Package org.openscience.cdk.isomorphism.matchers

Class RGroupQuery

java.lang.Object

org.openscience.cdk.isomorphism.matchers.QueryChemObject

org.openscience.cdk.isomorphism.matchers.RGroupQuery

All Implemented Interfaces:

Cloneable, ICDKObject, IChemObject, IRGroupQuery

public class RGroupQuery
extends QueryChemObject
implements IChemObject, IRGroupQuery

Represents information contained in a Symyx RGfile (R-group query file).
It contains a root structure (the scaffold if you like), a map with R-group definitions (each of which can contain multiple substitutes) and a map with attachment points. The attachment points define a connection order for the substitutes, which is relevant when an Rgroup is connected to the scaffold with more than one bond.

This class can also be used to produce all the valid configurations for the combination of its root,definitions and conditions.

This Javadoc does not contain a code sample how to create a new RGroupQuery from scratch, because a sensible RGroupQuery has quite a few attributes to be set including a root plus a bunch of substituents, which are all atom containers. So that would be a lot of sample code here.
The best way to get a feel for the way the RGroup objects are populated is to run the RGroupQueryReaderTest and look at the sample input RGroup query files contained in the CDK and how they translate into RGroupXX objects. The JChempaint application can visualize the input files for you.

Author:

Mark Rijnbeek

Source code:

main

Belongs to CDK module:

isomorphism

Keywords:

Rgroup, R group, R-group

Constructor Summary

Constructors

Constructor	Description
RGroupQuery(IChemObjectBuilder builder)

Method Summary

Modifier and Type	Method	Description
boolean	areRootAtomsDefined()	Checks validity of RGroupQuery.
boolean	areSubstituentsDefined()	Checks validity of the RGroupQuery.
List<IAtomContainer>	getAllConfigurations()	Produces all combinations of the root structure (scaffold) with the R-groups substituted in valid ways, using each R-group's definitions and conditions.
List<IAtom>	getAllRgroupQueryAtoms()	Returns all R# type atoms (pseudo atoms) found in the root structure.
int	getAtomContainerCount()	Return the total number of atom containers (count the root plus all substituents).
Map<Integer,IRGroupList>	getRGroupDefinitions()	Getter for the R-group definitions (substituents).
List<IAtom>	getRgroupQueryAtoms(Integer rgroupNumber)	Returns all R# type atoms (pseudo atoms) found in the root structure for a certain provided RGgroup number.
Map<IAtom,Map<Integer,IBond>>	getRootAttachmentPoints()	Getter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
IAtomContainer	getRootStructure()	Getter for the root structure of this R-Group.
List<IAtomContainer>	getSubstituents()	Return all the substituent atom containers, in other words the atom containers defined in this RGroupQuery except for the root structure.
static boolean	isValidRgroupQueryLabel(String Rxx)	Validates a Pseudo atom's label to be valid RGroup query label (R1..R32).
void	setRGroupDefinitions(Map<Integer,IRGroupList> rGroupDefinitions)	Setter for the R-group definitions (substituents).
void	setRootAttachmentPoints(Map<IAtom,Map<Integer,IBond>> rootAttachmentPoints)	Setter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
void	setRootStructure(IAtomContainer rootStructure)	Setter for the root structure of this R-Group.

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryChemObject

addListener, addProperties, clone, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, matches, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, addProperties, clone, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

Constructor Details

RGroupQuery

public RGroupQuery(IChemObjectBuilder builder)

Method Details

getRgroupQueryAtoms

public List<IAtom> getRgroupQueryAtoms(Integer rgroupNumber)

Returns all R# type atoms (pseudo atoms) found in the root structure for a certain provided RGgroup number.

Parameters:

rgroupNumber - R# number, 1..32

Returns:

list of (pseudo) atoms with the provided rgroupNumber as label

getAllRgroupQueryAtoms

public List<IAtom> getAllRgroupQueryAtoms()

Returns all R# type atoms (pseudo atoms) found in the root structure.

Returns:

list of (pseudo) R# atoms

isValidRgroupQueryLabel

public static boolean isValidRgroupQueryLabel(String Rxx)

Validates a Pseudo atom's label to be valid RGroup query label (R1..R32).

