Package org.openscience.cdk.tools

Class AtomTypeTools

java.lang.Object

org.openscience.cdk.tools.AtomTypeTools

public class AtomTypeTools
extends Object

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

Fields

Modifier and Type	Field	Description
static final int	BENZENE_RING
static final int	FURAN_RING
static final int	PYRIDINE_RING
static final int	PYRIMIDINE_RING
static final int	PYROLE_RING
static final int	THIOPHENE_RING

Constructor Summary

Constructors

Constructor	Description
AtomTypeTools()	Constructor for the MMFF94AtomTypeMatcher object.

Method Summary

Modifier and Type	Method	Description
IRingSet	assignAtomTypePropertiesToAtom(IAtomContainer molecule)
IRingSet	assignAtomTypePropertiesToAtom(IAtomContainer molecule, boolean aromaticity)	Method assigns certain properties to an atom.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

PYROLE_RING

public static final int PYROLE_RING

See Also:

• Constant Field Values

FURAN_RING

public static final int FURAN_RING

See Also:

• Constant Field Values

THIOPHENE_RING

public static final int THIOPHENE_RING

See Also:

• Constant Field Values

PYRIDINE_RING

public static final int PYRIDINE_RING

See Also:

• Constant Field Values

PYRIMIDINE_RING

public static final int PYRIMIDINE_RING

See Also:

• Constant Field Values

BENZENE_RING

public static final int BENZENE_RING

See Also:

• Constant Field Values

Constructor Details

AtomTypeTools

public AtomTypeTools()

Constructor for the MMFF94AtomTypeMatcher object.

Method Details

assignAtomTypePropertiesToAtom

public IRingSet assignAtomTypePropertiesToAtom(IAtomContainer molecule)
                                        throws Exception

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