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 Structure.findGroup(java.lang.String chainId, java.lang.String pdbResnum)
          request a particular group from a structure.
 Group StructureImpl.findGroup(java.lang.String chainName, java.lang.String pdbResnum)
           
 Group Structure.findGroup(java.lang.String chainId, java.lang.String pdbResnum, int modelnr)
          request a particular group from a structure.
 Group StructureImpl.findGroup(java.lang.String chainId, java.lang.String pdbResnum, int modelnr)
           
 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(java.lang.String pdbresnum)
           
 Group Chain.getGroupByPDB(java.lang.String pdbresnum)
          get a group by its PDB residue numbering.
 Group[] ChainImpl.getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd)
          Get all groups that are located between two PDB residue numbers.
 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, boolean ignoreMissing)
          Get all groups that are located between two PDB residue numbers.
 Group[] Chain.getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd, boolean ignoreMissing)
          Get all groups that are located between two PDB residue numbers.
 Group Atom.getParent()
          Returns the parent Group of the Atom.
 Group AtomImpl.getParent()
           
 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
 java.util.List<Group> ChainImpl.getAtomGroups()
          Return all groups that have been specified in the ATOM section of this chain .
 java.util.List<Group> Chain.getAtomGroups()
          Return all groups that have been specified in the ATOM section of this chain .
 java.util.List<Group> ChainImpl.getAtomGroups(java.lang.String type)
          Get the Groups of a certain type, that are listed int the ATOM records of the PDB file.
 java.util.List<Group> Chain.getAtomGroups(java.lang.String type)
          Return a List of all groups of a special type (e.g.
 java.util.List<Group> ChainImpl.getGroups()
          Deprecated. use getAtomGroups instead
 java.util.List<Group> Chain.getGroups()
          Deprecated. use getAtomGroups or getSeqResGroups instead
 java.util.List<Group> ChainImpl.getGroups(java.lang.String type)
          Deprecated. use getAtomGroups instead
 java.util.List<Group> Chain.getGroups(java.lang.String type)
          Deprecated. use getAtomGroups or getSeqResGroups instead
 java.util.List<Group> ChainImpl.getSeqResGroups()
          Return all groups of this chain.
 java.util.List<Group> Chain.getSeqResGroups()
          Return all groups of this chain.
 java.util.List<Group> ChainImpl.getSeqResGroups(java.lang.String type)
          Return a List of all groups of a special type (e.g.
 java.util.List<Group> Chain.getSeqResGroups(java.lang.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 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.
 

Method parameters in org.biojava.bio.structure with type arguments of type Group
 void ChainImpl.setAtomGroups(java.util.List<Group> groups)
          Set all groups that have been specified in the ATOM section of this chain .
 void Chain.setAtomGroups(java.util.List<Group> groups)
          Set all groups that have been specified in the ATOM section of this chain .
 void ChainImpl.setSeqResGroups(java.util.List<Group> groups)
          Set the list of SeqResGroups for this chain.
 void Chain.setSeqResGroups(java.util.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(java.util.List<Group> seqRes, java.util.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(java.util.List<Group> seqRes, java.util.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).
 java.lang.String SeqRes2AtomAligner.getFullAtomSequence(java.util.List<Group> groups)
          returns the full sequence of the Atom records of a chain with X instead of HETATMSs.