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## org.biojava.bio.structure
Interface Group

All Known Subinterfaces:
  AminoAcid

All Known Implementing Classes:
  AminoAcidImpl, HetatomImpl, NucleotideImpl

    public interface Group

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`

Method Summary
`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 .
`Atom` | `getAtom(int position)` Get at atom by position.
`Atom` | `getAtom(String name)` Get an atom.
`List<Atom>` | `getAtoms()` Get list of atoms.
`Chain` | `getParent()` Returns the parent Chain of the Group.
`String` | `getPDBCode()` Return the PDBcode (residue number + insertion code ) of this group.
`String` | `getPDBName()` Get the PDB 3 character name for this group.
`Map<String,Object>` | `getProperties()` return properties.
`Object` | `getProperty(String key)` get a single property .
`String` | `getType()` get Type of group, e.g.
`boolean` | `has3D()` returns true or false, depending if this group has 3D coordinates or not.
`boolean` | `hasAminoAtoms()` calculate if a groups has all atoms required for an amino acid.
`boolean` | `hasAtom(String name)` Teturns flag whether a particular atom is existing within this group .
`Iterator<Atom>` | `iterator()` get an Atom Iterator.
`void` | `setAtoms(List<Atom> atoms)` Set the atoms of this group.
`void` | `setParent(Chain parent)` Set the back-reference (to its parent Chain).
`void` | `setPDBCode(String pdbcode)` Specifies the PDBCode (residue number + insertion code) value.
`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 .
`int` | `size()` getnumber of atoms.

Method Detail

### getPDBCode

    String getPDBCode()

  Return the PDBcode (residue number + insertion code ) of this group. The residue number is treated as a String for the following reasons: Every amino acid in a PDB file is identified uniquely by 3 things: The chain ID, the residue number and the insertion code. To make sure one does not forget about the insertion code, in BJ it is appended to the residue number. To add to this, residue numbers can be negative, non-consecutive and also non-sequential. As such it is often easiest, to treat them as public identifiers and within your own code work with the internal atom or group positions...

  Returns:
    a String representing the PDBCode value
  See Also:
    `setPDBCode(java.lang.String)`

### setPDBCode

    void setPDBCode(String pdbcode)

  Specifies the PDBCode (residue number + insertion code) value.

  Parameters:
    `pdbcode` - a String specifying the PDBCode value
  See Also:
    `getPDBCode()`

### size

    int size()

  getnumber of atoms.

  Returns:
    number of atoms of this Group

### has3D

    boolean has3D()

  returns 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

    String getType()

  get Type of group, e.g. amino, hetatom, 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:
    an 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)
                 throws StructureException

  Get an atom. Throws StructureException if atom not found.

  Parameters:
    `name` - a String
  Returns:
    an Atom object
  Throws:
    `StructureException` - if atom not found.

### getAtom

    Atom getAtom(int position)
                 throws StructureException

  Get at atom by position.

  Parameters:
    `position` - an int
  Returns:
    an Atom object
  Throws:
    `StructureException` - if not atom at this position

### hasAtom

    boolean hasAtom(String name)

  Teturns flag whether a particular atom is existing within this group .

  Parameters:
    `name` - a String ...
  Returns:
    true if Atom with name is existing within this group

### getPDBName

    String getPDBName()

  Get the PDB 3 character 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)
                    throws PDBParseException

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

  Parameters:
    `s` - a String specifying the PDBName value
  Throws:
    `PDBParseException` - ...
  See Also:
    `getPDBName()`

### hasAminoAtoms

    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 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, CB)
  See Also:
    `getType()`

### setProperties

    void setProperties(Map<String,Object> properties)

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

  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)`

### 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

### setParent

    void setParent(Chain parent)

  Set the back-reference (to its parent Chain).

  Parameters:
    `parent` - the parent Chain
  See Also:
    `getParent()`

### getParent

    Chain getParent()

  Returns the parent Chain of the Group.

  Returns:
    Chain the Chain object that contains the Group
  See Also:
    `setParent(Chain)`

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