Interface IRGroupQuery
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- 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:
- main
- Belongs to CDK module:
- isomorphism
- Keywords:
- Rgroup, R group, R-group
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Field Summary
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Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED
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Method Summary
All Methods Instance Methods Abstract 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.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.ICDKObject
getBuilder
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Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, clear, clone, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString
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Method Detail
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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()
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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)
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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()
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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)
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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()
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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>)
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getAtomContainerCount
int getAtomContainerCount()
Return the total number of atom containers (count the root plus all substituents).- Returns:
- count.
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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
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areSubstituentsDefined
boolean areSubstituentsDefined()
Checks validity of the RGroupQuery. Each distinct R# in the root must have a a correspondingRGroupList
definition.
In file terms: $RGP blocks must be defined for each R-group number.- Returns:
- true when valid
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areRootAtomsDefined
boolean areRootAtomsDefined()
Checks validity of RGroupQuery. EachRGroupList
definition must have one or more corresponding R# atoms in the root block.- Returns:
- true when valid
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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
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