test_class.declarator: candidate
test_class.modifier: private static
test_class.original_string: private static Chain candidate;
test_class.type: Chain
test_class.var_name: candidate
test_class.declarator: reference
test_class.modifier: private static
test_class.original_string: private static Chain reference;
test_class.type: Chain
test_class.var_name: reference
test_class.file: singa-structure/src/test/java/bio/singa/structure/algorithms/superimposition/SubstructureSuperimposerTest.java
test_class.identifier: SubstructureSuperimposerTest
test_case.body: @Test
      void shouldCalculateMappedFullCandidates() {
          SubstructureSuperimposition superimposition = SubstructureSuperimposer
                  .calculateIdealSubstructureSuperimposition(reference, candidate, StructuralEntityFilter.AtomFilter.isBackbone());
          assertEquals(24, superimposition.getMappedFullCandidate().stream()
                  .map(LeafSubstructure::getAllAtoms)
                  .mapToLong(Collection::size)
                  .sum());
      }
test_case.class_method_signature: SubstructureSuperimposerTest.shouldCalculateMappedFullCandidates()
test_case.full_signature: @Test void shouldCalculateMappedFullCandidates()
test_case.identifier: shouldCalculateMappedFullCandidates
test_case.invocations: calculateIdealSubstructureSuperimposition isBackbone assertEquals sum mapToLong map stream getMappedFullCandidate
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldCalculateMappedFullCandidates()
focal_class.declarator: logger = LoggerFactory.getLogger(SubstructureSuperimposition.class)
focal_class.modifier: private static final
focal_class.original_string: private static final Logger logger = LoggerFactory.getLogger(SubstructureSuperimposition.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.declarator: DEFAULT_ATOM_FILTER = AtomFilter.isArbitrary()
focal_class.modifier: private static final
focal_class.original_string: private static final Predicate<Atom> DEFAULT_ATOM_FILTER = AtomFilter.isArbitrary();
focal_class.type: Predicate<Atom>
focal_class.var_name: DEFAULT_ATOM_FILTER
focal_class.declarator: reference
focal_class.modifier: protected final
focal_class.original_string: protected final List<LeafSubstructure<?>> reference;
focal_class.type: List<LeafSubstructure<?>>
focal_class.var_name: reference
focal_class.declarator: candidate
focal_class.modifier: protected final
focal_class.original_string: protected final List<LeafSubstructure<?>> candidate;
focal_class.type: List<LeafSubstructure<?>>
focal_class.var_name: candidate
focal_class.declarator: atomFilter
focal_class.modifier: private final
focal_class.original_string: private final Predicate<Atom> atomFilter;
focal_class.type: Predicate<Atom>
focal_class.var_name: atomFilter
focal_class.declarator: representationScheme
focal_class.modifier: private final
focal_class.original_string: private final RepresentationScheme representationScheme;
focal_class.type: RepresentationScheme
focal_class.var_name: representationScheme
focal_class.declarator: translation
focal_class.modifier: private
focal_class.original_string: private Vector translation;
focal_class.type: Vector
focal_class.var_name: translation
focal_class.declarator: rotation
focal_class.modifier: private
focal_class.original_string: private Matrix rotation;
focal_class.type: Matrix
focal_class.var_name: rotation
focal_class.file: singa-structure/src/main/java/bio/singa/structure/algorithms/superimposition/SubstructureSuperimposer.java
focal_class.identifier: SubstructureSuperimposer
focal_class.class_method_signature: SubstructureSuperimposer.SubstructureSuperimposer(LeafSubstructureContainer reference, LeafSubstructureContainer candidate)
focal_class.full_signature: private  SubstructureSuperimposer(LeafSubstructureContainer reference, LeafSubstructureContainer candidate)
focal_class.identifier: SubstructureSuperimposer
focal_class.modifiers: private
focal_class.parameters: (LeafSubstructureContainer reference, LeafSubstructureContainer candidate)
focal_class.signature:  SubstructureSuperimposer(LeafSubstructureContainer reference, LeafSubstructureContainer candidate)
focal_class.class_method_signature: SubstructureSuperimposer.SubstructureSuperimposer(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter,
                                       RepresentationScheme representationScheme)
focal_class.full_signature: private  SubstructureSuperimposer(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter,
                                       RepresentationScheme representationScheme)
focal_class.identifier: SubstructureSuperimposer
focal_class.modifiers: private
focal_class.parameters: (LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter,
                                       RepresentationScheme representationScheme)
focal_class.signature:  SubstructureSuperimposer(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter,
                                       RepresentationScheme representationScheme)
focal_class.class_method_signature: SubstructureSuperimposer.SubstructureSuperimposer(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate,
                                       Predicate<Atom> atomFilter, RepresentationScheme representationScheme)
focal_class.full_signature: private  SubstructureSuperimposer(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate,
                                       Predicate<Atom> atomFilter, RepresentationScheme representationScheme)
focal_class.identifier: SubstructureSuperimposer
focal_class.modifiers: private
focal_class.parameters: (List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate,
                                       Predicate<Atom> atomFilter, RepresentationScheme representationScheme)
focal_class.signature:  SubstructureSuperimposer(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate,
                                       Predicate<Atom> atomFilter, RepresentationScheme representationScheme)
focal_class.class_method_signature: SubstructureSuperimposer.SubstructureSuperimposer(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)
focal_class.full_signature: protected  SubstructureSuperimposer(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)
focal_class.identifier: SubstructureSuperimposer
focal_class.modifiers: protected
focal_class.parameters: (List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)
focal_class.signature:  SubstructureSuperimposer(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)
focal_class.class_method_signature: SubstructureSuperimposer.SubstructureSuperimposer(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate,
                                       RepresentationScheme representationScheme)
focal_class.full_signature: private  SubstructureSuperimposer(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate,
                                       RepresentationScheme representationScheme)
focal_class.identifier: SubstructureSuperimposer
focal_class.modifiers: private
focal_class.parameters: (List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate,
                                       RepresentationScheme representationScheme)
