test_class.declarator: logger     = LoggingToolFactory.createLoggingTool(CircularFingerprinterTest.class)
test_class.modifier: private static
test_class.original_string: private static ILoggingTool   logger     = LoggingToolFactory.createLoggingTool(CircularFingerprinterTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.declarator: trivialMol = null
test_class.modifier: private static
test_class.original_string: private static IAtomContainer trivialMol = null;
test_class.type: IAtomContainer
test_class.var_name: trivialMol
test_class.file: descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprinterTest.java
test_class.identifier: CircularFingerprinterTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test public void testUseStereoElements() throws CDKException {
          final String smiles1  = "CC[C@@H](C)O";
          final String smiles2  = "CC[C@H](O)C";
          final String molfile = "\n"
                               + "  CDK     10121722462D          \n"
                               + "\n"
                               + "  5  4  0  0  0  0            999 V2000\n"
                               + "   -4.1837    2.6984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
                               + "   -3.4692    3.1109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
                               + "   -2.7547    2.6984    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0\n"
                               + "   -2.0403    3.1109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
                               + "   -2.7547    1.8734    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
                               + "  1  2  1  0  0  0  0\n"
                               + "  2  3  1  0  0  0  0\n"
                               + "  3  4  1  0  0  0  0\n"
                               + "  3  5  1  1  0  0  0\n"
                               + "M  END\n";
          IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
          MDLV2000Reader mdlr = new MDLV2000Reader(new StringReader(molfile));
          SmilesParser smipar = new SmilesParser(bldr);
  
          IAtomContainer mol1 = smipar.parseSmiles(smiles1);
          IAtomContainer mol2 = smipar.parseSmiles(smiles2);
          IAtomContainer mol3 = mdlr.read(bldr.newAtomContainer());
  
          CircularFingerprinter fpr = new CircularFingerprinter();
  
          // when stereo-chemistry is perceived we don't have coordinates from the
          // SMILES and so get a different fingerprint
          fpr.setPerceiveStereo(true);
          org.hamcrest.MatcherAssert.assertThat(fpr.getFingerprint(mol1), is(fpr.getFingerprint(mol2)));
          org.hamcrest.MatcherAssert.assertThat(fpr.getFingerprint(mol2), is(not(fpr.getFingerprint(mol3))));
  
          fpr.setPerceiveStereo(false);
          org.hamcrest.MatcherAssert.assertThat(fpr.getFingerprint(mol1), is(fpr.getFingerprint(mol2)));
          org.hamcrest.MatcherAssert.assertThat(fpr.getFingerprint(mol2), is(fpr.getFingerprint(mol3)));
      }
test_case.class_method_signature: CircularFingerprinterTest.testUseStereoElements()
test_case.full_signature: @Test public void testUseStereoElements()
test_case.identifier: testUseStereoElements
test_case.invocations: getInstance parseSmiles parseSmiles read newAtomContainer setPerceiveStereo assertThat getFingerprint is getFingerprint assertThat getFingerprint is not getFingerprint setPerceiveStereo assertThat getFingerprint is getFingerprint assertThat getFingerprint is getFingerprint
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testUseStereoElements()
focal_class.declarator: CLASS_ECFP0 = 1
focal_class.modifier: public static final
focal_class.original_string: public static final int CLASS_ECFP0 = 1;
focal_class.type: int
focal_class.var_name: CLASS_ECFP0
focal_class.declarator: CLASS_ECFP2 = 2
focal_class.modifier: public static final
focal_class.original_string: public static final int CLASS_ECFP2 = 2;
focal_class.type: int
focal_class.var_name: CLASS_ECFP2
focal_class.declarator: CLASS_ECFP4 = 3
focal_class.modifier: public static final
focal_class.original_string: public static final int CLASS_ECFP4 = 3;
focal_class.type: int
focal_class.var_name: CLASS_ECFP4
focal_class.declarator: CLASS_ECFP6 = 4
focal_class.modifier: public static final
focal_class.original_string: public static final int CLASS_ECFP6 = 4;
focal_class.type: int
focal_class.var_name: CLASS_ECFP6
focal_class.declarator: CLASS_FCFP0 = 5
focal_class.modifier: public static final
