Group (biojava 5.0.0 API)

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:
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

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

Method Summary

All Methods Instance Methods Abstract 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.
`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 alternate locations.
`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()` Test if this group has alternate locations.
`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()` Tests in the Chemical Component Dictionary, if this group is an amino acid
`boolean`	`isHetAtomInFile()` Tells whether the group is annotated as HETATM in the file.
`boolean`	`isNucleotide()` Tests in the Chemical Component Dictionary, if this group is a nucleotide
`boolean`	`isPolymeric()` tests in the Chemical Component Dictionary, if this group is a polymeric group
`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()
```
    tests in the Chemical Component Dictionary, if this group is a polymeric group
    
    Returns:
    
    true if a polymeric group
  - isAminoAcid
```
boolean isAminoAcid()
```
    Tests in the Chemical Component Dictionary, if this group is an amino acid
    
    Returns:
    
    true if an amino acid
  - isNucleotide
```
boolean isNucleotide()
```
    Tests in the Chemical Component Dictionary, if this group is a nucleotide
    
    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()
```
    Test if this group has alternate locations.
    
    Returns:
    
    boolean flag if there are alternate locations.
  - getAltLocs
```
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(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 -

Interface Group

Field Summary

Method Summary

Field Detail

SEC_STRUC

Method Detail

size

has3D

setPDBFlag

getType

addAtom

getAtoms

setAtoms

clearAtoms

getAtom

getAtom

hasAtom

getPDBName

setPDBName

hasAminoAtoms

isPolymeric

isAminoAcid

isNucleotide

setProperties

getProperties

setProperty

getProperty

iterator

clone

setChain

getChain

getResidueNumber

setResidueNumber

setResidueNumber

getChainId

setChemComp

getChemComp

hasAltLoc

getAltLocs

addAltLoc

isWater

getAltLocGroup

trimToSize

toSDF

isHetAtomInFile

setHetAtomInFile