Uses of Class
org.biojava.nbio.structure.contact.AtomContactSet

Packages that use AtomContactSet

Package	Description
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.contact

Uses of AtomContactSet in org.biojava.nbio.structure

Methods in org.biojava.nbio.structure that return AtomContactSet

Modifier and Type	Method	Description
static AtomContactSet	StructureTools.getAtomsCAInContact(Chain chain, double cutoff)	Returns the set of intra-chain contacts for the given chain for C-alpha atoms (including non-standard aminoacids appearing as HETATM groups), i.e. the contact map.
static AtomContactSet	StructureTools.getAtomsInContact(Chain chain, double cutoff)	Returns the set of intra-chain contacts for the given chain for all non-H atoms of non-hetatoms, i.e. the contact map.
static AtomContactSet	StructureTools.getAtomsInContact(Chain chain, String[] atomNames, double cutoff)	Returns the set of intra-chain contacts for the given chain for given atom names, i.e. the contact map.
static AtomContactSet	StructureTools.getAtomsInContact(Chain chain1, Chain chain2, double cutoff, boolean hetAtoms)	Returns the set of inter-chain contacts between the two given chains for all non-H atoms.
static AtomContactSet	StructureTools.getAtomsInContact(Chain chain1, Chain chain2, String[] atomNames, double cutoff, boolean hetAtoms)	Returns the set of inter-chain contacts between the two given chains for the given atom names.
static AtomContactSet	StructureTools.getRepresentativeAtomsInContact(Chain chain, double cutoff)	Returns the set of intra-chain contacts for the given chain for C-alpha or C3' atoms (including non-standard aminoacids appearing as HETATM groups), i.e. the contact map.

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

Methods in org.biojava.nbio.structure.contact that return AtomContactSet

Modifier and Type	Method	Description
AtomContactSet	Grid.getAtomContacts()	Returns all contacts, i.e. all atoms that are within the cutoff distance.
AtomContactSet	Grid.getContacts()	Deprecated. use Grid.getAtomContacts() instead
AtomContactSet	StructureInterface.getContacts()

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

Modifier and Type	Method	Description
void	StructureInterface.setContacts(AtomContactSet contacts)

Constructors in org.biojava.nbio.structure.contact with parameters of type AtomContactSet

Modifier	Constructor	Description
	GroupContactSet(AtomContactSet atomContacts)	Constructs a GroupContactSet by collapsing the given AtomContactSet into residue-residue (group-group) contacts.
	StructureInterface(Atom[] firstMolecule, Atom[] secondMolecule, String firstMoleculeId, String secondMoleculeId, AtomContactSet contacts, CrystalTransform firstTransf, CrystalTransform secondTransf)	Constructs a StructureInterface