test_class.file: legacy/src/test/java/org/openscience/cdk/smsd/filters/ChemicalFiltersTest.java
test_class.identifier: ChemicalFiltersTest
test_case.body: @Test
      public void testGetSortedEnergy() throws InvalidSmilesException, CDKException {
          SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
          IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");
  
          Isomorphism smsd1 = new Isomorphism(Algorithm.DEFAULT, true);
          smsd1.init(queryac, target, true, true);
          smsd1.setChemFilters(false, false, true);
          Double score = 610.0;
          assertEquals(score, smsd1.getEnergyScore(0));
      }
test_case.class_method_signature: ChemicalFiltersTest.testGetSortedEnergy()
test_case.full_signature: @Test public void testGetSortedEnergy()
test_case.identifier: testGetSortedEnergy
test_case.invocations: getInstance parseSmiles parseSmiles init setChemFilters assertEquals getEnergyScore
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetSortedEnergy()
focal_class.declarator: allMCS        = null
focal_class.modifier: private
focal_class.original_string: private List<Map<Integer, Integer>> allMCS        = null;
focal_class.type: List<Map<Integer, Integer>>
focal_class.var_name: allMCS
focal_class.declarator: firstSolution = null
focal_class.modifier: private
focal_class.original_string: private Map<Integer, Integer>       firstSolution = null;
focal_class.type: Map<Integer, Integer>
focal_class.var_name: firstSolution
focal_class.declarator: allAtomMCS    = null
focal_class.modifier: private
focal_class.original_string: private List<Map<IAtom, IAtom>>     allAtomMCS    = null;
focal_class.type: List<Map<IAtom, IAtom>>
focal_class.var_name: allAtomMCS
focal_class.declarator: firstAtomMCS  = null
focal_class.modifier: private
focal_class.original_string: private Map<IAtom, IAtom>           firstAtomMCS  = null;
focal_class.type: Map<IAtom, IAtom>
focal_class.var_name: firstAtomMCS
focal_class.declarator: stereoScore   = null
focal_class.modifier: private
focal_class.original_string: private List<Double>                stereoScore   = null;
focal_class.type: List<Double>
focal_class.var_name: stereoScore
focal_class.declarator: fragmentSize  = null
focal_class.modifier: private
focal_class.original_string: private List<Integer>               fragmentSize  = null;
focal_class.type: List<Integer>
focal_class.var_name: fragmentSize
focal_class.declarator: bEnergies     = null
focal_class.modifier: private
focal_class.original_string: private List<Double>                bEnergies     = null;
focal_class.type: List<Double>
focal_class.var_name: bEnergies
focal_class.declarator: rMol          = null
focal_class.modifier: private
focal_class.original_string: private IAtomContainer              rMol          = null;
focal_class.type: IAtomContainer
focal_class.var_name: rMol
focal_class.declarator: pMol          = null
focal_class.modifier: private
focal_class.original_string: private IAtomContainer              pMol          = null;
focal_class.type: IAtomContainer
focal_class.var_name: pMol
focal_class.file: legacy/src/main/java/org/openscience/cdk/smsd/filters/ChemicalFilters.java
focal_class.identifier: ChemicalFilters
focal_class.class_method_signature: ChemicalFilters.ChemicalFilters(List<Map<Integer, Integer>> allMCS, List<Map<IAtom, IAtom>> allAtomMCS,
              Map<Integer, Integer> firstSolution, Map<IAtom, IAtom> firstAtomMCS, IAtomContainer sourceMol,
              IAtomContainer targetMol)
focal_class.full_signature: public  ChemicalFilters(List<Map<Integer, Integer>> allMCS, List<Map<IAtom, IAtom>> allAtomMCS,
              Map<Integer, Integer> firstSolution, Map<IAtom, IAtom> firstAtomMCS, IAtomContainer sourceMol,
              IAtomContainer targetMol)
focal_class.identifier: ChemicalFilters
focal_class.modifiers: public
focal_class.parameters: (List<Map<Integer, Integer>> allMCS, List<Map<IAtom, IAtom>> allAtomMCS,
              Map<Integer, Integer> firstSolution, Map<IAtom, IAtom> firstAtomMCS, IAtomContainer sourceMol,
