org.openscience.cdk.isomorphism.matchers

Class RGroup

java.lang.Object

org.openscience.cdk.isomorphism.matchers.RGroup

public class RGroup
extends Object

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

Keywords:

Rgroup, R group, R-group

Field Summary

Fields

Modifier and Type	Field and Description
static String	ROOT_LABEL Standard label/title to be used for the root atom container.

Constructor Summary

Constructors

Constructor and Description
RGroup()

Method Summary

Methods

Modifier and Type	Method and Description
IAtom	getFirstAttachmentPoint()
IAtomContainer	getGroup()
IAtom	getSecondAttachmentPoint()
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)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ROOT_LABEL

public static final String ROOT_LABEL

Standard label/title to be used for the root atom container.

See Also:

Constant Field Values

Constructor Detail

RGroup

public RGroup()

Method Detail

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"

setFirstAttachmentPoint

public void setFirstAttachmentPoint(IAtom firstAttachmentPoint)

getFirstAttachmentPoint

public IAtom getFirstAttachmentPoint()

setSecondAttachmentPoint

public void setSecondAttachmentPoint(IAtom secondAttachmentPoint)

getSecondAttachmentPoint

public IAtom getSecondAttachmentPoint()

setGroup

public void setGroup(IAtomContainer group)

getGroup

public IAtomContainer getGroup()