test_class.file: singa-structure/src/test/java/bio/singa/structure/model/oak/StructuresTest.java
test_class.identifier: StructuresTest
test_case.body: @Test
      void calculateDistanceMatrix() {
          Chain chain = StructureParser.pdb()
                  .pdbIdentifier("1HRR")
                  .parse()
                  .getFirstChain();
          final LabeledSymmetricMatrix<LeafSubstructure<?>> distanceMatrix = Structures.calculateDistanceMatrix(chain);
          assertTrue(distanceMatrix.getMainDiagonal().isZero());
          assertEquals(5.461240152199864, distanceMatrix.getElement(5, 3));
          assertEquals(3.792725405298938, distanceMatrix.getElement(17, 18));
          assertEquals(20.372810778093434, distanceMatrix.getElement(23, 11));
      }
test_case.class_method_signature: StructuresTest.calculateDistanceMatrix()
test_case.full_signature: @Test void calculateDistanceMatrix()
test_case.identifier: calculateDistanceMatrix
test_case.invocations: getFirstChain parse pdbIdentifier pdb calculateDistanceMatrix assertTrue isZero getMainDiagonal assertEquals getElement assertEquals getElement assertEquals getElement
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void calculateDistanceMatrix()
focal_class.file: singa-structure/src/main/java/bio/singa/structure/model/oak/Structures.java
focal_class.identifier: Structures
focal_class.class_method_signature: Structures.Structures()
focal_class.full_signature: private  Structures()
focal_class.identifier: Structures
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.signature:  Structures()
focal_class.class_method_signature: Structures.calculateDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)
focal_class.full_signature: public static LabeledSymmetricMatrix<LeafSubstructure<?>> calculateDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)
focal_class.identifier: calculateDistanceMatrix
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer leafSubstructureContainer)
focal_class.return: LabeledSymmetricMatrix<LeafSubstructure<?>>
focal_class.signature: LabeledSymmetricMatrix<LeafSubstructure<?>> calculateDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)
focal_class.class_method_signature: Structures.calculateSquaredDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)
focal_class.full_signature: public static LabeledSymmetricMatrix<LeafSubstructure<?>> calculateSquaredDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)
focal_class.identifier: calculateSquaredDistanceMatrix
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer leafSubstructureContainer)
focal_class.return: LabeledSymmetricMatrix<LeafSubstructure<?>>
focal_class.signature: LabeledSymmetricMatrix<LeafSubstructure<?>> calculateSquaredDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)
focal_class.class_method_signature: Structures.calculateExtent(LeafSubstructureContainer leafSubstructureContainer)
focal_class.full_signature: public static double calculateExtent(LeafSubstructureContainer leafSubstructureContainer)
focal_class.identifier: calculateExtent
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer leafSubstructureContainer)
focal_class.return: double
focal_class.signature: double calculateExtent(LeafSubstructureContainer leafSubstructureContainer)
focal_class.class_method_signature: Structures.calculateSquaredExtent(LeafSubstructureContainer leafSubstructureContainer)
focal_class.full_signature: public static double calculateSquaredExtent(LeafSubstructureContainer leafSubstructureContainer)
focal_class.identifier: calculateSquaredExtent
focal_class.modifiers: public static
focal_class.parameters: (LeafSubstructureContainer leafSubstructureContainer)
focal_class.return: double
focal_class.signature: double calculateSquaredExtent(LeafSubstructureContainer leafSubstructureContainer)
focal_class.class_method_signature: Structures.calculateAtomDistanceMatrix(AtomContainer atomContainer)
focal_class.full_signature: public static LabeledSymmetricMatrix<Atom> calculateAtomDistanceMatrix(AtomContainer atomContainer)
focal_class.identifier: calculateAtomDistanceMatrix
focal_class.modifiers: public static
focal_class.parameters: (AtomContainer atomContainer)
focal_class.return: LabeledSymmetricMatrix<Atom>
focal_class.signature: LabeledSymmetricMatrix<Atom> calculateAtomDistanceMatrix(AtomContainer atomContainer)
focal_class.class_method_signature: Structures.calculateAtomDistanceMatrix(List<Atom> atoms)
focal_class.full_signature: public static LabeledSymmetricMatrix<Atom> calculateAtomDistanceMatrix(List<Atom> atoms)
focal_class.identifier: calculateAtomDistanceMatrix
focal_class.modifiers: public static
focal_class.parameters: (List<Atom> atoms)
focal_class.return: LabeledSymmetricMatrix<Atom>
focal_class.signature: LabeledSymmetricMatrix<Atom> calculateAtomDistanceMatrix(List<Atom> atoms)
focal_class.class_method_signature: Structures.isAlphaCarbonStructure(Structure structure)
