JChemSearch (JChem API documentation (c)1998-2008 ChemAxon Ltd.)

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chemaxon.jchem.db
Class JChemSearch

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

All Implemented Interfaces:: SearchConstants, java.io.Serializable, TableTypeConstants

public class JChemSearch
extends ErrorHandler
implements java.io.Serializable, SearchConstants, TableTypeConstants

JavaBean for structure searching in structure tables of relational databases.

Example for using the class:

    searcher = new JChemSearch();
    searcher.setQueryStructure("c1cnccc1Cl");
    searcher.setConnectionHandler(conHandler);
    searcher.setStructureTable("cduser.structures");
    
    searchOptions = new JChemSearchOptions();
    searchOptions.setSearchType(JChemSearch.SIMILARITY);
    searchOptions.setDissimilarityThreshold(0.8);
    searchOptions.setMaxResultCount(100);
    searchOptions.setMaxTime(60000);
    searcher.setSearchOptions(searchOptions);
    
    searcher.setRunMode(JChemSearch.RUN_MODE_SYNCH_COMPLETE);
    searcher.run();

This class can be used as an ActiveX component. To avoid problems caused by exceptions in environments where exceptions can not be handled, exceptions are caught and stored using the chemaxon.util.ErrorHandler super class in methods with name like <method name>_NE (where NE means "no exception").

Author:: Ferenc Csizmadia, Szilard Dorant
See Also:: Serialized Form

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

Field Summary
`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`	`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`	`QM_ALWAYS_SMARTS` Deprecated. since JChem 3.2. Will always use the default mode in the future.
`static int`	`QM_ALWAYS_SMILES` Deprecated. since JChem 3.2. Will always use the default mode in the future.
`static int`	`QM_DEFAULT` Deprecated. since JChem 3.2. Will always use the default mode in the future.
`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.

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, PROPERTY_NOT_SET_ERROR, SQL_ERROR, UNIDENTIFIED_ERROR

Fields inherited from interface chemaxon.sss.SearchConstants

ABS_STEREO_ALWAYS_ON, ABS_STEREO_CHIRAL_FLAG, ABS_STEREO_TABLE_OPTION, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SIMILARITY_THRESHOLD, DISSIMILARITY, EXACT, EXACT_FRAGMENT, EXACT_FRAGMENT_OFF, EXACT_FRAGMENT_ON, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, IMPLICIT_H_MATCHING_ENABLED, ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, KEEP_QUERY_ORDER, MARKUSH_AROM_FINAL_CHECK, MARKUSH_AROM_NO_FINAL_CHECK, MARKUSH_AROM_OFF, MARKUSH_DISABLED, MARKUSH_ENABLED, MARKUSH_HIT_ORIGINAL, MARKUSH_HIT_SUPERGRAPH, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, MIX_SGROUP_MATCHING_OFF, MIX_SGROUP_MATCHING_ON, NO_ABAS, NO_SCREEN, OPTION_CHARGE_MATCHING, OPTION_EXACT_FRAGMENT, OPTION_ISOTOPE_MATCHING, OPTION_KEEP_QUERY_ORDER, OPTION_MARKUSH_AROM, OPTION_MARKUSH_ENABLED, OPTION_MARKUSH_HIT, OPTION_MIX_SGROUP_MATCHING, OPTION_RADICAL_MATCHING, OPTION_STEREO_MODEL, OPTION_TAUTOMER_SEARCH, OPTION_VAGUE_BOND, OPTION_VALENCE_MATCHING, PERFECT, R_NODE_PLACEHOLDER, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, REARRANGE_QUERY, REGULAR_SEARCH, SEARCH_MODE_NAMES, SEARCH_OPTIONS_LENGTH, SIMILARITY, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, VAGUE_BOND_DEFAULT, VAGUE_BOND_LEVEL1, VAGUE_BOND_LEVEL2, VAGUE_BOND_LEVEL3, VAGUE_BOND_LEVEL4, VAGUE_BOND_OFF, VALENCE_MATCHING_IGNORE, VALENCE_MATCHING_ON

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
`JChemSearch()` Creates new JChemSearch class
`JChemSearch(java.lang.String indexedTable, java.lang.String indexedColumn)` For internal use only.

