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

Packages that use Group

Package	Description
org.biojava.nbio.protmod.structure
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align	Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.fatcat.calc
org.biojava.nbio.structure.align.gui
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.asa
org.biojava.nbio.structure.basepairs
org.biojava.nbio.structure.contact
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.io.mmcif	Input and Output of mmcif files.
org.biojava.nbio.structure.io.mmtf
org.biojava.nbio.structure.secstruc
org.biojava.nbio.structure.symmetry.utils

Uses of Group in org.biojava.nbio.protmod.structure

Methods in org.biojava.nbio.protmod.structure that return types with arguments of type Group

Modifier and Type	Method and Description
static List<Group>	StructureUtil.getAminoAcids(Chain chain) Get all amino acids in a chain.

Methods in org.biojava.nbio.protmod.structure with parameters of type Group

Modifier and Type	Method and Description
static List<Atom[]>	StructureUtil.findAtomLinkages(Group group1, Group group2, boolean ignoreNCLinkage, double bondLengthTolerance) Find linkages between two groups within tolerance of bond length, from potential atoms.
static List<Atom[]>	StructureUtil.findAtomLinkages(Group group1, Group group2, List<String> potentialNamesOfAtomOnGroup1, List<String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance) Find linkages between two groups within tolerance of bond length, from potential atoms.
static Atom[]	StructureUtil.findLinkage(Group group1, Group group2, String nameOfAtomOnGroup1, String nameOfAtomOnGroup2, double bondLengthTolerance) Find a linkage between two groups within tolerance of bond length.
static Atom[]	StructureUtil.findNearestAtomLinkage(Group group1, Group group2, List<String> potentialNamesOfAtomOnGroup1, List<String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance) Find a linkage between two groups within tolerance of bond length, from potential atoms.
static List<String>	StructureUtil.getAtomNames(Group group)
static StructureGroup	StructureUtil.getStructureGroup(Group group, boolean isAminoAcid)

Uses of Group in org.biojava.nbio.structure

Subinterfaces of Group in org.biojava.nbio.structure

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

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

Modifier and Type	Class and 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.nbio.structure that return Group

Modifier and Type	Method and Description
static Group[]	StructureTools.cloneGroups(Atom[] ca) Clone a set of representative Atoms, but returns the parent groups
Group	StructureImpl.findGroup(String chainName, String pdbResnum) Request a particular group from a structure.
Group	Structure.findGroup(String authId, String pdbResnum) Request a particular group from a structure.
Group	StructureImpl.findGroup(String chainName, String pdbResnum, int modelnr) Request a particular group from a structure.
Group	Structure.findGroup(String authId, String pdbResnum, int modelnr) Request a particular group from a structure.
Group	Group.getAltLocGroup(Character altLoc) Gets the alternate location group to this group that has the alt-loc character code passed.
Group	HetatomImpl.getAltLocGroup(Character altLoc)
Group	Chain.getAtomGroup(int position) Return the Group at given position, from within Groups with observed density in the chain, i.e.
Group	ChainImpl.getAtomGroup(int position) Return the Group at given position, from within Groups with observed density in the chain, i.e.
Group	Atom.getGroup() Return the parent Group of the Atom.
Group	AtomImpl.getGroup() Return the parent Group of the Atom.
Group	Chain.getGroupByPDB(ResidueNumber resNum) Get a group by its PDB residue numbering.
Group	ChainImpl.getGroupByPDB(ResidueNumber resNum) Get a group by its PDB residue numbering.
static Group	StructureTools.getGroupByPDBResidueNumber(Structure struc, ResidueNumber pdbResNum) Get a group represented by a ResidueNumber.
Group[]	Chain.getGroupsByPDB(ResidueNumber pdbresnumStart, ResidueNumber pdbresnumEnd) Get all groups that are located between two PDB residue numbers.
Group[]	ChainImpl.getGroupsByPDB(ResidueNumber start, ResidueNumber end) Get all groups that are located between two PDB residue numbers.
Group[]	Chain.getGroupsByPDB(ResidueNumber pdbresnumStart, ResidueNumber pdbresnumEnd, boolean ignoreMissing) Get all groups that are located between two PDB residue numbers.
Group[]	ChainImpl.getGroupsByPDB(ResidueNumber start, ResidueNumber end, boolean ignoreMissing)
Group	Chain.getSeqResGroup(int position) Return the Group at given position, from within groups in the SEQRES records of the chain, i.e.
Group	ChainImpl.getSeqResGroup(int position) Return the Group at given position, from within groups in the SEQRES records of the chain, i.e.
Group	GroupIterator.next() get next Group.

