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 shouldRunFit3DAlignmentWithExchangesAndFiltering() {
          Structure target = StructureParser.pdb()
                  .pdbIdentifier("2mnr")
                  .everything()
                  .parse();
          StructuralMotif structuralMotif = StructuralMotif.fromLeafSubstructures(StructureParser.local()
                  .inputStream(Resources.getResourceAsStream("motif_KDEEH.pdb"))
                  .parse()
                  .getAllLeafSubstructures());
          structuralMotif.addExchangeableFamily(LeafIdentifier.fromSimpleString("A-164"), AminoAcidFamily.HISTIDINE);
          structuralMotif.addExchangeableFamily(LeafIdentifier.fromSimpleString("A-247"), AminoAcidFamily.ASPARTIC_ACID);
          structuralMotif.addExchangeableFamily(LeafIdentifier.fromSimpleString("A-247"), AminoAcidFamily.ASPARAGINE);
          structuralMotif.addExchangeableFamily(LeafIdentifier.fromSimpleString("A-297"), AminoAcidFamily.LYSINE);
  
          Fit3D fit3d = Fit3DBuilder.create()
                  .query(structuralMotif)
                  .target(target.getFirstModel())
                  .atomFilter(StructuralEntityFilter.AtomFilter.isArbitrary())
                  .filterEnvironments(3.0)
                  .run();
  
          List<Fit3DMatch> matches = fit3d.getMatches();
          assertEquals(0.0000, matches.get(0).getRmsd(), 1E-6);
      }
test_case.class_method_signature: Fit3DAlignmentTest.shouldRunFit3DAlignmentWithExchangesAndFiltering()
test_case.full_signature: @Test void shouldRunFit3DAlignmentWithExchangesAndFiltering()
test_case.identifier: shouldRunFit3DAlignmentWithExchangesAndFiltering
test_case.invocations: parse everything pdbIdentifier pdb fromLeafSubstructures getAllLeafSubstructures parse inputStream local getResourceAsStream addExchangeableFamily fromSimpleString addExchangeableFamily fromSimpleString addExchangeableFamily fromSimpleString addExchangeableFamily fromSimpleString run filterEnvironments atomFilter target query create getFirstModel isArbitrary getMatches assertEquals getRmsd get
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldRunFit3DAlignmentWithExchangesAndFiltering()
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()