org.biojava.bio.structure

Class HetatomImpl

java.lang.Object

org.biojava.bio.structure.HetatomImpl

All Implemented Interfaces:

java.io.Serializable, Group

Direct Known Subclasses:

AminoAcidImpl, NucleotideImpl, SecStrucGroup

public class HetatomImpl
extends java.lang.Object
implements Group, java.io.Serializable

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

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.List<Atom>	atoms
protected boolean	pdb_flag
protected java.lang.String	pdb_name
protected ResidueNumber	residueNumber
static java.lang.String	type this is a "hetatm".

Constructor Summary

Constructors

Constructor and Description
HetatomImpl()

Method Summary

Methods

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
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) return an atom by its position in the internal List.
Atom	getAtom(java.lang.String name) get an atom throws StructureException if atom not found.
Atom	getAtomByPDBname(java.lang.String name) Get an atom by the full PDB name e.g.
java.util.List<Atom>	getAtoms() get all atoms of this group .
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.
long	getId() the Hibernate database ID
Chain	getParent() Returns the parent Chain of the Group
java.lang.String	getPDBCode() Deprecated. replaced by #getSeqNum
java.lang.String	getPDBName() Returns the PDBName.
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() Returns the type value.
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 this allows to include chemically modified amino acids that are labeled hetatoms into some computations ...
boolean	hasAtom(java.lang.String fullName) test is an Atom with name is existing.
boolean	isWater() Determines if this group is water.
java.util.Iterator<Atom>	iterator() return an AtomIterator.
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	setId(long id) the Hibernate database ID
void	setParent(Chain parent) Set the back-reference (to its parent Chain)
void	setPDBCode(java.lang.String pdb_code) Deprecated. replaced by setResidueNumber(ResidueNumber)
void	setPDBFlag(boolean flag) flag if group has 3D data.
void	setPDBName(java.lang.String s) set three character name of Group .
void	setProperties(java.util.Map<java.lang.String,java.lang.Object> props) 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 resNum, 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.
java.lang.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 java.lang.String type

this is a "hetatm".

See Also:

Constant Field Values

pdb_flag

protected boolean pdb_flag

pdb_name

protected java.lang.String pdb_name

residueNumber

protected ResidueNumber residueNumber

atoms

protected java.util.List<Atom> atoms

Constructor Detail

HetatomImpl

public HetatomImpl()

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

getPDBCode

@Deprecated
public java.lang.String getPDBCode()

Deprecated. replaced by #getSeqNum

Returns the PDBCode.

Specified by:

getPDBCode in interface Group

Returns:

a String representing the PDBCode value

See Also:

setPDBCode(java.lang.String)

setPDBCode

@Deprecated
public void setPDBCode(java.lang.String pdb_code)

Deprecated. replaced by setResidueNumber(ResidueNumber)

set the PDB code.

Specified by:

setPDBCode in interface Group

Parameters:

pdb_code - a String specifying the PDBCode value

See Also:

getPDBCode()

setPDBName

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

set three character name of Group .

Specified by:

setPDBName in interface Group

Parameters:

s - a String specifying the PDBName value

Throws:

PDBParseException - ...

See Also:

getPDBName()

getPDBName

public java.lang.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()

getnumber of atoms.

Specified by:

size in interface Group

Returns:

number of atoms

getAtoms

public java.util.List<Atom> getAtoms()

get all atoms of this group . returns a List of all atoms in this Group

Specified by:

getAtoms in interface Group

Returns:

an List object representing the atoms value

See Also:

Group.setAtoms(List)

setAtoms

public void setAtoms(java.util.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(java.lang.String name)
             throws StructureException

get an atom throws StructureException if atom not found.

Specified by:

getAtom in interface Group

Parameters:

name - a String

Returns:

an Atom object

Throws:

StructureException - ...

getAtomByPDBname

public Atom getAtomByPDBname(java.lang.String name)
                      throws StructureException

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

Specified by:

getAtomByPDBname in interface Group

Parameters:

name - a String

Returns:

an Atom object

Throws:

StructureException - ...

getAtom

public Atom getAtom(int position)
             throws StructureException

return an atom by its position in the internal List.

Specified by:

getAtom in interface Group

Parameters:

position - an int

Returns:

an Atom object

Throws:

StructureException - ...

hasAtom

public boolean hasAtom(java.lang.String fullName)

test is an Atom with name is existing.

Specified by:

hasAtom in interface Group

Parameters:

fullName - a String ...

Returns:

true if Atom with name is existing within this group

getType

public java.lang.String getType()

Returns the type value.

Specified by:

getType in interface Group

Returns:

a String representing the type value

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

hasAminoAtoms

public 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 parent 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, CB)

See Also:

getType()

setProperties

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

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

Specified by:

setProperties in interface Group

Parameters:

props - a Map object specifying the properties value

See Also:

getProperties()

getProperties

public java.util.Map<java.lang.String,java.lang.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(java.lang.String key,
               java.lang.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 java.lang.Object getProperty(java.lang.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 java.util.Iterator<Atom> iterator()

return an AtomIterator.

Specified by:

iterator in interface Group

Returns:

an Iterator object

clone

public java.lang.Object clone()

returns and identical copy of this Group object .

Specified by:

clone in interface Group

Overrides:

clone in class java.lang.Object

Returns:

and identical copy of this Group object

setParent

public void setParent(Chain parent)

Set the back-reference (to its parent Chain)

Specified by:

setParent in interface Group

Parameters:

parent - the parent Chain

See Also:

Group.setChain(Chain), Group.getChain()

getParent

public Chain getParent()

Returns the parent Chain of the Group

Specified by:

getParent in interface Group

Returns:

Chain the Chain object that contains the Group

See Also:

Group.setChain(Chain)

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 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()

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(java.lang.String chainId,
                    java.lang.Integer resNum,
                    java.lang.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

Test if this group has alternate locations.

Specified by:

hasAltLoc in interface Group

Returns:

boolean flag if there are alternate locations.

getAltLocs

public java.util.List<Group> getAltLocs()

Description copied from interface: Group

Get the list of alternate locations.

Specified by:

getAltLocs in interface Group

Returns:

List of other groups that are on alternate locations

getAltLocGroup

public Group getAltLocGroup(java.lang.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

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