Methods in org.biojava.nbio.structure that return types with arguments of type Group

Modifier and Type	Method and Description
static List<Group>	StructureTools.filterLigands(List<Group> allGroups) Removes all polymeric and solvent groups from a list of groups
static Set<Group>	StructureTools.getAllGroupsFromSubset(Atom[] atoms) Expand a set of atoms into all groups from the same structure.
static Set<Group>	StructureTools.getAllGroupsFromSubset(Atom[] atoms, GroupType types) Expand a set of atoms into all groups from the same structure.
List<Group>	Group.getAltLocs() Get the list of other alternate location groups.
List<Group>	HetatomImpl.getAltLocs()
List<Group>	Chain.getAtomGroups() Return all Groups with observed density in the chain, i.e.
List<Group>	ChainImpl.getAtomGroups() Return all Groups with observed density in the chain, i.e.
List<Group>	Chain.getAtomGroups(GroupType type) Return a List of all (observed) Groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
List<Group>	ChainImpl.getAtomGroups(GroupType type) Return a List of all (observed) Groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
List<Group>	Chain.getAtomLigands() Deprecated. since biojava 5.0 this does not apply anymore. Chains contain either polymeric groups or non-polymeric groups
List<Group>	ChainImpl.getAtomLigands() Gets all groups that are not polymer groups and that are not solvent groups.
static Map<Group,Double>	StructureTools.getGroupDistancesWithinShell(Structure structure, Atom centroid, Set<ResidueNumber> excludeResidues, double radius, boolean includeWater, boolean useAverageDistance) Finds Groups in structure that contain at least one Atom that is within radius Angstroms of centroid.
List<Group>	Site.getGroups()
static Set<Group>	StructureTools.getGroupsWithinShell(Structure structure, Atom atom, Set<ResidueNumber> excludeResidues, double distance, boolean includeWater)
static Set<Group>	StructureTools.getGroupsWithinShell(Structure structure, Group group, double distance, boolean includeWater) Returns a Set of Groups in a structure within the distance specified of a given group.
static List<Group>	StructureTools.getLigandsByProximity(Collection<Group> target, Atom[] query, double cutoff) Finds all ligand groups from the target which fall within the cutoff distance of some atom from the query set.
List<Group>	Chain.getSeqResGroups() Returns a list of all groups in SEQRES records of the chain, i.e.
List<Group>	ChainImpl.getSeqResGroups() Returns a list of all groups in SEQRES records of the chain, i.e.
List<Group>	Chain.getSeqResGroups(GroupType type) Returns a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
List<Group>	ChainImpl.getSeqResGroups(GroupType type) Returns a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
static List<Group>	StructureTools.getUnalignedGroups(Atom[] ca) List of groups from the structure not included in ca (e.g. ligands).

