Interface Group

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void addAtom​(Atom atom)
      add an atom to this group.
      void clearAtoms()
      Remove all atoms from this group.
      java.lang.Object clone()
      returns and identical copy of this Group object .
      Atom getAtom​(int position)
      Get at atom by position.
      Atom getAtom​(java.lang.String name)
      Get an atom.
      java.util.List<Atom> getAtoms()
      Get list of atoms.
      Chain getParent()
      Returns the parent Chain of the Group.
      java.lang.String getPDBCode()
      Return the PDBcode (residue number + insertion code ) of this group.
      java.lang.String getPDBName()
      Get the PDB 3 character name for this group.
      java.util.Map<java.lang.String,​java.lang.Object> getProperties()
      return properties.
      java.lang.Object getProperty​(java.lang.String key)
      get a single property .
      java.lang.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​(java.lang.String name)
      Teturns flag whether a particular atom is existing within this group .
      java.util.Iterator<Atom> iterator()
      get an Atom Iterator.
      void setAtoms​(java.util.List<Atom> atoms)
      Set the atoms of this group.
      void setParent​(Chain parent)
      Set the back-reference (to its parent Chain).
      void setPDBCode​(java.lang.String pdbcode)
      Specifies the PDBCode (residue number + insertion code) value.
      void setPDBFlag​(boolean flag)
      flag if group has 3D data .
      void setPDBName​(java.lang.String s)
      Set the PDB 3 letter name for this group.
      void setProperties​(java.util.Map<java.lang.String,​java.lang.Object> properties)
      properties of this amino acid.
      void setProperty​(java.lang.String key, java.lang.Object value)
      set a single property .
      int size()
      getnumber of atoms.
    • Method Detail

      • getPDBCode

        java.lang.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​(java.lang.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

        java.lang.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

        java.util.List<Atom> getAtoms()
        Get list of atoms.
        Returns:
        an List object representing the atoms
        See Also:
        setAtoms(List)
      • setAtoms

        void setAtoms​(java.util.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​(java.lang.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​(java.lang.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

        java.lang.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​(java.lang.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​(java.util.Map<java.lang.String,​java.lang.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()
      • setProperty

        void setProperty​(java.lang.String key,
                         java.lang.Object value)
        set a single property .
        Parameters:
        key - a String
        value - an Object
        See Also:
        getProperty(java.lang.String)
      • iterator

        java.util.Iterator<Atom> iterator()
        get an Atom Iterator.
        Returns:
        an Iterator object
      • clone

        java.lang.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)