focal_class.original_string: public static final int CLASS_FCFP0 = 5;
focal_class.type: int
focal_class.var_name: CLASS_FCFP0
focal_class.declarator: CLASS_FCFP2 = 6
focal_class.modifier: public static final
focal_class.original_string: public static final int CLASS_FCFP2 = 6;
focal_class.type: int
focal_class.var_name: CLASS_FCFP2
focal_class.declarator: CLASS_FCFP4 = 7
focal_class.modifier: public static final
focal_class.original_string: public static final int CLASS_FCFP4 = 7;
focal_class.type: int
focal_class.var_name: CLASS_FCFP4
focal_class.declarator: CLASS_FCFP6 = 8
focal_class.modifier: public static final
focal_class.original_string: public static final int CLASS_FCFP6 = 8;
focal_class.type: int
focal_class.var_name: CLASS_FCFP6
focal_class.declarator: ATOMCLASS_ECFP = 1
focal_class.modifier: private final
focal_class.original_string: private final int      ATOMCLASS_ECFP = 1;
focal_class.type: int
focal_class.var_name: ATOMCLASS_ECFP
focal_class.declarator: ATOMCLASS_FCFP = 2
focal_class.modifier: private final
focal_class.original_string: private final int      ATOMCLASS_FCFP = 2;
focal_class.type: int
focal_class.var_name: ATOMCLASS_FCFP
focal_class.declarator: mol
focal_class.modifier: private
focal_class.original_string: private IAtomContainer mol;
focal_class.type: IAtomContainer
focal_class.var_name: mol
focal_class.declarator: length
focal_class.modifier: private final
focal_class.original_string: private final int      length;
focal_class.type: int
focal_class.var_name: length
focal_class.declarator: identity
focal_class.modifier: private
focal_class.original_string: private int[]          identity;
focal_class.type: int[]
focal_class.var_name: identity
focal_class.declarator: resolvedChiral
focal_class.modifier: private
focal_class.original_string: private boolean[]      resolvedChiral;
focal_class.type: boolean[]
focal_class.var_name: resolvedChiral
focal_class.declarator: atomGroup
focal_class.modifier: private
focal_class.original_string: private int[][]        atomGroup;
focal_class.type: int[][]
focal_class.var_name: atomGroup
focal_class.declarator: crc            = new CRC32()
focal_class.modifier: private
focal_class.original_string: private CRC32          crc            = new CRC32();
focal_class.type: CRC32
focal_class.var_name: crc
focal_class.declarator: fplist         = new ArrayList<FP>()
focal_class.modifier: private
focal_class.original_string: private ArrayList<FP>  fplist         = new ArrayList<FP>();
focal_class.type: ArrayList<FP>
focal_class.var_name: fplist
focal_class.declarator: amask
focal_class.modifier: private
focal_class.original_string: private boolean[]      amask;
focal_class.type: boolean[]
focal_class.var_name: amask
focal_class.declarator: hcount
focal_class.modifier: private
focal_class.original_string: private int[]          hcount;
focal_class.type: int[]
focal_class.var_name: hcount
focal_class.declarator: atomAdj
focal_class.modifier: private
focal_class.original_string: private int[][]        atomAdj, bondAdj;
focal_class.type: int[][]
focal_class.var_name: atomAdj
focal_class.declarator: ringBlock
focal_class.modifier: private
focal_class.original_string: private int[]          ringBlock;
focal_class.type: int[]
focal_class.var_name: ringBlock
focal_class.declarator: smallRings
focal_class.modifier: private
focal_class.original_string: private int[][]        smallRings;
focal_class.type: int[][]
focal_class.var_name: smallRings
focal_class.declarator: bondOrder
focal_class.modifier: private
focal_class.original_string: private int[]          bondOrder;
focal_class.type: int[]
focal_class.var_name: bondOrder
focal_class.declarator: atomArom
focal_class.modifier: private
focal_class.original_string: private boolean[]      atomArom, bondArom;
focal_class.type: boolean[]
focal_class.var_name: atomArom
focal_class.declarator: tetra
focal_class.modifier: private
focal_class.original_string: private int[][]        tetra;
focal_class.type: int[][]
focal_class.var_name: tetra
focal_class.declarator: maskDon
focal_class.modifier: private
focal_class.original_string: private boolean[]      maskDon, maskAcc, maskPos, maskNeg, maskAro, maskHal;
focal_class.type: boolean[]
focal_class.var_name: maskDon
focal_class.declarator: bondSum
focal_class.modifier: private
focal_class.original_string: private int[]          bondSum;
focal_class.type: int[]
focal_class.var_name: bondSum
focal_class.declarator: hasDouble
focal_class.modifier: private
focal_class.original_string: private boolean[]      hasDouble;
