test_class.declarator: queryMotif
test_class.modifier: private
test_class.original_string: private StructuralMotif queryMotif;
test_class.type: StructuralMotif
test_class.var_name: queryMotif
test_class.declarator: target
test_class.modifier: private
test_class.original_string: private  Structure target;
test_class.type: Structure
test_class.var_name: target
test_class.file: singa-structure/src/test/java/bio/singa/structure/algorithms/superimposition/fit3d/Fit3DAlignmentTest.java
test_class.identifier: Fit3DAlignmentTest
test_case.body: @Test
      void shouldHandleInsertionCodeMotifs() {
          Structure structure = StructureParser.pdb()
                  .pdbIdentifier("2w0l")
                  .parse();
  
          List<LeafIdentifier> leafIdentifiers = LeafIdentifiers.of("A-95A", "A-98", "A-100");
          StructuralMotif structuralMotif = StructuralMotif.fromLeafIdentifiers(structure, leafIdentifiers);
  
          Fit3D fit3d = Fit3DBuilder.create()
                  .query(structuralMotif)
                  .target(structure.getFirstChain())
                  .run();
          assertEquals(0.00, fit3d.getMatches().get(0).getRmsd(), 1E-6);
  
          leafIdentifiers = LeafIdentifiers.of("A-95", "A-98", "A-100");
          structuralMotif = StructuralMotif.fromLeafIdentifiers(structure, leafIdentifiers);
          fit3d = Fit3DBuilder.create()
                  .query(structuralMotif)
                  .target(structure.getFirstChain())
                  .run();
          assertEquals(0.00, fit3d.getMatches().get(0).getRmsd(), 1E-6);
      }
test_case.class_method_signature: Fit3DAlignmentTest.shouldHandleInsertionCodeMotifs()
test_case.full_signature: @Test void shouldHandleInsertionCodeMotifs()
test_case.identifier: shouldHandleInsertionCodeMotifs
test_case.invocations: parse pdbIdentifier pdb of fromLeafIdentifiers run target query create getFirstChain assertEquals getRmsd get getMatches of fromLeafIdentifiers run target query create getFirstChain assertEquals getRmsd get getMatches
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldHandleInsertionCodeMotifs()
focal_class.declarator: logger = LoggerFactory.getLogger(Fit3DAlignment.class)
focal_class.modifier: private static final
focal_class.original_string: private static final Logger logger = LoggerFactory.getLogger(Fit3DAlignment.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.declarator: queryMotif
focal_class.modifier: private final
focal_class.original_string: private final StructuralMotif queryMotif;
focal_class.type: StructuralMotif
focal_class.var_name: queryMotif
focal_class.declarator: target
focal_class.modifier: private final
focal_class.original_string: private final LeafSubstructureContainer target;
focal_class.type: LeafSubstructureContainer
focal_class.var_name: target
focal_class.declarator: squaredDistanceTolerance
focal_class.modifier: private final
focal_class.original_string: private final double squaredDistanceTolerance;
focal_class.type: double
focal_class.var_name: squaredDistanceTolerance
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: statisticalModel
focal_class.modifier: private final
focal_class.original_string: private final StatisticalModel statisticalModel;
focal_class.type: StatisticalModel
focal_class.var_name: statisticalModel
focal_class.declarator: rmsdCutoff
focal_class.modifier: private final
focal_class.original_string: private final double rmsdCutoff;
focal_class.type: double
focal_class.var_name: rmsdCutoff
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: mapEcNumbers
focal_class.modifier: private final
focal_class.original_string: private final boolean mapEcNumbers;
focal_class.type: boolean
focal_class.var_name: mapEcNumbers
focal_class.declarator: mapPfamIdentifiers
focal_class.modifier: private final
focal_class.original_string: private final boolean mapPfamIdentifiers;
focal_class.type: boolean
focal_class.var_name: mapPfamIdentifiers
focal_class.declarator: mapUniProtIdentifiers
focal_class.modifier: private final
focal_class.original_string: private final boolean mapUniProtIdentifiers;
focal_class.type: boolean
focal_class.var_name: mapUniProtIdentifiers
focal_class.declarator: filterEnvironments
focal_class.modifier: private final
focal_class.original_string: private final boolean filterEnvironments;
focal_class.type: boolean
focal_class.var_name: filterEnvironments
focal_class.declarator: squaredFilterThreshold
focal_class.modifier: private final
focal_class.original_string: private final double squaredFilterThreshold;
focal_class.type: double
focal_class.var_name: squaredFilterThreshold
focal_class.declarator: pairwiseQueryMotifDistanceMap
focal_class.modifier: private
focal_class.original_string: private Map<Integer, List<Double>> pairwiseQueryMotifDistanceMap;
focal_class.type: Map<Integer, List<Double>>
focal_class.var_name: pairwiseQueryMotifDistanceMap
focal_class.declarator: queryMotifSquaredDistanceMatrix
focal_class.modifier: private
focal_class.original_string: private LabeledSymmetricMatrix<LeafSubstructure<?>> queryMotifSquaredDistanceMatrix;
focal_class.type: LabeledSymmetricMatrix<LeafSubstructure<?>>
