org.openscience.cdk.isomorphism.matchers

Interface IRGroupQuery

All Superinterfaces:

Cloneable, ICDKObject, IChemObject

All Known Implementing Classes:

RGroupQuery

public interface IRGroupQuery
extends IChemObject

Interface definition for Rgroup query classes. These must provide a root structure, root attachment points and Rgroup definitions.

Author:

Mark Rijnbeek

Source code:

master

Belongs to CDK module:

isomorphism

Keywords:

Rgroup, R group, R-group

Method Summary

Modifier and Type	Method and 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.
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).
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.
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 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

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

getBuilder

Method Detail

setRootStructure

void setRootStructure(IAtomContainer rootStructure)

Setter for the root structure of this R-Group.

Parameters:

rootStructure - the root structure (or scaffold) container

See Also:

getRootStructure()

getRootStructure

IAtomContainer getRootStructure()

Getter for the root structure of this R-Group.

Returns:

the root structure (or scaffold) container

See Also:

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

setRootAttachmentPoints

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

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

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:

getRootAttachmentPoints()

getRootAttachmentPoints

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

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

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:

setRootAttachmentPoints(Map)

setRGroupDefinitions

void setRGroupDefinitions(Map<Integer,IRGroupList> rGroupDefinitions)

Setter for the R-group definitions (substituents).

Parameters:

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

See Also:

getRGroupDefinitions()

getRGroupDefinitions

Map<Integer,IRGroupList> getRGroupDefinitions()

Getter for the R-group definitions (substituents).

Returns:

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

See Also:

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

getAtomContainerCount

int getAtomContainerCount()

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

Returns:

count.

getSubstituents

List<IAtomContainer> getSubstituents()

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

Returns:

list with all substituents

areSubstituentsDefined

boolean areSubstituentsDefined()

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.

Returns:

true when valid

areRootAtomsDefined

boolean areRootAtomsDefined()

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

Returns:

true when valid

getAllConfigurations

List<IAtomContainer> getAllConfigurations()
                                   throws Exception

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

Returns:

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

Throws:

Exception