test_class.declarator: fragmenter
test_class.modifier: static
test_class.original_string: static MurckoFragmenter fragmenter;
test_class.type: MurckoFragmenter
test_class.var_name: fragmenter
test_class.declarator: smilesParser
test_class.modifier: static
test_class.original_string: static SmilesParser     smilesParser;
test_class.type: SmilesParser
test_class.var_name: smilesParser
test_class.file: tool/fragment/src/test/java/org/openscience/cdk/fragment/MurckoFragmenterTest.java
test_class.identifier: MurckoFragmenterTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testGetFragmentsAsContainers() throws Exception {
  
          IAtomContainer biphenyl = TestMoleculeFactory.makeBiphenyl();
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(biphenyl);
          Aromaticity.cdkLegacy().apply(biphenyl);
  
          MurckoFragmenter fragmenter = new MurckoFragmenter(true, 6);
          fragmenter.generateFragments(biphenyl);
          IAtomContainer[] fragments = fragmenter.getFragmentsAsContainers();
  
          assertThat(fragments.length, is(2));
          assertThat(fragments[0].getAtomCount(), is(12));
          assertThat(fragments[1].getAtomCount(), is(6));
      }
test_case.class_method_signature: MurckoFragmenterTest.testGetFragmentsAsContainers()
test_case.full_signature: @Test public void testGetFragmentsAsContainers()
test_case.identifier: testGetFragmentsAsContainers
test_case.invocations: makeBiphenyl percieveAtomTypesAndConfigureAtoms apply cdkLegacy generateFragments getFragmentsAsContainers assertThat is assertThat getAtomCount is assertThat getAtomCount is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetFragmentsAsContainers()
focal_class.declarator: IS_SIDECHAIN_ATOM    = "sidechain"
focal_class.modifier: private static final
focal_class.original_string: private static final String IS_SIDECHAIN_ATOM    = "sidechain";
focal_class.type: String
focal_class.var_name: IS_SIDECHAIN_ATOM
focal_class.declarator: IS_LINKER_ATOM       = "linker"
focal_class.modifier: private static final
focal_class.original_string: private static final String IS_LINKER_ATOM       = "linker";
focal_class.type: String
focal_class.var_name: IS_LINKER_ATOM
focal_class.declarator: IS_CONNECTED_TO_RING = "rcon"
focal_class.modifier: private static final
focal_class.original_string: private static final String IS_CONNECTED_TO_RING = "rcon";
focal_class.type: String
focal_class.var_name: IS_CONNECTED_TO_RING
focal_class.declarator: generator
focal_class.original_string: MoleculeHashGenerator       generator;
focal_class.type: MoleculeHashGenerator
focal_class.var_name: generator
focal_class.declarator: smigen
focal_class.original_string: SmilesGenerator             smigen;
focal_class.type: SmilesGenerator
focal_class.var_name: smigen
focal_class.declarator: frameMap             = new HashMap<Long, IAtomContainer>()
focal_class.original_string: Map<Long, IAtomContainer>   frameMap             = new HashMap<Long, IAtomContainer>();
focal_class.type: Map<Long, IAtomContainer>
focal_class.var_name: frameMap
focal_class.declarator: ringMap              = new HashMap<Long, IAtomContainer>()
focal_class.original_string: Map<Long, IAtomContainer>   ringMap              = new HashMap<Long, IAtomContainer>();
focal_class.type: Map<Long, IAtomContainer>
focal_class.var_name: ringMap
focal_class.declarator: singleFrameworkOnly  = false
focal_class.original_string: boolean                     singleFrameworkOnly  = false;
focal_class.type: boolean
focal_class.var_name: singleFrameworkOnly
focal_class.declarator: ringFragments        = true
focal_class.original_string: boolean                     ringFragments        = true;
focal_class.type: boolean
focal_class.var_name: ringFragments
focal_class.declarator: minimumFragmentSize  = 5
focal_class.original_string: int                         minimumFragmentSize  = 5;
focal_class.type: int
focal_class.var_name: minimumFragmentSize
focal_class.file: tool/fragment/src/main/java/org/openscience/cdk/fragment/MurckoFragmenter.java
focal_class.identifier: MurckoFragmenter
focal_class.interfaces: implements IFragmenter
focal_class.class_method_signature: MurckoFragmenter.MurckoFragmenter()
focal_class.full_signature: public  MurckoFragmenter()
focal_class.identifier: MurckoFragmenter
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  MurckoFragmenter()
focal_class.class_method_signature: MurckoFragmenter.MurckoFragmenter(boolean singleFrameworkOnly, int minimumFragmentSize)
