Class RGroup
java.lang.Object
org.openscience.cdk.isomorphism.matchers.RGroup
- All Implemented Interfaces:
IRGroup
Represents a single substitute structure in an
RGroupList
. 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
and RGroupQuery
.
- Author:
- Mark Rijnbeek
- Source code:
- main
- Belongs to CDK module:
- isomorphism
- Keywords:
- Rgroup, R group, R-group
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
Standard label/title to be used for the root atom container. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionGet the first attachment point of the RGroup.getGroup()
Get the connection table of atoms/bonds for this Rgroup.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 Details
-
ROOT_LABEL
Standard label/title to be used for the root atom container.- See Also:
-
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Constructor Details
-
RGroup
public RGroup()
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Method Details
-
makeLabel
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
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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
-
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
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getGroup
Description copied from interface:IRGroup
Get the connection table of atoms/bonds for this Rgroup.
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