              IAtomContainer targetMol)
focal_class.signature:  ChemicalFilters(List<Map<Integer, Integer>> allMCS, List<Map<IAtom, IAtom>> allAtomMCS,
              Map<Integer, Integer> firstSolution, Map<IAtom, IAtom> firstAtomMCS, IAtomContainer sourceMol,
              IAtomContainer targetMol)
focal_class.class_method_signature: ChemicalFilters.clear()
focal_class.full_signature: private void clear()
focal_class.identifier: clear
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void clear()
focal_class.class_method_signature: ChemicalFilters.clear(Map<Integer, Map<Integer, Integer>> sortedAllMCS,
              Map<Integer, Map<IAtom, IAtom>> sortedAllAtomMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Integer> fragmentScoreMap, Map<Integer, Double> energySelectionMap)
focal_class.full_signature: private void clear(Map<Integer, Map<Integer, Integer>> sortedAllMCS,
              Map<Integer, Map<IAtom, IAtom>> sortedAllAtomMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Integer> fragmentScoreMap, Map<Integer, Double> energySelectionMap)
focal_class.identifier: clear
focal_class.modifiers: private
focal_class.parameters: (Map<Integer, Map<Integer, Integer>> sortedAllMCS,
              Map<Integer, Map<IAtom, IAtom>> sortedAllAtomMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Integer> fragmentScoreMap, Map<Integer, Double> energySelectionMap)
focal_class.return: void
focal_class.signature: void clear(Map<Integer, Map<Integer, Integer>> sortedAllMCS,
              Map<Integer, Map<IAtom, IAtom>> sortedAllAtomMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Integer> fragmentScoreMap, Map<Integer, Double> energySelectionMap)
focal_class.class_method_signature: ChemicalFilters.addSolution(int counter, int key, Map<Integer, Map<IAtom, IAtom>> allFragmentAtomMCS,
              Map<Integer, Map<Integer, Integer>> allFragmentMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Double> energyScoreMap, Map<Integer, Integer> fragmentScoreMap)
focal_class.full_signature: private void addSolution(int counter, int key, Map<Integer, Map<IAtom, IAtom>> allFragmentAtomMCS,
              Map<Integer, Map<Integer, Integer>> allFragmentMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Double> energyScoreMap, Map<Integer, Integer> fragmentScoreMap)
focal_class.identifier: addSolution
focal_class.modifiers: private
focal_class.parameters: (int counter, int key, Map<Integer, Map<IAtom, IAtom>> allFragmentAtomMCS,
              Map<Integer, Map<Integer, Integer>> allFragmentMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Double> energyScoreMap, Map<Integer, Integer> fragmentScoreMap)
focal_class.return: void
focal_class.signature: void addSolution(int counter, int key, Map<Integer, Map<IAtom, IAtom>> allFragmentAtomMCS,
              Map<Integer, Map<Integer, Integer>> allFragmentMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Double> energyScoreMap, Map<Integer, Integer> fragmentScoreMap)
focal_class.class_method_signature: ChemicalFilters.initializeMaps(Map<Integer, Map<Integer, Integer>> sortedAllMCS,
              Map<Integer, Map<IAtom, IAtom>> sortedAllAtomMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Integer> fragmentScoreMap, Map<Integer, Double> energySelectionMap)
focal_class.full_signature: private void initializeMaps(Map<Integer, Map<Integer, Integer>> sortedAllMCS,
              Map<Integer, Map<IAtom, IAtom>> sortedAllAtomMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Integer> fragmentScoreMap, Map<Integer, Double> energySelectionMap)
focal_class.identifier: initializeMaps
focal_class.modifiers: private
focal_class.parameters: (Map<Integer, Map<Integer, Integer>> sortedAllMCS,
              Map<Integer, Map<IAtom, IAtom>> sortedAllAtomMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Integer> fragmentScoreMap, Map<Integer, Double> energySelectionMap)
focal_class.return: void
focal_class.signature: void initializeMaps(Map<Integer, Map<Integer, Integer>> sortedAllMCS,
              Map<Integer, Map<IAtom, IAtom>> sortedAllAtomMCS, Map<Integer, Double> stereoScoreMap,
