Package org.biojava.nbio.structure

Interface Group

    • 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

      • addAtom

        void addAtom​(Atom atom)
        Add an atom to this group.
        Parameters:
        atom - an Atom object

      • 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()

        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

      • 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()
        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()

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

      • 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