Method Summary
`void`	`cleanResults()` Cleans stored search results.
`static void`	`clearCache()` Clears the cache that stores fingerprints and structures.
`int`	`getAbsoluteStereo()` Deprecated. since JChem 5.0. use `JChemSearchOptions.getAbsoluteStereo()` instead
`int[]`	`getAvailableNewHits(int arraySize)` Used with run mode = `RUN_MODE_ASYNCH_PROGRESSIVE`.
`java.util.Hashtable`	`getCachedTables()` Gets the names and sizes of tables currently in the cache.
`java.lang.String`	`getCacheError()` For checking for cache errors.
`java.sql.Connection`	`getConnection()` Getter for property connection.
`ConnectionHandler`	`getConnectionHandler()` Getter for property connectionHandler.
`int`	`getCurrentId()` Getter for property currentId.
`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.
`float`	`getDissimilarityThreshold()` Deprecated. since JChem 5.0. Use `JChemSearchOptions.getDissimilarityThreshold()` instead
`int`	`getDoubleBondStereoMatchingMode()` Deprecated. since JChem 5.0. use `SearchOptions.getDoubleBondStereoMatchingMode()` instead
`java.lang.Throwable`	`getException()` Getter for property exception.
`java.lang.String`	`getFilter()` Deprecated. Since 5.0 Use `SearchOptions.getChemTermsFilter()` instead.
`java.lang.String`	`getFilterConfigFileName()` Deprecated. Since 5.0 Use `SearchOptions.getChemTermsFilterConfig()` instead.
`java.lang.String`	`getFilterQuery()` Deprecated. since JChem 5.0. use `JChemSearchOptions.getFilterQuery()` instead
`java.lang.String`	`getFilterTable()` Deprecated. since 2.3. Please use `setFilterQuery(String)` instead.
`int`	`getHCountMatching()` Deprecated. since JChem 5.0. use `SearchOptions.getHCountMatching()` instead
`Molecule[]`	`getHitsAsMolecules(int[] idList, HitColoringAndAlignmentOptions options, java.util.ArrayList dataFieldNames, java.util.ArrayList dataFieldValues)` Returns hits ready for display.
`int`	`getMaxResultCount()` Deprecated. since JChem 5.0. use `JChemSearchOptions.getMaxResultCount()` instead
`long`	`getMaxTime()` Deprecated. since JChem 5.0. use `JChemSearchOptions.getMaxTime()` instead
`int`	`getNextHit()` Used with run mode = `RUN_MODE_ASYNCH_PROGRESSIVE`.
`int`	`getOption(int option)` Deprecated. since 5.0, use getters in see `getSearchOptions()` see `SearchOptions` see `JChemSearchOptions`
`int`	`getOrder()` Getter for property order.
`java.lang.String`	`getProgressMessage()` Getter for property progressMessage.
`int`	`getQueryMode()` Deprecated. since JChem 3.2. Will always use the default mode in the future.
`java.lang.String`	`getQueryStructure()` Getter for property queryStructure.
`int`	`getResult(int index)` Indexed getter for property results.
`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 screeened structures.
`long`	`getScreeningTime()` Gets the screening time.
`JChemSearchOptions`	`getSearchOptions()` Returns the SearchOptions object associated with this Search object.
`long`	`getSearchTime()` Gets the total search time.
`int`	`getSearchType()` Deprecated. since JChem 5.0 use `SearchOptions.getSearchType()` instead
`float`	`getSimilarity(int index)` Deprecated. Use `getDissimilarity(int)` instead.
`float`	`getSimilarityThreshold()` Deprecated. Use `getDissimilarityThreshold()` instead
`java.lang.String`	`getStructureTable()` Getter for property structureTable.
`boolean`	`getTautomerSearch()` Deprecated. since JChem 5.0. use `SearchOptions.isTautomerSearch()` instead
`int`	`getTimeout()` Gets the current timout setting.
`int`	`getVagueBondLevel()` Deprecated. since JChem 5.0. use `SearchOptions.getVagueBondLevel()` instead
