Package org.openscience.cdk.isomorphism.matchers

Class RGroup

java.lang.Object

org.openscience.cdk.isomorphism.matchers.RGroup

All Implemented Interfaces:

IRGroup

public class RGroup
extends Object
implements 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

Keywords:

Rgroup, R group, R-group

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor	Description
RGroup()

Method Summary

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)	Deprecated. use IPseudoAtom with attachNum to explicitly indicate attachment
void	setGroup(IAtomContainer group)
void	setSecondAttachmentPoint(IAtom secondAttachmentPoint)	Deprecated. use IPseudoAtom with attachNum to explicitly indicate attachment

Methods inherited from class java.lang.Object

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

Field Details

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 Details

RGroup

public RGroup()

Method Details

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

@Deprecated
public void setFirstAttachmentPoint(IAtom firstAttachmentPoint)

Deprecated.

use IPseudoAtom with attachNum to explicitly indicate attachment

This function is used to set/move the attachment point on an RGroup. It does not set coordinates or adjust hydrogen counts and will modifying the underlying structure add/move bonds and atoms.

Parameters:

firstAttachmentPoint - the atom ato attach to

getFirstAttachmentPoint

public IAtom getFirstAttachmentPoint()

Description copied from interface: IRGroup

Get the first attachment point of the RGroup.

Specified by:

getFirstAttachmentPoint in interface IRGroup

Returns:

the first attachment point

setSecondAttachmentPoint

@Deprecated
public void setSecondAttachmentPoint(IAtom secondAttachmentPoint)

Deprecated.

use IPseudoAtom with attachNum to explicitly indicate attachment

This function is used to set/move the attachment point on an RGroup. It does not set coordinates or adjust hydrogen counts and will modifying the underlying structure add/move bonds and atoms.

Parameters:

secondAttachmentPoint - the atom ato attach to

getSecondAttachmentPoint

public IAtom getSecondAttachmentPoint()

Description copied from interface: IRGroup

Get the optional second attachment point of the RGroup.

Specified by:

getSecondAttachmentPoint in interface IRGroup

Returns:

the second attachment point or null.

setGroup

public void setGroup(IAtomContainer group)

getGroup

public IAtomContainer getGroup()

Description copied from interface: IRGroup

Get the connection table of atoms/bonds for this Rgroup.

Specified by:

getGroup in interface IRGroup

Returns:

the connection table