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. |
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MolSearch APIHitColoringAndAlignmentOptions 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 CartridgeUse the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.alignmentMode:{off|rotate|partialClean}jcsearch command line toolUse 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. |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### Coloring Specifies whether the hit atoms and bonds should be colored or not. |
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MolSearch APIHitColoringAndAlignmentOptions 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 CartridgeUse the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.coloring:{y|n}jcsearch command line toolUse the following command line parameter:--hitColoring:n/yDefault value is 'n'. If the output format is MRV, colors the hits depend on search type. |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### Hit color Determines the color of the substructure hit. |
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MolSearch APIHitColoringAndAlignmentOptions 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 CartridgeUse the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.hitColor:<color-value>jcsearch command line toolUse the following command line parameter:--hitColorIn case of hitColoring specify color of hit atoms and bonds. Examples: "red", "green", "blue", "#00FF00" |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### Hit homology color Specifies color of the user defined homologies in a substructure hit. |
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MolSearch APIHitColoringAndAlignmentOptions 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.setHitColor(Color.RED); Molecule[] results = searcher.getHitsAsMolecules(idList, displayOptions, dataFieldNames, dataFiledValues); JChem Oracle CartridgeUse the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.hitHomologyColor:<color-value>jcsearch command line toolUse the following command line parameter:--hitHomologyColorIn case of hitColoring specify color of user defined homologies. Examples: "red", "green", "blue", "#00FF00". |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### Non-hit color Determines the color of the target which is not part of the substructure. |
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MolSearch APIHitColoringAndAlignmentOptions 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 CartridgeUse the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.nonHitColor:<color-value>jcsearch command line toolUse the following command line parameter:--nonHitColorIn case of hitColoring specify color of non-hit atoms and bonds. Examples: "red", "green", "blue", "#00FF00" |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### Non-hit color 3D Determines the color of the 3D target which is not part of the substructure. |
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MolSearch APIHitColoringAndAlignmentOptions 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 CartridgeUse the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.nonHitColor3D:<color-value>jcsearch command line toolUse the following command line parameter:--nonHitColor3DIn case of hitColoring in 3D molecules specify color of non-hit atoms and bonds. Examples: "red", "green", "blue", "#00FF00". |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### Markush display mode In case of Markush searching and hit coloring specifies the type of the resulting molecule. Ignore tetrahedral stereo |
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MolSearch APIHitColoringAndAlignmentOptions 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 CartridgeUse 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 toolUse 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. |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### 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. |
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MolSearch APIHitColoringAndAlignmentOptions 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 CartridgeUse the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.removeUnusedDef:{y|n}jcsearch command line toolUse the following command line parameter:--removeUnusedDef:n/y |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### 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. |
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MolSearch APIHitColoringAndAlignmentOptions 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 CartridgeUse 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 toolUse 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 |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### 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. |
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MolSearch APIHitColoringAndAlignmentOptions 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 CartridgeUse the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.queryDisplay:{y|n} (default:n)jcsearch command line toolUse the following command line parameter:--queryDisplay:n/y |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |
| #### 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. |
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MolSearch APIHitColoringAndAlignmentOptions 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 CartridgeUse the jcf_hitColorAndAlign operator with hitColorAndAlignOptions.displayLabelsAndBoxes:{y|n} (default:n)jcsearch command line toolUse the following command line parameter:--displayLabelsAndBoxes:n/y |
| See the availability of the option in further ChemAxon products: InstantJChem JChem for Excel * Plexus Suite Home |