focal_class.type: boolean[]
focal_class.var_name: hasDouble
focal_class.declarator: aliphatic
focal_class.modifier: private
focal_class.original_string: private boolean[]      aliphatic;
focal_class.type: boolean[]
focal_class.var_name: aliphatic
focal_class.declarator: isOxide
focal_class.modifier: private
focal_class.original_string: private boolean[]      isOxide;
focal_class.type: boolean[]
focal_class.var_name: isOxide
focal_class.declarator: lonePair
focal_class.modifier: private
focal_class.original_string: private boolean[]      lonePair;
focal_class.type: boolean[]
focal_class.var_name: lonePair
focal_class.declarator: tetrazole
focal_class.modifier: private
focal_class.original_string: private boolean[]      tetrazole;
focal_class.type: boolean[]
focal_class.var_name: tetrazole
focal_class.declarator: classType
focal_class.modifier: private
focal_class.original_string: private int     classType, atomClass;
focal_class.type: int
focal_class.var_name: classType
focal_class.declarator: optPerceiveStereo = false
focal_class.modifier: private
focal_class.original_string: private boolean optPerceiveStereo = false;
focal_class.type: boolean
focal_class.var_name: optPerceiveStereo
focal_class.file: descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/CircularFingerprinter.java
focal_class.identifier: CircularFingerprinter
focal_class.interfaces: implements IFingerprinter
focal_class.class_method_signature: CircularFingerprinter.CircularFingerprinter()
focal_class.full_signature: public  CircularFingerprinter()
focal_class.identifier: CircularFingerprinter
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  CircularFingerprinter()
focal_class.class_method_signature: CircularFingerprinter.CircularFingerprinter(int classType)
focal_class.full_signature: public  CircularFingerprinter(int classType)
focal_class.identifier: CircularFingerprinter
focal_class.modifiers: public
focal_class.parameters: (int classType)
focal_class.signature:  CircularFingerprinter(int classType)
focal_class.class_method_signature: CircularFingerprinter.CircularFingerprinter(int classType, int len)
focal_class.full_signature: public  CircularFingerprinter(int classType, int len)
focal_class.identifier: CircularFingerprinter
focal_class.modifiers: public
focal_class.parameters: (int classType, int len)
focal_class.signature:  CircularFingerprinter(int classType, int len)
focal_class.class_method_signature: CircularFingerprinter.setPerceiveStereo(boolean val)
focal_class.full_signature: public void setPerceiveStereo(boolean val)
focal_class.identifier: setPerceiveStereo
focal_class.modifiers: public
focal_class.parameters: (boolean val)
focal_class.return: void
focal_class.signature: void setPerceiveStereo(boolean val)
focal_class.class_method_signature: CircularFingerprinter.getParameters()
focal_class.full_signature: @Override protected List<Map.Entry<String, String>> getParameters()
focal_class.identifier: getParameters
focal_class.modifiers: @Override protected
focal_class.parameters: ()
focal_class.return: List<Map.Entry<String, String>>
focal_class.signature: List<Map.Entry<String, String>> getParameters()
focal_class.class_method_signature: CircularFingerprinter.calculate(IAtomContainer mol)
focal_class.full_signature: public void calculate(IAtomContainer mol)
focal_class.identifier: calculate
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer mol)
focal_class.return: void
focal_class.signature: void calculate(IAtomContainer mol)
focal_class.class_method_signature: CircularFingerprinter.getFPCount()
focal_class.full_signature: public int getFPCount()
focal_class.identifier: getFPCount
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getFPCount()
focal_class.class_method_signature: CircularFingerprinter.getFP(int N)
focal_class.full_signature: public FP getFP(int N)
focal_class.identifier: getFP
focal_class.modifiers: public
focal_class.parameters: (int N)
focal_class.return: FP
focal_class.signature: FP getFP(int N)
focal_class.class_method_signature: CircularFingerprinter.getBitFingerprint(IAtomContainer mol)
focal_class.full_signature: @Override public IBitFingerprint getBitFingerprint(IAtomContainer mol)
focal_class.identifier: getBitFingerprint
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer mol)
focal_class.return: IBitFingerprint
focal_class.signature: IBitFingerprint getBitFingerprint(IAtomContainer mol)
focal_class.class_method_signature: CircularFingerprinter.getCountFingerprint(IAtomContainer mol)
