JChemSearch (JChem Base API documentation (c) 1998-2021 ChemAxon Ltd.)

java.lang.Object
- chemaxon.util.ErrorHandler
- - chemaxon.jchem.db.JChemSearch

All Implemented Interfaces:: TableTypeConstants, chemaxon.license.Licensable, SearchConstants

@PublicAPI
public class JChemSearch
extends ErrorHandler
implements SearchConstants, TableTypeConstants, chemaxon.license.Licensable

JavaBean for structure searching in structure tables of relational databases. For more information, see the corresponding section of the user's guide.

Example for using the class:

 searcher = new JChemSearch();
 searcher.setQueryStructure("c1cnccc1Cl");
 searcher.setConnectionHandler(conHandler);
 searcher.setStructureTable("cduser.structures");
 
 searchOptions = new JChemSearchOptions(JChemSearch.SIMILARITY);
 searchOptions.setDissimilarityThreshold(0.8F);
 searchOptions.setMaxResultCount(100);
 searcher.setSearchOptions(searchOptions);
 
 searcher.setRunMode(JChemSearch.RUN_MODE_SYNCH_COMPLETE);
 searcher.run();

Author:: JChem Base team, Ferenc Csizmadia, Szilard Dorant, Tamas Csizmazia, Robert Wagner, Nora Mate, Peter Kovacs (pkovacs), Edvard Buki, Vencel Bors, Peter Kovacs (pkovacs84), Zoltan Nagy, Gabor Hornyak

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class JChemSearch.DissimilarityMetrics
Class for presenting the available dissimilarity metrics for similarity search.

Nested Classes
Modifier and Type	Class and Description
`static class`	`JChemSearch.DissimilarityMetrics` Class for presenting the available dissimilarity metrics for similarity search.

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`APPEND_TO_RESULT_TABLE` Constant for the generation of result tables.
`static int`	`CREATE_OR_REPLACE_RESULT_TABLE` Constant for the generation of result tables.
`static int`	`MAXIMAL_ACCEPTEDSEARCHTIME_MINUTES` Deprecated.
`static int`	`NO_ORDERING` Constant for ordering the result.
`static int`	`NO_RESULT_TABLE` Constant for the generation of result tables.
`static int`	`ORDERING_BY_FILTER_ID_LIST` Constant for ordering the result.
`static int`	`ORDERING_BY_ID` Constant for ordering the result.
`static int`	`ORDERING_BY_ID_OR_SIMILARITY` Constant for ordering the result.
`static int`	`RUN_MODE_ASYNCH_COMPLETE` Runs the search in a new thread; `run()` or `setRunning(boolean)` return immediately.
`static int`	`RUN_MODE_ASYNCH_PROGRESSIVE` Runs the search in a new thread; `run()` or `setRunning(boolean)` return immediately.
`static int`	`RUN_MODE_SYNCH_COMPLETE` The "runner" methods (`run()` or `setRunning(boolean)` return only after all hits has been found.
`protected JChemSearchOptions`	`searchOptions` Object to store all search parameters.

Fields inherited from class chemaxon.util.ErrorHandler
CLASS_NOT_FOUND_ERROR, DATABASE_SEARCH_ERROR, exception, ILLEGAL_ACCESS_ERROR, INSTANTIATION_ERROR, IO_ERROR, MAX_SEARCH_FREQUENCY_EXCEEDED_ERROR, MOL_FORMAT_ERROR, NO_ERROR, SQL_ERROR, UNIDENTIFIED_ERROR

Fields inherited from interface chemaxon.sss.SearchConstants
ABS_STEREO_ALWAYS_ON, ABS_STEREO_CHIRAL_FLAG, ABS_STEREO_TABLE_OPTION, ATTACHED_DATA_MATCH_EXACT, ATTACHED_DATA_MATCH_GENERAL, ATTACHED_DATA_MATCH_IGNORE, ATTACHMENT_ATOM, ATTACHMENT_LABEL, ATTACHMENT_MAP, ATTACHMENT_NONE, ATTACHMENT_POINT, ATTACHMENT_RLABEL, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SEARCHTYPE, DISSIMILARITY_PROPERTY_NAME, DUPLICATE, FULL, FULL_FRAGMENT, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, HIT_EXCLUDEDQ, HIT_LP, HIT_MULTICENTER, HIT_NON_R, HIT_ORDERING_NONE, HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST, HIT_R, HIT_R_EMPTY_MATCH, HIT_UNMAPABLE, IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, IMPLICIT_H_MATCHING_ENABLED, IMPLICIT_H_MATCHING_IGNORE, ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, MARKUSH_HIT_INNER, MARKUSH_HIT_ORIGINAL, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, NO_ABAS, NO_SCREEN, POSITION_ON_0TH_HEAVY_ATOM, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, SEARCH_MODE_NAMES, SEARCH_TYPE_NAMES, SIMILARITY, STEREO_DIASTEREOMER, STEREO_ENANTIOMER, STEREO_EXACT, STEREO_IGNORE, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, STEREO_SPECIFIC, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_DEFAULT, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO, UNDEF_R_MATCHING_ALL, UNDEF_R_MATCHING_GROUP, UNDEF_R_MATCHING_GROUP_H, UNDEF_R_MATCHING_GROUP_H_EMPTY, UNDEF_R_MATCHING_UNDEF_R, VAGUE_BOND_DEFAULT, VAGUE_BOND_LEVEL_HALF, VAGUE_BOND_LEVEL1, VAGUE_BOND_LEVEL2, VAGUE_BOND_LEVEL3, VAGUE_BOND_LEVEL4, VAGUE_BOND_OFF

