RgDecompResults (JChem Base API documentation (c) 1998-2019 ChemAxon Ltd.)

java.lang.Object
- chemaxon.sss.search.RgDecompResults

```
@PublicAPI
public class RgDecompResults
extends java.lang.Object
```
Convenience class for generating, storing and returning results of a search in different forms: as r-group decomposition or Markush molecule. Used as return class of JChemSearch.getHitsAsRgDecomp(int[], int).
When RgDecompResults is used only for storing results use the constructor designed for that purpose. When generating the results, set the parameters (query, targets (and optionally their original identifiers), search options, attachment type) using the appropriate constructor or setters then call run() method.
Available setters:
If a query does not contain undefined r-atoms (r-atom without corresponding r-group definition) then implicit Hydrogens are exchanged to undefined r-atoms and results are obtained using this new query.
hasResults() shows whether the class can actually provide valid results. Results can be achieved by calling different methods:
- scaffold of query (getScaffold())
- number of ligands (getLigandsNumber())
- matched target indexes (getIncludedIds())
- non-matched target indexes (getSkippedIds())
- hits in a Markush molecule (getHitsAsMarkush())
- r-group decomposed hits (getHitsAsRgDecomp())
- r-group decomposed hits in colored table format (getHitsAsTable()). Format of the table (first row is header row, following rows contain targets, 1 hit/target):
```
 [query]:     molecule        R1         R2         R3    ...
 ---------------------------------------------------------
 [target1]:   molecule1    ligand1.1  ligand1.2  ligand1.3
 [target2]:   molecule2    ligand2.1  ligand2.2  ligand2.3
 
```
  As an example see decomposition table
More details about r-group decomposition can be found here.
For more sophisticated usages (e.g. all hits of query in a specific target) see our RGroupDecomposition API documentation.
Since:

JChem 5.3 Date 1-Oct-2009

Author:

Tamas Csizmazia

Constructor Summary

Constructors
Constructor and Description
`RgDecompResults(Molecule scaffold, int noLigands, Molecule[][] rgDecomps, RgMolecule markush, int[] skippedIds)` This constructor is used only for storing results.
`RgDecompResults(Molecule scaffold, int noLigands, Molecule[][] rgDecomps, RgMolecule markush, int[] skippedIds, int[] originalIds)` This constructor is used only for storing results.
`RgDecompResults(Molecule query, Molecule[] targets, SearchOptions options, int attachmentType)` Constructor used for generating results.
`RgDecompResults(Molecule query, Molecule[] targets, SearchOptions options, int attachmentType, int[] originalIds)` Constructor used for generating results.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Decomposition[]`	`getDecompositions()` Returns the `Decomposition` objects corresponding to the targets.
`RgMolecule`	`getHitsAsMarkush()` Returns a single RgMolecule that consists of the scaffold and all the possible ligands as rgroup-definitions.
`Molecule[][]`	`getHitsAsRgDecomp()` Returns All ligands of all targets.
`Molecule[][]`	`getHitsAsTable()` Returns the table elements in Molecule[][] format.
`int[]`	`getIncludedIds()` Returns indexes of those targets that are matched by query.
`int`	`getLigandsNumber()` Returns the number of ligands in one target structure.
`Molecule`	`getScaffold()` Returns scaffold of the query (r-groups are added automatically if needed).
`int[]`	`getSkippedIds()` Returns indexes of those targets that are not matched by query.
`boolean`	`hasResults()`
`void`	`run()` Generates the results if no valid results are available (see `hasResults()`)
`void`	`setAttachmentType(int attachmentType)`
`void`	`setOriginalIds(int[] originalIds)`
`void`	`setQuery(Molecule query)`
`void`	`setSearchOptions(SearchOptions options)`
`void`	`setTargets(Molecule[] targets)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - RgDecompResults
```
public RgDecompResults(Molecule scaffold,
                       int noLigands,
                       Molecule[][] rgDecomps,
                       RgMolecule markush,
                       int[] skippedIds)
```
    This constructor is used only for storing results. For retrieving stored results see getScaffold(), getLigandsNumber(), getHitsAsRgDecomp(), getHitsAsMarkush(), getHitsAsTable(), getIncludedIds() and getSkippedIds().
    
    Parameters:
    
    scaffold - Scaffold of the query with added rgroups.
    
    noLigands - Number of ligands in a decomposition.
    
    rgDecomps - Ligands of decomposition for all targets.
    
    markush - Scaffold and ligands collected in one Markush structure
    
    skippedIds - Indexes of those targets that are not matched by query.
  - RgDecompResults
```
public RgDecompResults(Molecule scaffold,
                       int noLigands,
                       Molecule[][] rgDecomps,
                       RgMolecule markush,
                       int[] skippedIds,
                       int[] originalIds)
```
    This constructor is used only for storing results. For retrieving stored results see getScaffold(), getLigandsNumber(), getHitsAsRgDecomp(), getHitsAsMarkush(), getHitsAsTable(), getIncludedIds() and getSkippedIds().
    
    Parameters:
    
    scaffold - Scaffold of the query with added r-groups.
    
    noLigands - Number of ligands in a decomposition.
    
    rgDecomps - Ligands of decomposition for all targets.
    
    markush - Scaffold and ligands collected in one Markush structure
    
    skippedIds - Indexes of those targets that are not matched by query.
    
    originalIds - Target identifiers to be returned by getSkippedIds() and getIncludedIds() instead of indexes of targets.
  - RgDecompResults
```
public RgDecompResults(Molecule query,
                       Molecule[] targets,
                       SearchOptions options,
                       int attachmentType)
```
    Constructor used for generating results.
    
