ambit2.smarts

Class SmartsToChemObject

java.lang.Object

net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

ambit2.smarts.SmartsToChemObject

All Implemented Interfaces:

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

public class SmartsToChemObject
extends net.idea.modbcum.p.DefaultAmbitProcessor<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected org.openscience.cdk.interfaces.IChemObjectBuilder	builder
boolean	forceAromaticBondsAlways
boolean	forceAromaticBondsForNonRingAtoms
static String	markProperty

Fields inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
SmartsToChemObject(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Summary

Modifier and Type	Method and Description
void	analyzeSubExpressionsFromLowAnd(SmartsAtomExpression atExp, SmartsAtomExpression sub)
void	analyzeSubExpressionsFromLowAnd(SmartsBondExpression boExp, SmartsBondExpression sub)
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	convertKekuleSmartsToAromatic(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	convertKekuleSmartsToAromatic(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query, org.openscience.cdk.interfaces.IRingSet ringSet)
org.openscience.cdk.interfaces.IAtomContainer	extractAtomContainer(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query) Version of the function when the Ring data is not supplied outside
org.openscience.cdk.interfaces.IAtomContainer	extractAtomContainer(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query, org.openscience.cdk.interfaces.IRingSet ringSet) Maximal possible atom container from this query is generated.
org.openscience.cdk.interfaces.IAtomContainer	extractAtomContainerFullyConnected(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
org.openscience.cdk.interfaces.IAtomContainer	extractAtomContainerFullyConnected(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query, org.openscience.cdk.interfaces.IRingSet ringSet) Maximal possible atom container from this query is generated BUT this container is always fully connected as the original query.
org.openscience.cdk.interfaces.IChemObjectBuilder	getBuilder()
int	getExpressionAtomType(SmartsAtomExpression atExp, SmartsAtomExpression sub)
int	getExpressionBondType(SmartsBondExpression boExp, SmartsBondExpression sub)
int	getRecursiveExpressionAtomType(SmartsAtomExpression atExp, int n)
static List<SmartsAtomExpression>	getSubExpressions(SmartsAtomExpression a, int separator)
List<SmartsBondExpression>	getSubExpressions(SmartsBondExpression b, int separator)
org.openscience.cdk.interfaces.IAtomContainer	process(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer target)
void	setBuilder(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
org.openscience.cdk.interfaces.IAtom	smartsExpressionToAtom(SmartsAtomExpression a) This function tries to convert the SmartsAtomExpression to a IAtom with defined atom type.
org.openscience.cdk.interfaces.IBond	smartsExpressionToBond(SmartsBondExpression b)
org.openscience.cdk.interfaces.IAtom	toAtom(org.openscience.cdk.interfaces.IAtom a) This function tries to convert this object to a classic CDK Atom If it is impossible to determine the atom type null is returned
org.openscience.cdk.interfaces.IBond	toBond(org.openscience.cdk.interfaces.IBond b)

Methods inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

addPropertyChangeListener, addPropertyChangeListener, close, getID, isEnabled, open, removePropertyChangeListener, removePropertyChangeListener, setEnabled, toString

Methods inherited from class java.lang.Object

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

Field Detail

markProperty

public static final String markProperty

See Also:

Constant Field Values

forceAromaticBondsAlways

public boolean forceAromaticBondsAlways

forceAromaticBondsForNonRingAtoms

public boolean forceAromaticBondsForNonRingAtoms

builder

protected org.openscience.cdk.interfaces.IChemObjectBuilder builder

Constructor Detail

SmartsToChemObject

public SmartsToChemObject(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Detail

getBuilder

public org.openscience.cdk.interfaces.IChemObjectBuilder getBuilder()

setBuilder

public void setBuilder(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

extractAtomContainer

public org.openscience.cdk.interfaces.IAtomContainer extractAtomContainer(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query,
                                                                          org.openscience.cdk.interfaces.IRingSet ringSet)

Maximal possible atom container from this query is generated. This container may be fragmented since some original atoms or bonds could be removed. Following rule is applied: each query atom/bond which is a simple expression is converted to a normal IAtom/IBond object Also some heuristics are applied in order to get information from more complicated atoms expressions (when possible).

Parameters:

query -

Returns:

atomcontainer

extractAtomContainerFullyConnected

public org.openscience.cdk.interfaces.IAtomContainer extractAtomContainerFullyConnected(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query,
                                                                                        org.openscience.cdk.interfaces.IRingSet ringSet)

Maximal possible atom container from this query is generated BUT this container is always fully connected as the original query. The "removed" atoms and bonds are marked with a set property This object is useful for visualization purposes.

convertKekuleSmartsToAromatic

public org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer convertKekuleSmartsToAromatic(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query,
                                                                                                  org.openscience.cdk.interfaces.IRingSet ringSet)
                                                                                           throws Exception

Throws:

Exception

process

public org.openscience.cdk.interfaces.IAtomContainer process(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer target)
                                                      throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

extractAtomContainer

public org.openscience.cdk.interfaces.IAtomContainer extractAtomContainer(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)

Version of the function when the Ring data is not supplied outside

extractAtomContainerFullyConnected

public org.openscience.cdk.interfaces.IAtomContainer extractAtomContainerFullyConnected(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)

convertKekuleSmartsToAromatic

public org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer convertKekuleSmartsToAromatic(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
                                                                                           throws Exception

Throws:

Exception

toAtom

public org.openscience.cdk.interfaces.IAtom toAtom(org.openscience.cdk.interfaces.IAtom a)

This function tries to convert this object to a classic CDK Atom If it is impossible to determine the atom type null is returned

Parameters:

a -

Returns:

atom

smartsExpressionToAtom

public org.openscience.cdk.interfaces.IAtom smartsExpressionToAtom(SmartsAtomExpression a)

This function tries to convert the SmartsAtomExpression to a IAtom with defined atom type. When this is impossible null object is returned

getSubExpressions

public static List<SmartsAtomExpression> getSubExpressions(SmartsAtomExpression a,
                                                           int separator)

analyzeSubExpressionsFromLowAnd

public void analyzeSubExpressionsFromLowAnd(SmartsAtomExpression atExp,
                                            SmartsAtomExpression sub)

getExpressionAtomType

public int getExpressionAtomType(SmartsAtomExpression atExp,
                                 SmartsAtomExpression sub)

getRecursiveExpressionAtomType

public int getRecursiveExpressionAtomType(SmartsAtomExpression atExp,
                                          int n)

toBond

public org.openscience.cdk.interfaces.IBond toBond(org.openscience.cdk.interfaces.IBond b)

smartsExpressionToBond

public org.openscience.cdk.interfaces.IBond smartsExpressionToBond(SmartsBondExpression b)

getSubExpressions

public List<SmartsBondExpression> getSubExpressions(SmartsBondExpression b,
                                                    int separator)

analyzeSubExpressionsFromLowAnd

public void analyzeSubExpressionsFromLowAnd(SmartsBondExpression boExp,
                                            SmartsBondExpression sub)

getExpressionBondType

public int getExpressionBondType(SmartsBondExpression boExp,
                                 SmartsBondExpression sub)