test_class.declarator: leaf162
test_class.modifier: private static
test_class.original_string: private static LeafSubstructure<?> leaf162;
test_class.type: LeafSubstructure<?>
test_class.var_name: leaf162
test_class.declarator: leaf620A
test_class.modifier: private static
test_class.original_string: private static LeafSubstructure<?> leaf620A;
test_class.type: LeafSubstructure<?>
test_class.var_name: leaf620A
test_class.declarator: leafToModify
test_class.modifier: private static
test_class.original_string: private static OakAminoAcid leafToModify;
test_class.type: OakAminoAcid
test_class.var_name: leafToModify
test_class.file: singa-structure/src/test/java/bio/singa/structure/model/oak/OakLeafSubstructureTest.java
test_class.identifier: OakLeafSubstructureTest
test_case.body: @Test
      void removeAtom() {
          // ATOM   2966  OE2 GLU A 161      45.631  55.119  -0.991  1.00 14.27           O
          final int expected = leafToModify.getAllAtoms().size() - 1;
          leafToModify.removeAtom(2966);
          final int actual = leafToModify.getAllAtoms().size();
          assertEquals(expected, actual);
      }
test_case.class_method_signature: OakLeafSubstructureTest.removeAtom()
test_case.full_signature: @Test void removeAtom()
test_case.identifier: removeAtom
test_case.invocations: size getAllAtoms removeAtom size getAllAtoms assertEquals
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void removeAtom()
focal_class.declarator: leafIdentifier
focal_class.modifier: private final
focal_class.original_string: private final LeafIdentifier leafIdentifier;
focal_class.type: LeafIdentifier
focal_class.var_name: leafIdentifier
focal_class.declarator: family
focal_class.modifier: private final
focal_class.original_string: private final FamilyType family;
focal_class.type: FamilyType
focal_class.var_name: family
focal_class.declarator: divergingThreeLetterCode
focal_class.modifier: private final
focal_class.original_string: private final String divergingThreeLetterCode;
focal_class.type: String
focal_class.var_name: divergingThreeLetterCode
focal_class.declarator: atoms
focal_class.modifier: private final
focal_class.original_string: private final Map<Integer, OakAtom> atoms;
focal_class.type: Map<Integer, OakAtom>
focal_class.var_name: atoms
focal_class.declarator: bonds
focal_class.modifier: private final
focal_class.original_string: private final Map<Integer, OakBond> bonds;
focal_class.type: Map<Integer, OakBond>
focal_class.var_name: bonds
focal_class.declarator: exchangeableFamilies
focal_class.modifier: private final
focal_class.original_string: private final Set<FamilyType> exchangeableFamilies;
focal_class.type: Set<FamilyType>
focal_class.var_name: exchangeableFamilies
focal_class.declarator: nextEdgeIdentifier = 0
focal_class.modifier: private
focal_class.original_string: private int nextEdgeIdentifier = 0;
focal_class.type: int
focal_class.var_name: nextEdgeIdentifier
focal_class.declarator: annotatedAsHetAtom
focal_class.modifier: private
focal_class.original_string: private boolean annotatedAsHetAtom;
focal_class.type: boolean
focal_class.var_name: annotatedAsHetAtom
focal_class.file: singa-structure/src/main/java/bio/singa/structure/model/oak/OakLeafSubstructure.java
focal_class.identifier: OakLeafSubstructure
focal_class.interfaces: implements LeafSubstructure<FamilyType>
focal_class.class_method_signature: OakLeafSubstructure.OakLeafSubstructure(LeafIdentifier leafIdentifier, FamilyType family)
focal_class.full_signature: public  OakLeafSubstructure(LeafIdentifier leafIdentifier, FamilyType family)
focal_class.identifier: OakLeafSubstructure
focal_class.modifiers: public
focal_class.parameters: (LeafIdentifier leafIdentifier, FamilyType family)
focal_class.signature:  OakLeafSubstructure(LeafIdentifier leafIdentifier, FamilyType family)
focal_class.class_method_signature: OakLeafSubstructure.OakLeafSubstructure(LeafIdentifier identifer, FamilyType aminoAcidFamily, String threeLetterCode)
focal_class.full_signature: public  OakLeafSubstructure(LeafIdentifier identifer, FamilyType aminoAcidFamily, String threeLetterCode)
focal_class.identifier: OakLeafSubstructure
focal_class.modifiers: public
focal_class.parameters: (LeafIdentifier identifer, FamilyType aminoAcidFamily, String threeLetterCode)
focal_class.signature:  OakLeafSubstructure(LeafIdentifier identifer, FamilyType aminoAcidFamily, String threeLetterCode)
