Package org.openscience.cdk.tools
Class AtomTypeTools
- java.lang.Object
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- org.openscience.cdk.tools.AtomTypeTools
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Field Summary
Fields Modifier and Type Field Description static int
BENZENE_RING
static int
FURAN_RING
static int
PYRIDINE_RING
static int
PYRIMIDINE_RING
static int
PYROLE_RING
static int
THIOPHENE_RING
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Constructor Summary
Constructors Constructor Description AtomTypeTools()
Constructor for the MMFF94AtomTypeMatcher object.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description IRingSet
assignAtomTypePropertiesToAtom(IAtomContainer molecule)
IRingSet
assignAtomTypePropertiesToAtom(IAtomContainer molecule, boolean aromaticity)
Method assigns certain properties to an atom.
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Field Detail
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PYROLE_RING
public static final int PYROLE_RING
- See Also:
- Constant Field Values
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FURAN_RING
public static final int FURAN_RING
- See Also:
- Constant Field Values
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THIOPHENE_RING
public static final int THIOPHENE_RING
- See Also:
- Constant Field Values
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PYRIDINE_RING
public static final int PYRIDINE_RING
- See Also:
- Constant Field Values
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PYRIMIDINE_RING
public static final int PYRIMIDINE_RING
- See Also:
- Constant Field Values
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BENZENE_RING
public static final int BENZENE_RING
- See Also:
- Constant Field Values
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Method Detail
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assignAtomTypePropertiesToAtom
public IRingSet assignAtomTypePropertiesToAtom(IAtomContainer molecule) throws Exception
- Throws:
Exception
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assignAtomTypePropertiesToAtom
public IRingSet assignAtomTypePropertiesToAtom(IAtomContainer molecule, boolean aromaticity) throws Exception
Method assigns certain properties to an atom. Necessary for the atom type matching Properties:- aromaticity)
- ChemicalGroup (CDKChemicalRingGroupConstant)
- SSSR
- Ring/Group, ringSize, aromaticity
- SphericalMatcher (HoSe Code)
- Parameters:
aromaticity
- boolean true/false true if aromaticity should be calculated- Returns:
- sssrf ringSetofTheMolecule
- Throws:
Exception
- Description of the Exception
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