com.chemaxon.markush.composer

Class MarkushComposer

java.lang.Object

com.chemaxon.markush.composer.MarkushComposer

@PublicAPI
 @Beta
public class MarkushComposer
extends java.lang.Object

Composes Markush structure(s) from a list of compounds.

The generated Markush structures will represent all given molecules as enumerated structures, but many additional molecules are also represented in typical cases (due to additional combinations of the variable parts of the Markush structures).

This is a Beta class, it may change in future releases.

Author:

Gabor Botka, Janos Kendi, Peter Kovacs (pkovacs84)

Constructor Summary

Constructors

Constructor and Description
MarkushComposer()

Method Summary

Modifier and Type	Method and Description
RgMolecule	getPreferredResult() Returns the most relevant structure in getResults(), which represents the most input molecules.
java.util.List<RgMolecule>	getResults() Returns the generated Markush structures.
boolean	isStrictScaffoldChecking() Indicates whether input structures not containing the specified scaffold should be ignored (true) or not (false).
void	run() Executes the Markush Composer algorithm.
void	setMolecules(java.util.List<Molecule> molecules) Sets the input molecules for Markush composition.
void	setOptions(MarkushComposerOptions options) Sets the options for Markush composition.
void	setScaffold(Molecule scaffold) Sets a user-defined scaffold for Markush composition.
void	setStrictScaffoldChecking(boolean strictScaffoldChecking) Sets whether input structures not containing the specified scaffold should be ignored (true) or not (false).

Methods inherited from class java.lang.Object

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

Constructor Detail

MarkushComposer

public MarkushComposer()

Method Detail

setMolecules

public void setMolecules(java.util.List<Molecule> molecules)

Sets the input molecules for Markush composition.

setOptions

public void setOptions(MarkushComposerOptions options)

Sets the options for Markush composition.

setScaffold

public void setScaffold(Molecule scaffold)

Sets a user-defined scaffold for Markush composition.

By default, the composer algorithm automatically detects the scaffold structure to be used, but this method overrides this behavior and forces the usage of a certain scaffold. The given scaffold structure may contain list atoms, list bonds, and R-atoms (undefined R-groups). If R-atoms are also specified, then the algorithm will not generate R-groups at other positions of the scaffold, only the predefined R-groups will be used.

Parameters:

scaffold - the scaffold structure to be used during Markush composition

run

public void run()
         throws com.chemaxon.markush.composer.MarkushComposerException

Executes the Markush Composer algorithm.

Throws:

MarkushComposerException - in the following cases:

• if an unsupported input molecule is specified
• if the user-defined scaffold is unsupported
• if one or more input molecules do not match the user-defined scaffold (if it is set)
• if an unexpected error occurs during the algorithm

getResults

public java.util.List<RgMolecule> getResults()

Returns the generated Markush structures.

getPreferredResult

public RgMolecule getPreferredResult()

Returns the most relevant structure in getResults(), which represents the most input molecules.

Returns:

the most relevant result structure

isStrictScaffoldChecking

public boolean isStrictScaffoldChecking()

Indicates whether input structures not containing the specified scaffold should be ignored (true) or not (false).

See Also:

setScaffold(Molecule)

setStrictScaffoldChecking

public void setStrictScaffoldChecking(boolean strictScaffoldChecking)

Sets whether input structures not containing the specified scaffold should be ignored (true) or not (false). The default value is true.

See Also:

setScaffold(Molecule)