test_class.declarator: structuralMotif
test_class.modifier: private static
test_class.original_string: private static StructuralMotif structuralMotif;
test_class.type: StructuralMotif
test_class.var_name: structuralMotif
test_class.file: singa-structure/src/test/java/bio/singa/structure/model/oak/StructuralMotifsTest.java
test_class.identifier: StructuralMotifsTest
test_case.body: @Test
      void shouldCalculateRmsdMatrix() throws IOException {
          List<StructuralMotif> input = Files.list(Paths.get(Resources.getResourceAsFileLocation("consensus_alignment")))
                  .map(path -> StructureParser.local()
                          .fileLocation(path.toString())
                          .parse())
                  .map(Structure::getAllLeafSubstructures)
                  .map(StructuralMotif::fromLeafSubstructures)
                  .collect(Collectors.toList());
          assertEquals(StructuralMotifs.calculateRmsdMatrix(input, false).getRowDimension(), input.size());
      }
test_case.class_method_signature: StructuralMotifsTest.shouldCalculateRmsdMatrix()
test_case.full_signature: @Test void shouldCalculateRmsdMatrix()
test_case.identifier: shouldCalculateRmsdMatrix
test_case.invocations: collect map map map list get getResourceAsFileLocation parse fileLocation local toString toList assertEquals getRowDimension calculateRmsdMatrix size
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldCalculateRmsdMatrix()
focal_class.file: singa-structure/src/main/java/bio/singa/structure/model/oak/StructuralMotifs.java
focal_class.identifier: StructuralMotifs
focal_class.class_method_signature: StructuralMotifs.StructuralMotifs()
focal_class.full_signature: private  StructuralMotifs()
focal_class.identifier: StructuralMotifs
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.signature:  StructuralMotifs()
focal_class.class_method_signature: StructuralMotifs.assignComplexExchanges(StructuralMotif structuralMotif, EnumSet<MatcherFamily> familyGroup)
focal_class.full_signature: public static void assignComplexExchanges(StructuralMotif structuralMotif, EnumSet<MatcherFamily> familyGroup)
focal_class.identifier: assignComplexExchanges
focal_class.modifiers: public static
focal_class.parameters: (StructuralMotif structuralMotif, EnumSet<MatcherFamily> familyGroup)
focal_class.return: void
focal_class.signature: void assignComplexExchanges(StructuralMotif structuralMotif, EnumSet<MatcherFamily> familyGroup)
focal_class.class_method_signature: StructuralMotifs.calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                                boolean idealSuperimposition)
focal_class.full_signature: public static LabeledSymmetricMatrix<StructuralMotif> calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                                boolean idealSuperimposition)
focal_class.identifier: calculateRmsdMatrix
focal_class.modifiers: public static
focal_class.parameters: (List<StructuralMotif> structuralMotifs,
                                                                                boolean idealSuperimposition)
focal_class.return: LabeledSymmetricMatrix<StructuralMotif>
focal_class.signature: LabeledSymmetricMatrix<StructuralMotif> calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                                boolean idealSuperimposition)
focal_class.class_method_signature: StructuralMotifs.calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                                Predicate<Atom> atomFilter,
                                                                                boolean idealSuperimposition)
focal_class.full_signature: public static LabeledSymmetricMatrix<StructuralMotif> calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                                Predicate<Atom> atomFilter,
                                                                                boolean idealSuperimposition)
focal_class.identifier: calculateRmsdMatrix
focal_class.modifiers: public static
focal_class.parameters: (List<StructuralMotif> structuralMotifs,
                                                                                Predicate<Atom> atomFilter,
                                                                                boolean idealSuperimposition)
focal_class.return: LabeledSymmetricMatrix<StructuralMotif>
focal_class.signature: LabeledSymmetricMatrix<StructuralMotif> calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                                Predicate<Atom> atomFilter,
                                                                                boolean idealSuperimposition)
focal_method.body: public static LabeledSymmetricMatrix<StructuralMotif> calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                                boolean idealSuperimposition) {
          return calculateRmsdMatrix(structuralMotifs, StructuralEntityFilter.AtomFilter.isArbitrary(), idealSuperimposition);
      }
focal_method.class_method_signature: StructuralMotifs.calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                                boolean idealSuperimposition)
focal_method.full_signature: public static LabeledSymmetricMatrix<StructuralMotif> calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                                boolean idealSuperimposition)
focal_method.identifier: calculateRmsdMatrix
focal_method.invocations: calculateRmsdMatrix isArbitrary
focal_method.modifiers: public static
focal_method.parameters: (List<StructuralMotif> structuralMotifs,
                                                                                boolean idealSuperimposition)
focal_method.return: LabeledSymmetricMatrix<StructuralMotif>
focal_method.signature: LabeledSymmetricMatrix<StructuralMotif> calculateRmsdMatrix(List<StructuralMotif> structuralMotifs,
                                                                                boolean idealSuperimposition)