              Map<Integer, Integer> fragmentScoreMap, Map<Integer, Double> energySelectionMap)
focal_class.class_method_signature: ChemicalFilters.sortResultsByStereoAndBondMatch()
focal_class.full_signature: public synchronized void sortResultsByStereoAndBondMatch()
focal_class.identifier: sortResultsByStereoAndBondMatch
focal_class.modifiers: public synchronized
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void sortResultsByStereoAndBondMatch()
focal_class.class_method_signature: ChemicalFilters.sortResultsByFragments()
focal_class.full_signature: public synchronized void sortResultsByFragments()
focal_class.identifier: sortResultsByFragments
focal_class.modifiers: public synchronized
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void sortResultsByFragments()
focal_class.class_method_signature: ChemicalFilters.sortResultsByEnergies()
focal_class.full_signature: public synchronized void sortResultsByEnergies()
focal_class.identifier: sortResultsByEnergies
focal_class.modifiers: public synchronized
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void sortResultsByEnergies()
focal_class.class_method_signature: ChemicalFilters.makeBondMapsOfAtomMaps(IAtomContainer ac1, IAtomContainer ac2,
              Map<Integer, Integer> mappings)
focal_class.full_signature: private Map<IBond, IBond> makeBondMapsOfAtomMaps(IAtomContainer ac1, IAtomContainer ac2,
              Map<Integer, Integer> mappings)
focal_class.identifier: makeBondMapsOfAtomMaps
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer ac1, IAtomContainer ac2,
              Map<Integer, Integer> mappings)
focal_class.return: Map<IBond, IBond>
focal_class.signature: Map<IBond, IBond> makeBondMapsOfAtomMaps(IAtomContainer ac1, IAtomContainer ac2,
              Map<Integer, Integer> mappings)
focal_class.class_method_signature: ChemicalFilters.getMappedMoleculeFragmentSize(Map<IAtom, IAtom> mcsAtomSolution)
focal_class.full_signature: private synchronized int getMappedMoleculeFragmentSize(Map<IAtom, IAtom> mcsAtomSolution)
focal_class.identifier: getMappedMoleculeFragmentSize
focal_class.modifiers: private synchronized
focal_class.parameters: (Map<IAtom, IAtom> mcsAtomSolution)
focal_class.return: int
focal_class.signature: int getMappedMoleculeFragmentSize(Map<IAtom, IAtom> mcsAtomSolution)
focal_class.class_method_signature: ChemicalFilters.getMappedMoleculeEnergies(Map<Integer, Integer> mcsAtomSolution)
focal_class.full_signature: private synchronized Double getMappedMoleculeEnergies(Map<Integer, Integer> mcsAtomSolution)
focal_class.identifier: getMappedMoleculeEnergies
focal_class.modifiers: private synchronized
focal_class.parameters: (Map<Integer, Integer> mcsAtomSolution)
focal_class.return: Double
focal_class.signature: Double getMappedMoleculeEnergies(Map<Integer, Integer> mcsAtomSolution)
focal_class.class_method_signature: ChemicalFilters.sortMapByValueInAccendingOrder(Map<Integer, Double> map)
focal_class.full_signature: static Map<Integer, Double> sortMapByValueInAccendingOrder(Map<Integer, Double> map)
focal_class.identifier: sortMapByValueInAccendingOrder
focal_class.modifiers: static
focal_class.parameters: (Map<Integer, Double> map)
focal_class.return: Map<Integer, Double>
focal_class.signature: Map<Integer, Double> sortMapByValueInAccendingOrder(Map<Integer, Double> map)
focal_class.class_method_signature: ChemicalFilters.sortMapByValueInDecendingOrder(Map<Integer, Double> map)
focal_class.full_signature: static Map<Integer, Double> sortMapByValueInDecendingOrder(Map<Integer, Double> map)
focal_class.identifier: sortMapByValueInDecendingOrder
focal_class.modifiers: static
focal_class.parameters: (Map<Integer, Double> map)
focal_class.return: Map<Integer, Double>
focal_class.signature: Map<Integer, Double> sortMapByValueInDecendingOrder(Map<Integer, Double> map)
focal_class.class_method_signature: ChemicalFilters.getSortedEnergy()
focal_class.full_signature: public List<Double> getSortedEnergy()
focal_class.identifier: getSortedEnergy
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<Double>