focal_class.full_signature: public  MurckoFragmenter(boolean singleFrameworkOnly, int minimumFragmentSize)
focal_class.identifier: MurckoFragmenter
focal_class.modifiers: public
focal_class.parameters: (boolean singleFrameworkOnly, int minimumFragmentSize)
focal_class.signature:  MurckoFragmenter(boolean singleFrameworkOnly, int minimumFragmentSize)
focal_class.class_method_signature: MurckoFragmenter.MurckoFragmenter(boolean singleFrameworkOnly, int minimumFragmentSize, MoleculeHashGenerator generator)
focal_class.full_signature: public  MurckoFragmenter(boolean singleFrameworkOnly, int minimumFragmentSize, MoleculeHashGenerator generator)
focal_class.identifier: MurckoFragmenter
focal_class.modifiers: public
focal_class.parameters: (boolean singleFrameworkOnly, int minimumFragmentSize, MoleculeHashGenerator generator)
focal_class.signature:  MurckoFragmenter(boolean singleFrameworkOnly, int minimumFragmentSize, MoleculeHashGenerator generator)
focal_class.class_method_signature: MurckoFragmenter.setComputeRingFragments(boolean val)
focal_class.full_signature: public void setComputeRingFragments(boolean val)
focal_class.identifier: setComputeRingFragments
focal_class.modifiers: public
focal_class.parameters: (boolean val)
focal_class.return: void
focal_class.signature: void setComputeRingFragments(boolean val)
focal_class.class_method_signature: MurckoFragmenter.generateFragments(IAtomContainer atomContainer)
focal_class.full_signature: @Override public void generateFragments(IAtomContainer atomContainer)
focal_class.identifier: generateFragments
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: void
focal_class.signature: void generateFragments(IAtomContainer atomContainer)
focal_class.class_method_signature: MurckoFragmenter.scaffold(final IAtomContainer mol)
focal_class.full_signature: public static IAtomContainer scaffold(final IAtomContainer mol)
focal_class.identifier: scaffold
focal_class.modifiers: public static
focal_class.parameters: (final IAtomContainer mol)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer scaffold(final IAtomContainer mol)
focal_class.class_method_signature: MurckoFragmenter.addRingFragment(IAtomContainer mol)
focal_class.full_signature: private void addRingFragment(IAtomContainer mol)
focal_class.identifier: addRingFragment
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol)
focal_class.return: void
focal_class.signature: void addRingFragment(IAtomContainer mol)
focal_class.class_method_signature: MurckoFragmenter.run(IAtomContainer atomContainer, Set<Long> fragmentSet)
focal_class.full_signature: private void run(IAtomContainer atomContainer, Set<Long> fragmentSet)
focal_class.identifier: run
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, Set<Long> fragmentSet)
focal_class.return: void
focal_class.signature: void run(IAtomContainer atomContainer, Set<Long> fragmentSet)
focal_class.class_method_signature: MurckoFragmenter.removeSideChains(IAtomContainer atomContainer)
focal_class.full_signature: private IAtomContainer removeSideChains(IAtomContainer atomContainer)
focal_class.identifier: removeSideChains
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer removeSideChains(IAtomContainer atomContainer)
focal_class.class_method_signature: MurckoFragmenter.markLinkers(IAtomContainer atomContainer)
focal_class.full_signature: private void markLinkers(IAtomContainer atomContainer)
focal_class.identifier: markLinkers
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: void
focal_class.signature: void markLinkers(IAtomContainer atomContainer)
focal_class.class_method_signature: MurckoFragmenter.markSideChains(IAtomContainer atomContainer)
focal_class.full_signature: private void markSideChains(IAtomContainer atomContainer)
focal_class.identifier: markSideChains
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: void
focal_class.signature: void markSideChains(IAtomContainer atomContainer)
focal_class.class_method_signature: MurckoFragmenter.getSmilesFromAtomContainers(Collection<IAtomContainer> mols)
focal_class.full_signature: private List<String> getSmilesFromAtomContainers(Collection<IAtomContainer> mols)
focal_class.identifier: getSmilesFromAtomContainers
focal_class.modifiers: private
focal_class.parameters: (Collection<IAtomContainer> mols)
focal_class.return: List<String>
focal_class.signature: List<String> getSmilesFromAtomContainers(Collection<IAtomContainer> mols)