focal_class.full_signature: @Override public ICountFingerprint getCountFingerprint(IAtomContainer mol)
focal_class.identifier: getCountFingerprint
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer mol)
focal_class.return: ICountFingerprint
focal_class.signature: ICountFingerprint getCountFingerprint(IAtomContainer mol)
focal_class.class_method_signature: CircularFingerprinter.getRawFingerprint(IAtomContainer mol)
focal_class.full_signature: @Override public Map<String, Integer> getRawFingerprint(IAtomContainer mol)
focal_class.identifier: getRawFingerprint
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer mol)
focal_class.return: Map<String, Integer>
focal_class.signature: Map<String, Integer> getRawFingerprint(IAtomContainer mol)
focal_class.class_method_signature: CircularFingerprinter.getSize()
focal_class.full_signature: @Override public int getSize()
focal_class.identifier: getSize
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getSize()
focal_class.class_method_signature: CircularFingerprinter.initialIdentityECFP(int aidx)
focal_class.full_signature: private int initialIdentityECFP(int aidx)
focal_class.identifier: initialIdentityECFP
focal_class.modifiers: private
focal_class.parameters: (int aidx)
focal_class.return: int
focal_class.signature: int initialIdentityECFP(int aidx)
focal_class.class_method_signature: CircularFingerprinter.initialIdentityFCFP(int aidx)
focal_class.full_signature: private int initialIdentityFCFP(int aidx)
focal_class.identifier: initialIdentityFCFP
focal_class.modifiers: private
focal_class.parameters: (int aidx)
focal_class.return: int
focal_class.signature: int initialIdentityFCFP(int aidx)
focal_class.class_method_signature: CircularFingerprinter.circularIterate(int iter, int atom)
focal_class.full_signature: private int circularIterate(int iter, int atom)
focal_class.identifier: circularIterate
focal_class.modifiers: private
focal_class.parameters: (int iter, int atom)
focal_class.return: int
focal_class.signature: int circularIterate(int iter, int atom)
focal_class.class_method_signature: CircularFingerprinter.growAtoms(int[] atoms)
focal_class.full_signature: private int[] growAtoms(int[] atoms)
focal_class.identifier: growAtoms
focal_class.modifiers: private
focal_class.parameters: (int[] atoms)
focal_class.return: int[]
focal_class.signature: int[] growAtoms(int[] atoms)
focal_class.class_method_signature: CircularFingerprinter.considerNewFP(FP newFP)
focal_class.full_signature: private void considerNewFP(FP newFP)
focal_class.identifier: considerNewFP
focal_class.modifiers: private
focal_class.parameters: (FP newFP)
focal_class.return: void
focal_class.signature: void considerNewFP(FP newFP)
focal_class.class_method_signature: CircularFingerprinter.excavateMolecule()
focal_class.full_signature: private void excavateMolecule()
focal_class.identifier: excavateMolecule
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void excavateMolecule()
focal_class.class_method_signature: CircularFingerprinter.markRingBlocks()
focal_class.full_signature: private void markRingBlocks()
focal_class.identifier: markRingBlocks
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void markRingBlocks()
focal_class.class_method_signature: CircularFingerprinter.recursiveRingFind(int[] path, int psize, int capacity, int rblk, ArrayList<int[]> rings)
focal_class.full_signature: private void recursiveRingFind(int[] path, int psize, int capacity, int rblk, ArrayList<int[]> rings)
focal_class.identifier: recursiveRingFind
focal_class.modifiers: private
focal_class.parameters: (int[] path, int psize, int capacity, int rblk, ArrayList<int[]> rings)
focal_class.return: void
focal_class.signature: void recursiveRingFind(int[] path, int psize, int capacity, int rblk, ArrayList<int[]> rings)
focal_class.class_method_signature: CircularFingerprinter.detectStrictAromaticity()
focal_class.full_signature: private void detectStrictAromaticity()
focal_class.identifier: detectStrictAromaticity
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void detectStrictAromaticity()
focal_class.class_method_signature: CircularFingerprinter.rubricTetrahedralsCdk()
focal_class.full_signature: private void rubricTetrahedralsCdk()
focal_class.identifier: rubricTetrahedralsCdk
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void rubricTetrahedralsCdk()
focal_class.class_method_signature: CircularFingerprinter.rubricTetrahedral(int aidx)
focal_class.full_signature: private int[] rubricTetrahedral(int aidx)
focal_class.identifier: rubricTetrahedral