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

Modifier and Type	Method and Description
void	Group.addAltLoc(Group g) Add a group that is an alternate location for this group.
void	HetatomImpl.addAltLoc(Group group)
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 Chain	StructureTools.addGroupToStructure(Structure s, Group g, int model, Chain chainGuess, boolean clone) Adds a particular group to a structure.
protected void	HetatomImpl.cloneAtomsAndBonds(Group newGroup)
int	EntityInfo.getAlignedResIndex(Group g, Chain c) Given a Group g of Chain c (member of this EntityInfo) return the corresponding position in the alignment of all member sequences (1-based numbering), i.e. the index (1-based) in the SEQRES sequence.
static Set<Group>	StructureTools.getGroupsWithinShell(Structure structure, Group group, double distance, boolean includeWater) Returns a Set of Groups in a structure within the distance specified of a given group.
static boolean	StructureTools.hasDeuteratedEquiv(Atom atom, Group currentGroup) Check to see if a Hydrogen has a Deuterated brother in the group.
static boolean	StructureTools.hasNonDeuteratedEquiv(Atom atom, Group currentGroup) Check to see if an Deuterated atom has a non deuterated brother in the group.
boolean	AtomPositionMap.GroupMatcher.matches(Group group)
static void	Calc.rotate(Group group, double[][] rotationmatrix) Rotate a Group.
static void	Calc.rotate(Group group, Matrix m) Rotate a group object.
void	Atom.setGroup(Group parent) Set the back-reference to its parent Group.
void	AtomImpl.setGroup(Group parent) Set the back-reference to its parent Group.
static void	Calc.shift(Group group, Atom a) Shift a Group with a vector.
static void	Calc.transform(Group group, javax.vecmath.Matrix4d m) Transforms a group object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix).
static void	Calc.translate(Group group, javax.vecmath.Vector3d v) Translates a group object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)

Method parameters in org.biojava.nbio.structure with type arguments of type Group

Modifier and Type	Method and Description
static void	StructureTools.addGroupsToStructure(Structure s, Collection<Group> groups, int model, boolean clone) Add a list of groups to a new structure.
static List<Group>	StructureTools.filterLigands(List<Group> allGroups) Removes all polymeric and solvent groups from a list of groups
static List<Group>	StructureTools.getLigandsByProximity(Collection<Group> target, Atom[] query, double cutoff) Finds all ligand groups from the target which fall within the cutoff distance of some atom from the query set.
void	Chain.setAtomGroups(List<Group> groups) Set all Groups with observed density in the chain, i.e.
void	ChainImpl.setAtomGroups(List<Group> groups) Set all Groups with observed density in the chain, i.e.
void	Site.setGroups(List<Group> residues)
void	Chain.setSeqResGroups(List<Group> seqResGroups) Sets the list of SeqResGroups for this chain.
void	ChainImpl.setSeqResGroups(List<Group> groups) Sets the list of SeqResGroups for this chain.

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

Constructor and Description
AtomIterator(Group g) Constructs an AtomIterator object.
StructureImpl(Group g) Construct a Structure object that only contains a single group

Constructor parameters in org.biojava.nbio.structure with type arguments of type Group

Constructor and Description
Site(String siteID, List<Group> groups)

Uses of Group in org.biojava.nbio.structure.align

Methods in org.biojava.nbio.structure.align that return Group

Modifier and Type	Method and Description
static Group[]	AFPTwister.twistOptimized(AFPChain afpChain, Atom[] ca1, Atom[] ca2) superimposing according to the optimized alignment
static Group[]	AFPTwister.twistPDB(AFPChain afpChain, Atom[] ca1, Atom[] ca2) calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B

Uses of Group in org.biojava.nbio.structure.align.ce

Method parameters in org.biojava.nbio.structure.align.ce with type arguments of type Group

Modifier and Type	Method and Description
static Atom[]	GuiWrapper.getAtomArray(Atom[] ca, List<Group> hetatoms, List<Group> nucs)
static Atom[]	GuiWrapper.getAtomArray(Atom[] ca, List<Group> hetatoms, List<Group> nucs)

Uses of Group in org.biojava.nbio.structure.align.fatcat.calc

Methods in org.biojava.nbio.structure.align.fatcat.calc that return Group

Modifier and Type	Method and Description
Group[]	FatCatAligner.getTwistedGroups()

