Package org.biojava.nbio.structure

Interface Group

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:

  • Field Summary

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

  • Method Summary

    Modifier and Type
    Method
    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 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.
    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()
    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 name)
    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()
    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(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.
    void
    setResidueNumber(ResidueNumber residueNumber)
    Sets the ResidueNumber for this Group
    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 Details

  • Method Details

    • 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

      void setAtoms(List<Atom> atoms)
      Set the atoms of this group.
      Parameters:
      atoms - a list of atoms
      See Also:

    • 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()

      Note this method will return only the atom in the default alternative location (be it '.' or a letter).

      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

      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:

    • 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:

    • isPolymeric

      boolean isPolymeric()
      Check if this group is a polymeric group, from the definition in Chemical Component Dictionary
      Returns:
      true if a polymeric group

    • isAminoAcid

      boolean isAminoAcid()
      Check if this group is an aminoacid group, from the definition in Chemical Component Dictionary
      Returns:
      true if an amino acid

    • isNucleotide

      boolean isNucleotide()
      Check if this group is a nucleotide group, from the definition in Chemical Component Dictionary
      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

      Map<String,Object> getProperties()
      Return properties.
      Returns:
      a HashMap object representing the properties value
      See Also:

    • setProperty

      void setProperty(String key, Object value)
      Set a single property .
      Parameters:
      key - a String
      value - an Object
      See Also:

    • getProperty

      Object getProperty(String key)
      Get a single property .
      Parameters:
      key - a String
      Returns:
      an Object
      See Also:

    • 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

      Chain getChain()
      Returns the parent Chain of the Group.
      Returns:
      Chain the Chain object that contains the Group
      Since:
      3.0
      See Also:

    • 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:

    • 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()
      Check if this group has alternate location groups.
      Returns:
      boolean flag if there are alternate locations.
      See Also:

    • getAltLocs

      List<Group> getAltLocs()
      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.

      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.
      Parameters:
      g - the altloc group to add

    • isWater

      boolean isWater()
      Determines if this group is water.
      Returns:
      true if it's water, false otherwise.
      See Also:

    • 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 -