Uses of Class
org.biojava.nbio.structure.contact.AtomContactSet
Packages that use AtomContactSet
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Uses of AtomContactSet in org.biojava.nbio.structure
Methods in org.biojava.nbio.structure that return AtomContactSetModifier and TypeMethodDescriptionstatic 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.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.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.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. -
Uses of AtomContactSet in org.biojava.nbio.structure.contact
Methods in org.biojava.nbio.structure.contact that return AtomContactSetModifier and TypeMethodDescriptionGrid.getAtomContacts()
Returns all contacts, i.e.Grid.getContacts()
Deprecated.StructureInterface.getContacts()
Methods in org.biojava.nbio.structure.contact with parameters of type AtomContactSetConstructors in org.biojava.nbio.structure.contact with parameters of type AtomContactSetModifierConstructorDescriptionGroupContactSet
(AtomContactSet atomContacts) Constructs aGroupContactSet
by collapsing the givenAtomContactSet
into residue-residue (group-group) contacts.StructureInterface
(Atom[] firstMolecule, Atom[] secondMolecule, String firstMoleculeId, String secondMoleculeId, AtomContactSet contacts, CrystalTransform firstTransf, CrystalTransform secondTransf) Constructs a StructureInterface
Grid.getAtomContacts()
instead