@PublicAPI @Beta public class MarkushComposer extends java.lang.Object
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.
Constructor and Description |
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MarkushComposer() |
Modifier and Type | Method and Description |
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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.
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boolean |
isStrictScaffoldChecking()
Indicates whether input structures not containing the specified scaffold should be ignored (true) or not (false).
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void |
run()
Executes the Markush Composer algorithm.
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void |
setMolecules(java.util.List<Molecule> molecules)
Sets the input molecules for Markush composition.
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void |
setOptions(MarkushComposerOptions options)
Sets the options for Markush composition.
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void |
setScaffold(Molecule scaffold)
Sets a user-defined scaffold for Markush composition.
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void |
setStrictScaffoldChecking(boolean strictScaffoldChecking)
Sets whether input structures not containing the specified scaffold should be ignored (true) or not (false).
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public void setMolecules(java.util.List<Molecule> molecules)
public void setOptions(MarkushComposerOptions options)
public void setScaffold(Molecule scaffold)
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.
scaffold
- the scaffold structure to be used during Markush compositionpublic void run() throws com.chemaxon.markush.composer.MarkushComposerException
MarkushComposerException
- in the following cases:
public java.util.List<RgMolecule> getResults()
public RgMolecule getPreferredResult()
getResults()
, which represents the most input molecules.public boolean isStrictScaffoldChecking()
setScaffold(Molecule)
public void setStrictScaffoldChecking(boolean strictScaffoldChecking)
setScaffold(Molecule)