## Uses of Interface
org.biojava.bio.structure.Group

Packages that use Group
org.biojava.bio.structure: Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.io: Input and Output of Structures

Uses of Group in org.biojava.bio.structure

Subinterfaces of Group in org.biojava.bio.structure
`interface` `AminoAcid` A `Group` that represents an AminoAcid.

Classes in org.biojava.bio.structure that implement Group
`class` `AminoAcidImpl` AminoAcid inherits most from Hetatom.
`class` `HetatomImpl` Generic Implementation of a Group interface.
`class` `NucleotideImpl` A nucleotide group is almost the same as a Hetatm group.

Methods in org.biojava.bio.structure that return Group
`Group` `StructureImpl.findGroup(String chainName, String pdbResnum)`
`Group` `Structure.findGroup(String chainId, String pdbResnum)` request a particular group from a structure.
`Group` `StructureImpl.findGroup(String chainId, String pdbResnum, int modelnr)`
`Group` `Structure.findGroup(String chainId, String pdbResnum, int modelnr)` request a particular group from a structure.
`Group` `ChainImpl.getAtomGroup(int position)` return the group at position .
`Group` `Chain.getAtomGroup(int position)` return the Group at position X.
`Group` `ChainImpl.getGroup(int position)` Deprecated. use getAtomGroup or getSeqResGroup instead
`Group` `Chain.getGroup(int position)` Deprecated. use getAtomGroup or getSeqResGroup instead
`Group` `ChainImpl.getGroupByPDB(String pdbresnum)`
`Group` `Chain.getGroupByPDB(String pdbresnum)` get a group by its PDB residue numbering.
`Group[]` `ChainImpl.getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd)` Get all groups that are located between two PDB residue numbers.
`Group[]` `Chain.getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd)` Get all groups that are located between two PDB residue numbers.
`Group[]` `ChainImpl.getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd, boolean ignoreMissing)` Get all groups that are located between two PDB residue numbers.
`Group[]` `Chain.getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd, boolean ignoreMissing)` Get all groups that are located between two PDB residue numbers.
`Group` `AtomImpl.getParent()`
`Group` `Atom.getParent()` Returns the parent Group of the Atom.
`Group` `ChainImpl.getSeqResGroup(int position)` return the Group at position X.
`Group` `Chain.getSeqResGroup(int position)` return the Group at position X.
`Group` `GroupIterator.next()` get next Group.

Methods in org.biojava.bio.structure that return types with arguments of type Group
`List<Group>` `ChainImpl.getAtomGroups()` Return all groups that have been specified in the ATOM section of this chain .
`List<Group>` `Chain.getAtomGroups()` Return all groups that have been specified in the ATOM section of this chain .
`List<Group>` `ChainImpl.getAtomGroups(String type)` Get the Groups of a certain type, that are listed int the ATOM records of the PDB file.
`List<Group>` `Chain.getAtomGroups(String type)` Return a List of all groups of a special type (e.g.
`List<Group>` `ChainImpl.getGroups()` Deprecated. use getAtomGroups instead
`List<Group>` `Chain.getGroups()` Deprecated. use getAtomGroups or getSeqResGroups instead
`List<Group>` `ChainImpl.getGroups(String type)` Deprecated. use getAtomGroups instead
`List<Group>` `Chain.getGroups(String type)` Deprecated. use getAtomGroups or getSeqResGroups instead
`List<Group>` `ChainImpl.getSeqResGroups()` Return all groups of this chain.
`List<Group>` `Chain.getSeqResGroups()` Return all groups of this chain.
`List<Group>` `ChainImpl.getSeqResGroups(String type)` Return a List of all groups of a special type (e.g.
`List<Group>` `Chain.getSeqResGroups(String type)` Return a List of all groups of a special type (e.g.

Methods in org.biojava.bio.structure with parameters of type Group
`void` `ChainImpl.addGroup(Group group)` add a group to the list of ATOM record group of this chain.
`void` `Chain.addGroup(Group group)` add a group to the list of ATOM record group of this chain.
`static void` `Calc.rotate(Group group, double[][] rotationmatrix)` rotate a structure .
`static void` `Calc.rotate(Group group, Matrix m)` Rotate a group object.
`void` `AtomImpl.setParent(Group parent)`
`void` `Atom.setParent(Group parent)` Sets the back-reference to its parent Group.
`static void` `Calc.shift(Group group, Atom a)` Shift a Group with a vector.

Method parameters in org.biojava.bio.structure with type arguments of type Group
`void` `ChainImpl.setAtomGroups(List<Group> groups)` Set all groups that have been specified in the ATOM section of this chain .
`void` `Chain.setAtomGroups(List<Group> groups)` Set all groups that have been specified in the ATOM section of this chain .
`void` `ChainImpl.setSeqResGroups(List<Group> groups)` Set the list of SeqResGroups for this chain.
`void` `Chain.setSeqResGroups(List<Group> seqResGroups)` Set the list of SeqResGroups for this chain.

Constructors in org.biojava.bio.structure with parameters of type Group
`AtomIterator(Group g)` Constructs an AtomIterator object.
`StructureImpl(Group g)` construct a Structure object that only contains a single group

Uses of Group in org.biojava.bio.structure.io

Method parameters in org.biojava.bio.structure.io with type arguments of type Group
`boolean` `SeqRes2AtomAligner.align(List<Group> seqRes, List<Group> atomRes)` aligns two chains of groups, where the first chain is representing the list of amino acids as obtained from the SEQRES records, and the second chain represents the groups obtained from the ATOM records (and containing the actual ATOM information).
`boolean` `SeqRes2AtomAligner.align(List<Group> seqRes, List<Group> atomRes)` aligns two chains of groups, where the first chain is representing the list of amino acids as obtained from the SEQRES records, and the second chain represents the groups obtained from the ATOM records (and containing the actual ATOM information).
`String` `SeqRes2AtomAligner.getFullAtomSequence(List<Group> groups)` returns the full sequence of the Atom records of a chain with X instead of HETATMSs.