com.chemaxon.virtuallib.sc.model.sdf

Class RgDefiniton

java.lang.Object

com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton

All Implemented Interfaces:

Serializable

public class RgDefiniton
extends Object
implements Serializable

Group of Rg fragments.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	RgDefiniton.EnumeratedExtension
static class	RgDefiniton.ScoredExtension

Constructor Summary

Constructors

Constructor and Description
RgDefiniton(Scaffold scaffold, com.chemaxon.calculations.sc.util.IntListSet indices) Construct.

Method Summary

Modifier and Type	Method and Description
void	addFragment(RgFrag fragment) Add fragment.
List<RgDefiniton.EnumeratedExtension>	allSingleAtomExtensions() All single atom based growth candidates.
List<RgFrag>	getFragments() Get fragments list.
com.chemaxon.calculations.sc.util.IntListSet	getIndices() Get covered RG indices.
int	getTotalRealAtomCount() Sum of chemical atom counts from all definitions.
List<RgDefiniton.ScoredExtension>	scoreExtensions(List<RgDefiniton.EnumeratedExtension> in)
String	toString()
String	toString(boolean multiline) Details into human readable String.

Methods inherited from class java.lang.Object

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

Constructor Detail

RgDefiniton

public RgDefiniton(Scaffold scaffold,
                   com.chemaxon.calculations.sc.util.IntListSet indices)

Construct.

Parameters:

scaffold - Scaffold

indices - Rn indices used by this group.

Throws:

IllegalArgumentException - when indices is empty

Method Detail

addFragment

public void addFragment(RgFrag fragment)

Add fragment.

Parameters:

fragment - Fragment definition to add

Throws:

IllegalArgumentException - when fragment is incompatible

getFragments

public List<RgFrag> getFragments()

Get fragments list.

Returns:

List of fragments

toString

public String toString(boolean multiline)

Details into human readable String.

Parameters:

multiline - Write multi line String

Returns:

Human readable String

getIndices

public com.chemaxon.calculations.sc.util.IntListSet getIndices()

Get covered RG indices.

Returns:

Covered RG indices.

toString

public String toString()

Overrides:

toString in class Object

getTotalRealAtomCount

public int getTotalRealAtomCount()

Sum of chemical atom counts from all definitions.

Returns:

Sum of chemical atom counts from all definitions

scoreExtensions

public List<RgDefiniton.ScoredExtension> scoreExtensions(List<RgDefiniton.EnumeratedExtension> in)

allSingleAtomExtensions

public List<RgDefiniton.EnumeratedExtension> allSingleAtomExtensions()

All single atom based growth candidates.

Returns:

All single atom based extension candidates with unique filtering