HetatomImpl

java.lang.Object
- org.biojava.nbio.structure.HetatomImpl

All Implemented Interfaces:

java.io.Serializable, Group

Direct Known Subclasses:

AminoAcidImpl, NucleotideImpl
```
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

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class HetatomImpl.PerformanceBehavior
Behaviors for how to balance memory vs.

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

Field Summary

Fields
Modifier and Type	Field	Description
`protected java.util.List<Atom>`	`atoms`
`protected ChemComp`	`chemComp`
`protected boolean`	`pdb_flag`	stores if 3d coordinates are available.
`protected java.lang.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 Description

HetatomImpl()
Construct a Hetatom instance.

Constructors
Constructor	Description
`HetatomImpl()`	Construct a Hetatom instance.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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)`	Get at atom by position.
`Atom`	`getAtom(java.lang.String name)`	Get an atom given its PDB name.
`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.
`long`	`getId()`	the Hibernate database ID
`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.
`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()`	Test if this group has alternate locations.
`boolean`	`hasAminoAtoms()`	Calculate if this group has all atoms required for an amino acid backbone.
`boolean`	`hasAtom(java.lang.String fullName)`	Tell whether a particular atom exists within this group.
`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`	`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(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.
`void`	`setResidueNumber(ResidueNumber residueNumber)`	sets the ResidueNumber for this Group
`int`	`size()`	Get number of atoms.
`java.lang.String`	`toSDF()`	Function to get the Group as an MDL molblock
`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 GroupType type
```
    The GroupType is HETATM
  - pdb_flag
```
protected boolean pdb_flag
```
    stores if 3d coordinates are available.
  - pdb_name
```
protected java.lang.String pdb_name
```
    3 letter name of amino acid in pdb file.
  - residueNumber
```
protected ResidueNumber residueNumber
```
  - atoms
```
protected java.util.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(java.lang.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 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()
```
    Get number of atoms.
    
    Specified by:
    
    size in interface Group
    
    Returns:
    
    number of atoms of this Group
  - getAtoms
```
public java.util.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(java.util.List<Atom> atoms)
```
    Set the atoms of this group.
    
    Specified by:
    
    setAtoms in interface Group
    
    Parameters:
    
    atoms - a list of atoms
  - getAtom
```
public Atom getAtom(java.lang.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(java.lang.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 java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.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()
  - setProperties
```
public void setProperties(java.util.Map<java.lang.String,java.lang.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 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
  - 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.
  - 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 java.lang.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

Class HetatomImpl

Nested Class Summary

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

type

pdb_flag

pdb_name

residueNumber

atoms

performanceBehavior

chemComp

Constructor Detail

HetatomImpl

Method Detail

has3D

setPDBFlag

setPDBName

getPDBName

addAtom

clearAtoms

size

getAtoms

setAtoms

getAtom

getAtom

hasAtom

getType

toString

hasAminoAtoms

setProperties

getProperties

setProperty

getProperty

iterator

clone

getId

setId

getChemComp

setChemComp

setChain

getChain

getChainId

getResidueNumber

setResidueNumber

setResidueNumber

hasAltLoc

getAltLocs

getAltLocGroup

addAltLoc

isWater

trimToSize

toSDF