Package org.openscience.cdk.tools.scaffold

Enum Class ScaffoldGenerator.ScaffoldModeOption

java.lang.Object

java.lang.Enum<ScaffoldGenerator.ScaffoldModeOption>

org.openscience.cdk.tools.scaffold.ScaffoldGenerator.ScaffoldModeOption

All Implemented Interfaces:

Serializable, Comparable<ScaffoldGenerator.ScaffoldModeOption>, java.lang.constant.Constable

Enclosing class:

ScaffoldGenerator

public static enum ScaffoldGenerator.ScaffoldModeOption
extends Enum<ScaffoldGenerator.ScaffoldModeOption>

Enum with which the type of scaffolds to be generated can be set. These scaffolds are then used for the rest of the processing.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
BASIC_FRAMEWORK	All side chains are removed and all atoms are converted into carbons.
BASIC_WIRE_FRAME	All side chains are removed, all bonds are converted into single bonds and all atoms are converted into carbons.
ELEMENTAL_WIRE_FRAME	All side chains are removed and multiple bonds are converted to single bonds, but the atomic elements remain.
MURCKO_FRAMEWORK	Murcko frameworks are generated.
SCAFFOLD	Terminal side chains of the molecule are removed except for any atoms non-single bonded directly to linkers or rings, as it is e.g. defined in "The Scaffold Tree − Visualization of the Scaffold Universe by Hierarchical Scaffold Classification".

Method Summary

Modifier and Type	Method	Description
static ScaffoldGenerator.ScaffoldModeOption	valueOf(String name)	Returns the enum constant of this class with the specified name.
static ScaffoldGenerator.ScaffoldModeOption[]	values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

SCAFFOLD

public static final ScaffoldGenerator.ScaffoldModeOption SCAFFOLD

Terminal side chains of the molecule are removed except for any atoms non-single bonded directly to linkers or rings, as it is e.g. defined in "The Scaffold Tree − Visualization of the Scaffold Universe by Hierarchical Scaffold Classification".

MURCKO_FRAMEWORK

public static final ScaffoldGenerator.ScaffoldModeOption MURCKO_FRAMEWORK

Murcko frameworks are generated. Based on "The Properties of Known Drugs. 1. Molecular Frameworks" by Bemis and Murcko 1996. All terminal side chains are removed and only linkers and rings are retained.

BASIC_WIRE_FRAME

public static final ScaffoldGenerator.ScaffoldModeOption BASIC_WIRE_FRAME

All side chains are removed, all bonds are converted into single bonds and all atoms are converted into carbons. Naming is based on "Molecular Anatomy: a new multi‑dimensional hierarchical scaffold analysis tool" by Manelfi et al. 2021.

ELEMENTAL_WIRE_FRAME

public static final ScaffoldGenerator.ScaffoldModeOption ELEMENTAL_WIRE_FRAME

All side chains are removed and multiple bonds are converted to single bonds, but the atomic elements remain.

BASIC_FRAMEWORK

public static final ScaffoldGenerator.ScaffoldModeOption BASIC_FRAMEWORK

All side chains are removed and all atoms are converted into carbons. The order of the remaining bonds is not changed. Naming is based on "Molecular Anatomy: a new multi‑dimensional hierarchical scaffold analysis tool" by Manelfi et al. 2021.

Method Details

values

public static ScaffoldGenerator.ScaffoldModeOption[] values()

Returns an array containing the constants of this enum class, in the order they are declared.

Returns:

an array containing the constants of this enum class, in the order they are declared

valueOf

public static ScaffoldGenerator.ScaffoldModeOption valueOf(String name)

Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum class has no constant with the specified name

NullPointerException - if the argument is null