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

All Methods Static Methods Instance Methods Concrete Methods
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 Detail
  - RGroupQuery
```
public RGroupQuery(IChemObjectBuilder builder)
```
- Method Detail
  - 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>)

Class RGroupQuery

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

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

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

Constructor Detail

RGroupQuery

Method Detail

getRgroupQueryAtoms

getAllRgroupQueryAtoms

isValidRgroupQueryLabel

areSubstituentsDefined

areRootAtomsDefined

getAllConfigurations

getAtomContainerCount

getSubstituents

setRootStructure

getRootStructure

setRootAttachmentPoints

getRootAttachmentPoints

setRGroupDefinitions

getRGroupDefinitions