Fields inherited from interface chemaxon.jchem.db.TableTypeConstants
FP_DEFAULT_BITS_PER_PATTERN, FP_DEFAULT_LENGTH_IN_INTS, FP_DEFAULT_PATTERN_LENGTH, MYSQL_DEFAULT_TABLE_TYPE, MYSQL_FORCE_INNO_DB, MYSQL_FORCE_MYISAM, TABLE_TYPE_ANY_STRUCTURES, TABLE_TYPE_DEFAULT, TABLE_TYPE_EXPLANATIONS, TABLE_TYPE_IS_NOT_SUPPORTED, TABLE_TYPE_MARKUSH_LIBRARIES, TABLE_TYPE_MOLECULES, TABLE_TYPE_NAMES, TABLE_TYPE_QUERY_STRUCTURES, TABLE_TYPE_REACTIONS

Constructor Summary

Constructors
Constructor and Description
`JChemSearch()` Creates new JChemSearch class
`JChemSearch(chemaxon.jchem.db.distributed.DistributedNodes distributedNodes)` Creates a new JChemSearch class for distributed search.
`JChemSearch(chemaxon.jchem.db.distributed.DistributedNodes distributedNodes, java.lang.String indexedTable, java.lang.String indexedColumn)` For internal use only.
`JChemSearch(java.lang.String indexedTable, java.lang.String indexedColumn)` For internal use only.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`checkException()` Throws the exception stored in the object.
`void`	`cleanResults()` Cleans stored search results.
`java.util.List<byte[]>`	`getAvailableExtraInformation(int minimumHitSize)` For internal use only.
`int[]`	`getAvailableNewHits(int minimumHitSize)` Used with run mode = `RUN_MODE_ASYNCH_PROGRESSIVE`.
`java.lang.String`	`getCacheError()` For checking for cache errors.
`long`	`getCacheLoadTime()` Gets the time spent with cache loading for the target structure table.
`double`	`getCacheSize()` Returns the size of the cache for the target structure table.
`double`	`getCacheSizeEstimate()` Returns an estimate of the cache size for the target structure table.
`java.sql.Connection`	`getConnection()` Getter for property connection.
`ConnectionHandler`	`getConnectionHandler()` Getter for property connectionHandler.
`float[]`	`getDissimilarity()` Getter for dissimilarity results.
`float`	`getDissimilarity(int index)` Indexed getter for property dissimilarity.
`static JChemSearch.DissimilarityMetrics`	`getDissimilarityMetrics(ConnectionHandler ch, java.lang.String tableName)` Returns the available dissimilarity metrics for the given table.
`static JChemSearch.DissimilarityMetrics`	`getDissimilarityMetrics(ConnectionHandler ch, java.lang.String tableName, java.lang.String indexedTable, java.lang.String indexedColumn)`
`int`	`getEnumerationCount()` Gets the number of enumerates used while screening the database
`java.util.List<byte[]>`	`getExtraInformation()` For internal use only.
`long`	`getFirstHitTime()` Gets the first hit's retrieving time (measured from start of screening).
`HitDisplayTool`	`getHitsAsHitDisplayTool(int[] idList, HitColoringAndAlignmentOptions options, java.util.List<java.lang.String> dataFieldNames, java.util.List<java.lang.Object[]> dataFieldValues, java.util.List<? super Molecule> molecules, java.util.List<byte[]> sources)` Gets a HitDisplayTool object from which the results can be retrieved.
`Molecule[]`	`getHitsAsMolecules(int[] idList, HitColoringAndAlignmentOptions options, java.util.List<java.lang.String> dataFieldNames, java.util.List<java.lang.Object[]> dataFieldValues)` Returns hits ready for display.
`RgDecompResults`	`getHitsAsRgDecomp(int[] hits, int attachmentType)` Returns hits as result of r-group decomposition according to the original query.
`int`	`getNextHit()` Used with run mode = `RUN_MODE_ASYNCH_PROGRESSIVE`.
`int`	`getNumberOfProcessingThreads()` Gets the number of processing threads.
`int`	`getOrder()` Getter for property order.
`java.lang.String`	`getProgressMessage()` Getter for property progressMessage.
`java.lang.String`	`getQueryStructure()` Getter for property queryStructure.
`int`	`getResult(int index)` Indexed getter for property results.
`chemaxon.jchem.db.SearchCoreReturnedValue`	`getResultContext()` For internal use only.
`int`	`getResultCount()` Getter for property resultCount.
`int[]`	`getResults()` Returns an `int` array containing the `cd_id` values of found compounds.
`java.lang.String`	`getResultTable()` Getter for property resultTable.
`int`	`getResultTableMode()` Getter for property resultTableMode.
`int`	`getRunMode()` Retruns the current run mode.
`int`	`getScreenedCount()` Gets the number of total screened structures.
`int`	`getScreenedCountTotal()` Gets the number of total screened structures.
`int`	`getScreenedCountUnique()` Gets the number of unique screened structures.
`int[]`	`getScreenedResults()` Gets the screened unique structures' ids.
`long`	`getScreeningTime()` Gets the screening time.
`JChemSearchOptions`	`getSearchOptions()` Returns the SearchOptions object associated with this Search object.
`long`	`getSearchTime()` Gets the total search time.
`java.lang.String`	`getStructureTable()` Getter for property structureTable.
`boolean`	`hasMoreHits()` Used with run mode = `RUN_MODE_ASYNCH_PROGRESSIVE`.
`boolean`	`isInfoToStdError()` Getter for property infoToStdError.
`boolean`	`isLicensed()`
`boolean`	`isMaxResultCountReached()` Getter for property maxResultCountReached.
`boolean`	`isMaxTimeReached()` Getter for property maxTimeReached.
`boolean`	`isRunning()` Getter for property running.
`boolean`	`isTargetMarkush()` Gets whether target structure table is a Markush table
`void`	`run()` Starts searching.
`void`	`setConnectionHandler(ConnectionHandler connectionHandler)` Sets the database connection.
`void`	`setFilterIDList(int[] ids)` Specifies a list of cd_id values that are allowed to be included in the result set.
`void`	`setFilterIDNotList(int[] ids)` Specifies a list of cd_id values that should not be included in the result set.
`void`	`setInfoToStdError(boolean infoToStdError)` Setter for property infoToStdError.
`void`	`setLicenseEnvironment(java.lang.String env)`
`void`	`setNumberOfProcessingThreads(int threads)` Sets the number of processing threads.
`void`	`setOrder(int order)` Setter for property order.
`void`	`setProgressMessage(java.lang.String message)`
`void`	`setQueryFingerprint(int[] queryFp)` Currently internal use only.
`void`	`setQueryStructure(Molecule queryMol)` Sets the query structure.
`void`	`setQueryStructure(java.lang.String queryStructure)` Setter for property queryStructure.
`void`	`setResultTable(java.lang.String resultTable)` Setter for property resultTable.
`void`	`setResultTableMode(int resultTableMode)` Setter for property resultTableMode.
`void`	`setRunMode(int runMode)` Specifies whether the search is performed synchronously or asychronously and if performed asynchronously, whether the hits can be obtained as soon as they are found or only after the search has completed.
`void`	`setRunning(boolean run)` Setter for property running.
`void`	`setSearchOptions(JChemSearchOptions options)` Sets search parameters.
`void`	`setStructureTable(java.lang.String structureTable)` Setter for property structureTable.
`void`	`setTargetCollection(chemaxon.jchem.base.storage.search.CurrentTargetCollection targetCollection)` For internal use only.
`void`	`setThreadPriority(int priority)` Sets the priority of the processing threads.
`java.lang.String`	`toString()`
`void`	`waitUntilSearchComplete()` Used with run mode = `RUN_MODE_ASYNCH_PROGRESSIVE`.