focal_class.modifiers: private
focal_class.parameters: (int aidx)
focal_class.return: int[]
focal_class.signature: int[] rubricTetrahedral(int aidx)
focal_class.class_method_signature: CircularFingerprinter.calculateBioTypes()
focal_class.full_signature: private void calculateBioTypes()
focal_class.identifier: calculateBioTypes
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void calculateBioTypes()
focal_class.class_method_signature: CircularFingerprinter.considerBioTypeAromaticity(final int[] ring)
focal_class.full_signature: private void considerBioTypeAromaticity(final int[] ring)
focal_class.identifier: considerBioTypeAromaticity
focal_class.modifiers: private
focal_class.parameters: (final int[] ring)
focal_class.return: void
focal_class.signature: void considerBioTypeAromaticity(final int[] ring)
focal_class.class_method_signature: CircularFingerprinter.considerBioTypeTetrazole(final int[] ring)
focal_class.full_signature: private void considerBioTypeTetrazole(final int[] ring)
focal_class.identifier: considerBioTypeTetrazole
focal_class.modifiers: private
focal_class.parameters: (final int[] ring)
focal_class.return: void
focal_class.signature: void considerBioTypeTetrazole(final int[] ring)
focal_class.class_method_signature: CircularFingerprinter.determineDonor(int aidx)
focal_class.full_signature: private boolean determineDonor(int aidx)
focal_class.identifier: determineDonor
focal_class.modifiers: private
focal_class.parameters: (int aidx)
focal_class.return: boolean
focal_class.signature: boolean determineDonor(int aidx)
focal_class.class_method_signature: CircularFingerprinter.determineAcceptor(int aidx)
focal_class.full_signature: private boolean determineAcceptor(int aidx)
focal_class.identifier: determineAcceptor
focal_class.modifiers: private
focal_class.parameters: (int aidx)
focal_class.return: boolean
focal_class.signature: boolean determineAcceptor(int aidx)
focal_class.class_method_signature: CircularFingerprinter.determinePositive(int aidx)
focal_class.full_signature: private boolean determinePositive(int aidx)
focal_class.identifier: determinePositive
focal_class.modifiers: private
focal_class.parameters: (int aidx)
focal_class.return: boolean
focal_class.signature: boolean determinePositive(int aidx)
focal_class.class_method_signature: CircularFingerprinter.determineNegative(int aidx)
focal_class.full_signature: private boolean determineNegative(int aidx)
focal_class.identifier: determineNegative
focal_class.modifiers: private
focal_class.parameters: (int aidx)
focal_class.return: boolean
focal_class.signature: boolean determineNegative(int aidx)
focal_class.class_method_signature: CircularFingerprinter.determineHalide(int aidx)
focal_class.full_signature: private boolean determineHalide(int aidx)
focal_class.identifier: determineHalide
focal_class.modifiers: private
focal_class.parameters: (int aidx)
focal_class.return: boolean
focal_class.signature: boolean determineHalide(int aidx)
focal_class.class_method_signature: CircularFingerprinter.bondOrderBioType(int bidx)
focal_class.full_signature: private int bondOrderBioType(int bidx)
focal_class.identifier: bondOrderBioType
focal_class.modifiers: private
focal_class.parameters: (int bidx)
focal_class.return: int
focal_class.signature: int bondOrderBioType(int bidx)
focal_class.class_method_signature: CircularFingerprinter.appendInteger(int[] a, int v)
focal_class.full_signature: private int[] appendInteger(int[] a, int v)
focal_class.identifier: appendInteger
focal_class.modifiers: private
focal_class.parameters: (int[] a, int v)
focal_class.return: int[]
focal_class.signature: int[] appendInteger(int[] a, int v)
focal_class.class_method_signature: CircularFingerprinter.findBond(int a1, int a2)
focal_class.full_signature: private int findBond(int a1, int a2)
focal_class.identifier: findBond
focal_class.modifiers: private
focal_class.parameters: (int a1, int a2)
focal_class.return: int
focal_class.signature: int findBond(int a1, int a2)
focal_class.superclass: extends AbstractFingerprinter
focal_method.body: public void setPerceiveStereo(boolean val) {
          this.optPerceiveStereo = val;
      }
focal_method.class_method_signature: CircularFingerprinter.setPerceiveStereo(boolean val)
focal_method.full_signature: public void setPerceiveStereo(boolean val)
focal_method.identifier: setPerceiveStereo
focal_method.modifiers: public
focal_method.parameters: (boolean val)
focal_method.return: void
focal_method.signature: void setPerceiveStereo(boolean val)