`boolean`	`hasMoreHits()` Used with run mode = `RUN_MODE_ASYNCH_PROGRESSIVE`.
`boolean`	`isDeleteFilterTableWhenReady()` Deprecated. since 2.3. Please use `setFilterQuery(String)` instead.
`boolean`	`isExactChargeMatching()` Deprecated. since JChem 3.2 Please use `SearchOptions.getChargeMatching()` instead.
`boolean`	`isExactIsotopeMatching()` Deprecated. since JChem 3.2 Please use `SearchOptions.getIsotopeMatching()` instead.
`boolean`	`isExactQueryAtomMatching()` Deprecated. since JChem 5.0. use `SearchOptions.isExactQueryAtomMatching()` instead
`boolean`	`isExactRadicalMatching()` Deprecated. since JChem 3.2 Please use `SearchOptions.getRadicalMatching()` instead.
`boolean`	`isExactStereoMatching()` Deprecated. since JChem 5.0. use `SearchOptions.isExactStereoMatching()` instead
`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`	`isStereoSearch()` Deprecated. since JChem 5.0. use `SearchOptions.isStereoSearch()` instead
`boolean`	`isStructureCaching()` Getter for property structureCaching.
`boolean`	`isWaitingForResult()` Deprecated. Replaced by `getRunMode()`.
`void`	`run_NE()` Starts searching.
`void`	`run()` Starts searching.
`void`	`setAbsoluteStereo(int absoluteStereo)` Deprecated. since JChem 5.0. use `JChemSearchOptions.setAbsoluteStereo(int)` instead
`void`	`setCacheExpirationTime(double hours)` Sets the expiration time for the structure cache.
`void`	`setConnection(java.sql.Connection connection)` Deprecated. It is recommended to use `setConnectionHandler` instead.
`void`	`setConnectionHandler(ConnectionHandler connectionHandler)` Setter for property connectionHandler.
`void`	`setDeleteFilterTableWhenReady(boolean deleteFilterTableWhenReady)` Deprecated. since 2.3. Please use `setFilterQuery(String)` instead.
`void`	`setDescriptorConfig(java.lang.String descriptorConfig)` Deprecated. since JChem 5.0 use `JChemSearchOptions.setDescriptorConfig(String)` instead
`void`	`setDescriptorName(java.lang.String descriptorName)` Deprecated. since JChem 5.0 use `JChemSearchOptions.setDescriptorName(String)` instead
`void`	`setDissimilarityMetric(java.lang.String dissimilarityMetric)` Deprecated. since JChem 5.0. Use `JChemSearchOptions.setDissimilarityMetric(String)` instead
`void`	`setDissimilarityThreshold(float dissimilarityThreshold)` Deprecated. since JChem 5.0. Use `JChemSearchOptions.setDissimilarityThreshold(float)` instead
`void`	`setDoubleBondStereoMatchingMode(int mode)` Deprecated. since JChem 5.0. use `SearchOptions.setDoubleBondStereoMatchingMode(int)` instead
`void`	`setExactChargeMatching(boolean exactChargeMatching)` Deprecated. since JChem 3.2 Please use `SearchOptions.setChargeMatching(int)` instead.
`void`	`setExactIsotopeMatching(boolean exactIsotopeMatching)` Deprecated. since JChem 3.2 Please use `SearchOptions.setIsotopeMatching(int)` instead.
`void`	`setExactQueryAtomMatching(boolean exactQueryAtomMatching)` Deprecated. since JChem 5.0. use `SearchOptions.setExactQueryAtomMatching(boolean)` instead
`void`	`setExactRadicalMatching(boolean exactRadicalMatching)` Deprecated. since JChem 3.2 Please use `SearchOptions.setRadicalMatching(int)` instead.
`void`	`setExactStereoMatching(boolean exactStereoMatching)` Deprecated. since JChem 5.0. use `SearchOptions.setExactStereoMatching(boolean)` instead
`void`	`setFilter(java.lang.String filterExpression)` Deprecated. Since 5.0 Use `SearchOptions.setChemTermsFilter(String)` instead.
`void`	`setFilterConfigFileName(java.lang.String fileName)` Deprecated. Since 5.0 Use `SearchOptions.setChemTermsFilterConfig(String)` instead, using the content of the file as parameter.
