public interface IRGroupQuery extends IChemObject
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,RGroupList> |
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,RGroupList> 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.
|
addListener, addProperties, clone, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString
getBuilder
void setRootStructure(IAtomContainer rootStructure)
rootStructure
- the root structure (or scaffold) containergetRootStructure()
IAtomContainer getRootStructure()
setRootStructure(org.openscience.cdk.interfaces.IAtomContainer)
void setRootAttachmentPoints(Map<IAtom,Map<Integer,IBond>> rootAttachmentPoints)
rootAttachmentPoints
- Map with per R-group pseudo atom another map with an Integer and an IBond, the integer indicating 1st or 2nd attachment.getRootAttachmentPoints()
Map<IAtom,Map<Integer,IBond>> getRootAttachmentPoints()
setRootAttachmentPoints(Map)
void setRGroupDefinitions(Map<Integer,RGroupList> rGroupDefinitions)
rGroupDefinitions
- map with an Integer and an RGroupList (substituent list), the Integer being the R-Group number (1..32).getRGroupDefinitions()
Map<Integer,RGroupList> getRGroupDefinitions()
setRGroupDefinitions(java.util.Map<java.lang.Integer, org.openscience.cdk.isomorphism.matchers.RGroupList>)
int getAtomContainerCount()
List<IAtomContainer> getSubstituents()
boolean areSubstituentsDefined()
RGroupList
definition.boolean areRootAtomsDefined()
RGroupList
definition must have one or more corresponding
R# atoms in the root block.List<IAtomContainer> getAllConfigurations() throws Exception
Exception
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