focal_class.var_name: queryMotifSquaredDistanceMatrix
focal_class.declarator: squaredQueryExtent
focal_class.modifier: private
focal_class.original_string: private double squaredQueryExtent;
focal_class.type: double
focal_class.var_name: squaredQueryExtent
focal_class.declarator: squaredDistanceMatrix
focal_class.modifier: private
focal_class.original_string: private LabeledSymmetricMatrix<LeafSubstructure<?>> squaredDistanceMatrix;
focal_class.type: LabeledSymmetricMatrix<LeafSubstructure<?>>
focal_class.var_name: squaredDistanceMatrix
focal_class.declarator: environments
focal_class.modifier: private
focal_class.original_string: private List<List<LeafSubstructure<?>>> environments;
focal_class.type: List<List<LeafSubstructure<?>>>
focal_class.var_name: environments
focal_class.declarator: candidates
focal_class.modifier: private
focal_class.original_string: private HashMap<List<LeafSubstructure<?>>, List<List<LeafSubstructure<?>>>> candidates;
focal_class.type: HashMap<List<LeafSubstructure<?>>, List<List<LeafSubstructure<?>>>>
focal_class.var_name: candidates
focal_class.declarator: matches
focal_class.modifier: private
focal_class.original_string: private List<Fit3DMatch> matches;
focal_class.type: List<Fit3DMatch>
focal_class.var_name: matches
focal_class.file: singa-structure/src/main/java/bio/singa/structure/algorithms/superimposition/fit3d/Fit3DAlignment.java
focal_class.identifier: Fit3DAlignment
focal_class.interfaces: implements Fit3D
focal_class.class_method_signature: Fit3DAlignment.Fit3DAlignment(Fit3DBuilder.Builder builder)
focal_class.full_signature:   Fit3DAlignment(Fit3DBuilder.Builder builder)
focal_class.identifier: Fit3DAlignment
focal_class.parameters: (Fit3DBuilder.Builder builder)
focal_class.signature:  Fit3DAlignment(Fit3DBuilder.Builder builder)
focal_class.class_method_signature: Fit3DAlignment.generateLabelHashCode(StructuralFamily<?> structuralFamily1, StructuralFamily<?> structuralFamily2)
focal_class.full_signature: public static int generateLabelHashCode(StructuralFamily<?> structuralFamily1, StructuralFamily<?> structuralFamily2)
focal_class.identifier: generateLabelHashCode
focal_class.modifiers: public static
focal_class.parameters: (StructuralFamily<?> structuralFamily1, StructuralFamily<?> structuralFamily2)
focal_class.return: int
focal_class.signature: int generateLabelHashCode(StructuralFamily<?> structuralFamily1, StructuralFamily<?> structuralFamily2)
focal_class.class_method_signature: Fit3DAlignment.calculateStatistics()
focal_class.full_signature: private void calculateStatistics()
focal_class.identifier: calculateStatistics
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void calculateStatistics()
focal_class.class_method_signature: Fit3DAlignment.mapIdentifiers()
focal_class.full_signature: private void mapIdentifiers()
focal_class.identifier: mapIdentifiers
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void mapIdentifiers()
focal_class.class_method_signature: Fit3DAlignment.getMatches()
focal_class.full_signature: @Override public List<Fit3DMatch> getMatches()
focal_class.identifier: getMatches
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: List<Fit3DMatch>
focal_class.signature: List<Fit3DMatch> getMatches()
focal_class.class_method_signature: Fit3DAlignment.getFraction()
focal_class.full_signature: @Override public double getFraction()
focal_class.identifier: getFraction
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: double
focal_class.signature: double getFraction()
focal_class.class_method_signature: Fit3DAlignment.computeMatches()
focal_class.full_signature: private void computeMatches()
focal_class.identifier: computeMatches
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void computeMatches()
focal_class.class_method_signature: Fit3DAlignment.computeAlignments(List<LeafSubstructure<?>> candidate)
focal_class.full_signature: private void computeAlignments(List<LeafSubstructure<?>> candidate)
focal_class.identifier: computeAlignments
focal_class.modifiers: private
focal_class.parameters: (List<LeafSubstructure<?>> candidate)
focal_class.return: void
focal_class.signature: void computeAlignments(List<LeafSubstructure<?>> candidate)
focal_class.class_method_signature: Fit3DAlignment.generateCandidates()
focal_class.full_signature: private void generateCandidates()
focal_class.identifier: generateCandidates
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void generateCandidates()
focal_class.class_method_signature: Fit3DAlignment.composeEnvironments()
focal_class.full_signature: private void composeEnvironments()
focal_class.identifier: composeEnvironments
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void composeEnvironments()
focal_method.body: @Override
      public List<Fit3DMatch> getMatches() {
          return matches;
      }
focal_method.class_method_signature: Fit3DAlignment.getMatches()
focal_method.full_signature: @Override public List<Fit3DMatch> getMatches()
focal_method.identifier: getMatches
focal_method.modifiers: @Override public
focal_method.parameters: ()
focal_method.return: List<Fit3DMatch>
focal_method.signature: List<Fit3DMatch> getMatches()