Package org.openscience.cdk.tools
Class AtomTypeTools
java.lang.Object
org.openscience.cdk.tools.AtomTypeTools
AtomTypeTools is a helper class for assigning atom types to an atom.
- Author:
- cho
- Source code:
- main
- Belongs to CDK module:
- extra
- Created on:
- 2005-18-07
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
static final int
static final int
static final int
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionassignAtomTypePropertiesToAtom
(IAtomContainer molecule) assignAtomTypePropertiesToAtom
(IAtomContainer molecule, boolean aromaticity) Method assigns certain properties to an atom.
-
Field Details
-
PYROLE_RING
public static final int PYROLE_RING- See Also:
-
FURAN_RING
public static final int FURAN_RING- See Also:
-
THIOPHENE_RING
public static final int THIOPHENE_RING- See Also:
-
PYRIDINE_RING
public static final int PYRIDINE_RING- See Also:
-
PYRIMIDINE_RING
public static final int PYRIMIDINE_RING- See Also:
-
BENZENE_RING
public static final int BENZENE_RING- See Also:
-
-
Constructor Details
-
AtomTypeTools
public AtomTypeTools()Constructor for the MMFF94AtomTypeMatcher object.
-
-
Method Details
-
assignAtomTypePropertiesToAtom
- Throws:
Exception
-
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
-