Hitdisplay specific search options¶

In this section search options concerning hit display are summarized andtheir usage is shown in different search interfaces.

Alignment

Coloring

Hit color

Hit homology color

Non-hit color

Non-hit color 3D

Markush display mode

Remove unused definition

Similarity

Query display

Display labels and boxes

Alignment¶

Specifies alignment mode of the hit structures.
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setAlignmentMode( HitColoringAndAlignmentOptions.ALIGNMENT_OFF /
                HitColoringAndAlignmentOptions.ALIGNMENT_ROTATE /
                HitColoringAndAlignmentOptions.ALIGNMENT_PARTIAL_CLEAN );
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setAlignmentMode( HitColoringAndAlignmentOptions.ALIGNMENT_OFF /
                HitColoringAndAlignmentOptions.ALIGNMENT_ROTATE /
                HitColoringAndAlignmentOptions.ALIGNMENT_PARTIAL_CLEAN );
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.

alignmentMode:{off|rotate|partialClean}

jcsearch command line tool

Use one of the following command line parameters to align the hits if output format is MRV.

    --align:r rotate if query molecule has 0 dimension, it will be cleaned in 2D for alignment;
    --align:p partial clean (template based clean) if query molecule has 0 dimension, same as rotate.

Coloring¶

Specifies whether the hit atoms and bonds should be colored or not.
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setColoringEnabled( true / false );
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setColoringEnabled( true / false );
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.

coloring:{y|n}

jcsearch command line tool

Use the following command line parameter:

--hitColoring:n/y

Default value is 'n'. If the output format is MRV, colors the hits depend on search type.

Hit color¶

Determines the color of the substructure hit.
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setHitColor(Color.RED);
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setHitColor(Color.RED);
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.

hitColor:<color-value>

jcsearch command line tool

Use the following command line parameter:

--hitColor

In case of hitColoring specify color of hit atoms and bonds. Examples: "red", "green", "blue", "#00FF00"

Hit homology color¶

Specifies color of the user defined homologies in a substructure hit.
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setHitHomologyColor(Color.RED);
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setHitHomologyColor(Color.RED);
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.

hitHomologyColor:<color-value>

jcsearch command line tool

Use the following command line parameter:

--hitHomologyColor

In case of hitColoring specify color of user defined homologies. Examples: "red", "green", "blue", "#00FF00".

Non-hit color¶

Determines the color of the target which is not part of the substructure.
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setNonHitColor(Color.GRAY);
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setNonHitColor(Color.GRAY);
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.

nonHitColor:<color-value>

jcsearch command line tool

Use the following command line parameter:

--nonHitColor

In case of hitColoring specify color of non-hit atoms and bonds. Examples: "red", "green", "blue", "#00FF00"

Non-hit color 3D¶

Determines the color of the 3D target which is not part of the substructure.
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setNonHitColor3D(Color.GRAY);
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setNonHitColor3D(Color.GRAY);
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.
nonHitColor3D:<color-value>

jcsearch command line tool

Use the following command line parameter:

--nonHitColor3D

In case of hitColoring in 3D molecules specify color of non-hit atoms and bonds. Examples: "red", "green", "blue", "#00FF00".

Markush display mode¶

In case of Markush searching and hit coloring specifies the type of the resulting molecule. Ignore tetrahedral stereo
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setMarkushDisplayMode( HitColoringAndAlignmentOptions.ORIGINAL_MARKUSH /
                HitColoringAndAlignmentOptions.MARKUSH_REDUCTION /
                HitColoringAndAlignmentOptions.MARKUSH_REDUCTION_HGEXPANSION );
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setMarkushDisplayMode( HitColoringAndAlignmentOptions.ORIGINAL_MARKUSH /
                HitColoringAndAlignmentOptions.MARKUSH_REDUCTION /
                HitColoringAndAlignmentOptions.MARKUSH_REDUCTION_HGEXPANSION );
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.
markushDisplayMode: <o/r/rhg>

    o: (default) the result is shown on the given target structure;
    r: Markush reduction to hit, the Markush structure is reduced according to the hit;
    rhg: Markush reduction to hit and the homology groups are expanded according to the matching part of the query, which can also be a single H atom or an empty set.

jcsearch command line tool

Use the following command line parameter:

--markushDisplayMode:o/r/rhg

    o: (default) the result is shown on the given target structure;
    r: Markush reduction to hit, the Markush structure is reduced according to the hit;
    rhg: Markush reduction to hit and the homology groups are expanded according to the matching part of the query, which can also be a single H atom or an empty set.

Remove unused definition¶

Sets removing unused R-group definitions in case of Markush search. By removing unused definitions readability is increased. Default value is false.
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setRemoveUnusedDefinitions( true / false );
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setRemoveUnusedDefinitions( true / false );
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.
removeUnusedDef:{y|n}

jcsearch command line tool

Use the following command line parameter:
--removeUnusedDef:n/y

Similarity¶

It can be applied only in case of similarity search. Describes which score is displayed within the result of a similarity search. Similarity score is displayed by default.
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setSimilarityScoreDisplay( HitColoringAndAlignmentOptions.SIMILARITY /
                HitColoringAndAlignmentOptions.DISSIMILARITY / HitColoringAndAlignmentOptions.SIMILARITY_OFF );
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setSimilarityScoreDisplay( HitColoringAndAlignmentOptions.SIMILARITY /
                HitColoringAndAlignmentOptions.DISSIMILARITY / HitColoringAndAlignmentOptions.SIMILARITY_OFF );
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.
similarity:{s|d|o}

    s: similarity score is displayed (default);
    d: dissimilarity score is displayed;
    o: neither similarity nor dissimilarity score is displayed.

jcsearch command line tool

Use the following command line parameter:
--similarity:s/d/o

    s: similarity score is displayed (default);
    d: dissimilarity score is displayed;
    o: neither similarity nor dissimilarity score is displayed

Query display¶

It can be applied only in case of similarity search. Describes whether query structure is displayed within the result of a similarity search. Query is not displayed by default.
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setQueryDisplay( true / false );
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setQueryDisplay( true / false );
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.
queryDisplay:{y|n} (default:n)

jcsearch command line tool

Use the following command line parameter:
--queryDisplay:n/y

Display labels and boxes¶

It can be applied only in case of similarity search. Describes whether labels and bounding boxes for the parts of the result of a similarity search - target, query, score - are displayed.

Labels and boxes are not displayed by default.
MolSearch API

        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setDisplayLabelsAndBoxes( true / false );
        MolSearchOptions searchOptions = new MolSearchOptions(SearchConstants.SUBSTRUCTURE);
        // ...
        HitDisplayTool hdt = new HitDisplayTool(displayOptions, searchOptions, queryMol);
        Molecule result = hdt.getHit(targetMol);

JChemSearch API

        JChemSearch searcher = new JChemSearch();
        // ...
        searcher.run();
        int[] idList = searcher.getResults();
        List<String> dataFieldNames = new ArrayList<String>();
        // ... (add required field names)
        List<Object[]> dataFieldValues = new ArrayList<Object[]>(); // will store field values for the required fields
        // ...
        HitColoringAndAlignmentOptions displayOptions = new HitColoringAndAlignmentOptions();
        displayOptions.setDisplayLabelsAndBoxes( true / false );
        Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues);

JChem Oracle Cartridge

Use the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.
displayLabelsAndBoxes:{y|n} (default:n)

jcsearch command line tool

Use the following command line parameter:
--displayLabelsAndBoxes:n/y