focal_class.class_method_signature: OakLeafSubstructure.OakLeafSubstructure(OakLeafSubstructure<FamilyType> leafSubstructure)
focal_class.full_signature: public  OakLeafSubstructure(OakLeafSubstructure<FamilyType> leafSubstructure)
focal_class.identifier: OakLeafSubstructure
focal_class.modifiers: public
focal_class.parameters: (OakLeafSubstructure<FamilyType> leafSubstructure)
focal_class.signature:  OakLeafSubstructure(OakLeafSubstructure<FamilyType> leafSubstructure)
focal_class.class_method_signature: OakLeafSubstructure.getIdentifier()
focal_class.full_signature: @Override public LeafIdentifier getIdentifier()
focal_class.identifier: getIdentifier
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: LeafIdentifier
focal_class.signature: LeafIdentifier getIdentifier()
focal_class.class_method_signature: OakLeafSubstructure.containsAtomWithName(String atomName)
focal_class.full_signature: @Override public boolean containsAtomWithName(String atomName)
focal_class.identifier: containsAtomWithName
focal_class.modifiers: @Override public
focal_class.parameters: (String atomName)
focal_class.return: boolean
focal_class.signature: boolean containsAtomWithName(String atomName)
focal_class.class_method_signature: OakLeafSubstructure.getAtomByName(String atomName)
focal_class.full_signature: @Override public Optional<Atom> getAtomByName(String atomName)
focal_class.identifier: getAtomByName
focal_class.modifiers: @Override public
focal_class.parameters: (String atomName)
focal_class.return: Optional<Atom>
focal_class.signature: Optional<Atom> getAtomByName(String atomName)
focal_class.class_method_signature: OakLeafSubstructure.isAnnotatedAsHeteroAtom()
focal_class.full_signature: @Override public boolean isAnnotatedAsHeteroAtom()
focal_class.identifier: isAnnotatedAsHeteroAtom
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isAnnotatedAsHeteroAtom()
focal_class.class_method_signature: OakLeafSubstructure.setAnnotatedAsHetAtom(boolean annotatedAsHetAtom)
focal_class.full_signature: public void setAnnotatedAsHetAtom(boolean annotatedAsHetAtom)
focal_class.identifier: setAnnotatedAsHetAtom
focal_class.modifiers: public
focal_class.parameters: (boolean annotatedAsHetAtom)
focal_class.return: void
focal_class.signature: void setAnnotatedAsHetAtom(boolean annotatedAsHetAtom)
focal_class.class_method_signature: OakLeafSubstructure.getThreeLetterCode()
focal_class.full_signature: @Override public String getThreeLetterCode()
focal_class.identifier: getThreeLetterCode
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getThreeLetterCode()
focal_class.class_method_signature: OakLeafSubstructure.getFamily()
focal_class.full_signature: @Override public FamilyType getFamily()
focal_class.identifier: getFamily
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: FamilyType
focal_class.signature: FamilyType getFamily()
focal_class.class_method_signature: OakLeafSubstructure.getAllAtoms()
focal_class.full_signature: @Override public List<Atom> getAllAtoms()
focal_class.identifier: getAllAtoms
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: List<Atom>
focal_class.signature: List<Atom> getAllAtoms()
focal_class.class_method_signature: OakLeafSubstructure.getAtom(Integer atomIdentifier)
focal_class.full_signature: @Override public Optional<Atom> getAtom(Integer atomIdentifier)
focal_class.identifier: getAtom
focal_class.modifiers: @Override public
focal_class.parameters: (Integer atomIdentifier)
focal_class.return: Optional<Atom>
focal_class.signature: Optional<Atom> getAtom(Integer atomIdentifier)
focal_class.class_method_signature: OakLeafSubstructure.addAtom(OakAtom atom)
focal_class.full_signature: public void addAtom(OakAtom atom)
focal_class.identifier: addAtom
focal_class.modifiers: public
focal_class.parameters: (OakAtom atom)
focal_class.return: void
focal_class.signature: void addAtom(OakAtom atom)
focal_class.class_method_signature: OakLeafSubstructure.removeAtom(Integer atomIdentifier)
focal_class.full_signature: @Override public void removeAtom(Integer atomIdentifier)
focal_class.identifier: removeAtom
focal_class.modifiers: @Override public
focal_class.parameters: (Integer atomIdentifier)
focal_class.return: void
focal_class.signature: void removeAtom(Integer atomIdentifier)
focal_class.class_method_signature: OakLeafSubstructure.getBonds()
focal_class.full_signature: public Collection<OakBond> getBonds()