`void`	`setFilterIDList(int[] ids)` Specifies a list of cd_id's that are allowed to be included in the result set.
`void`	`setFilterIDNotList(int[] ids)` Specifies a list of cd_id's that should not to be included in the result set.
`void`	`setFilterQuery(java.lang.String filterQuery)` Deprecated. since JChem 5.0 use `JChemSearchOptions.setFilterQuery(String)`
`void`	`setFilterTable(java.lang.String filterTable)` Deprecated. since 2.3. Please use `setFilterQuery(String)` instead.
`void`	`setHCountMatching(int HCountMatching)` Deprecated. since JChem 5.0. use `SearchOptions.setHCountMatching(int)` instead
`void`	`setInfoToStdError(boolean infoToStdError)` Setter for property infoToStdError.
`void`	`setLicenseEnvironment(java.lang.String env)`
`void`	`setMatchCountBetween(int hitLimitLow, boolean isLowerLimitIncluded, int hitLimitHigh, boolean isHigherLimitIncluded)` Deprecated. since JChem 5.0 use `JChemSearchOptions.setMatchCountOptions(int, boolean, int, boolean)` instead
`void`	`setMatchCountInRelation(java.lang.String relation, int hitLimit)` Deprecated. since JChem 5.0 use `JChemSearchOptions.setMatchCountOptions(String, int)` instead
`void`	`setMaxCacheSize(int maxCacheSizeMB)` Sets the desired cache memory allocation policy.
`void`	`setMaxResultCount(int maxResultCount)` Deprecated. since JChem 5.0. use `JChemSearchOptions.setMaxResultCount(int)` instead
`void`	`setMaxTime(long maxTime)` Deprecated. since JChem 5.0. use `JChemSearchOptions.setMaxTime(long)` instead
`void`	`setMinNonCachedMemory(int minNonCachedMemoryMB)` Sets the desired cache memory allocation policy.
`void`	`setNumberOfProcessingThreads(int threads)` Sets the number of processing threads.
`void`	`setOption(int option, int value)` Deprecated. since 5.0, use setters in SearchOptions see `getSearchOptions()` see `SearchOptions` see `JChemSearchOptions`
`void`	`setOrder(int order)` Setter for property order.
`void`	`setQueryMode(int queryMode)` Deprecated. since JChem 3.2. Will always use the default mode in the future.
`void`	`setQueryStructure(Molecule queryMol)` Sets the query structure.
`void`	`setQueryStructure(java.lang.String queryStructure)` Setter for property queryStructure.
`void`	`setRegCode(long code)` Sets the registration code.
`void`	`setResultTable(java.lang.String resultTable)` Setter for property resultTable.
`void`	`setResultTableMode(int resultTableMode)` Setter for property resultTableMode.
`void`	`setReturnsNonHits(boolean value)` Deprecated. since JChem 5.0 use `JChemSearchOptions.setReturnsNonHits(boolean)` instead
`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`	`setSearchType(int searchType)` Deprecated. since JChem 5.0 use `SearchOptions.setSearchType(int)` instead
`void`	`setSimilarityThreshold(float similarityThreshold)` Deprecated. Use `instead`
`void`	`setStereoSearch(boolean stereoSearch)` Deprecated. since JChem 5.0. use `SearchOptions.setStereoSearch(boolean)` instead
`void`	`setStructureTable(java.lang.String structureTable)` Setter for property structureTable.
`void`	`setTautomerSearch(boolean value)` Deprecated. since JChem 5.0. use `SearchOptions.setTautomerSearch(boolean)` instead
`void`	`setThreadPriority(int priority)` Sets the priority of the processing threads.
`void`	`setTimeout(int seconds)` Sets the timeout value in seconds.
`void`	`setVagueBondLevel(int level)` Deprecated. since JChem 5.0. use `SearchOptions.setVagueBondLevel(int)` instead
`void`	`setWaitingForResult(boolean waitingForResult)` Deprecated. replaced by `setRunMode(int)`.
`void`	`waitUntilSearchComplete()` Waits until after the search has completed.

