ambit2.smarts

Class CMLUtilities

java.lang.Object

ambit2.smarts.CMLUtilities

public class CMLUtilities
extends Object

SMARTSProp is a per atom property & hvnNrrrrrrrrRRRRRRRR extractSMARTSProperties(IAtomContainer mol) setCMLSMARTSProperties(IAtomContainer mol) mol.getAtom(i).setProperty("SMARTSProp", prop); if already set,

Author:

nina

Field Summary

Fields

Modifier and Type	Field and Description
static String	ExplicitH
static int	MAXRINGS
static String	RingData
static String	RingData2
static String	SMARTSProp

Constructor Summary

Constructors

Constructor and Description
CMLUtilities()

Method Summary

Modifier and Type	Method and Description
void	extractCMLAtomProperties(org.openscience.cdk.interfaces.IAtom atom, String CMLProperty) Converts per-atom string property into internal structure
void	extractSMARTSProperties(org.openscience.cdk.interfaces.IAtomContainer mol) Retrieves properties (set by setCMLSmartsProperties Expects SMARTSProp to be set for each atom !
void	setCMLSMARTSProperties(org.openscience.cdk.interfaces.IAtomContainer mol) Generates attributes and sets atom & bond attributes for every atom as atom properties

Methods inherited from class java.lang.Object

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

Field Detail

SMARTSProp

public static final String SMARTSProp

See Also:

Constant Field Values

RingData

public static final String RingData

See Also:

Constant Field Values

RingData2

public static final String RingData2

See Also:

Constant Field Values

ExplicitH

public static final String ExplicitH

See Also:

Constant Field Values

MAXRINGS

public static final int MAXRINGS

See Also:

Constant Field Values

Constructor Detail

CMLUtilities

public CMLUtilities()

Method Detail

setCMLSMARTSProperties

public void setCMLSMARTSProperties(org.openscience.cdk.interfaces.IAtomContainer mol)

Generates attributes and sets atom & bond attributes for every atom as atom properties

Parameters:

mol -

extractSMARTSProperties

public void extractSMARTSProperties(org.openscience.cdk.interfaces.IAtomContainer mol)

Retrieves properties (set by setCMLSmartsProperties Expects SMARTSProp to be set for each atom !

Parameters:

mol -

extractCMLAtomProperties

public void extractCMLAtomProperties(org.openscience.cdk.interfaces.IAtom atom,
                                     String CMLProperty)

Converts per-atom string property into internal structure

Parameters:

atom -

CMLProperty -