Class RGroup
- java.lang.Object
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- org.openscience.cdk.isomorphism.matchers.RGroup
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- All Implemented Interfaces:
IRGroup
public class RGroup extends Object implements IRGroup
Represents a single substitute structure in anRGroupList
.The order of attachment points is provided (first and second only, conform RGFile spec). This order is relevant when the structure connects to the root with more than one bond.
See also
RGroupList
andRGroupQuery
.- Author:
- Mark Rijnbeek
- Source code:
- main
- Belongs to CDK module:
- isomorphism
- Keywords:
- Rgroup, R group, R-group
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Field Summary
Fields Modifier and Type Field Description static String
ROOT_LABEL
Standard label/title to be used for the root atom container.
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Constructor Summary
Constructors Constructor Description RGroup()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description IAtom
getFirstAttachmentPoint()
Get the first attachment point of the RGroup.IAtomContainer
getGroup()
Get the connection table of atoms/bonds for this Rgroup.IAtom
getSecondAttachmentPoint()
Get the optional second attachment point of the RGroup.static String
makeLabel(int rgroupNum)
Makes a label/title to be used for a substituent.void
setFirstAttachmentPoint(IAtom firstAttachmentPoint)
void
setGroup(IAtomContainer group)
void
setSecondAttachmentPoint(IAtom secondAttachmentPoint)
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Field Detail
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ROOT_LABEL
public static final String ROOT_LABEL
Standard label/title to be used for the root atom container.- See Also:
- Constant Field Values
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Method Detail
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makeLabel
public static String makeLabel(int rgroupNum)
Makes a label/title to be used for a substituent.- Parameters:
rgroupNum
- R-Group number (1..32)- Returns:
- label for substituent, like "R3"
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setFirstAttachmentPoint
public void setFirstAttachmentPoint(IAtom firstAttachmentPoint)
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getFirstAttachmentPoint
public IAtom getFirstAttachmentPoint()
Description copied from interface:IRGroup
Get the first attachment point of the RGroup.- Specified by:
getFirstAttachmentPoint
in interfaceIRGroup
- Returns:
- the first attachment point
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setSecondAttachmentPoint
public void setSecondAttachmentPoint(IAtom secondAttachmentPoint)
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getSecondAttachmentPoint
public IAtom getSecondAttachmentPoint()
Description copied from interface:IRGroup
Get the optional second attachment point of the RGroup.- Specified by:
getSecondAttachmentPoint
in interfaceIRGroup
- Returns:
- the second attachment point or null.
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setGroup
public void setGroup(IAtomContainer group)
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getGroup
public IAtomContainer getGroup()
Description copied from interface:IRGroup
Get the connection table of atoms/bonds for this Rgroup.
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