Package org.biojava.nbio.structure

Class HetatomImpl

java.lang.Object
org.biojava.nbio.structure.HetatomImpl
All Implemented Interfaces:
Serializable, Group
Direct Known Subclasses:
AminoAcidImpl, NucleotideImpl
public class HetatomImpl extends Object implements Group, 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:

  • Field Details

    • 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 String pdb_name
      3 letter name of amino acid in pdb file.

    • residueNumber

      protected ResidueNumber residueNumber

    • atoms

      protected List<Atom> atoms

    • performanceBehavior

      public static HetatomImpl.PerformanceBehavior performanceBehavior

    • chemComp

      protected ChemComp chemComp

  • Constructor Details

    • HetatomImpl

      public HetatomImpl()
      Construct a Hetatom instance.

  • Method Details

    • 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(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

      public String getPDBName()
      Returns the PDBName.
      Specified by:
      getPDBName in interface Group
      Returns:
      a String representing the PDBName value
      See Also:

    • 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 List<Atom> getAtoms()
      Get list of atoms.
      Specified by:
      getAtoms in interface Group
      Returns:
      a List object representing the atoms
      See Also:

    • setAtoms

      public void setAtoms(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(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(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 String toString()
      Overrides:
      toString in class 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:

    • setProperties

      public void setProperties(Map<String,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:

    • getProperties

      public Map<String,Object> getProperties()
      return properties.
      Specified by:
      getProperties in interface Group
      Returns:
      a HashMap object representing the properties value
      See Also:

    • setProperty

      public void setProperty(String key, Object value)
      set a single property .
      Specified by:
      setProperty in interface Group
      Parameters:
      key - a String
      value - an Object
      See Also:

    • getProperty

      public Object getProperty(String key)
      get a single property .
      Specified by:
      getProperty in interface Group
      Parameters:
      key - a String
      Returns:
      an Object
      See Also:

    • iterator

      public Iterator<Atom> iterator()
      return an AtomIterator.
      Specified by:
      iterator in interface Group
      Returns:
      an Iterator object

    • clone

      public Object clone()
      returns and identical copy of this Group object .
      Specified by:
      clone in interface Group
      Overrides:
      clone in class 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:

    • 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:

    • getChainId

      public 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:

    • 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(String chainId, Integer resNum, 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 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(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 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