms

protected List<Atom> atoms

performanceBehavior

public static HetatomImpl.PerformanceBehavior performanceBehavior

chemComp

protected ChemComp chemComp

Constructor Detail

HetatomImpl

public HetatomImpl()

Construct a Hetatom instance.

Method Detail

has3D

public boolean has3D()

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

Specified by:

has3D in interface Group

Returns:

true if Group has 3D coordinates

setPDBFlag

public void setPDBFlag(boolean flag)

flag if group has 3D data.

Specified by:

setPDBFlag in interface Group

Parameters:

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

setPDBName

public void setPDBName(String s)

Set three character name of Group .

Specified by:

setPDBName in interface Group

Parameters:

s - a String specifying the PDBName value

See Also:

getPDBName()

getPDBName

public String getPDBName()

Returns the PDBName.

Specified by:

getPDBName in interface Group

Returns:

a String representing the PDBName value

See Also:

setPDBName(java.lang.String)

addAtom

public void addAtom(Atom atom)

Add an atom to this group.

Specified by:

addAtom in interface Group

Parameters:

atom - an Atom object

clearAtoms

public void clearAtoms()

remove all atoms

Specified by:

clearAtoms in interface Group

size

public int size()

Get number of atoms.

Specified by:

size in interface Group

Returns:

number of atoms of this Group

getAtoms

public List<Atom> getAtoms()

Get list of atoms.

Specified by:

getAtoms in interface Group

Returns:

a List object representing the atoms

See Also:

Group.setAtoms(List)

setAtoms

public void setAtoms(List<Atom> atoms)

Set the atoms of this group.

Specified by:

setAtoms in interface Group

Parameters:

atoms - a list of atoms

See Also:

Atom}

getAtom

public 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()

Specified by:

getAtom in interface Group

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

public Atom getAtom(int position)

Get at atom by position.

Specified by:

getAtom in interface Group

Parameters:

position - an int

Returns:

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

hasAtom

public boolean hasAtom(String fullName)

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.

Specified by:

hasAtom in interface Group

Parameters:

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

Returns:

true if Atom with name exists within this group

getType

public GroupType getType()

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

Specified by:

getType in interface Group

Returns:

a String representing the type value

toString

public String toString()

Overrides:

toString in class Object

hasAminoAtoms

public 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 Group.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
 

Specified by:

hasAminoAtoms in interface Group

Returns:

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

See Also:

Group.getType()

isPolymeric

public boolean isPolymeric()

Description copied from interface: Group

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

Specified by:

isPolymeric in interface Group

Returns:

true if a polymeric group

isAminoAcid

public boolean isAminoAcid()

Description copied from interface: Group

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

Specified by:

isAminoAcid in interface Group

Returns:

true if an amino acid

isNucleotide

public boolean isNucleotide()

Description copied from interface: Group

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

Specified by:

isNucleotide in interface Group

Returns:

true if a nucleotide

setProperties

public void setProperties(Map<String,Object> props)

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

Specified by:

setProperties in interface Group

Parameters:

props - a Map object specifying the properties value

See Also:

Group.getProperties()

getProperties

public Map<String,Object> getProperties()

return properties.

Specified by:

getProperties in interface Group

Returns:

a HashMap object representing the properties value

See Also:

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

setProperty

public void setProperty(String key,
                        Object value)

set a single property .

Specified by:

setProperty in interface Group

Parameters:

key - a String

value - an Object

See Also:

getProperties(), getProperty(java.lang.String)

getProperty

public Object getProperty(String key)

get a single property .

Specified by:

getProperty in interface Group

Parameters:

key - a String

Returns:

an Object

See Also:

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

iterator

public Iterator<Atom> iterator()

return an AtomIterator.

Specified by:

iterator in interface Group

Returns:

an Iterator object

clone

public Object clone()

returns and identical copy of this Group object .

Specified by:

clone in interface Group

Overrides:

clone in class Object

Returns:

and identical copy of this Group object

cloneAtomsAndBonds

protected void cloneAtomsAndBonds(Group newGroup)

getId

public long getId()

the Hibernate database ID

Returns:

the id

setId

public void setId(long id)

the Hibernate database ID

Parameters:

id - the hibernate id

getChemComp

public ChemComp getChemComp()

Description copied from interface: Group

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

Specified by:

getChemComp in interface Group

Returns:

the Chemical Component definition for this Group.

setChemComp

public void setChemComp(ChemComp cc)

Description copied from interface: Group

Set the Chemical Component that closer describes this group.

Specified by:

setChemComp in interface Group

Parameters:

cc - the chemical component

setChain

public void setChain(Chain chain)

Sets the back-reference to its parent Chain.

Specified by:

setChain in interface Group

Parameters:

chain - the parent Chain

See Also:

Group.getChain()

getChain

public Chain getChain()

Returns the parent Chain of the Group.

Specified by:

getChain in interface Group

Returns:

Chain the Chain object that contains the Group

See Also:

Group.setChain(Chain)

getChainId

public 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.

Specified by:

getChainId in interface Group

Returns:

the ID of the chain

getResidueNumber

public ResidueNumber getResidueNumber()

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

Specified by:

getResidueNumber in interface Group

Returns:

ResidueNumber for the group.

See Also:

ResidueNumber

setResidueNumber

public void setResidueNumber(ResidueNumber residueNumber)

Description copied from interface: Group

Sets the ResidueNumber for this Group

Specified by:

setResidueNumber in interface Group

Parameters:

residueNumber - the PDB residueNumber

setResidueNumber

public void setResidueNumber(String chainId,
                             Integer resNum,
                             Character iCode)

Description copied from interface: Group

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.

Specified by:

setResidueNumber in interface Group

hasAltLoc

public boolean hasAltLoc()

Description copied from interface: Group

Check if this group has alternate location groups.

Specified by:

hasAltLoc in interface Group

Returns:

boolean flag if there are alternate locations.

See Also:

Group.getAltLocs()

getAltLocs

public List<Group> getAltLocs()

Description copied from interface: Group

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.

Specified by:

getAltLocs in interface Group

Returns:

List of other groups that are on alternate locations

getAltLocGroup

public Group getAltLocGroup(Character altLoc)

Description copied from interface: Group

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

Specified by:

getAltLocGroup in interface Group

Parameters:

altLoc - the alternate location code of the group desired

Returns:

the alternate location group if found, or null otherwise

addAltLoc

public void addAltLoc(Group group)

Description copied from interface: Group

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

Specified by:

addAltLoc in interface Group

Parameters:

group - the altloc group to add

isWater

public boolean isWater()

Description copied from interface: Group

Determines if this group is water.

Specified by:

isWater in interface Group

Returns:

true if it's water, false otherwise.

See Also:

GroupType.WATERNAMES

trimToSize

public void trimToSize()

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

Specified by:

trimToSize in interface Group

toSDF

public String toSDF()

Description copied from interface: Group

Function to get the Group as an MDL molblock

Specified by:

toSDF in interface Group

Returns:

the string of the MDL molblock

isHetAtomInFile

public boolean isHetAtomInFile()

Description copied from interface: Group

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.

Specified by:

isHetAtomInFile in interface Group

Returns:

setHetAtomInFile

public void setHetAtomInFile(boolean isHetAtomInFile)

Description copied from interface: Group

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.

Specified by:

setHetAtomInFile in interface Group