Methods in org.biojava.nbio.structure.align.fatcat.calc with parameters of type Group

Modifier and Type	Method and Description
void	FatCatAligner.setTwistedGroups(Group[] twistedGroups)

Uses of Group in org.biojava.nbio.structure.align.gui

Methods in org.biojava.nbio.structure.align.gui with parameters of type Group

Modifier and Type	Method and Description
static StructureAlignmentJmol	DisplayAFP.display(AFPChain afpChain, Group[] twistedGroups, Atom[] ca1, Atom[] ca2, List<Group> hetatms1, List<Group> hetatms2) Note: ca2, hetatoms2 and nucleotides2 should not be rotated.

Method parameters in org.biojava.nbio.structure.align.gui with type arguments of type Group

Modifier and Type	Method and Description
static StructureAlignmentJmol	DisplayAFP.display(AFPChain afpChain, Group[] twistedGroups, Atom[] ca1, Atom[] ca2, List<Group> hetatms1, List<Group> hetatms2) Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
static StructureAlignmentJmol	DisplayAFP.display(AFPChain afpChain, Group[] twistedGroups, Atom[] ca1, Atom[] ca2, List<Group> hetatms1, List<Group> hetatms2) Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
static Atom[]	DisplayAFP.getAtomArray(Atom[] ca, List<Group> hetatms) Returns the first atom for each group

Uses of Group in org.biojava.nbio.structure.align.util

Methods in org.biojava.nbio.structure.align.util that return Group

Modifier and Type	Method and Description
static Group[]	AlignmentTools.prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Rotate the Atoms/Groups so they are aligned for the 3D visualisation

Methods in org.biojava.nbio.structure.align.util with parameters of type Group

Modifier and Type	Method and Description
static void	AlignmentTools.shiftCA2(AFPChain afpChain, Atom[] ca2, Matrix m, Atom shift, Group[] twistedGroups) only shift CA positions.

Uses of Group in org.biojava.nbio.structure.asa

Methods in org.biojava.nbio.structure.asa that return Group

Modifier and Type	Method and Description
Group	GroupAsa.getGroup()

Constructors in org.biojava.nbio.structure.asa with parameters of type Group

Constructor and Description
GroupAsa(Group g)

Uses of Group in org.biojava.nbio.structure.basepairs

Methods in org.biojava.nbio.structure.basepairs that return types with arguments of type Group

Modifier and Type	Method and Description
List<Pair<Group>>	TertiaryBasePairParameters.findPairs(List<Chain> chains) This is an alternative implementation of findPair() that looks for anything that would fit the criteria for a base-pair, useful for the context of tertiary structure of RNA.
List<Pair<Group>>	BasePairParameters.findPairs(List<Chain> chains) This method performs a search for base pairs in the structure.
List<Pair<Group>>	MismatchedBasePairParameters.findPairs(List<Chain> chains) This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.

Method parameters in org.biojava.nbio.structure.basepairs with type arguments of type Group

Modifier and Type	Method and Description
javax.vecmath.Matrix4d	BasePairParameters.basePairReferenceFrame(Pair<Group> pair) This method calculates the central frame (4x4 transformation matrix) of a single base pair.

Uses of Group in org.biojava.nbio.structure.contact

Methods in org.biojava.nbio.structure.contact that return types with arguments of type Group

Modifier and Type	Method and Description
Pair<List<Group>>	StructureInterface.getCoreResidues(double bsaToAsaCutoff, double minAsaForSurface) Returns the residues belonging to the interface core, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is above the given bsaToAsaCutoff
Pair<List<Group>>	StructureInterface.getInterfacingResidues(double minAsaForSurface) Returns the residues belonging to the interface, i.e. the residues at the surface with BSA>0
Pair<Group>	GroupContact.getPair()
Pair<List<Group>>	StructureInterface.getRimResidues(double bsaToAsaCutoff, double minAsaForSurface) Returns the residues belonging to the interface rim, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is below the given bsaToAsaCutoff
Pair<List<Group>>	StructureInterface.getSurfaceResidues(double minAsaForSurface) Returns the residues belonging to the surface

