test_class.declarator: bindingSite1
test_class.modifier: private
test_class.original_string: private StructuralMotif bindingSite1;
test_class.type: StructuralMotif
test_class.var_name: bindingSite1
test_class.declarator: bindingSite2
test_class.modifier: private
test_class.original_string: private StructuralMotif bindingSite2;
test_class.type: StructuralMotif
test_class.var_name: bindingSite2
test_class.file: singa-structure/src/test/java/bio/singa/structure/algorithms/superimposition/fit3d/Fit3DSiteAlignmentTest.java
test_class.identifier: Fit3DSiteAlignmentTest
test_case.body: @Test
      void shouldAlignBindingSitesKuhnMunkres() {
          Fit3D fit3d = Fit3DBuilder.create()
                  .site(bindingSite1)
                  .vs(bindingSite2)
                  .kuhnMunkres(SubstitutionMatrix.MC_LACHLAN, false)
                  .run();
          assertEquals(10.367884580510683, fit3d.getMatches().get(0).getRmsd(), 1E-6);
      }
test_case.class_method_signature: Fit3DSiteAlignmentTest.shouldAlignBindingSitesKuhnMunkres()
test_case.full_signature: @Test void shouldAlignBindingSitesKuhnMunkres()
test_case.identifier: shouldAlignBindingSitesKuhnMunkres
test_case.invocations: run kuhnMunkres vs site create assertEquals getRmsd get getMatches
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void shouldAlignBindingSitesKuhnMunkres()
focal_class.declarator: logger = LoggerFactory.getLogger(Fit3DSiteAlignment.class)
focal_class.modifier: private static final
focal_class.original_string: private static final Logger logger = LoggerFactory.getLogger(Fit3DSiteAlignment.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.declarator: PERMUTATION_CUTOFF = 3
focal_class.modifier: private static final
focal_class.original_string: private static final int PERMUTATION_CUTOFF = 3;
focal_class.type: int
focal_class.var_name: PERMUTATION_CUTOFF
focal_class.declarator: site1
focal_class.modifier: private final
focal_class.original_string: private final StructuralMotif site1;
focal_class.type: StructuralMotif
focal_class.var_name: site1
focal_class.declarator: site2
focal_class.modifier: private final
focal_class.original_string: private final StructuralMotif site2;
focal_class.type: StructuralMotif
focal_class.var_name: site2
focal_class.declarator: site1Partitions
focal_class.modifier: private final
focal_class.original_string: private final LinkedHashSet<List<LeafSubstructure<?>>> site1Partitions;
focal_class.type: LinkedHashSet<List<LeafSubstructure<?>>>
focal_class.var_name: site1Partitions
focal_class.declarator: site2Partitions
focal_class.modifier: private final
focal_class.original_string: private final LinkedHashSet<List<LeafSubstructure<?>>> site2Partitions;
focal_class.type: LinkedHashSet<List<LeafSubstructure<?>>>
focal_class.var_name: site2Partitions
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: 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: 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: distanceTolerance
focal_class.modifier: private final
focal_class.original_string: private final double distanceTolerance;
focal_class.type: double
focal_class.var_name: distanceTolerance
focal_class.declarator: exhaustive
focal_class.modifier: private final
focal_class.original_string: private final boolean exhaustive;
focal_class.type: boolean
focal_class.var_name: exhaustive
focal_class.declarator: restrictToExchanges
focal_class.modifier: private final
focal_class.original_string: private final boolean restrictToExchanges;
focal_class.type: boolean
focal_class.var_name: restrictToExchanges
focal_class.declarator: substitutionMatrix
focal_class.modifier: private final
focal_class.original_string: private final SubstitutionMatrix substitutionMatrix;
focal_class.type: SubstitutionMatrix
focal_class.var_name: substitutionMatrix
focal_class.declarator: containsNonAminoAcids
focal_class.modifier: private final
focal_class.original_string: private final boolean containsNonAminoAcids;
focal_class.type: boolean
focal_class.var_name: containsNonAminoAcids
focal_class.declarator: kuhnMunkres
focal_class.modifier: private final
focal_class.original_string: private final boolean kuhnMunkres;
focal_class.type: boolean
focal_class.var_name: kuhnMunkres
focal_class.declarator: cutoffScore
focal_class.modifier: private final
focal_class.original_string: private final double cutoffScore;
focal_class.type: double
focal_class.var_name: cutoffScore
focal_class.declarator: matches
focal_class.modifier: private final
focal_class.original_string: private final List<Fit3DMatch> matches;
focal_class.type: List<Fit3DMatch>
focal_class.var_name: matches
focal_class.declarator: currentAlignmentSize
focal_class.modifier: private
focal_class.original_string: private int currentAlignmentSize;
focal_class.type: int
focal_class.var_name: currentAlignmentSize
focal_class.declarator: currentSimilarityMatrix
focal_class.modifier: private
focal_class.original_string: private LabeledRegularMatrix<List<LeafSubstructure<?>>> currentSimilarityMatrix;
focal_class.type: LabeledRegularMatrix<List<LeafSubstructure<?>>>
focal_class.var_name: currentSimilarityMatrix
focal_class.declarator: currentBestMatchingPair
focal_class.modifier: private
focal_class.original_string: private Pair<List<LeafSubstructure<?>>> currentBestMatchingPair;
focal_class.type: Pair<List<LeafSubstructure<?>>>
focal_class.var_name: currentBestMatchingPair
focal_class.declarator: currentBestScore
focal_class.modifier: private
focal_class.original_string: private double currentBestScore;
focal_class.type: double
focal_class.var_name: currentBestScore
focal_class.declarator: currentBestSuperimposition
focal_class.modifier: private
focal_class.original_string: private SubstructureSuperimposition currentBestSuperimposition;
focal_class.type: SubstructureSuperimposition
focal_class.var_name: currentBestSuperimposition
focal_class.declarator: alignmentString
focal_class.modifier: private
focal_class.original_string: private String alignmentString;