focal_class.full_signature: public static boolean isAlphaCarbonStructure(Structure structure)
focal_class.identifier: isAlphaCarbonStructure
focal_class.modifiers: public static
focal_class.parameters: (Structure structure)
focal_class.return: boolean
focal_class.signature: boolean isAlphaCarbonStructure(Structure structure)
focal_class.class_method_signature: Structures.isBackboneStructure(Structure structure)
focal_class.full_signature: public static boolean isBackboneStructure(Structure structure)
focal_class.identifier: isBackboneStructure
focal_class.modifiers: public static
focal_class.parameters: (Structure structure)
focal_class.return: boolean
focal_class.signature: boolean isBackboneStructure(Structure structure)
focal_class.class_method_signature: Structures.convertToSpheres(AtomContainer atomContainer)
focal_class.full_signature: public static List<Sphere> convertToSpheres(AtomContainer atomContainer)
focal_class.identifier: convertToSpheres
focal_class.modifiers: public static
focal_class.parameters: (AtomContainer atomContainer)
focal_class.return: List<Sphere>
focal_class.signature: List<Sphere> convertToSpheres(AtomContainer atomContainer)
focal_class.class_method_signature: Structures.calculateTorsionAngle(Atom a, Atom b, Atom c, Atom d)
focal_class.full_signature: public static double calculateTorsionAngle(Atom a, Atom b, Atom c, Atom d)
focal_class.identifier: calculateTorsionAngle
focal_class.modifiers: public static
focal_class.parameters: (Atom a, Atom b, Atom c, Atom d)
focal_class.return: double
focal_class.signature: double calculateTorsionAngle(Atom a, Atom b, Atom c, Atom d)
focal_class.class_method_signature: Structures.renumberStructure(OakStructure structure, Map<LeafIdentifier, Integer> renumberingMap)
focal_class.full_signature: public static OakStructure renumberStructure(OakStructure structure, Map<LeafIdentifier, Integer> renumberingMap)
focal_class.identifier: renumberStructure
focal_class.modifiers: public static
focal_class.parameters: (OakStructure structure, Map<LeafIdentifier, Integer> renumberingMap)
focal_class.return: OakStructure
focal_class.signature: OakStructure renumberStructure(OakStructure structure, Map<LeafIdentifier, Integer> renumberingMap)
focal_class.class_method_signature: Structures.getClosestDistance(AtomContainer atomContainer1, AtomContainer atomContainer2)
focal_class.full_signature: public static double getClosestDistance(AtomContainer atomContainer1, AtomContainer atomContainer2)
focal_class.identifier: getClosestDistance
focal_class.modifiers: public static
focal_class.parameters: (AtomContainer atomContainer1, AtomContainer atomContainer2)
focal_class.return: double
focal_class.signature: double getClosestDistance(AtomContainer atomContainer1, AtomContainer atomContainer2)
focal_class.class_method_signature: Structures.assignBFactors(Structure structure, Map<UniqueAtomIdentifer, Double> factors)
focal_class.full_signature: public static void assignBFactors(Structure structure, Map<UniqueAtomIdentifer, Double> factors)
focal_class.identifier: assignBFactors
focal_class.modifiers: public static
focal_class.parameters: (Structure structure, Map<UniqueAtomIdentifer, Double> factors)
focal_class.return: void
focal_class.signature: void assignBFactors(Structure structure, Map<UniqueAtomIdentifer, Double> factors)
focal_class.class_method_signature: Structures.mapAtomsByCoordinate(Structure structure, Set<Vector3D> coordinates, double eps)
focal_class.full_signature: public static Map<Vector3D, UniqueAtomIdentifer> mapAtomsByCoordinate(Structure structure, Set<Vector3D> coordinates, double eps)
focal_class.identifier: mapAtomsByCoordinate
focal_class.modifiers: public static
focal_class.parameters: (Structure structure, Set<Vector3D> coordinates, double eps)
focal_class.return: Map<Vector3D, UniqueAtomIdentifer>
focal_class.signature: Map<Vector3D, UniqueAtomIdentifer> mapAtomsByCoordinate(Structure structure, Set<Vector3D> coordinates, double eps)
focal_method.body: public static LabeledSymmetricMatrix<LeafSubstructure<?>> calculateDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer) {
          return VectorMetricProvider.EUCLIDEAN_METRIC.calculateDistancesPairwise(leafSubstructureContainer.getAllLeafSubstructures(), LeafSubstructure::getPosition);
      }
focal_method.class_method_signature: Structures.calculateDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)
focal_method.full_signature: public static LabeledSymmetricMatrix<LeafSubstructure<?>> calculateDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)
focal_method.identifier: calculateDistanceMatrix
focal_method.invocations: calculateDistancesPairwise getAllLeafSubstructures
focal_method.modifiers: public static
focal_method.parameters: (LeafSubstructureContainer leafSubstructureContainer)
focal_method.return: LabeledSymmetricMatrix<LeafSubstructure<?>>
focal_method.signature: LabeledSymmetricMatrix<LeafSubstructure<?>> calculateDistanceMatrix(LeafSubstructureContainer leafSubstructureContainer)