Methods inherited from class chemaxon.util.ErrorHandler
checkError, getError, getErrorMessage, getException, getStackTrace

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

- Field Detail
  - NO_RESULT_TABLE
```
public static final int NO_RESULT_TABLE
```
    Constant for the generation of result tables. Meaning: Don't store the results in a table. (Value=0)
    
    See Also:
    
    Constant Field Values
  - CREATE_OR_REPLACE_RESULT_TABLE
```
public static final int CREATE_OR_REPLACE_RESULT_TABLE
```
    Constant for the generation of result tables. Meaning: Create a result table. If a table with same name exists, replace it with the new one. (Value=2)
    
    See Also:
    
    Constant Field Values
  - APPEND_TO_RESULT_TABLE
```
public static final int APPEND_TO_RESULT_TABLE
```
    Constant for the generation of result tables. Meaning: Append to an existing result table. Create a new one if it doesn't exist (Value=3)
    
    See Also:
    
    Constant Field Values
  - NO_ORDERING
```
public static final int NO_ORDERING
```
    Constant for ordering the result. Meaning: Don't order the result (Value=0)
    
    See Also:
    
    Constant Field Values
  - ORDERING_BY_ID
```
public static final int ORDERING_BY_ID
```
    Constant for ordering the result. Meaning: Order the result according to the cd_id values (Value=1)
    
    See Also:
    
    Constant Field Values
  - ORDERING_BY_ID_OR_SIMILARITY
```
public static final int ORDERING_BY_ID_OR_SIMILARITY
```
    Constant for ordering the result. Meaning: Order the result according to the calculated dissimilarity in the case of dissimilarity searching, use the cd_id values otherwise (Value=2)
    
    See Also:
    
    Constant Field Values
  - ORDERING_BY_FILTER_ID_LIST
```
public static final int ORDERING_BY_FILTER_ID_LIST
```
    Constant for ordering the result. Meaning: Order the result according to the filterIDList
    
    See Also:
    
    Constant Field Values
  - RUN_MODE_SYNCH_COMPLETE
```
public static final int RUN_MODE_SYNCH_COMPLETE
```
    The "runner" methods (run() or setRunning(boolean) return only after all hits has been found.
    
    Since:
    
    JChem 5.0
    
    See Also:
    
    Constant Field Values
  - RUN_MODE_ASYNCH_COMPLETE
```
public static final int RUN_MODE_ASYNCH_COMPLETE
```
    Runs the search in a new thread; run() or setRunning(boolean) return immediately. Exceptions are not thrown by the run() method they should be checked by the checkException() or ErrorHandler.checkError() methods.
    
    Since:
    
    JChem 5.0
    
    See Also:
    
    Constant Field Values
  - RUN_MODE_ASYNCH_PROGRESSIVE
```
public static final int RUN_MODE_ASYNCH_PROGRESSIVE
```
    Runs the search in a new thread; run() or setRunning(boolean) return immediately. The methods hasMoreHits(), getNextHit() and getAvailableNewHits(int) can be used retrieve hits as soon as they become available. Exceptions are not thrown by the run() method they should be checked by the checkException() or ErrorHandler.checkError() methods.
    This mode doesn't support
    - SIMILARITY search, (SearchOptions.SearchOptions(int)),
    - MD - search,
    - Inverse hits (JChemSearchOptions.setReturnsNonHits(boolean))
    - return order other than NO_ORDERING (setOrder(int) ).
    Since:
    
    JChem 5.0
    
    See Also:
    
