Hitdisplay specific search options

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

 

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