org.openscience.cdk.isomorphism.matchers

Interface IRGroupList

All Known Implementing Classes:

RGroupList

public interface IRGroupList

Represents a list of Rgroup substitutes to be associated with some key in an IRGroupQuery.

Author:

John Mayfield

Method Summary

Modifier and Type	Method and Description
String	getOccurrence() Occurrence required: n : exactly n ; n - m : n through m ; > n : greater than n ; < n : fewer than n ; default (blank) is > 0 ; Any non-contradictory combination of the preceding values is also allowed; for example "1, 3-7, 9, >11".
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.
boolean	isRestH() Indicates that sites labeled with this Rgroup may only be substituted with a member of the Rgroup or with hydrogen.
List<Integer>	matchOccurence(int maxAttachments) Matches the 'occurrence' condition with a provided maximum number of RGroup attachments.

Method Detail

getRGroupNumber

int getRGroupNumber()

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

Returns:

the Rgroup number

getRequiredRGroupNumber

int getRequiredRGroupNumber()

Access the dependant Rgroup number if R1 then R2.

Returns:

the required Rgroup number.

getRGroups

List<IRGroup> getRGroups()

Access the list of possible RGroups.

Returns:

the rgroups.

isRestH

boolean isRestH()

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

matchOccurence

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.

Parameters:

maxAttachments - number of attachments

Returns:

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

getOccurrence

String getOccurrence()

Occurrence required:

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

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