    Constant Field Values
  - searchOptions
```
protected final JChemSearchOptions searchOptions
```
    Object to store all search parameters. This is used during the search and stores the settings of the previous search.
  - MAXIMAL_ACCEPTEDSEARCHTIME_MINUTES
```
@Deprecated
public static final int MAXIMAL_ACCEPTEDSEARCHTIME_MINUTES
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - JChemSearch
```
public JChemSearch()
```
    Creates new JChemSearch class
  - JChemSearch
```
public JChemSearch(java.lang.String indexedTable,
                   java.lang.String indexedColumn)
```
    For internal use only.
    
    Parameters:
    
    indexedTable - the name of the table
    
    indexedColumn - the name of the column
  - JChemSearch
```
public JChemSearch(chemaxon.jchem.db.distributed.DistributedNodes distributedNodes,
                   java.lang.String indexedTable,
                   java.lang.String indexedColumn)
```
    For internal use only.
    
    Parameters:
    
    distributedNodes - the distributed nodes
    
    indexedTable - the name of the table
    
    indexedColumn - the name of the column
  - JChemSearch
```
public JChemSearch(chemaxon.jchem.db.distributed.DistributedNodes distributedNodes)
```
    Creates a new JChemSearch class for distributed search. For internal use only.
    
    Parameters:
    
    distributedNodes - the distributed nodes
- Method Detail
  - checkException
```
public void checkException()
                    throws java.lang.Exception
```
    Description copied from class: ErrorHandler
    
    Throws the exception stored in the object. Needed because Tomcat errorpages don't handle errors of type Throwable that are not inheritors of Exception.
    
    Overrides:
    
    checkException in class ErrorHandler
    
    Throws:
    
    java.lang.Exception - the exception stored, boxed as Exception
  - getConnectionHandler
```
public ConnectionHandler getConnectionHandler()
```
    Getter for property connectionHandler.
    
    Returns:
    
    Value of property connectionHandler.
  - setConnectionHandler
```
public void setConnectionHandler(ConnectionHandler connectionHandler)
```
    Sets the database connection.
    
    Parameters:
    
    connectionHandler - a ConnectionHandler object containing a live connection to the database
  - getConnection
```
public java.sql.Connection getConnection()
```
    Getter for property connection.
    
    Returns:
    
    Value of property connection.
  - getDissimilarityMetrics
```
public static JChemSearch.DissimilarityMetrics getDissimilarityMetrics(ConnectionHandler ch,
                                                                       java.lang.String tableName)
                                                                throws java.sql.SQLException
```
    Returns the available dissimilarity metrics for the given table.
    
    Parameters:
    
    ch - ConnectionHandler with live connection
    
    tableName - the name of the JChem structure table
    
    Returns:
    
    the information about the available metrics, or null if no metrics are available
    
    Throws:
    
    java.sql.SQLException - in case it encounters an sql problem.
    
    Since:
    
    JChem 3.2
    
    See Also:
    
    JChemSearchOptions.setDissimilarityMetric(String), MolecularDescriptor.getDefaultDissimilarityMetricThresholds(), MolecularDescriptor.getDissimilarityMetrics(), MolecularDescriptor.getDefaultMetricIndex(), MolecularDescriptor.getMetricName(int)
  - getDissimilarityMetrics
```
public static JChemSearch.DissimilarityMetrics getDissimilarityMetrics(ConnectionHandler ch,
                                                                       java.lang.String tableName,
                                                                       java.lang.String indexedTable,
                                                                       java.lang.String indexedColumn)
                                                                throws java.sql.SQLException
```
    Throws:
    
    java.sql.SQLException
  - getCacheError
```
public java.lang.String getCacheError()
```
    For checking for cache errors. Should be called after the search is finished.
    
    Returns:
    
    the error text, or null in case of normal execution.
    
    Since:
    
    JChem 3.0
  - getQueryStructure
```
public java.lang.String getQueryStructure()
```
    Getter for property queryStructure.
    
    Returns:
    
    Value of property queryStructure.
  - setQueryStructure
```
public void setQueryStructure(java.lang.String queryStructure)
```
    Setter for property queryStructure. The query structure may be in MDL Molfile, Smiles or other format recognized by JChem. If the specified value is null or empty string, then it is interpreted as an empty query structure. (For more information, see the user's guide.)
    NOTE for Daylight formats: If search type is SearchConstants.DUPLICATE, SearchConstants.SUPERSTRUCTURE or SearchConstants.SIMILARITY, treats SMILES/SMARTS input strings as SMILES, otherwise as SMARTS.
    
    Parameters:
    
    queryStructure - New value of property queryStructure.
  - setQueryStructure
```
public void setQueryStructure(Molecule queryMol)
```
    Sets the query structure. If the specified value is null, then it is interpreted as an empty query structure. (For more information, see the user's guide.)
    
    Parameters:
    
    queryMol - the query structure.
  - setQueryFingerprint
```
public void setQueryFingerprint(int[] queryFp)
```
    Currently internal use only.
    
    Parameters:
    
    queryFp - the query fingerprint.
  - getStructureTable
```
public java.lang.String getStructureTable()
```
    Getter for property structureTable.
    
    Returns:
    
    Value of property structureTable.
  - setStructureTable
```
public void setStructureTable(java.lang.String structureTable)
```
    Setter for property structureTable. It specifies the name of the table to be searched for structures containing the query.
    
    Parameters:
    
    structureTable - New value of property structureTable.
  - setFilterIDList
```
public void setFilterIDList(int[] ids)
```
    Specifies a list of cd_id values that are allowed to be included in the result set. Useful for narrowing the result set of the search (e.g., based on the {#getResults() results} of a previous search).