focal_class.class_method_signature: MurckoFragmenter.getFragments()
focal_class.full_signature: @Override public String[] getFragments()
focal_class.identifier: getFragments
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] getFragments()
focal_class.class_method_signature: MurckoFragmenter.getFragmentsAsContainers()
focal_class.full_signature: @Override public IAtomContainer[] getFragmentsAsContainers()
focal_class.identifier: getFragmentsAsContainers
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IAtomContainer[]
focal_class.signature: IAtomContainer[] getFragmentsAsContainers()
focal_class.class_method_signature: MurckoFragmenter.getRingSystems()
focal_class.full_signature: public String[] getRingSystems()
focal_class.identifier: getRingSystems
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] getRingSystems()
focal_class.class_method_signature: MurckoFragmenter.getRingSystemsAsContainers()
focal_class.full_signature: public IAtomContainer[] getRingSystemsAsContainers()
focal_class.identifier: getRingSystemsAsContainers
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: IAtomContainer[]
focal_class.signature: IAtomContainer[] getRingSystemsAsContainers()
focal_class.class_method_signature: MurckoFragmenter.getFrameworks()
focal_class.full_signature: public String[] getFrameworks()
focal_class.identifier: getFrameworks
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] getFrameworks()
focal_class.class_method_signature: MurckoFragmenter.getFrameworksAsContainers()
focal_class.full_signature: public IAtomContainer[] getFrameworksAsContainers()
focal_class.identifier: getFrameworksAsContainers
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: IAtomContainer[]
focal_class.signature: IAtomContainer[] getFrameworksAsContainers()
focal_class.class_method_signature: MurckoFragmenter.isring(IAtom atom)
focal_class.full_signature: private boolean isring(IAtom atom)
focal_class.identifier: isring
focal_class.modifiers: private
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean isring(IAtom atom)
focal_class.class_method_signature: MurckoFragmenter.islinker(IAtom atom)
focal_class.full_signature: private boolean islinker(IAtom atom)
focal_class.identifier: islinker
focal_class.modifiers: private
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean islinker(IAtom atom)
focal_class.class_method_signature: MurckoFragmenter.issidechain(IAtom atom)
focal_class.full_signature: private boolean issidechain(IAtom atom)
focal_class.identifier: issidechain
focal_class.modifiers: private
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean issidechain(IAtom atom)
focal_class.class_method_signature: MurckoFragmenter.islinker(IBond bond)
focal_class.full_signature: private boolean islinker(IBond bond)
focal_class.identifier: islinker
focal_class.modifiers: private
focal_class.parameters: (IBond bond)
focal_class.return: boolean
focal_class.signature: boolean islinker(IBond bond)
focal_class.class_method_signature: MurckoFragmenter.isZeroAtomLinker(IBond bond)
focal_class.full_signature: private boolean isZeroAtomLinker(IBond bond)
focal_class.identifier: isZeroAtomLinker
focal_class.modifiers: private
focal_class.parameters: (IBond bond)
focal_class.return: boolean
focal_class.signature: boolean isZeroAtomLinker(IBond bond)
focal_class.class_method_signature: MurckoFragmenter.hasframework(IAtomContainer atomContainer)
focal_class.full_signature: private boolean hasframework(IAtomContainer atomContainer)
focal_class.identifier: hasframework
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: boolean
focal_class.signature: boolean hasframework(IAtomContainer atomContainer)
focal_method.body: @Override
      public IAtomContainer[] getFragmentsAsContainers() {
          List<IAtomContainer> allfrags = new ArrayList<IAtomContainer>();
          allfrags.addAll(frameMap.values());
          allfrags.addAll(ringMap.values());
          return allfrags.toArray(new IAtomContainer[0]);
      }
focal_method.class_method_signature: MurckoFragmenter.getFragmentsAsContainers()
focal_method.full_signature: @Override public IAtomContainer[] getFragmentsAsContainers()
focal_method.identifier: getFragmentsAsContainers
focal_method.invocations: addAll values addAll values toArray
focal_method.modifiers: @Override public
focal_method.parameters: ()
focal_method.return: IAtomContainer[]
focal_method.signature: IAtomContainer[] getFragmentsAsContainers()