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

Packages that use Group
org.biojava.bio.structure Interfaces and classes for protein structure (PDB). 
 

Uses of Group in org.biojava.bio.structure
 

Subinterfaces of Group in org.biojava.bio.structure
 interface AminoAcid
          AminoAcid inherits most from Hetatom.
 

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(java.lang.String chainName, java.lang.String pdbResnum)
           
 Group Structure.findGroup(java.lang.String chainId, java.lang.String pdbResnum)
          request a particular group from a structure.
 Group StructureImpl.findGroup(java.lang.String chainId, java.lang.String pdbResnum, int modelnr)
           
 Group Structure.findGroup(java.lang.String chainId, java.lang.String pdbResnum, int modelnr)
          request a particular group from a structure.
 Group Chain.getGroup(int position)
          return the amino acid at position X.
 Group ChainImpl.getGroup(int position)
          return the amino acid at position .
 Group Chain.getGroupByPDB(java.lang.String pdbresnum)
          get a group by its PDB residue numbering.
 Group ChainImpl.getGroupByPDB(java.lang.String pdbresnum)
           
 Group[] Chain.getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd)
          get all groups that are located between two PDB residue numbers
 Group[] ChainImpl.getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd)
           
 Group Atom.getParent()
          Returns the parent Group of the Atom returns null if the referenced object is not Group
 Group AtomImpl.getParent()
           
 

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

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