    If the given array is empty, no hits will be returned. Resetting the list is possible by calling the method with null parameter.
    
    Parameters:
    
    ids - the cd_id values in an array
    
    Since:
    
    JChem 3.1
  - setFilterIDNotList
```
public void setFilterIDNotList(int[] ids)
```
    Specifies a list of cd_id values that should not be included in the result set.
    
    Parameters:
    
    ids - the cd_id values in an array
    
    Since:
    
    JChem 3.1.2
  - isInfoToStdError
```
public boolean isInfoToStdError()
```
    Getter for property infoToStdError.
    
    Returns:
    
    Value of property infoToStdError.
  - setInfoToStdError
```
public void setInfoToStdError(boolean infoToStdError)
```
    Setter for property infoToStdError. If set to true, information useful for testing will be written in the servlet server's error log file. (Default: false)
    
    Parameters:
    
    infoToStdError - New value of property infoToStdError.
  - getRunMode
```
public int getRunMode()
```
    Retruns the current run mode.
    
    Returns:
    
    the current run mode.
    
    Since:
    
    JChem 5.0
    
    See Also:
    
    setRunMode(int)
  - setRunMode
```
public void setRunMode(int runMode)
```
    Specifies whether the search is performed synchronously or asychronously and if performed asynchronously, whether the hits can be obtained as soon as they are found or only after the search has completed. The default run mode is RUN_MODE_SYNCH_COMPLETE
    Parameters:
    runMode - Accepted values:
    
    RUN_MODE_SYNCH_COMPLETE
    RUN_MODE_ASYNCH_COMPLETE
    RUN_MODE_ASYNCH_PROGRESSIVE
    Since:
    
    JChem 5.0
  - setSearchOptions
```
public void setSearchOptions(JChemSearchOptions options)
```
    Sets search parameters.
    
    Parameters:
    
    options - search options. Will be copied, modification of the original object does not affect future searches unless this method is called again. The timeout limit of the new options will be applied to further searches.
    
    Since:
    
    JChem 5.0
    
    See Also:
    
    getSearchOptions()
  - getSearchOptions
```
public JChemSearchOptions getSearchOptions()
```
    Returns the SearchOptions object associated with this Search object. The object returned is linked with this Search object, so modifications in the returned SearchOptions object (e.g timeout limit) will change directly the behaviour of this Search object.
    
    Returns:
    
    the current serarch options.
    
    Since:
    
    JChem 5.0
    
    See Also:
    
    setSearchOptions(JChemSearchOptions)
  - getOrder
```
public int getOrder()
```
    Getter for property order.
    
    Returns:
    
    Value of property order.
  - setOrder
```
public void setOrder(int order)
```
    Setter for property order. Determines the order of the result.
    
    Parameters:
    
    order - New value of property order. Acceptable values: NO_ORDERING, ORDERING_BY_ID, ORDERING_BY_ID_OR_SIMILARITY (default), and ORDERING_BY_FILTER_ID_LIST .
    If an "ORDER BY" clause is used in filter query, and no inverse hit list is requested, this setting is ignored, and the "ORDER BY" clause takes precedence.
  - setResultTable
```
public void setResultTable(java.lang.String resultTable)
```
    Setter for property resultTable. Sets the result table that will contain the cd_id of hits. In the case of searching similar structures, the similarity value is also stored in column similarity.
    
    Parameters:
    
    resultTable - New value of property resultTable.
    
    See Also:
    
    setResultTableMode, getResult
  - getResultTableMode
```
public int getResultTableMode()
```
    Getter for property resultTableMode.
    
    Returns:
    
    Value of property resultTableMode.
  - setResultTableMode
```
public void setResultTableMode(int resultTableMode)
```
    Setter for property resultTableMode. It instructs the searcher about the way of handling the result table. Modes:
    - NO_RESULT_TABLE Don't store the results in a table. (Value=0)
    - CREATE_OR_REPLACE_RESULT_TABLE Create a result table. If a table with the same name exists, replace it with the new one. (Value=1)
    - APPEND_TO_RESULT_TABLE Append to an existing result table. Create a new one if it doesn't exist (Value=2)
    (Default: NO_RESULT_TABLE)
    Parameters:
    
    resultTableMode - New value of property resultTableMode.
    
    See Also:
    
    setResultTable
  - getResultTable
```
public java.lang.String getResultTable()
```
    Getter for property resultTable.
    
    Returns:
    
    Value of property resultTable.
  - setNumberOfProcessingThreads
```
public void setNumberOfProcessingThreads(int threads)
```
    Sets the number of processing threads.
    
    Parameters:
    
    threads - the number of threads.
    If set to 0, the number of threads will be equal to the number of logical processors available for the Java Vitual Machine (default).
    NOTE: Under Java Runtime Environment 1.3.1 or older the number of processors cannot be determined. In this case the default number of threads is 16.
    
    Since:
    
    JChem 3.0
  - getNumberOfProcessingThreads
```
public int getNumberOfProcessingThreads()
```
    Gets the number of processing threads.
    
    Returns:
    
    number of threads executed the database search.
  - setThreadPriority
```
public void setThreadPriority(int priority)
```
    Sets the priority of the processing threads. Only effective, if setRunMode(int) is set to either RUN_MODE_ASYNCH_COMPLETE or RUN_MODE_ASYNCH_PROGRESSIVE .
    
    Parameters:
    
    priority - the priority ranging 1 (Thread.MIN_PRIORITY) to 10 (Thread.MAX_PRIORITY).
    The default and recommended setting is 1 ( Thread.MIN_PRIORITY).
    NOTE: if all other threads are not constantly calculating, a low priority setting will not slow down the search process, and it will help user interfaces to be responsive.
    
    Since:
    
    JChem 3.0
  - getResult
```
public int getResult(int index)
```
    Indexed getter for property results. Returns a cd_id value of the found compound specified by index. If result table is generated, getResult throws NullPointerException.
    
    Parameters:
    
    index - Index of the property.
    
    Returns:
    
    Value of the property at index.
    
    See Also:
    
    setResultTable
  - getResultContext
```
public chemaxon.jchem.db.SearchCoreReturnedValue getResultContext()