focal_class.signature:  SubstructureSuperimposer(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate,
                                       RepresentationScheme representationScheme)
focal_class.class_method_signature: SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate)
focal_class.full_signature: public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate)
focal_class.identifier: calculateIdealSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate)
focal_class.class_method_signature: SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          Predicate<Atom> atomFilter)
focal_class.full_signature: public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          Predicate<Atom> atomFilter)
focal_class.identifier: calculateIdealSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          Predicate<Atom> atomFilter)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          Predicate<Atom> atomFilter)
focal_class.class_method_signature: SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          RepresentationScheme representationScheme)
focal_class.full_signature: public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          RepresentationScheme representationScheme)
focal_class.identifier: calculateIdealSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          RepresentationScheme representationScheme)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          RepresentationScheme representationScheme)
focal_class.class_method_signature: SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate)
focal_class.full_signature: public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate)
focal_class.identifier: calculateIdealSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate)
focal_class.class_method_signature: SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          Predicate<Atom> atomFilter)
focal_class.full_signature: public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          Predicate<Atom> atomFilter)
focal_class.identifier: calculateIdealSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          Predicate<Atom> atomFilter)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          Predicate<Atom> atomFilter)
focal_class.class_method_signature: SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          RepresentationScheme representationScheme)
focal_class.full_signature: public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          RepresentationScheme representationScheme)
focal_class.identifier: calculateIdealSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          RepresentationScheme representationScheme)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          RepresentationScheme representationScheme)
focal_class.class_method_signature: SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.full_signature: public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.identifier: calculateKuhnMunkresSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.class_method_signature: SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                Predicate<Atom> atomFilter,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.full_signature: public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                Predicate<Atom> atomFilter,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.identifier: calculateKuhnMunkresSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                Predicate<Atom> atomFilter,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                Predicate<Atom> atomFilter,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.class_method_signature: SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                RepresentationScheme representationScheme,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.full_signature: public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                RepresentationScheme representationScheme,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.identifier: calculateKuhnMunkresSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                RepresentationScheme representationScheme,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                                List<LeafSubstructure<?>> candidate,
                                                                                                RepresentationScheme representationScheme,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.class_method_signature: SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.full_signature: public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.identifier: calculateKuhnMunkresSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.class_method_signature: SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                Predicate<Atom> atomFilter,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.full_signature: public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                Predicate<Atom> atomFilter,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.identifier: calculateKuhnMunkresSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                Predicate<Atom> atomFilter,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                Predicate<Atom> atomFilter,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.class_method_signature: SubstructureSuperimposer.calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                RepresentationScheme representationScheme,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.full_signature: public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                RepresentationScheme representationScheme,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.identifier: calculateKuhnMunkresSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                RepresentationScheme representationScheme,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                                LeafSubstructureContainer candidate,
                                                                                                RepresentationScheme representationScheme,
                                                                                                SubstitutionMatrix substitutionMatrix,
                                                                                                boolean considerExchanges)
focal_class.class_method_signature: SubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate)
focal_class.full_signature: public static SubstructureSuperimposition calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate)
focal_class.identifier: calculateSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate)
focal_class.class_method_signature: SubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate,
                                                                                     Predicate<Atom> atomFilter)
focal_class.full_signature: public static SubstructureSuperimposition calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate,
                                                                                     Predicate<Atom> atomFilter)
