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

Packages that use Group

Package	Description
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

Modifier and Type	Interface	Description
interface	AminoAcid	A Group that represents an AminoAcid.

Classes in org.biojava.bio.structure that implement Group

Modifier and Type	Class	Description
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

Modifier and Type	Method	Description
Group	Structure.findGroup(java.lang.String chainId, java.lang.String pdbResnum)	request a particular group from a structure.
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 chainName, java.lang.String pdbResnum)
Group	StructureImpl.findGroup(java.lang.String chainId, java.lang.String pdbResnum, int modelnr)
Group	Chain.getAtomGroup(int position)	return the Group at position X.
Group	ChainImpl.getAtomGroup(int position)	return the group at position .
Group	Chain.getGroup(int position)	Deprecated. use getAtomGroup or getSeqResGroup instead
Group	ChainImpl.getGroup(int position)	Deprecated. use getAtomGroup or getSeqResGroup instead
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[]	Chain.getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd, boolean ignoreMissing)	Get all groups that are located between two PDB residue numbers.
Group[]	ChainImpl.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	Atom.getParent()	Returns the parent Group of the Atom.
Group	AtomImpl.getParent()
Group	Chain.getSeqResGroup(int position)	return the Group at position X.
Group	ChainImpl.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

Modifier and Type	Method	Description
java.util.List<Group>	Chain.getAtomGroups()	Return all groups that have been specified in the ATOM section of this chain .
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.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.getGroups()	Deprecated. use getAtomGroups or getSeqResGroups instead
java.util.List<Group>	Chain.getGroups(java.lang.String type)	Deprecated. use getAtomGroups or getSeqResGroups instead
java.util.List<Group>	ChainImpl.getGroups()	Deprecated. use getAtomGroups instead
java.util.List<Group>	ChainImpl.getGroups(java.lang.String type)	Deprecated. use getAtomGroups instead
java.util.List<Group>	Chain.getSeqResGroups()	Return all groups of this chain.
java.util.List<Group>	Chain.getSeqResGroups(java.lang.String type)	Return a List of all groups of a special type (e.g.
java.util.List<Group>	ChainImpl.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.

Methods in org.biojava.bio.structure with parameters of type Group

Modifier and Type	Method	Description
void	Chain.addGroup(Group group)	add a group to the list of ATOM record group of this chain.
void	ChainImpl.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

Modifier and Type	Method	Description
void	Chain.setAtomGroups(java.util.List<Group> groups)	Set all groups that have been specified in the ATOM section of this chain .
void	ChainImpl.setAtomGroups(java.util.List<Group> groups)	Set all groups that have been specified in the ATOM section of this chain .
void	Chain.setSeqResGroups(java.util.List<Group> seqResGroups)	Set the list of SeqResGroups for this chain.
void	ChainImpl.setSeqResGroups(java.util.List<Group> groups)	Set the list of SeqResGroups for this chain.

Constructors in org.biojava.bio.structure with parameters of type Group

Constructor	Description
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

Modifier and Type	Method	Description
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.