focal_class.signature: List<Double> getSortedEnergy()
focal_class.class_method_signature: ChemicalFilters.getSortedFragment()
focal_class.full_signature: public List<Integer> getSortedFragment()
focal_class.identifier: getSortedFragment
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<Integer>
focal_class.signature: List<Integer> getSortedFragment()
focal_class.class_method_signature: ChemicalFilters.getStereoMatches()
focal_class.full_signature: public List<Double> getStereoMatches()
focal_class.identifier: getStereoMatches
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<Double>
focal_class.signature: List<Double> getStereoMatches()
focal_class.class_method_signature: ChemicalFilters.getMappedFragment(IAtomContainer molecule, Collection<IAtom> atomsMCS)
focal_class.full_signature: private List<Object> getMappedFragment(IAtomContainer molecule, Collection<IAtom> atomsMCS)
focal_class.identifier: getMappedFragment
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer molecule, Collection<IAtom> atomsMCS)
focal_class.return: List<Object>
focal_class.signature: List<Object> getMappedFragment(IAtomContainer molecule, Collection<IAtom> atomsMCS)
focal_class.class_method_signature: ChemicalFilters.getAtomScore(double score, Map<IAtom, IAtom> atomMapMCS, IAtomContainer reactant,
              IAtomContainer product)
focal_class.full_signature: private double getAtomScore(double score, Map<IAtom, IAtom> atomMapMCS, IAtomContainer reactant,
              IAtomContainer product)
focal_class.identifier: getAtomScore
focal_class.modifiers: private
focal_class.parameters: (double score, Map<IAtom, IAtom> atomMapMCS, IAtomContainer reactant,
              IAtomContainer product)
focal_class.return: double
focal_class.signature: double getAtomScore(double score, Map<IAtom, IAtom> atomMapMCS, IAtomContainer reactant,
              IAtomContainer product)
focal_class.class_method_signature: ChemicalFilters.getBondScore(double score, Map<IBond, IBond> bondMaps)
focal_class.full_signature: private double getBondScore(double score, Map<IBond, IBond> bondMaps)
focal_class.identifier: getBondScore
focal_class.modifiers: private
focal_class.parameters: (double score, Map<IBond, IBond> bondMaps)
focal_class.return: double
focal_class.signature: double getBondScore(double score, Map<IBond, IBond> bondMaps)
focal_class.class_method_signature: ChemicalFilters.getBondFormalChargeMatches(IBond rBond, IBond pBond)
focal_class.full_signature: private double getBondFormalChargeMatches(IBond rBond, IBond pBond)
focal_class.identifier: getBondFormalChargeMatches
focal_class.modifiers: private
focal_class.parameters: (IBond rBond, IBond pBond)
focal_class.return: double
focal_class.signature: double getBondFormalChargeMatches(IBond rBond, IBond pBond)
focal_class.class_method_signature: ChemicalFilters.getBondTypeMatches(IBond queryBond, IBond targetBond)
focal_class.full_signature: private double getBondTypeMatches(IBond queryBond, IBond targetBond)
focal_class.identifier: getBondTypeMatches
focal_class.modifiers: private
focal_class.parameters: (IBond queryBond, IBond targetBond)
focal_class.return: double
focal_class.signature: double getBondTypeMatches(IBond queryBond, IBond targetBond)
focal_class.class_method_signature: ChemicalFilters.getRingMatchScore(List<Object> list)
focal_class.full_signature: private double getRingMatchScore(List<Object> list)
focal_class.identifier: getRingMatchScore
focal_class.modifiers: private
focal_class.parameters: (List<Object> list)
focal_class.return: double
focal_class.signature: double getRingMatchScore(List<Object> list)
focal_class.class_method_signature: ChemicalFilters.getEnergy(IAtomContainer educt, IAtomContainer product)
focal_class.full_signature: private double getEnergy(IAtomContainer educt, IAtomContainer product)
focal_class.identifier: getEnergy
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer educt, IAtomContainer product)
focal_class.return: double
focal_class.signature: double getEnergy(IAtomContainer educt, IAtomContainer product)