Methods in org.biojava.nbio.structure.contact with parameters of type Group

Modifier and Type	Method and Description
GroupContact	GroupContactSet.getContact(Group group1, Group group2) Returns the corresponding GroupContact or null if no contact exists between the 2 given groups
boolean	GroupContactSet.hasContact(Group group1, Group group2) Tell whether the given group pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers

Method parameters in org.biojava.nbio.structure.contact with type arguments of type Group

Modifier and Type	Method and Description
void	GroupContact.setPair(Pair<Group> pair)

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

Methods in org.biojava.nbio.structure.io with parameters of type Group

Modifier and Type	Method and Description
String	GroupToSDF.getText(Group thisGroup)
static String	FileConvert.toPDB(Group g) Convert a Group object to PDB representation

Method parameters in org.biojava.nbio.structure.io with type arguments of type Group

Modifier and Type	Method and Description
static String	SeqRes2AtomAligner.getFullAtomSequence(List<Group> groups, Map<Integer,Integer> positionIndex, boolean isNucleotideChain) Returns the full sequence of the Atom records of a parent with X instead of HETATMSs.
static ProteinSequence	StructureSequenceMatcher.getProteinSequenceForStructure(Structure struct, Map<Integer,Group> groupIndexPosition) Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups.

Uses of Group in org.biojava.nbio.structure.io.mmcif

Methods in org.biojava.nbio.structure.io.mmcif that return Group

Modifier and Type	Method and Description
static Group	ChemCompGroupFactory.getGroupFromChemCompDictionary(String recordName)

Methods in org.biojava.nbio.structure.io.mmcif with parameters of type Group

Modifier and Type	Method and Description
static List<AtomSite>	MMCIFFileTools.convertGroupToAtomSites(Group g, int model, String chainName, String chainId) Converts a Group into a List of AtomSite objects.

Uses of Group in org.biojava.nbio.structure.io.mmtf

Methods in org.biojava.nbio.structure.io.mmtf with parameters of type Group

Modifier and Type	Method and Description
static List<Atom>	MmtfUtils.getAtomsForGroup(Group inputGroup) Get a list of atoms for a group.
static int	MmtfUtils.getSecStructType(Group group) Get the secondary structure as defined by DSSP.
static void	MmtfUtils.insertSeqResGroup(Chain chain, Group group, int sequenceIndexId) Insert the group in the given position in the sequence.
static void	MmtfUtils.setSecStructType(Group group, int dsspIndex) Get the secondary structure as defined by DSSP.

Uses of Group in org.biojava.nbio.structure.secstruc

Fields in org.biojava.nbio.structure.secstruc declared as Group

Modifier and Type	Field and Description
protected Group	SecStrucInfo.parent

Methods in org.biojava.nbio.structure.secstruc that return Group

Modifier and Type	Method and Description
Group	SecStrucInfo.getGroup()

Method parameters in org.biojava.nbio.structure.secstruc with type arguments of type Group

Modifier and Type	Method and Description
static List<SecStrucElement>	SecStrucTools.getSecStrucElements(List<Group> groups) Obtain the List of secondary structure elements (SecStrucElement) of a List of Groups (assumed to be sequential, this is, connected in the original Structure).

Constructors in org.biojava.nbio.structure.secstruc with parameters of type Group

Constructor and Description
SecStrucInfo(Group g, String ass, SecStrucType t)
SecStrucState(Group g, String ass, SecStrucType t)

Uses of Group in org.biojava.nbio.structure.symmetry.utils

Methods in org.biojava.nbio.structure.symmetry.utils that return types with arguments of type Group

Modifier and Type	Method and Description
static List<Group>	SymmetryTools.getGroups(Atom[] rAtoms) Returns the List of Groups of the corresponding representative Atom array.