Methods inherited from class chemaxon.util.ErrorHandler

checkError, checkException, getError, getErrorMessage, getStackTrace

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, 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

QM_DEFAULT

public static final int QM_DEFAULT

Deprecated. since JChem 3.2. Will always use the default mode in the future.

If search type is SearchConstants.PERFECT, SearchConstants.SUPERSTRUCTURE or SearchConstants.SIMILARITY, treats SMILES/SMARTS input strings as SMILES, otherwise as SMARTS.

See Also:: Constant Field Values

QM_ALWAYS_SMILES

public static final int QM_ALWAYS_SMILES

Deprecated. since JChem 3.2. Will always use the default mode in the future.

Always treats SMILES/SMARTS input strings as SMILES.

See Also:: Constant Field Values

QM_ALWAYS_SMARTS

public static final int QM_ALWAYS_SMARTS

Deprecated. since JChem 3.2. Will always use the default mode in the future.

Always treats SMILES/SMARTS input strings as SMARTS.

See Also:: Constant Field Values

RUN_MODE_SYNCH_COMPLETE

public static int RUN_MODE_SYNCH_COMPLETE

The "runner" methods (run() or setRunning(boolean) return only after all hits has been found. (Corresponds to calling setWaitingForResult(boolean) with true.)

Since:: JChem 5.0

RUN_MODE_ASYNCH_COMPLETE

public static int RUN_MODE_ASYNCH_COMPLETE

Runs the search in a new thread; run() or setRunning(boolean) return immediately. (Corresponds to calling setWaitingForResult(boolean) with false)

Since:: JChem 5.0

RUN_MODE_ASYNCH_PROGRESSIVE

public static 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.
This mode doesn't support

SIMILARITY search, (setSearchType(int)),
MD - search,
Inverse hits (setReturnsNonHits(boolean))
return order other than NO_ORDERING (setOrder(int)).

Since:: JChem 5.0

Constructor Detail

JChemSearch

public JChemSearch()

Creates new JChemSearch class

JChemSearch

public JChemSearch(java.lang.String indexedTable,
                   java.lang.String indexedColumn)

For internal use only.

Method Detail

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 the search returns all molecules.

NOTE for Daylight formats: If search type is SearchConstants.PERFECT, 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 the search returns all molecules.

Parameters:: queryMol - the query structure.

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.

getSearchType

public int getSearchType()

Deprecated. since JChem 5.0 use SearchOptions.getSearchType() instead

Getter for property searchType.

Returns:: Value of property searchType.

setSearchType

public void setSearchType(int searchType)

Deprecated. since JChem 5.0 use SearchOptions.setSearchType(int) instead

Sets different search options according to a predefined search type. For full explanation see JChem Query Guide.
Acceptable values: SearchConstants.NO_SCREEN, SearchConstants.NO_ABAS, SearchConstants.SUBSTRUCTURE (default), SearchConstants.SUPERSTRUCTURE (no query fetures allowed), SearchConstants.SIMILARITY, SearchConstants.EXACT, SearchConstants.EXACT_FRAGMENT and SearchConstants.PERFECT.

WARNING: This method may affect other search settings, therefore if other search options are adjusted, this method should be called first! The following options are affected:

Parameters:: searchType - New value of property searchType.

setOption

public void setOption(int option,
                      int value)

Deprecated. since 5.0, use setters in SearchOptions
see getSearchOptions()

see SearchOptions

see JChemSearchOptions

Setter for some advanced search options.

Parameters:

option - Option identifier to be set.

value - Value of option to be set.
The list of accepted option identifiers:

Since:

JChem 3.2

getOption

public int getOption(int option)

Deprecated. since 5.0, use getters in
see getSearchOptions()

see SearchOptions

see JChemSearchOptions

Getter for some advanced search options.

Parameters:

option - Option identifier.
The list of accepted identifiers:

Returns:

the setting of the given option

Since:

JChem 3.2

getException

public java.lang.Throwable getException()

Getter for property exception. The ancestor's method is overloaded to allow handling exceptions occuring in the searching thread.