focal_class.identifier: getBonds
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Collection<OakBond>
focal_class.signature: Collection<OakBond> getBonds()
focal_class.class_method_signature: OakLeafSubstructure.addBondBetween(OakBond edge, OakAtom source, OakAtom target)
focal_class.full_signature: public int addBondBetween(OakBond edge, OakAtom source, OakAtom target)
focal_class.identifier: addBondBetween
focal_class.modifiers: public
focal_class.parameters: (OakBond edge, OakAtom source, OakAtom target)
focal_class.return: int
focal_class.signature: int addBondBetween(OakBond edge, OakAtom source, OakAtom target)
focal_class.class_method_signature: OakLeafSubstructure.addBondBetween(OakAtom source, OakAtom target)
focal_class.full_signature: public int addBondBetween(OakAtom source, OakAtom target)
focal_class.identifier: addBondBetween
focal_class.modifiers: public
focal_class.parameters: (OakAtom source, OakAtom target)
focal_class.return: int
focal_class.signature: int addBondBetween(OakAtom source, OakAtom target)
focal_class.class_method_signature: OakLeafSubstructure.addBondBetween(OakAtom source, OakAtom target, CovalentBondType bondType)
focal_class.full_signature: public int addBondBetween(OakAtom source, OakAtom target, CovalentBondType bondType)
focal_class.identifier: addBondBetween
focal_class.modifiers: public
focal_class.parameters: (OakAtom source, OakAtom target, CovalentBondType bondType)
focal_class.return: int
focal_class.signature: int addBondBetween(OakAtom source, OakAtom target, CovalentBondType bondType)
focal_class.class_method_signature: OakLeafSubstructure.getExchangeableFamilies()
focal_class.full_signature: @Override public Set<FamilyType> getExchangeableFamilies()
focal_class.identifier: getExchangeableFamilies
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Set<FamilyType>
focal_class.signature: Set<FamilyType> getExchangeableFamilies()
focal_class.class_method_signature: OakLeafSubstructure.addExchangeableFamily(FamilyType exchangeableType)
focal_class.full_signature: @Override public void addExchangeableFamily(FamilyType exchangeableType)
focal_class.identifier: addExchangeableFamily
focal_class.modifiers: @Override public
focal_class.parameters: (FamilyType exchangeableType)
focal_class.return: void
focal_class.signature: void addExchangeableFamily(FamilyType exchangeableType)
focal_class.class_method_signature: OakLeafSubstructure.equals(Object o)
focal_class.full_signature: @Override public boolean equals(Object o)
focal_class.identifier: equals
focal_class.modifiers: @Override public
focal_class.parameters: (Object o)
focal_class.return: boolean
focal_class.signature: boolean equals(Object o)
focal_class.class_method_signature: OakLeafSubstructure.hashCode()
focal_class.full_signature: @Override public int hashCode()
focal_class.identifier: hashCode
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int hashCode()
focal_class.class_method_signature: OakLeafSubstructure.toString()
focal_class.full_signature: @Override public String toString()
focal_class.identifier: toString
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String toString()
focal_class.class_method_signature: OakLeafSubstructure.getNextEdgeIdentifier()
focal_class.full_signature: public int getNextEdgeIdentifier()
focal_class.identifier: getNextEdgeIdentifier
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getNextEdgeIdentifier()
focal_method.body: @Override
      public void removeAtom(Integer atomIdentifier) {
          final OakAtom atom = atoms.get(atomIdentifier);
          if (atom != null) {
              for (OakAtom neighbor : atom.getNeighbours()) {
                  neighbor.getNeighbours().remove(atom);
              }
  
              atoms.remove(atom.getAtomIdentifier());
              bonds.entrySet().removeIf(edge -> edge.getValue().connectsAtom(atom));
          }
      }
focal_method.class_method_signature: OakLeafSubstructure.removeAtom(Integer atomIdentifier)
focal_method.full_signature: @Override public void removeAtom(Integer atomIdentifier)
focal_method.identifier: removeAtom
focal_method.invocations: get getNeighbours remove getNeighbours remove getAtomIdentifier removeIf entrySet connectsAtom getValue
focal_method.modifiers: @Override public
focal_method.parameters: (Integer atomIdentifier)
focal_method.return: void
focal_method.signature: void removeAtom(Integer atomIdentifier)