```
    For internal use only.
    
    Returns:
    
    the result
  - getResults
```
public int[] getResults()
```
    Returns an int array containing the cd_id values of found compounds. If a result table is generated in the database, it returns null.
    
    Returns:
    
    an array of cd_ids
  - getExtraInformation
```
public java.util.List<byte[]> getExtraInformation()
```
    For internal use only.
    
    Returns:
    
    extrainformation for all results
  - cleanResults
```
public void cleanResults()
```
    Cleans stored search results. Can be called to save memory while keeping the JChemSearch object. since JChem 3.0
  - getDissimilarity
```
public float getDissimilarity(int index)
```
    Indexed getter for property dissimilarity. Returns the calculated dissimilarity value of the found compound specified by index and the query structure. If searching has not been finished yet or if a result table is generated, getDissimilarity throws NullPointerException.
    
    Parameters:
    
    index - Index of the property.
    
    Returns:
    
    Value of the property at index.
    
    See Also:
    
    setResultTable
  - getDissimilarity
```
public float[] getDissimilarity()
```
    Getter for dissimilarity results. Returns the calculated dissimilarity values calculated for the last query strucutre. If searching has not been finished yet or if a result table is generated, getDissimilarity throws NullPointerException.
    
    Returns:
    
    the dissimilarity results.
    
    See Also:
    
    setResultTable
  - getProgressMessage
```
public java.lang.String getProgressMessage()
```
    Getter for property progressMessage. It returns a message that shows the state of the search. It can be used for showing the progress of the search.
    
    Returns:
    
    Value of property progressMessage.
  - isMaxResultCountReached
```
public boolean isMaxResultCountReached()
```
    Getter for property maxResultCountReached. It returns true if the search was stopped because the number of hits had reached the maximum value, false otherwise.
    
    Returns:
    
    Value of property maxResultCountReached.
  - isMaxTimeReached
```
public boolean isMaxTimeReached()
```
    Getter for property maxTimeReached. It returns true if the search stopped because the time that passed since the start of the searched had reached the maximum value, false otherwise.
    
    Returns:
    
    Value of property maxTimeReached.
  - getResultCount
```
public int getResultCount()
```
    Getter for property resultCount. It returns the number of hits found by the search.
    
    Returns:
    
    Value of property resultCount.
  - isRunning
```
public boolean isRunning()
```
    Getter for property running.
    
    Returns:
    
    Value of property running.
  - setRunning
```
public void setRunning(boolean run)
                throws java.sql.SQLException,
                       java.io.IOException,
                       DatabaseSearchException
```
    Setter for property running. If it is set to true and the search has not been started yet, then searching is unleashed. If it is set to false and a search is running, the the process will be stopped. (Default: false)
    
    Parameters:
    
    run - New value of property run.
    
    Throws:
    
    java.io.IOException - if an io error is encountered
    
    DatabaseSearchException - if a search error occurs
    
    java.sql.SQLException - if an sql exception is encountered
  - run
```
public void run()
         throws java.io.IOException,
                DatabaseSearchException,
                java.sql.SQLException
```
    Starts searching. Same as setRunning(true)
    
    Throws:
    
    java.io.IOException - if an io error is encountered
    
    DatabaseSearchException - if a search error occurs
    
    java.sql.SQLException - if an sql exception is encountered
  - hasMoreHits
```
public boolean hasMoreHits()
                    throws java.lang.InterruptedException
```
    Used with run mode = RUN_MODE_ASYNCH_PROGRESSIVE.
    Returns true if there are more hits to retrieve with getNextHit() or getAvailableNewHits(int), false otherwise.
    
    Returns:
    
    true if there are more hits to retrieve with getNextHit() or getAvailableNewHits(int), false otherwise.
    
    Throws:
    
    java.lang.InterruptedException - if the thread is interrupted during waiting
    
    Since:
    
    JChem 5.0
  - getNextHit
```
public int getNextHit()
               throws java.lang.InterruptedException
```
    Used with run mode = RUN_MODE_ASYNCH_PROGRESSIVE.
    Returns the next available hit. Waits until at least one is available or throws NoSuchElementException, there are no more hits to return.
    
    Returns:
    
    the next available hit. Waits until at least one is available or throws NoSuchElementException, there are no more hits to return.
    
    Throws:
    
    java.lang.InterruptedException - if the calling thread was interrupted while waiting for the next available hit.
    
    Since:
    
    JChem 5.0
  - getAvailableNewHits
```
public int[] getAvailableNewHits(int minimumHitSize)
                          throws java.lang.InterruptedException,
                                 DatabaseSearchException
```
    Used with run mode = RUN_MODE_ASYNCH_PROGRESSIVE.
    Returns all new hits available at the time of return, but at least minimumHitSize new hits.
    
    Parameters:
    
    minimumHitSize - the minimum number of hits to return, which will be waited if not yet available.
    
    Returns:
    
    all new hits available at the time of return, but at least minimumHitSize new hits.
    
    Throws:
    
    java.lang.InterruptedException - if the calling thread was interrupted while waiting.
    
    DatabaseSearchException - if there was an error during searching.
    
    Since:
    
    JChem 5.0
  - getAvailableExtraInformation
```
public java.util.List<byte[]> getAvailableExtraInformation(int minimumHitSize)
                                                    throws java.lang.InterruptedException,
                                                           DatabaseSearchException
```
    For internal use only.
    
    Parameters:
    
    minimumHitSize - minmum size of hits to collect
    
    Returns:
    
    list of extrainformation
    
    Throws:
    
    java.lang.InterruptedException - if the thread is interrupted during waiting
    
