com.chemaxon.virtuallib.sc.model.sdf

Class ScaffoldExtensionBuilder

java.lang.Object

com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder

All Implemented Interfaces:

Serializable

public class ScaffoldExtensionBuilder
extends Object
implements Serializable

Allows to "build" a scaffold extension by cutting down an r group fragment.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ScaffoldExtensionBuilder(RgFrag frag) Construct.

Method Summary

Modifier and Type	Method and Description
ScaffoldExtension	build(int firstR) Build scaffold extension.
ScaffoldExtensionBuilder	clone() Clone.
com.chemaxon.calculations.sc.util.IntListSet	getSelecteds() Get current state of selection.
boolean	isKeep(int atomIndex) Check if an atom is set to be kept.
boolean	isTerminal() Check if the current state is a terminal extension.
void	keepAtom(int atomIndex) Designate a fragment atom to keep.
void	keepAtoms(Iterable<Integer> atoms) Designate multiple fragment atoms to keep.
com.chemaxon.calculations.sc.util.IntListSet	selectedsWithMultipleUnselectedLigands() List selected atoms resulting in forbidden configuration.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

ScaffoldExtensionBuilder

public ScaffoldExtensionBuilder(RgFrag frag)

Construct.

Parameters:

frag - Underlying fragment

Method Detail

keepAtom

public void keepAtom(int atomIndex)

Designate a fragment atom to keep.

Parameters:

atomIndex - Atom index

Throws:

IllegalArgumentException - When the given atom is an attachment pseudo atom

keepAtoms

public void keepAtoms(Iterable<Integer> atoms)

Designate multiple fragment atoms to keep.

Parameters:

atoms - Atoms to keep index

Throws:

IllegalArgumentException - When the given atom is an attachment pseudo atom

isTerminal

public boolean isTerminal()

Check if the current state is a terminal extension.

Returns:

True if all chemical atoms are selected.

isKeep

public boolean isKeep(int atomIndex)

Check if an atom is set to be kept.

Parameters:

atomIndex - Atom index

Returns:

true when atom was marked to be kept by keepAtom(int);

selectedsWithMultipleUnselectedLigands

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

List selected atoms resulting in forbidden configuration. Each of the returned atoms have more than one non selected real atom neighbors. The represented candidate therefore would transform into a Markush where an R group is connected to a scaffold atom with more than one bonds.

Returns:

List of problematic selected atom indices

clone

public ScaffoldExtensionBuilder clone()

Clone.

Overrides:

clone in class Object

Returns:

Copy of the current state.

build

public ScaffoldExtension build(int firstR)

Build scaffold extension.

Parameters:

firstR - First R attachment index to use

Returns:

Immutable scaffold extension

Throws:

IllegalStateException - in case of consistency error, like empty structure or not attached substructure

getSelecteds

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

Get current state of selection.

Returns:

Current state of selection

toString

public String toString()

Overrides:

toString in class Object