Overrides:: getException in class ErrorHandler

Returns:: Value of property exception.

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

getCachedTables

public java.util.Hashtable getCachedTables()

Gets the names and sizes of tables currently in the cache.

Returns:: the names and allocated memory size in bytes as key - value (String - Long) pairs.
Since:: JChem 3.0

getMaxTime

public long getMaxTime()

Deprecated. since JChem 5.0. use JChemSearchOptions.getMaxTime() instead

Getter for property maxTime.

Returns:: Value of property maxTime.

setMaxTime

public void setMaxTime(long maxTime)

Deprecated. since JChem 5.0. use JChemSearchOptions.setMaxTime(long) instead

Setter for property maxTime. Sets the maximum amount of time in milliseconds, which is available for searching. If the time is passed searching stops. If maxTime is 0, then there is no limit. (Default: 0)

Parameters:: maxTime - New value of property maxTime.

getMaxResultCount

public int getMaxResultCount()

Deprecated. since JChem 5.0. use JChemSearchOptions.getMaxResultCount() instead

Getter for property maxResultCount.

Returns:: Value of property maxResultCount.

setMaxResultCount

public void setMaxResultCount(int maxResultCount)

Deprecated. since JChem 5.0. use JChemSearchOptions.setMaxResultCount(int) instead

Setter for property maxResultCount. Limits the number of molecules returned by the search to maxResultCount". This can save time when there would be too many results. If maxResultCount is 0, then there is no limit. (Default: 0)

NOTE: The search will stop after the maximum result count is reached. This is also true for SIMILARITY searches: after the search has found the given number of compounds that falls below the specified similarity threshold, it stops and returns them. To find the n most similar structures in table, please set maxResultCount to 0 (unlimitied, default), and use the first n results with ordering set by setOrder(int) to ORDERING_BY_ID_OR_SIMILARITY.

Parameters:: maxResultCount - New value of property maxResultCount.

getFilterQuery

public java.lang.String getFilterQuery()

Deprecated. since JChem 5.0. use JChemSearchOptions.getFilterQuery() instead

Getter for property filterQuery

Returns:: Value of property filterQuery.
Since:: JChem 2.3

setFilterQuery

public void setFilterQuery(java.lang.String filterQuery)

Deprecated. since JChem 5.0 use JChemSearchOptions.setFilterQuery(String)

Setter for property filterQuery. SQL query for filtering. The result should contain the cd_id values. Example:

    searcher.setFilterQuery("select cd_id from mystructures where cd_id>1000");

If the SELECT contains an "ORDER BY" clause, the results will be ordered accordingly, the setting for setOrder(int) will be ignored, except when an inverse hit list is requested.

NOTE: The filtered cd_id values are cached. Invoke setFilterQuery again before the next search, if the filter needs to be refreshed.

Parameters:: filterQuery - New value of property filterQuery.
Since:: JChem 2.3

setFilterIDList

public void setFilterIDList(int[] ids)

Specifies a list of cd_id's that are allowed to be included in the result set. Useful for narrowing the result of a previous search.

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's that should not to be included in the result set.

Parameters:: ids - the cd_id values in an array
Since:: JChem 3.1.2

getFilterTable

public java.lang.String getFilterTable()

Deprecated. since 2.3. Please use setFilterQuery(String) instead.

Getter for property filterTable.

Returns:: Value of property filterTable.

setFilterTable

public void setFilterTable(java.lang.String filterTable)

Deprecated. since 2.3. Please use setFilterQuery(String) instead.

Setter for property filterTable. Sets a table or a view to be used as a filter. (The structure table and the filter table will be joined by their cd_id columns during the search) This feature can also be used for ordering the results by columns outside the structure table.

Parameters:: filterTable - The name of an optional table used for decreasing the size of the set to be searched. It containes a subset of the id-s in the structure table. (The search will be peformed in the inner join of the structure table and the filter table.)
See Also:: setDeleteFilterTableWhenReady

isDeleteFilterTableWhenReady

public boolean isDeleteFilterTableWhenReady()

Deprecated. since 2.3. Please use setFilterQuery(String) instead.