    DatabaseSearchException - if the search ecountered a problem
  - waitUntilSearchComplete
```
public void waitUntilSearchComplete()
                             throws java.lang.InterruptedException
```
    Used with run mode = RUN_MODE_ASYNCH_PROGRESSIVE.
    Waits until after the search has completed.
    
    Throws:
    
    java.lang.InterruptedException - if the calling thread was interrupted while waiting.
    
    Since:
    
    JChem 5.0
  - getScreenedCount
```
public int getScreenedCount()
```
    Gets the number of total screened structures.
    
    Returns:
    
    the number of total screened structures, or -1 if the screened count was not calculated
    
    Since:
    
    JChem 5.6
  - getScreenedCountUnique
```
public int getScreenedCountUnique()
```
    Gets the number of unique screened structures.
    
    Returns:
    
    the number of unique screened structures, or -1 if the screened count was not calculated
    
    Since:
    
    JChem 5.6
  - getScreenedCountTotal
```
public int getScreenedCountTotal()
```
    Gets the number of total screened structures.
    
    Returns:
    
    the number of total screened structures, or -1 if the screened count was not calculated
    
    Since:
    
    JChem 5.6
  - getScreenedResults
```
public int[] getScreenedResults()
```
    Gets the screened unique structures' ids.
    
    Returns:
    
    the screened structures' ids
    
    Since:
    
    JChem 5.6
  - getScreeningTime
```
public long getScreeningTime()
```
    Gets the screening time.
    
    Returns:
    
    the screening time in milliseconds
  - getFirstHitTime
```
public long getFirstHitTime()
```
    Gets the first hit's retrieving time (measured from start of screening).
    
    Returns:
    
    the retrieving time of first hit in milliseconds
  - getSearchTime
```
public long getSearchTime()
```
    Gets the total search time.
    
    Returns:
    
    the search time in milliseconds (includes screening time) If the returned value is -1 then the search time is invalid (e.g search hasn't finished yet).
  - isTargetMarkush
```
public boolean isTargetMarkush()
```
    Gets whether target structure table is a Markush table
    
    Returns:
    
    true if target table is a Markush table, false if not
  - getEnumerationCount
```
public int getEnumerationCount()
```
    Gets the number of enumerates used while screening the database
    
    Returns:
    
    the number of enumerates for the query
  - isLicensed
```
public boolean isLicensed()
```
    Specified by:
    
    isLicensed in interface chemaxon.license.Licensable
  - setLicenseEnvironment
```
public void setLicenseEnvironment(java.lang.String env)
```
    Specified by:
    
    setLicenseEnvironment in interface chemaxon.license.Licensable
  - setProgressMessage
```
public void setProgressMessage(java.lang.String message)
```
  - getCacheLoadTime
```
public long getCacheLoadTime()
                      throws java.lang.IllegalStateException
```
    Gets the time spent with cache loading for the target structure table. Returns
    
    Returns:
    
    duration for the last successful cache loading in milliseconds
    
    Throws:
    
    java.lang.IllegalStateException - if no cache is loaded yet
  - getCacheSizeEstimate
```
public double getCacheSizeEstimate()
                            throws java.lang.IllegalStateException
```
    Returns an estimate of the cache size for the target structure table.
    
    Returns:
    
    estimated size of the cache for the target structure table in MBs
    
    Throws:
    
    java.lang.IllegalStateException - if no cache is loaded yet
  - getCacheSize
```
public double getCacheSize()
                    throws java.lang.IllegalStateException
```
    Returns the size of the cache for the target structure table.
    Warning: the calculation performed by this function may be slow and may consume a large amount of memory. Consider to use getCacheSizeEstimate() to obtain an estimation of the cache size much faster.
    
    Returns:
    
    the size of the cache for the target structure table in MBs
    
    Throws:
    
    java.lang.IllegalStateException - if no cache is loaded yet
  - getHitsAsRgDecomp
```
public RgDecompResults getHitsAsRgDecomp(int[] hits,
                                         int attachmentType)
                                  throws SearchException,
                                         MolFormatException,
                                         java.sql.SQLException
```
    Returns hits as result of r-group decomposition according to the original query. Various results are returned in one RgDecompResults object:
    - scaffold of query (RgDecompResults.getScaffold())
    - number of ligands (RgDecompResults.getLigandsNumber())
    - matched target indexes (RgDecompResults.getIncludedIds())
    - non-matched target indexes (RgDecompResults.getSkippedIds())
    - hits in a Markush molecule ( RgDecompResults.getHitsAsMarkush())
    - r-group decomposed hits (RgDecompResults.getHitsAsRgDecomp())
    - r-group decomposed hits in colored table format ( RgDecompResults.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.
    Parameters:
    
    hits - cd_ids of target structures
    
    attachmentType - Type of visualization of attachment of ligands.
    
    Returns:
    
    An RGDecompResults object.
    
    Throws:
    
    java.sql.SQLException - if an sql exception is encountered
    
    SearchException - Search failure
    
    MolFormatException - if the molecule can't be read
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    RgDecompResults
  - getHitsAsMolecules
```
public Molecule[] getHitsAsMolecules(int[] idList,
                                     HitColoringAndAlignmentOptions options,
                                     java.util.List<java.lang.String> dataFieldNames,
                                     java.util.List<java.lang.Object[]> dataFieldValues)
                              throws java.sql.SQLException,
                                     java.io.IOException,
                                     SearchException,
                                     chemaxon.enumeration.supergraph.SupergraphException,
                                     DatabaseSearchException
```