focal_class.class_method_signature: ChemicalFilters.getBondEnergy(IBond bond, BondEnergies bondEnergy)
focal_class.full_signature: private double getBondEnergy(IBond bond, BondEnergies bondEnergy)
focal_class.identifier: getBondEnergy
focal_class.modifiers: private
focal_class.parameters: (IBond bond, BondEnergies bondEnergy)
focal_class.return: double
focal_class.signature: double getBondEnergy(IBond bond, BondEnergies bondEnergy)
focal_class.class_method_signature: ChemicalFilters.getRingMatch(IRingSet rings, List<IAtom> atoms)
focal_class.full_signature: private double getRingMatch(IRingSet rings, List<IAtom> atoms)
focal_class.identifier: getRingMatch
focal_class.modifiers: private
focal_class.parameters: (IRingSet rings, List<IAtom> atoms)
focal_class.return: double
focal_class.signature: double getRingMatch(IRingSet rings, List<IAtom> atoms)
focal_class.class_method_signature: ChemicalFilters.getStereoBondChargeMatch(Map<Integer, Double> stereoScoreMap,
              Map<Integer, Map<Integer, Integer>> allStereoMCS, Map<Integer, Map<IAtom, IAtom>> allStereoAtomMCS)
focal_class.full_signature: private boolean getStereoBondChargeMatch(Map<Integer, Double> stereoScoreMap,
              Map<Integer, Map<Integer, Integer>> allStereoMCS, Map<Integer, Map<IAtom, IAtom>> allStereoAtomMCS)
focal_class.identifier: getStereoBondChargeMatch
focal_class.modifiers: private
focal_class.parameters: (Map<Integer, Double> stereoScoreMap,
              Map<Integer, Map<Integer, Integer>> allStereoMCS, Map<Integer, Map<IAtom, IAtom>> allStereoAtomMCS)
focal_class.return: boolean
focal_class.signature: boolean getStereoBondChargeMatch(Map<Integer, Double> stereoScoreMap,
              Map<Integer, Map<Integer, Integer>> allStereoMCS, Map<Integer, Map<IAtom, IAtom>> allStereoAtomMCS)
focal_class.class_method_signature: ChemicalFilters.getfragmentCount(IAtomContainer molecule)
focal_class.full_signature: private int getfragmentCount(IAtomContainer molecule)
focal_class.identifier: getfragmentCount
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: int
focal_class.signature: int getfragmentCount(IAtomContainer molecule)
focal_class.class_method_signature: ChemicalFilters.convertOrder(double srcOrder)
focal_class.full_signature: public static IBond.Order convertOrder(double srcOrder)
focal_class.identifier: convertOrder
focal_class.modifiers: public static
focal_class.parameters: (double srcOrder)
focal_class.return: IBond.Order
focal_class.signature: IBond.Order convertOrder(double srcOrder)
focal_class.class_method_signature: ChemicalFilters.convertBondOrder(IBond bond)
focal_class.full_signature: public static int convertBondOrder(IBond bond)
focal_class.identifier: convertBondOrder
focal_class.modifiers: public static
focal_class.parameters: (IBond bond)
focal_class.return: int
focal_class.signature: int convertBondOrder(IBond bond)
focal_class.class_method_signature: ChemicalFilters.convertBondStereo(IBond bond)
focal_class.full_signature: public static int convertBondStereo(IBond bond)
focal_class.identifier: convertBondStereo
focal_class.modifiers: public static
focal_class.parameters: (IBond bond)
focal_class.return: int
focal_class.signature: int convertBondStereo(IBond bond)
focal_class.class_method_signature: ChemicalFilters.convertStereo(int stereoValue)
focal_class.full_signature: public static IBond.Stereo convertStereo(int stereoValue)
focal_class.identifier: convertStereo
focal_class.modifiers: public static
focal_class.parameters: (int stereoValue)
focal_class.return: IBond.Stereo
focal_class.signature: IBond.Stereo convertStereo(int stereoValue)
focal_method.body: public List<Double> getSortedEnergy() {
          return Collections.unmodifiableList(bEnergies);
      }
focal_method.class_method_signature: ChemicalFilters.getSortedEnergy()
focal_method.full_signature: public List<Double> getSortedEnergy()
focal_method.identifier: getSortedEnergy
focal_method.invocations: unmodifiableList
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: List<Double>
focal_method.signature: List<Double> getSortedEnergy()