ambit2.core.processors

Class AbstractStructureProcessor

java.lang.Object

ambit2.core.processors.AbstractStructureProcessor

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Direct Known Subclasses:

FragmentProcessor, IsotopesProcessor, SMIRKSProcessor

public abstract class AbstractStructureProcessor
extends Object
implements net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Parent class for processors

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	at_property
protected static String	at_property_added
protected static String	at_property_removed
protected boolean	atomtypeasproperties
protected boolean	enabled
protected Logger	logger
protected boolean	sparseproperties

Constructor Summary

Constructors

Constructor and Description
AbstractStructureProcessor(Logger logger)

Method Summary

Modifier and Type	Method and Description
protected boolean	applicable(org.openscience.cdk.interfaces.IAtom atom) Used as criteria whether to assign atom types as properties e.g.
static org.openscience.cdk.interfaces.IAtomContainer	atomtypes2properties_init(org.openscience.cdk.interfaces.IAtomContainer mol)
static org.openscience.cdk.interfaces.IAtomContainer	atomtypes2properties(org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.interfaces.IAtomContainer	atomtypes2property(org.openscience.cdk.interfaces.IAtomContainer mol, Object compareWith, boolean sparseProperties)
org.openscience.cdk.interfaces.IAtomContainer	atomtypes2property(String property, org.openscience.cdk.interfaces.IAtomContainer mol, Object compareWith, boolean sparseProperties)
void	close()
long	getID()
boolean	isAtomtypeasproperties()
boolean	isEnabled()
boolean	isSparseproperties()
void	open()
void	setAtomtypeasproperties(boolean atomtypeasproperties) Assign atomtypes as atomcontainer properties
void	setEnabled(boolean value)
void	setSparseproperties(boolean sparseproperties) if true assigns empty properties

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.idea.modbcum.i.processors.IProcessor

process

Field Detail

logger

protected transient Logger logger

at_property

protected static final String at_property

See Also:

Constant Field Values

at_property_added

protected static final String at_property_added

See Also:

Constant Field Values

at_property_removed

protected static final String at_property_removed

See Also:

Constant Field Values

sparseproperties

protected boolean sparseproperties

atomtypeasproperties

protected boolean atomtypeasproperties

enabled

protected boolean enabled

Constructor Detail

AbstractStructureProcessor

public AbstractStructureProcessor(Logger logger)

Method Detail

isSparseproperties

public boolean isSparseproperties()

setSparseproperties

public void setSparseproperties(boolean sparseproperties)

if true assigns empty properties

Parameters:

sparseproperties -

isAtomtypeasproperties

public boolean isAtomtypeasproperties()

setAtomtypeasproperties

public void setAtomtypeasproperties(boolean atomtypeasproperties)

Assign atomtypes as atomcontainer properties

Parameters:

atomtypeasproperties -

isEnabled

public boolean isEnabled()

Specified by:

isEnabled in interface net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

setEnabled

public void setEnabled(boolean value)

Specified by:

setEnabled in interface net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

getID

public long getID()

Specified by:

getID in interface net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

close

public void close()
           throws Exception

Specified by:

close in interface net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

Exception

open

public void open()
          throws Exception

Specified by:

open in interface net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

Exception

atomtypes2property

public org.openscience.cdk.interfaces.IAtomContainer atomtypes2property(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                        Object compareWith,
                                                                        boolean sparseProperties)
                                                                 throws Exception

Throws:

Exception

applicable

protected boolean applicable(org.openscience.cdk.interfaces.IAtom atom)

Used as criteria whether to assign atom types as properties e.g. assign only if charged atoms. Subclass to define your own.

Parameters:

atom -

Returns:

atomtypes2property

public org.openscience.cdk.interfaces.IAtomContainer atomtypes2property(String property,
                                                                        org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                        Object compareWith,
                                                                        boolean sparseProperties)
                                                                 throws Exception

Throws:

Exception

atomtypes2properties

public static org.openscience.cdk.interfaces.IAtomContainer atomtypes2properties(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                          throws Exception

Throws:

Exception

atomtypes2properties_init

public static org.openscience.cdk.interfaces.IAtomContainer atomtypes2properties_init(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                               throws Exception

Throws:

Exception