Parameters:

Rxx - R-group label like R1 or R10

Returns:

true if R1..R32, otherwise false

areSubstituentsDefined

public boolean areSubstituentsDefined()

Description copied from interface: IRGroupQuery

Checks validity of the RGroupQuery. Each distinct R# in the root must have a a corresponding RGroupList definition.
In file terms: $RGP blocks must be defined for each R-group number.

Specified by:

areSubstituentsDefined in interface IRGroupQuery

Returns:

true when valid

areRootAtomsDefined

public boolean areRootAtomsDefined()

Description copied from interface: IRGroupQuery

Checks validity of RGroupQuery. Each RGroupList definition must have one or more corresponding R# atoms in the root block.

Specified by:

areRootAtomsDefined in interface IRGroupQuery

Returns:

true when valid

getAllConfigurations

public List<IAtomContainer> getAllConfigurations()
                                          throws CDKException

Description copied from interface: IRGroupQuery

Produces all combinations of the root structure (scaffold) with the R-groups substituted in valid ways, using each R-group's definitions and conditions.

Specified by:

getAllConfigurations in interface IRGroupQuery

Returns:

all valid combinations of the root structure (scaffold) with the R-groups substituted.

Throws:

CDKException

getAtomContainerCount

public int getAtomContainerCount()

Description copied from interface: IRGroupQuery

Return the total number of atom containers (count the root plus all substituents).

Specified by:

getAtomContainerCount in interface IRGroupQuery

Returns:

count.

getSubstituents

public List<IAtomContainer> getSubstituents()

Description copied from interface: IRGroupQuery

Return all the substituent atom containers, in other words the atom containers defined in this RGroupQuery except for the root structure.

Specified by:

getSubstituents in interface IRGroupQuery

Returns:

list with all substituents

setRootStructure

public void setRootStructure(IAtomContainer rootStructure)

Description copied from interface: IRGroupQuery

Setter for the root structure of this R-Group.

Specified by:

setRootStructure in interface IRGroupQuery

Parameters:

rootStructure - the root structure (or scaffold) container

See Also:

• IRGroupQuery.getRootStructure()

getRootStructure

public IAtomContainer getRootStructure()

Description copied from interface: IRGroupQuery

Getter for the root structure of this R-Group.

Specified by:

getRootStructure in interface IRGroupQuery

Returns:

the root structure (or scaffold) container

See Also:

• IRGroupQuery.setRootStructure(org.openscience.cdk.interfaces.IAtomContainer)

setRootAttachmentPoints

public void setRootAttachmentPoints(Map<IAtom,Map<Integer,IBond>> rootAttachmentPoints)

Description copied from interface: IRGroupQuery

Setter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.

Specified by:

setRootAttachmentPoints in interface IRGroupQuery

Parameters:

rootAttachmentPoints - Map with per R-group pseudo atom another map with an Integer and an IBond, the integer indicating 1st or 2nd attachment.

See Also:

• IRGroupQuery.getRootAttachmentPoints()

getRootAttachmentPoints

public Map<IAtom,Map<Integer,IBond>> getRootAttachmentPoints()

Description copied from interface: IRGroupQuery

Getter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.

Specified by:

getRootAttachmentPoints in interface IRGroupQuery

Returns:

Map with per R-group pseudo atom another map with an Integer and an IBond, the integer indicating 1st or 2nd attachment.

See Also:

• IRGroupQuery.setRootAttachmentPoints(Map)

setRGroupDefinitions

public void setRGroupDefinitions(Map<Integer,IRGroupList> rGroupDefinitions)

Description copied from interface: IRGroupQuery

Setter for the R-group definitions (substituents).

Specified by:

setRGroupDefinitions in interface IRGroupQuery

Parameters:

rGroupDefinitions - map with an Integer and an RGroupList (substituent list), the Integer being the R-Group number (1..32).

See Also:

• IRGroupQuery.getRGroupDefinitions()

getRGroupDefinitions

public Map<Integer,IRGroupList> getRGroupDefinitions()

Description copied from interface: IRGroupQuery

Getter for the R-group definitions (substituents).

Specified by:

getRGroupDefinitions in interface IRGroupQuery

Returns:

rGroupDefinitions Map with an Integer and an RGroupList (substituent list), the Integer being the R-Group number (1..32).

See Also:

• IRGroupQuery.setRGroupDefinitions(java.util.Map<java.lang.Integer, org.openscience.cdk.isomorphism.matchers.IRGroupList>)