focal_class.type: String
focal_class.var_name: alignmentString
focal_class.declarator: cutoffScoreReached
focal_class.modifier: private
focal_class.original_string: private boolean cutoffScoreReached;
focal_class.type: boolean
focal_class.var_name: cutoffScoreReached
focal_class.declarator: xieScore
focal_class.modifier: private
focal_class.original_string: private XieScore xieScore;
focal_class.type: XieScore
focal_class.var_name: xieScore
focal_class.declarator: psScore
focal_class.modifier: private
focal_class.original_string: private PsScore psScore;
focal_class.type: PsScore
focal_class.var_name: psScore
focal_class.declarator: assignment
focal_class.modifier: private
focal_class.original_string: private List<Pair<LeafSubstructure<?>>> assignment;
focal_class.type: List<Pair<LeafSubstructure<?>>>
focal_class.var_name: assignment
focal_class.file: singa-structure/src/main/java/bio/singa/structure/algorithms/superimposition/fit3d/Fit3DSiteAlignment.java
focal_class.identifier: Fit3DSiteAlignment
focal_class.interfaces: implements Fit3D
focal_class.class_method_signature: Fit3DSiteAlignment.Fit3DSiteAlignment(Fit3DBuilder.Builder builder)
focal_class.full_signature: public  Fit3DSiteAlignment(Fit3DBuilder.Builder builder)
focal_class.identifier: Fit3DSiteAlignment
focal_class.modifiers: public
focal_class.parameters: (Fit3DBuilder.Builder builder)
focal_class.signature:  Fit3DSiteAlignment(Fit3DBuilder.Builder builder)
focal_class.class_method_signature: Fit3DSiteAlignment.getPsScore()
focal_class.full_signature: @Override public PsScore getPsScore()
focal_class.identifier: getPsScore
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: PsScore
focal_class.signature: PsScore getPsScore()
focal_class.class_method_signature: Fit3DSiteAlignment.getXieScore()
focal_class.full_signature: @Override public XieScore getXieScore()
focal_class.identifier: getXieScore
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: XieScore
focal_class.signature: XieScore getXieScore()
focal_class.class_method_signature: Fit3DSiteAlignment.getAlignmentString()
focal_class.full_signature: @Override public String getAlignmentString()
focal_class.identifier: getAlignmentString
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getAlignmentString()
focal_class.class_method_signature: Fit3DSiteAlignment.extendAlignment()
focal_class.full_signature: private void extendAlignment()
focal_class.identifier: extendAlignment
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void extendAlignment()
focal_class.class_method_signature: Fit3DSiteAlignment.calculatePsScore()
focal_class.full_signature: private void calculatePsScore()
focal_class.identifier: calculatePsScore
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void calculatePsScore()
focal_class.class_method_signature: Fit3DSiteAlignment.calculateXieScore()
focal_class.full_signature: private void calculateXieScore()
focal_class.identifier: calculateXieScore
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void calculateXieScore()
focal_class.class_method_signature: Fit3DSiteAlignment.outputSummary()
focal_class.full_signature: private void outputSummary()
focal_class.identifier: outputSummary
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void outputSummary()
focal_class.class_method_signature: Fit3DSiteAlignment.getAlignedResidueFraction()
focal_class.full_signature: private double getAlignedResidueFraction()
focal_class.identifier: getAlignedResidueFraction
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: double
focal_class.signature: double getAlignedResidueFraction()
focal_class.class_method_signature: Fit3DSiteAlignment.extendPartitions()
focal_class.full_signature: private void extendPartitions()
focal_class.identifier: extendPartitions
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void extendPartitions()
focal_class.class_method_signature: Fit3DSiteAlignment.calculateSimilarities()
focal_class.full_signature: private void calculateSimilarities()
focal_class.identifier: calculateSimilarities
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void calculateSimilarities()
focal_class.class_method_signature: Fit3DSiteAlignment.createInitialPartitions(StructuralMotif structuralMotif)
focal_class.full_signature: private LinkedHashSet<List<LeafSubstructure<?>>> createInitialPartitions(StructuralMotif structuralMotif)
focal_class.identifier: createInitialPartitions
focal_class.modifiers: private
focal_class.parameters: (StructuralMotif structuralMotif)
focal_class.return: LinkedHashSet<List<LeafSubstructure<?>>>
focal_class.signature: LinkedHashSet<List<LeafSubstructure<?>>> createInitialPartitions(StructuralMotif structuralMotif)
focal_class.class_method_signature: Fit3DSiteAlignment.calculateAssignment()
focal_class.full_signature: private void calculateAssignment()
focal_class.identifier: calculateAssignment
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void calculateAssignment()
focal_class.class_method_signature: Fit3DSiteAlignment.calculateAlignment()
focal_class.full_signature: private void calculateAlignment()
focal_class.identifier: calculateAlignment
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void calculateAlignment()
focal_class.class_method_signature: Fit3DSiteAlignment.writeMatches(Path outputDirectory)
focal_class.full_signature: @Override public void writeMatches(Path outputDirectory)
focal_class.identifier: writeMatches
focal_class.modifiers: @Override public
focal_class.parameters: (Path outputDirectory)
focal_class.return: void
focal_class.signature: void writeMatches(Path outputDirectory)
focal_class.class_method_signature: Fit3DSiteAlignment.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: Fit3DSiteAlignment.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_method.body: @Override
      public List<Fit3DMatch> getMatches() {
          return matches;
      }
focal_method.class_method_signature: Fit3DSiteAlignment.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()