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Query DB structures Manipulation queries DB search Hits Memory - - PowerPoint PPT Presentation
Query DB structures Manipulation queries DB search Hits Memory - - PowerPoint PPT Presentation
Query DB structures Manipulation queries DB search Hits Memory search 2 Standardization of the query 3 DB search DB structures Manipulation queries DB search Hits Memory search Search in database Main classes of the search
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Standardization of the query
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DB search
DB
structures queries
DB search Hits Manipulation Memory search
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Main classes of the search process I.
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MolSearch JChemSearch StandardizedMolSearch
Search in database
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Main classes of the search process II.
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SearchOptions MolSearchOptions (MolSearch, StandardizedMolSearch) JChemSearchOptions (JChemSearch)
Search in database
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Search type Query Retrieved Not retrieved Duplicate Superstructure Full structure Full fragment Similarity Substructure
Structure search types
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Charge, isotopes, radical, valence
(on, exact, ignore)
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Search options
ON: Exact: Ignore:
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Stereo search
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Search options
- n
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Stereo search
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Search options
exact
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Stereo search
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Search options
enantiomer, diastereomer
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Stereo search
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Search options
- ff
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Tautomer search (off/on)
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Search options
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Vague bond search levels
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Search options
OFF default
- r aromatic
ignore type
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- Attached data search (off/on)
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Search options
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Search type is set in constructor!
JChemSearchOptions jcSearchOptions = new JChemSearchOptions(SearchConstants.SIMILARITY);
Setting search options
jcSearchOptions.setVagueBondLevel(SearchConstants.VAGUE_BOND_LEVEL2)
jcSearchOptions.setOptions("hcountmatching:g keepqueryorder:y");
Modifying search behaviour
jcSearchOptions.setMaxResultCount(10);
jcSearchOptions.setMaxTime(10000);
jcSearchOptions.setReturnsNonHits(true); (SearchUtil.java)
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Search in database
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Running a search - JChemSearch
JChemSearch jChemSearch = new JChemSearch(); jChemSearch.setConnectionHandler(connectionHandler); jChemSearch.setQueryStructure(query); // no need for aromatization! jChemSearch.setStructureTable(targetTable); jChemSearch.setSearchOptions(jcSearchOptions); jChemSearch.run(); (SearchUtil.java)
Cartridge example
SELECT id FROM mystructures WHERE jc_compare(smiles, 'Brc1ccccc1C=C Cc1cccc(Br)c1C Cc1ccccc1Br', 't:d') = 1;
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Search in database
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Reusing objects
jChemSearch.setSearchOptions(jcSearchOptions); jChemSearch.run(); … jcSearchOptions.setOption("vagueBond", "3"); … // JChemSearchOptions object must be set again! jChemSearch.setSearchOptions(jcSearchOptions);
jChemSearch.getSearchOptions().setOption("vagueBond", "3"); (DatabaseSearchExample.java)
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Search in database
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Manipulation
DB
structures queries
DB search Hits Manipulation Memory search
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Running search in a separate thread
jChemSearch.setRunMode(JChemSearch.RUN_MODE_ASYNCH_COMPLETE); jChemSearch.run(); while (jChemSearch.isRunning()) { String msg = jChemSearch.getProgressMessage(); int count = jChemSearch.getResultCount(); int lastId = jChemSearch.getCurrentId(); System.out.printf("Progress message: %s, result count: %d, " + "last cd_id: %d\n", msg, count, lastId); Thread.sleep(100); } System.out.println(jChemSearch.getResultCount() + " hit(s) found"); (AsyncSearchExample.java)
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Search in database - asynchronous mode
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Similarity search
Using default descriptor: chemical hashed fingerprint
jcso.setSearchType(SearchConstants.SIMILARITY); jcso.setDissimilarityThreshold(0.4);
Using other descriptors: a descriptor table have to be created first!
gMD = new GenerateMD(); ... // set connection handler, structure table name etc. gMD.setDescriptor("myDescriptor", "ECFP", settings, null); gMD.init(); gMD.run(); jcso.setDescriptorName("myDescriptor"); (SimilaritySearchExample.java)
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Search in database - similarity
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JChem Screen descriptors can be set up for JChem tables Available descriptors:
ECFP, FCFP – extended connectivity fingerprint pharmacophore fingerprint BCUT chemical fingerprint
Various metrics
Tanimoto Euclidean Tversky, Dice, Sub, Super, etc
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Search in database - descriptors
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Pre-filtering, ordering
Filtering target molecules:
jcSearchOptions.setFilterQuery("SELECT cd_id FROM my_structures" + " WHERE cd_molweight < 500");
Filter queries can also be used for ordering:
jcSearchOptions.setFilterQuery("SELECT cd_id FROM my_structures” + " ORDER BY cd_molweight");
Filtering based on a separate table:
jcSearchOptions.setFilterQuery("SELECT cd_id" + " FROM stock_table" + " WHERE quantity > 20"); (SearchWithFilterQueryExample.java)
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