Getter for property deleteFilterTableWhenReady.

Returns:: Value of property deleteFilterTableWhenReady.

setDeleteFilterTableWhenReady

public void setDeleteFilterTableWhenReady(boolean deleteFilterTableWhenReady)

Deprecated. since 2.3. Please use setFilterQuery(String) instead.

Setter for property deleteFilterTableWhenReady. Determines if the filter table should be dropped after the search. (Default: false)

Parameters:: deleteFilterTableWhenReady - New value of property deleteFilterTableWhenReady.
See Also:: setFilterTable

getSimilarityThreshold

public float getSimilarityThreshold()

Deprecated. Use getDissimilarityThreshold() instead

Getter for property similarityThreshold.

Returns:: 1-dissimilarityThreshold, or zero if dissimilarityThreshold>1.

getDissimilarityThreshold

public float getDissimilarityThreshold()

Deprecated. since JChem 5.0. Use JChemSearchOptions.getDissimilarityThreshold() instead

Getter for property dissimilarityThreshold.

Returns:: Value of property dissimilarityThreshold.

setSimilarityThreshold

public void setSimilarityThreshold(float similarityThreshold)

Deprecated. Use instead

Setter for property similarityThreshold. Sets the threshold for similarity searches. The value has to be between 0 and 1. A greater threshold results less hits that are more similar to the query structure. (Default: 0.7)

Parameters:: similarityThreshold - New value of property similarityThreshold.

setDissimilarityThreshold

public void setDissimilarityThreshold(float dissimilarityThreshold)

Deprecated. since JChem 5.0. Use JChemSearchOptions.setDissimilarityThreshold(float) instead

Setter for property dissimilarityThreshold. Sets the threshold for similarity searches. A lower threshold results less hits that are more similar to the query structure. (Default: 0.3)

Parameters:: dissimilarityThreshold - New value of property dissimilarityThreshold.

setDissimilarityMetric

public void setDissimilarityMetric(java.lang.String dissimilarityMetric)

Deprecated. since JChem 5.0. Use JChemSearchOptions.setDissimilarityMetric(String) instead

Sets the metric to be used during similarity search.

Parameters:: dissimilarityMetric - the name of the metric to be used. Specify null for the default metric.
Since:: JChem 3.2
See Also:: getDissimilarityMetrics(chemaxon.util.ConnectionHandler, String)

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 - ConnaectionHandler 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
Since:: JChem 3.2
See Also:: setDissimilarityMetric(String), MolecularDescriptor.getDefaultDissimilarityMetricThresholds(), MolecularDescriptor.getDissimilarityMetrics(), MolecularDescriptor.getDefaultMetricIndex(), MolecularDescriptor.getMetricName(int), setDissimilarityMetric(String)





setDescriptorName
public void setDescriptorName(java.lang.String descriptorName)

Deprecated. since JChem 5.0 
 use JChemSearchOptions.setDescriptorName(String) instead

Sets the name of descriptor used for descriptor similarity search





Parameters:
descriptorName - the descriptor identifier used for similatiry
 search. If not specified or null, structural fingerprint
 similarity search performed by default.
Since:
  JChem 2.0






setDescriptorConfig
public void setDescriptorConfig(java.lang.String descriptorConfig)

Deprecated. since JChem 5.0 
 use JChemSearchOptions.setDescriptorConfig(String) instead

Sets the configuration used for descriptor dissimilarity search





Parameters:
descriptorConfig - the configuration used for dissimilarity search
 calculation. Default value: null (means default configuration)
Since:
  JChem 2.0.0






isStructureCaching
public boolean isStructureCaching()

Getter for property structureCaching.






Returns:
Value of property structureCaching.





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.





getConnectionHandler
public ConnectionHandler getConnectionHandler()

Getter for property connectionHandler.






Returns:
Value of property connectionHandler.





setConnectionHandler
public void setConnectionHandler(ConnectionHandler connectionHandler)

Setter for property connectionHandler. By setting connectionHandler,
 you also set the connection
 property. The usage of connectionHandler is suggested in
 a JavaBean or  * ActiveX environment.





Parameters:
connectionHandler - New value of property connectionHandler.





getConnection
public java.sql.Connection getConnection()

Getter for property connection.






Returns:
Value of property connection.





setConnection
public void setConnection(java.sql.Connection connection)
                   throws java.beans.PropertyVetoException

Deprecated. It is recommended to use
setConnectionHandler instead.

Setter for property connection. 

 Assumes that the name of the property table is "JChemProperties"





Parameters:
connection - New value of property connection.
Throws:
java.beans.PropertyVetoException





isWaitingForResult
public boolean isWaitingForResult()

Deprecated. Replaced by getRunMode().

Getter for property waitingForResult.






Returns:
Value of property waitingForResult.





setWaitingForResult
public void setWaitingForResult(boolean waitingForResult)

Deprecated. replaced by setRunMode(int).

Setter for property waitingForResult.
 If the property is true, then processing waits until the end of the search.
 Otherwise searching takes place in a new thread
 and run() (or its alternative)
 returns immediately.
 (Default: false)





Parameters:
waitingForResult - New value of property waitingForResult.





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. Accepted
 values:
 
 RUN_MODE_SYNCH_COMPLETE (corresponds to calling
 setWaitingForResult(boolean) with true),
 
RUN_MODE_ASYNCH_COMPLETE (corresponds to calling
 setWaitingForResult(boolean) with false),
 
RUN_MODE_ASYNCH_PROGRESSIVE
 
 
 The default run mode is RUN_MODE_SYNCH_COMPLETE





Parameters:
runMode - 
Since:
  JChem 5.0






setReturnsNonHits
public void setReturnsNonHits(boolean value)

Deprecated. since JChem 5.0 use 
 JChemSearchOptions.setReturnsNonHits(boolean) instead

Determines if the inverse of the hit set should be returned.





Parameters:
value - set to true to get non-hit structures. Default
            is false.
Since:
  JChem 2.2






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.
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 will change 
 directly the behaviour of this Search object.





Since:
  JChem 5.0
See Also:
setSearchOptions(JChemSearchOptions)





getAbsoluteStereo
public int getAbsoluteStereo()

Deprecated. since JChem 5.0. use JChemSearchOptions.getAbsoluteStereo() instead

Returns the absolute stereo matching mode.






Returns:
the mathcing mode.
Since:
  JChem 2.2
See Also:
setAbsoluteStereo(int)





setAbsoluteStereo
public void setAbsoluteStereo(int absoluteStereo)

Deprecated. since JChem 5.0. use JChemSearchOptions.setAbsoluteStereo(int) instead

Sets the absolute stereo matching mode.





Param

chemaxon.jchem.db Class JChemSearch

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

QM_DEFAULT

QM_ALWAYS_SMILES

QM_ALWAYS_SMARTS

RUN_MODE_SYNCH_COMPLETE

RUN_MODE_ASYNCH_COMPLETE

RUN_MODE_ASYNCH_PROGRESSIVE

JChemSearch

JChemSearch

getQueryStructure

setQueryStructure

setQueryStructure

getStructureTable

setStructureTable

getSearchType

setSearchType

setOption

getOption

getException

getCacheError

getCachedTables

getMaxTime

setMaxTime

getMaxResultCount

setMaxResultCount

getFilterQuery

setFilterQuery

setFilterIDList

setFilterIDNotList

getFilterTable

setFilterTable

isDeleteFilterTableWhenReady

setDeleteFilterTableWhenReady

getSimilarityThreshold

getDissimilarityThreshold

setSimilarityThreshold

setDissimilarityThreshold

setDissimilarityMetric

getDissimilarityMetrics

setDescriptorName

setDescriptorConfig

isStructureCaching

isInfoToStdError

setInfoToStdError

getConnectionHandler

setConnectionHandler

getConnection

setConnection

isWaitingForResult

setWaitingForResult

getRunMode

setRunMode

setReturnsNonHits

setSearchOptions

getSearchOptions

getAbsoluteStereo

setAbsoluteStereo

chemaxon.jchem.db
Class JChemSearch