    Parameters:
    
    query - The query structure that is looked for in targets.
    
    targets - The target structures.
    
    options - Search options used in search.
    
    attachmentType - Type of attachment point representation in ligands. When creating Markush structure from results, this parameter is ignored and Decomposition#ATTACHMENT_POINT (default) is used instead.
    
    See Also:
    
    SearchConstants.ATTACHMENT_NONE, SearchConstants.ATTACHMENT_POINT, SearchConstants.ATTACHMENT_MAP, SearchConstants.ATTACHMENT_LABEL, SearchConstants.ATTACHMENT_ATOM, SearchConstants.ATTACHMENT_RLABEL
  - RgDecompResults
```
public RgDecompResults(Molecule query,
                       Molecule[] targets,
                       SearchOptions options,
                       int attachmentType,
                       int[] originalIds)
```
    Constructor used for generating results.
    
    Parameters:
    
    query - The query structure that is looked for in targets.
    
    targets - The target structures.
    
    options - Search options used in search.
    
    attachmentType - Type of attachment point representation in ligands. When creating Markush structure from results, this parameter is ignored and Decomposition#ATTACHMENT_POINT (default) is used instead.
    
    originalIds - Target identifiers to be returned by getSkippedIds() and getIncludedIds() instead of indexes of targets.
    
    See Also:
    
    SearchConstants.ATTACHMENT_NONE, SearchConstants.ATTACHMENT_POINT, SearchConstants.ATTACHMENT_MAP, SearchConstants.ATTACHMENT_LABEL, SearchConstants.ATTACHMENT_ATOM, SearchConstants.ATTACHMENT_RLABEL
- Method Detail
  - getScaffold
```
public Molecule getScaffold()
```
    Returns scaffold of the query (r-groups are added automatically if needed).
    
    Returns:
    
    Scaffold if valid results are available otherwise null.
  - getLigandsNumber
```
public int getLigandsNumber()
```
    Returns the number of ligands in one target structure.
    
    Returns:
    
    Number of ligands in a target structure if valid results are available, otherwise Integer.MIN_VALUE.
  - getHitsAsRgDecomp
```
public Molecule[][] getHitsAsRgDecomp()
```
    Returns All ligands of all targets. When a target does not contain the query structure the array contains null instead of array of ligands.
    
    Returns:
    
    Array of array of ligands for all target structures if valid results are available, otherwise null. The returned array contains ligands for all query atoms. If a query atom is not an r-atom the ligand is null.
  - getDecompositions
```
public Decomposition[] getDecompositions()
```
    Returns the Decomposition objects corresponding to the targets.
    
    Returns:
    
    the Decomposition objects corresponding to the targets if valid results are available, otherwise null.
    
    Since:
    
    JChem 5.10
  - getHitsAsTable
```
public Molecule[][] getHitsAsTable()
```
    Returns the table elements in Molecule[][] format. As an example see decomposition table
    Returns:
    A colored molecule table if valid results are available and there were matching targets for the query, otherwise null. Format of the table (first row is header row, following rows contain targets, 1 hit/target):
    [query]: molecule R1 R2 R3 ... --------------------------------------------------------- [target1]: molecule1 ligand1.1 ligand1.2 ligand1.3 [target2]: molecule2 ligand2.1 ligand2.2 ligand2.3
  - getHitsAsMarkush
```
public RgMolecule getHitsAsMarkush()
```
    Returns a single RgMolecule that consists of the scaffold and all the possible ligands as rgroup-definitions.
    
    Returns:
    
    An RgMolecule if valid results are available, otherwise null.
  - getSkippedIds
```
public int[] getSkippedIds()
```
    Returns indexes of those targets that are not matched by query.
    
    Returns:
    
    Array of skipped indexes if valid results are available, otherwise null. If original identifiers of targets are set then those are returned instead of array indexes.
  - getIncludedIds
```
public int[] getIncludedIds()
```
    Returns indexes of those targets that are matched by query.
    
    Returns:
    
    Array of included indexes if valid results are available, otherwise null. If original identifiers of targets are set then those are returned instead of array indexes.
  - run
```
public void run()
         throws SearchException
```
    Generates the results if no valid results are available (see hasResults())
    
    Throws:
    
    SearchException
  - setQuery
```
public void setQuery(Molecule query)
```
    Parameters:
    
    query - The query to set
  - setTargets
```
public void setTargets(Molecule[] targets)
```
    Parameters:
    
    targets - The targets to set
  - setSearchOptions
```
public void setSearchOptions(SearchOptions options)
```
    Parameters:
    
    options - The search options to set
  - setAttachmentType
```
public void setAttachmentType(int attachmentType)
```
    Parameters:
    
    attachmentType - The attachment type to set
  - setOriginalIds
```
public void setOriginalIds(int[] originalIds)
```
    Parameters:
    
    originalIds - Original identifiers of targets to set
  - hasResults
```
public boolean hasResults()
```
    Returns:
    
    true, if valid results are available

Class RgDecompResults

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

RgDecompResults

RgDecompResults

RgDecompResults

RgDecompResults

Method Detail

getScaffold

getLigandsNumber

getHitsAsRgDecomp

getDecompositions

getHitsAsTable

getHitsAsMarkush

getSkippedIds

getIncludedIds

run

setQuery

setTargets

setSearchOptions

setAttachmentType

setOriginalIds

hasResults