    Returns hits ready for display. If hit alignment or coloring is needed, the graph search must be repeated for the selected structures to obtain the atom indexes of hits. (Storing this data would consume too much memory for large hit sets) If alignment mode has been set to rotate, and query has 0 dimension, it will be cleaned in 2d. If alignment mode has been set to partial clean, this option will be changed to rotate in this case.
    
    Parameters:
    
    idList - the cd_id list of hits to be retrieved.
    
    options - the options for coloring and alignment. If null the structures will be displayed in their original form.
    
    dataFieldNames - fields of the jchem table that should be fetched together with the structure or null.
    
    dataFieldValues - an empty List required or it can be null. The fetched values will be stored in this object as Object[] elements.
    
    Returns:
    
    the hits as Molecules, colored and aligned if needed. If coloring is specified in case of SearchConstants.SUPERSTRUCTURE search mode, always the query structure is returned, the target subgraph is colored. If there is no hit for a target then the appropriate element of the result array is null.
    
    Throws:
    
    java.sql.SQLException - if the fetched row is deleted
    
    java.io.IOException - if an io error is encountered
    
    SearchException - Search failure during getting colored atoms
    
    chemaxon.enumeration.supergraph.SupergraphException - Search failure during getting colored atoms
    
    DatabaseSearchException - Search failure during getting colored atoms
    
    Since:
    
    JChem 5.0
  - getHitsAsHitDisplayTool
```
public HitDisplayTool getHitsAsHitDisplayTool(int[] idList,
                                              HitColoringAndAlignmentOptions options,
                                              java.util.List<java.lang.String> dataFieldNames,
                                              java.util.List<java.lang.Object[]> dataFieldValues,
                                              java.util.List<? super Molecule> molecules,
                                              java.util.List<byte[]> sources)
                                       throws java.sql.SQLException,
                                              java.io.IOException,
                                              SearchException,
                                              chemaxon.enumeration.supergraph.SupergraphException,
                                              DatabaseSearchException
```
    Gets a HitDisplayTool object from which the results can be retrieved. Parameters are similar to getHitsAsMolecules(int[], HitColoringAndAlignmentOptions, List, List) Additional parameters: molecules, sources Example usage:
```
 List<Molecule> molecules = new ArrayList<Molecule>();
 List<byte[]> sources = new ArrayList<byte[]>();
 HitDisplayTool colorUtil = getHitsAsHitDisplayTool(idList, options,
         dataFieldNames, dataFieldValues, molecules, sources);
 for (int x = 0, n = molecules.size(); x < n; x++) {
     if (molecules.get(x) == null) { // not found
         continue;
     }
     colorUtil.setMoleculeMarkushSourceTarget(molecules.get(x), sources.get(x));
     // fetch the hits using colorUtil.getNextHit() or colorUtil.getHits(int)
     // ...
 }
 
```
    Parameters:
    
    idList - the cd_id list of hits to be retrieved.
    
    options - the options for coloring and alignment. If null the structures will be displayed in their original form.
    
    dataFieldNames - fields of the jchem table that should be fetched together with the structure or null.
    
    dataFieldValues - an empty List required or it can be null. The fetched values will be stored in this object as Object[] elements.
    
    molecules - An empty list that will contain the molecules to be set on the hitdisplaytool object. For not found IDs (e.g. deleted) null is set.
    
    sources - An empty list that will contain the byte array sources to be set on the hitdisplaytool object.
    
    Returns:
    
    the hitDisplayTool object
    
    Throws:
    
    java.sql.SQLException - if an sql error encountered
    
    java.io.IOException - if an io exception is encountered
    
    SearchException - if there was an error during searching.
    
    chemaxon.enumeration.supergraph.SupergraphException - if there was an error during searching.
    
    DatabaseSearchException - if there was an error during searching.
    
    Since:
    
    version 5.4
  - setTargetCollection
```
@Beta
public void setTargetCollection(chemaxon.jchem.base.storage.search.CurrentTargetCollection targetCollection)
```
    For internal use only.
    
    Parameters:
    
    targetCollection - the targetcollection to use
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object

Class JChemSearch

Nested Class Summary

Field Summary

Fields inherited from class chemaxon.util.ErrorHandler

Fields inherited from interface chemaxon.sss.SearchConstants

Fields inherited from interface chemaxon.jchem.db.TableTypeConstants

Constructor Summary

Method Summary

Methods inherited from class chemaxon.util.ErrorHandler

Methods inherited from class java.lang.Object

Field Detail

NO_RESULT_TABLE

CREATE_OR_REPLACE_RESULT_TABLE

APPEND_TO_RESULT_TABLE

NO_ORDERING

ORDERING_BY_ID

ORDERING_BY_ID_OR_SIMILARITY

ORDERING_BY_FILTER_ID_LIST

RUN_MODE_SYNCH_COMPLETE

RUN_MODE_ASYNCH_COMPLETE

RUN_MODE_ASYNCH_PROGRESSIVE

searchOptions

MAXIMAL_ACCEPTEDSEARCHTIME_MINUTES

Constructor Detail

JChemSearch

JChemSearch

JChemSearch

JChemSearch

Method Detail

checkException

getConnectionHandler

setConnectionHandler

getConnection

getDissimilarityMetrics

getDissimilarityMetrics

getCacheError

getQueryStructure

setQueryStructure

setQueryStructure

setQueryFingerprint

getStructureTable

setStructureTable

setFilterIDList

setFilterIDNotList

isInfoToStdError

setInfoToStdError

getRunMode

setRunMode

setSearchOptions

getSearchOptions

getOrder

setOrder

setResultTable

getResultTableMode

setResultTableMode

getResultTable

setNumberOfProcessingThreads

getNumberOfProcessingThreads

setThreadPriority

getResult

getResultContext

getResults

getExtraInformation

cleanResults

getDissimilarity

getDissimilarity

getProgressMessage

isMaxResultCountReached

isMaxTimeReached

getResultCount

isRunning

setRunning

run

hasMoreHits

getNextHit

getAvailableNewHits

getAvailableExtraInformation

waitUntilSearchComplete

getScreenedCount

getScreenedCountUnique