org.openscience.cdk.isomorphism.matchers

Class RGroupList

java.lang.Object

org.openscience.cdk.isomorphism.matchers.RGroupList

All Implemented Interfaces:

IRGroupList

public class RGroupList
extends Object
implements IRGroupList

Represents a list of Rgroup substitutes to be associated with some RGroupQuery.

Author:

Mark Rijnbeek

Source code:

master

Belongs to CDK module:

isomorphism

Keywords:

Rgroup, R group, R-group

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_OCCURRENCE Default value for occurrence field.

Constructor Summary

Constructors

Constructor and Description
RGroupList(int rGroupNumber) Default constructor.
RGroupList(int rGroupNumber, boolean restH, String occurrence, int requiredRGroupNumber) Constructor with attributes given.

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
String	getOccurrence() Returns the occurrence value.
int	getRequiredRGroupNumber() Access the dependant Rgroup number if R1 then R2.
int	getRGroupNumber() Get the Rgroup number, for example R1 => 1.
List<IRGroup>	getRGroups() Access the list of possible RGroups.
int	hashCode()
boolean	isRestH() Indicates that sites labeled with this Rgroup may only be substituted with a member of the Rgroup or with hydrogen.
static boolean	isValidOccurrenceSyntax(String occ) Validates the occurrence value.
List<Integer>	matchOccurence(int maxAttachments) Matches the 'occurrence' condition with a provided maximum number of RGroup attachments.
void	setOccurrence(String occurrence) Picky setter for occurrence fields.
void	setRequiredRGroupNumber(int rGroupNumberImplicated)
void	setRestH(boolean restH)
void	setRGroupNumber(int rGroupNumber) Setter for rGroupNumber, checks for valid range.
void	setRGroups(List<IRGroup> rGroups)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_OCCURRENCE

public static final String DEFAULT_OCCURRENCE

Default value for occurrence field.

See Also:

Constant Field Values

Constructor Detail

RGroupList

public RGroupList(int rGroupNumber)

Default constructor.

RGroupList

public RGroupList(int rGroupNumber,
                  boolean restH,
                  String occurrence,
                  int requiredRGroupNumber)
           throws CDKException

Constructor with attributes given.

Parameters:

rGroupNumber - R-Group number

restH - restH

occurrence - occurrence

requiredRGroupNumber - number of other R-Group required

Throws:

CDKException

Method Detail

setRGroupNumber

public void setRGroupNumber(int rGroupNumber)

Setter for rGroupNumber, checks for valid range. Spec: "value from 1 to 32 *, labels position of Rgroup on root."

Parameters:

rGroupNumber - R-Group number

getRGroupNumber

public int getRGroupNumber()

Description copied from interface: IRGroupList

Get the Rgroup number, for example R1 => 1.

Specified by:

getRGroupNumber in interface IRGroupList

Returns:

the Rgroup number

setRestH

public void setRestH(boolean restH)

isRestH

public boolean isRestH()

Description copied from interface: IRGroupList

Indicates that sites labeled with this Rgroup may only be substituted with a member of the Rgroup or with hydrogen.

Specified by:

isRestH in interface IRGroupList

setRequiredRGroupNumber

public void setRequiredRGroupNumber(int rGroupNumberImplicated)

getRequiredRGroupNumber

public int getRequiredRGroupNumber()

Description copied from interface: IRGroupList

Access the dependant Rgroup number if R1 then R2.

Specified by:

getRequiredRGroupNumber in interface IRGroupList

Returns:

the required Rgroup number.

setRGroups

public void setRGroups(List<IRGroup> rGroups)

getRGroups

public List<IRGroup> getRGroups()

Description copied from interface: IRGroupList

Access the list of possible RGroups.

Specified by:

getRGroups in interface IRGroupList

Returns:

the rgroups.

getOccurrence

public String getOccurrence()

Returns the occurrence value.

Specified by:

getOccurrence in interface IRGroupList

Returns:

occurrence

setOccurrence

public void setOccurrence(String occurrence)
                   throws CDKException

Picky setter for occurrence fields. Validates user input to be conform the (Symyx) specification.

Parameters:

occurrence - occurence value

Throws:

CDKException

isValidOccurrenceSyntax

public static boolean isValidOccurrenceSyntax(String occ)

Validates the occurrence value.

• n : exactly n ;
• n - m : n through m ;
• > n : greater than n ;
• < n : fewer than n ;
• default (blank) is > 0 ;

Any combination of the preceding values is also allowed; for example "1, 3-7, 9, >11".

Parameters:

occ - String to validate.

Returns:

true if valid String provided.

matchOccurence

public List<Integer> matchOccurence(int maxAttachments)

Matches the 'occurrence' condition with a provided maximum number of RGroup attachments. Returns the valid occurrences (numeric) for these two combined. If none found, returns empty list.
Example: if R1 occurs 3 times attached to some root structure, then stating ">5" as an occurrence for that RGoupList does not make sense: the example R1 can occur 0..3 times. Empty would be returned.
If the occurence would be >2, then 3 would be returned. Etcetera.

Specified by:

matchOccurence in interface IRGroupList

Parameters:

maxAttachments - number of attachments

Returns:

valid values by combining a max for R# with the occurrence cond.

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object