focal_class.identifier: calculateSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate,
                                                                                     Predicate<Atom> atomFilter)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate,
                                                                                     Predicate<Atom> atomFilter)
focal_class.class_method_signature: SubstructureSuperimposer.calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate,
                                                                                     RepresentationScheme representationScheme)
focal_class.full_signature: public static SubstructureSuperimposition calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate,
                                                                                     RepresentationScheme representationScheme)
focal_class.identifier: calculateSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate,
                                                                                     RepresentationScheme representationScheme)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                     List<LeafSubstructure<?>> candidate,
                                                                                     RepresentationScheme representationScheme)
focal_class.class_method_signature: SubstructureSuperimposer.calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate)
focal_class.full_signature: public static SubstructureSuperimposition calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate)
focal_class.identifier: calculateSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate)
focal_class.class_method_signature: SubstructureSuperimposer.calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate,
                                                                                     Predicate<Atom> atomFilter)
focal_class.full_signature: public static SubstructureSuperimposition calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate,
                                                                                     Predicate<Atom> atomFilter)
focal_class.identifier: calculateSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate,
                                                                                     Predicate<Atom> atomFilter)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate,
                                                                                     Predicate<Atom> atomFilter)
focal_class.class_method_signature: SubstructureSuperimposer.calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate,
                                                                                     RepresentationScheme representationScheme)
focal_class.full_signature: public static SubstructureSuperimposition calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate,
                                                                                     RepresentationScheme representationScheme)
focal_class.identifier: calculateSubstructureSuperimposition
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate,
                                                                                     RepresentationScheme representationScheme)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                     LeafSubstructureContainer candidate,
                                                                                     RepresentationScheme representationScheme)
focal_class.class_method_signature: SubstructureSuperimposer.calculateSuperimposition()
focal_class.full_signature: protected SubstructureSuperimposition calculateSuperimposition()
focal_class.identifier: calculateSuperimposition
focal_class.modifiers: protected
focal_class.parameters: ()
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateSuperimposition()
focal_class.class_method_signature: SubstructureSuperimposer.defineAtoms()
focal_class.full_signature: protected Pair<List<Atom>> defineAtoms()
focal_class.identifier: defineAtoms
focal_class.modifiers: protected
focal_class.parameters: ()
focal_class.return: Pair<List<Atom>>
focal_class.signature: Pair<List<Atom>> defineAtoms()
focal_class.class_method_signature: SubstructureSuperimposer.defineIntersectingAtoms(Map.Entry<Pair<LeafSubstructure<?>>, Set<String>> pairListEntry)
focal_class.full_signature: private void defineIntersectingAtoms(Map.Entry<Pair<LeafSubstructure<?>>, Set<String>> pairListEntry)
focal_class.identifier: defineIntersectingAtoms
focal_class.modifiers: private
focal_class.parameters: (Map.Entry<Pair<LeafSubstructure<?>>, Set<String>> pairListEntry)
focal_class.return: void
focal_class.signature: void defineIntersectingAtoms(Map.Entry<Pair<LeafSubstructure<?>>, Set<String>> pairListEntry)
focal_class.class_method_signature: SubstructureSuperimposer.calculateIdealSuperimposition()
focal_class.full_signature: private SubstructureSuperimposition calculateIdealSuperimposition()
focal_class.identifier: calculateIdealSuperimposition
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateIdealSuperimposition()
focal_class.class_method_signature: SubstructureSuperimposer.calculateKuhnMunkresSuperimposition(SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
focal_class.full_signature: private SubstructureSuperimposition calculateKuhnMunkresSuperimposition(SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
focal_class.identifier: calculateKuhnMunkresSuperimposition
focal_class.modifiers: private
focal_class.parameters: (SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
focal_class.return: SubstructureSuperimposition
focal_class.signature: SubstructureSuperimposition calculateKuhnMunkresSuperimposition(SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
focal_class.class_method_signature: SubstructureSuperimposer.toAlignmentString(List<LeafSubstructure<?>> mappedCandidate, Pair<List<Atom>> alignmentAtoms)
focal_class.full_signature: private String toAlignmentString(List<LeafSubstructure<?>> mappedCandidate, Pair<List<Atom>> alignmentAtoms)
focal_class.identifier: toAlignmentString
focal_class.modifiers: private
focal_class.parameters: (List<LeafSubstructure<?>> mappedCandidate, Pair<List<Atom>> alignmentAtoms)
focal_class.return: String
focal_class.signature: String toAlignmentString(List<LeafSubstructure<?>> mappedCandidate, Pair<List<Atom>> alignmentAtoms)
focal_method.body: public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate) {
          return new SubstructureSuperimposer(reference, candidate).calculateIdealSuperimposition();
      }
focal_method.class_method_signature: SubstructureSuperimposer.calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate)
focal_method.full_signature: public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate)
focal_method.identifier: calculateIdealSubstructureSuperimposition
focal_method.invocations: calculateIdealSuperimposition
focal_method.modifiers: public static
focal_method.parameters: (List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate)
focal_method.return: SubstructureSuperimposition
focal_method.signature: SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate)