JChemSearch (JChem API documentation (c)1998-2009 ChemAxon Ltd.)

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

chemaxon.jchem.db
Class JChemSearch

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

All Implemented Interfaces:: TableTypeConstants, chemaxon.license.Licensable, SearchConstants, java.io.Serializable

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

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();

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`	`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, ATTACHED_DATA_MATCH_EXACT, ATTACHED_DATA_MATCH_GENERAL, ATTACHED_DATA_MATCH_IGNORE, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SIMILARITY_THRESHOLD, DISSIMILARITY, DUPLICATE, EXACT, EXACT_FRAGMENT, EXACT_FRAGMENT_OFF, EXACT_FRAGMENT_ON, FULL, FULL_FRAGMENT, 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_INNER, MARKUSH_HIT_ORIGINAL, 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, SEARCH_MODE_NAMES, SEARCH_OPTIONS_LENGTH, SIMILARITY, STEREO_DIASTEREOMER, STEREO_EXACT, STEREO_IGNORE, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, STEREO_SPECIFIC, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, UNDEF_R_MATCHING_ALL, UNDEF_R_MATCHING_GROUP, UNDEF_R_MATCHING_UNDEF_R, 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.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, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SIMILARITY_THRESHOLD, DISSIMILARITY, DUPLICATE, EXACT, EXACT_FRAGMENT, EXACT_FRAGMENT_OFF, EXACT_FRAGMENT_ON, FULL, FULL_FRAGMENT, 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_INNER, MARKUSH_HIT_ORIGINAL, 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, SEARCH_MODE_NAMES, SEARCH_OPTIONS_LENGTH, SIMILARITY, STEREO_DIASTEREOMER, STEREO_EXACT, STEREO_IGNORE, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, STEREO_SPECIFIC, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, UNDEF_R_MATCHING_ALL, UNDEF_R_MATCHING_GROUP, UNDEF_R_MATCHING_UNDEF_R, 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
`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.
`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
`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`	`isExactQueryAtomMatching()` Deprecated. since JChem 5.0. use `SearchOptions.isExactQueryAtomMatching()` instead
`boolean`	`isExactStereoMatching()` Deprecated. since JChem 5.0. use `SearchOptions.isExactStereoMatching()` instead
`boolean`	`isInfoToStdError()` Getter for property infoToStdError.
`boolean`	`isLicensed()` Returns information about the licensing of the product.
`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()` Deprecated. since JChem 5.2 use `run()`
`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`	`setConnectionHandler(ConnectionHandler connectionHandler)` Sets the database connection.
`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`	`setExactQueryAtomMatching(boolean exactQueryAtomMatching)` Deprecated. since JChem 5.0. use `SearchOptions.setExactQueryAtomMatching(boolean)` 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`	`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)` Every license can have a modifier environment that's typically an integration environment.
`void`	`setMatchCountBetween(int hitLimitLow, boolean isLowerLimitIncluded, int hitLimitHigh, boolean isHigherLimitIncluded)` Deprecated. since JChem 5.0 use `JChemSearchOptions.setMatchCountOptions(MatchCountOptions)` instead
`void`	`setMatchCountInRelation(java.lang.String relation, int hitLimit)` Deprecated. since JChem 5.0 use `JChemSearchOptions.setMatchCountOptions(MatchCountOptions)` 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`	`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`	`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()` Used with run mode = `RUN_MODE_ASYNCH_PROGRESSIVE`.

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

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.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 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.FULL, SearchConstants.FULL_FRAGMENT and SearchConstants.DUPLICATE.

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

getDissimilarityThreshold

public float getDissimilarityThreshold()

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

Getter for property dissimilarityThreshold.

Returns:: Value of property dissimilarityThreshold.

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)

Sets the database connection.





Parameters:
connectionHandler - a ConnectionHandler object conaining a live connection
 to the database





getConnection
public java.sql.Connection getConnection()

Getter for property connection.






Returns:
Value of property connection.





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.





Parameters:
absoluteStereo - the matching mode, one of the following constants:
 SearchConstants.ABS_STEREO_TABLE_OPTION,
 SearchConstants.ABS_STEREO_CHIRAL_FLAG,
 SearchConstants.ABS_STEREO_ALWAYS_ON,
Since:
  JChem 2.2






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, and
 ORDERING_BY_ID_OR_SIMILARITY
 (default).
 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.





getResultTable
public java.lang.String getResultTable()

Getter for property resultTable.






Returns:
Value of property resultTable.





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





setExactStereoMatching
public void setExactStereoMatching(boolean exactStereoMatching)

Deprecated. since JChem 5.0.
 use SearchOptions.setExactStereoMatching(boolean) instead

Specifies whether stereo information should match exactly - looking for
 query stereo properties in target.





Parameters:
exactStereoMatching - if set to true,
 stereo information must match
 exactly. For example "cis or unspecified" matches only
 "cis or unspecified", but matches neither "cis", "trans" or
 "unspecified". The same is true for chirality.
 Default value is false
Since:
  JChem 3.0






isExactStereoMatching
public boolean isExactStereoMatching()

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

Indicates whether stereo information should match exactly - looking
 for query stereo properties in target.






Returns:
true if stereo information must match exactly. Default value is
 false
Since:
  JChem 3.0






setExactQueryAtomMatching
public void setExactQueryAtomMatching(boolean exactQueryAtomMatching)

Deprecated. since JChem 5.0. use SearchOptions.setExactQueryAtomMatching(boolean) instead

Sets whether exact query atom matching should be used or not.





Since:
  JChem 3.0
See Also:
isExactQueryAtomMatching()





setStereoSearch
public void setStereoSearch(boolean stereoSearch)

Deprecated. since JChem 5.0. use SearchOptions.setStereoSearch(boolean) instead

Specifies, whether stereo search is performed.





Parameters:
stereoSearch - If set to false,
 no stereo information is
 considered during searching.(Default: true)
Since:
  JChem 3.0






isStereoSearch
public boolean isStereoSearch()

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

Indicates, whether stereo search is performed.






Returns:
true, is stereo features are considered during
 the search.
Since:
  Jchem 3.0






isExactQueryAtomMatching
public boolean isExactQueryAtomMatching()

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

Returns whether exact matching of query atom information is set.
  If true, query information (e.g. atom list, any atom, number
  of hydrogens, aromaticity, etc.) in atoms will not be evaluated,
  but rather exact matching of these information is required. It is
  useful for searching in query databases.
  Default is false.





Since:
  JChem 3.0






setHCountMatching
public void setHCountMatching(int HCountMatching)

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

Sets the H count matching mode.





Parameters:
HCountMatching - possible values:
Since:
  JChem 3.0
See Also:
SearchConstants.HCOUNT_MATCHING_AUTO, 
SearchConstants.HCOUNT_MATCHING_EQUAL, 
SearchConstants.HCOUNT_MATCHING_GREATER_OR_EQUAL





getHCountMatching
public int getHCountMatching()

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

Gets the H count matching mode.






Returns:
the H count matching mode.
Since:
  JChem 3.0
See Also:
setHCountMatching(int)





setDoubleBondStereoMatchingMode
public void setDoubleBondStereoMatchingMode(int mode)

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

Sets how double bond cis/trans stereo information should match during
 the search.





Parameters:
mode - The following options can be used:
 
  chemaxon.struc.StereoConstants.DBS_NONE:
     No double bond cis/trans is considered.
 
 chemaxon.struc.StereoConstants.DBS_MARKED:
     (Default) Double bond cis/trans stereo is checked for double bonds designated by the
     stereo search flag only.
 
 chemaxon.struc.StereoConstants.DBS_ALL: All
     double bonds are checked for cis/trans stereo matching.
 
Since:
  JChem 3.0






getDoubleBondStereoMatchingMode
public int getDoubleBondStereoMatchingMode()

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

Getter for property doubleBondStereoMatchingMode.






Returns:
the matching mode relating to double bond stereo.
Since:
  JChem 3.0
See Also:
setDoubleBondStereoMatchingMode(int)





setFilter
public void setFilter(java.lang.String filterExpression)

Deprecated. Since 5.0

 Use SearchOptions.setChemTermsFilter(String) instead.

Sets the filtering expression.





Parameters:
filterExpression - the filtering expression
Since:
  JChem 2.3
See Also:
MolSearch.setFilter(java.lang.String)





getFilter
public java.lang.String getFilter()

Deprecated. Since 5.0

 Use SearchOptions.getChemTermsFilter() instead.

Gets the filtering expression






Returns:
the filtering expression
Since:
  JChem 2.3
See Also:
MolSearch.setFilter(java.lang.String)





setFilterConfigFileName
public void setFilterConfigFileName(java.lang.String fileName)

Deprecated. Since 5.0
 Use SearchOptions.setChemTermsFilterConfig(String) instead,
 using the content of the file as parameter.

Sets the configutration file for Chemical Terms filter.





Parameters:
fileName - the name of the configuration file. Set to
 null for default configuration.
Since:
  JChem 3.0
See Also:
setFilter(String), 
MolSearch.setFilterConfig(java.io.File)





getFilterConfigFileName
public java.lang.String getFilterConfigFileName()

Deprecated. Since 5.0
 Use SearchOptions.getChemTermsFilterConfig() instead.

Gets the configutration file for Chemical Terms filter.






Returns:
the name of the configuration file.
Since:
  JChem 3.0
See Also:
MolSearch.setFilterConfig(java.io.File)





setMatchCountInRelation
public void setMatchCountInRelation(java.lang.String relation,
                                    int hitLimit)

Deprecated. since JChem 5.0
 use JChemSearchOptions.setMatchCountOptions(MatchCountOptions) instead

Sets the allowed match count for substructure search.





Parameters:
relation - The relational operation of the question. This
 operation will be used to compare the number of hits to
 hitLimit. Available values:
 
       "=" - tests equality to hitLimit.
     
  "<" - returns true if the number of found hits is
                less than hitLimit.
     
  "<=" - less than or equality
     
  ">" - greater than
     
  ">=" - greater than or equality
 
 Specifying null disables match count rules.
hitLimit - The limit for the number of hits.
Since:
  JChem 3.0
See Also:
Search.isMatchCountInRelation(String, int), 
setMatchCountBetween(int, boolean, int, boolean)





setMatchCountBetween
public void setMatchCountBetween(int hitLimitLow,
                                 boolean isLowerLimitIncluded,
                                 int hitLimitHigh,
                                 boolean isHigherLimitIncluded)

Deprecated. since JChem 5.0
 use JChemSearchOptions.setMatchCountOptions(MatchCountOptions) instead

Sets rules like "the query must match the target
 between 2 and 5 times (inclusively)" for substructure search.
 Makes this efficiently, which means it only searches
 for the number of hits necessary to decide the question.

 Example:
 
 isMatchCountBetween(2, true, 4, true) - true if the query can be found in
   the target exactly 2, 3 or 4 times.
 
 isMatchCountBetween(2, false, 4, false) - true if the query can be found in
   the target exactly 3 times.





Parameters:
hitLimitLow - The lower limit for the number of hits.
isLowerLimitIncluded - If true, equality is allowed with hitLimitLow.
hitLimitHigh - The upper limit for the number of hits.
 If you pass Integer.MAX_VALUE, it will be treated as infinity.
 (I.e. only the lower limit is applied.)
isHigherLimitIncluded - If true, equality is allowed with hitLimitHigh.
Since:
  JChem 3.0
See Also:
Search.isMatchCountBetween(int, boolean, int, boolean), 
setMatchCountInRelation(String, int)





setTautomerSearch
public void setTautomerSearch(boolean value)

Deprecated. since JChem 5.0.
 use SearchOptions.setTautomerSearch(boolean) instead

Sets if tautomers of the query should be enumerated for search.





Parameters:
value - set to true to enable enumeration of
 the tautomers of the query for search.
 The default is false.
Since:
  JChem 3.2






getTautomerSearch
public boolean getTautomerSearch()

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

Indicates if tautomers of the query should be enumerated for search.






Returns:
wheather tautomers of the query are enumerated for search.
Since:
  JChem 3.2
See Also:
setTautomerSearch(boolean)





setVagueBondLevel
public void setVagueBondLevel(int level)

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

Option for less strict evaluation of query bonds
 (e.g. ambiguious aromaticity).





Parameters:
level - the desired level. See
 SearchConstants.OPTION_VAGUE_BOND
Since:
  JChem 3.2






getVagueBondLevel
public int getVagueBondLevel()

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

Getter for vague bond level.






Returns:
the current vague bond level
Since:
  JChem 3.2
See Also:
setVagueBondLevel(int)





setMaxCacheSize
public void setMaxCacheSize(int maxCacheSizeMB)

Sets the desired cache memory allocation policy.
 
NOTE: the setting takes effect during the very first search in the
 running JVM, after that the call has no effect.
 If set to -1 (auto-detect)  or minFreeMem is not set to 0,
 the program tries to determine the maximum amount of memory available
 for allocation by calling the garbage collector and determinig the
 available memory.

 NOTE: Under Java Runtime Environment 1.3.1 or older the available
 memory size cannot be determined. In this case JChem allocates
 cache for tables until it detects OutOfMemoryError during loading.





Parameters:
maxCacheSizeMB - the maximum amount of memory the cache allowed to
 utitlize in megabytes.
 Set -1 for auto-detection (default):
 maxCacheSize = available_memory - minFreeMem
Since:
  JChem 3.0
See Also:
setMinNonCachedMemory(int)





setMinNonCachedMemory
public void setMinNonCachedMemory(int minNonCachedMemoryMB)

Sets the desired cache memory allocation policy.
 
NOTE: the setting takes effect during the very first search in the
 running JVM, after that the call has no effect.
 If not set to 0 or maxCacheSize is set
 to -1 (auto-detect),
 the program tries to determine the maximum amount of memory available
 for allocation by calling the garbage collector and determinig the
 available memory. 

 NOTE: Under Java Runtime Environment 1.3.1 or older the available
 memory size cannot be determined. In this case JChem allocates
 cache for tables until it detects OutOfMemoryError during loading.





Parameters:
minNonCachedMemoryMB - the minimum amount of memory that
 should be left free for future non-cache allocations in megabytes.
 
Set to 0 if not specified.
 
Set to -1 for auto-detection (default):
 
  10 % of all available space for future allocations
  
Not smaller, than 20 MB
  
Nor bigger, than 100 MB
 
Since:
  JChem 3.0
See Also:
setMaxCacheSize(int)





setCacheExpirationTime
public void setCacheExpirationTime(double hours)

Sets the expiration time for the structure cache.
 At the start of each search all tables are purged from cache that were
 searched before the specified time period. Naturally the currently
 searched table is never purged.





Parameters:
hours - the time in hours. The default value is 96.
 Set to 0 for no expiration.
Since:
  JChem 3.0
See Also:
setMaxCacheSize(int), 
setMinNonCachedMemory(int)





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






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





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.











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.





getCurrentId
public int getCurrentId()

Getter for property currentId.
 It returns the current cd_id of molecule being searched.
 It can be used for showing the progress of the search.






Returns:
Value of property currentId.





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.





setTimeout
public void setTimeout(int seconds)

Sets the timeout value in seconds. If the search is run in a thread,
 isRunning() must be constantly called within the specified time
 interval, otherwise the search stops. Useful if the user no longer
 monitors the search process, e.g. closes the browser window.





Parameters:
seconds - the timeout in seconds. Set to 0 to disable (default).
Since:
  JChem 3.0
See Also:
setRunMode(int)





getTimeout
public int getTimeout()

Gets the current timout setting.






Returns:
the current timeout setting.
Since:
  JChem 3.0
See Also:
setTimeout(int)





isRunning
public boolean isRunning()

Getter for property running.






Returns:
Value of property running.





setRunning
public void setRunning(boolean run)
                throws java.sql.SQLException,
                       MolFormatException,
                       java.io.IOException,
                       DatabaseSearchException,
                       PropertyNotSetException

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.sql.SQLException
MolFormatException
java.io.IOException
DatabaseSearchException
PropertyNotSetException





run
public void run()
         throws java.sql.SQLException,
                MolFormatException,
                java.io.IOException,
                DatabaseSearchException,
                PropertyNotSetException

Starts searching. Same as
 setRunning(true)






Throws:
java.sql.SQLException
MolFormatException
java.io.IOException
DatabaseSearchException
PropertyNotSetException





run_NE
public void run_NE()

Deprecated. since JChem 5.2 use run()

Starts searching. Same as
 setRunning(true), but
 Exceptions are caught and stored.











clearCache
public static void clearCache()

Clears the cache that stores fingerprints and structures.











getScreenedCount
public int getScreenedCount()

Gets the number of screeened structures.






Returns:
the number of screened structures





getScreeningTime
public long getScreeningTime()

Gets the screening time.






Returns:
the screening time in milliseconds





getSearchTime
public long getSearchTime()

Gets the total search time.






Returns:
the search time in milliseconds (includes screening time)





getHitsAsMolecules
public Molecule[] getHitsAsMolecules(int[] idList,
                                     HitColoringAndAlignmentOptions options,
                                     java.util.ArrayList dataFieldNames,
                                     java.util.ArrayList dataFieldValues)
                              throws java.sql.SQLException,
                                     java.io.IOException,
                                     chemaxon.sss.search.SearchException,
                                     chemaxon.enumeration.supergraph.SupergraphException,
                                     PropertyNotSetException,
                                     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 fo 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 ArrayList required or 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.
Throws:
java.sql.SQLException
java.io.IOException
chemaxon.sss.search.SearchException
chemaxon.enumeration.supergraph.SupergraphException
PropertyNotSetException
DatabaseSearchException
Since:

  JChem 5.0






setRegCode
public void setRegCode(long code)

Sets the registration code. FOR INTERNAL USE.
 
 Should be called before the very first search.





Parameters:
code - the code. If not 0, overrides the value
 found in the property table.
Since:
  JChem 3.1






isLicensed
public boolean isLicensed()

Description copied from interface: chemaxon.license.Licensable
Returns information about the licensing of the product.
 Example implementation:
 
 return LicenseHandler.isLicensed( LicenseHandler.MY_IDENTIFIER, licenseEnvironment );
 


Specified by:
isLicensed in interface chemaxon.license.Licensable



Returns:
true if the product is correctly licensed





setLicenseEnvironment
public void setLicenseEnvironment(java.lang.String env)

Description copied from interface: chemaxon.license.Licensable
Every license can have a modifier environment that's typically an integration environment.
 All being Licensable should be prepared to store and show a set environment to the LicenseHandler.
 Example implementation:
  private String licenseEnvironment = "";
 public void setLicenseEnvironment(String env) {
     licenseEnvironment = env;
 }
 


Specified by:
setLicenseEnvironment in interface chemaxon.license.Licensable


Parameters:
env - environment String to be stored and passed to the LicenseHandler in the isLicensed method





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
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 arraySize)
                          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 arraySize new hits.





Parameters:
arraySize - 
Returns:
all new hits available at the time of return, but at
         least arraySize new hits.
Throws:
java.lang.InterruptedException - if the calling thread was interrupted while waiting.
DatabaseSearchException
Since:
  JChem 5.0






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















  
      Overview 
      Package 
    Class 
      Tree 
      Deprecated 
      Index 
      Help 
  









 PREV CLASS 
 NEXT CLASS

  FRAMES   
 NO FRAMES   
 







  SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

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

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

getDissimilarityThreshold

setDissimilarityThreshold

setDissimilarityMetric

getDissimilarityMetrics

setDescriptorName

setDescriptorConfig

isStructureCaching

isInfoToStdError

setInfoToStdError

getConnectionHandler

setConnectionHandler

getConnection

isWaitingForResult

setWaitingForResult

getRunMode

setRunMode

setReturnsNonHits

setSearchOptions

getSearchOptions

getAbsoluteStereo

setAbsoluteStereo

getOrder

setOrder

getResultTable

setResultTable

getResultTableMode

setResultTableMode

setExactStereoMatching

isExactStereoMatching

setExactQueryAtomMatching

setStereoSearch

isStereoSearch

isExactQueryAtomMatching

setHCountMatching

getHCountMatching

setDoubleBondStereoMatchingMode

getDoubleBondStereoMatchingMode

setFilter

getFilter

setFilterConfigFileName

getFilterConfigFileName

setMatchCountInRelation

setMatchCountBetween

setTautomerSearch

getTautomerSearch

setVagueBondLevel

getVagueBondLevel

chemaxon.jchem.db
Class JChemSearch