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

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_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_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
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 JChemSearchOptions.getFilterQuery() 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() 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() 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 JChemSearchOptions.getFilterQuery() 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 JChemSearchOptions.getFilterQuery() 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) Every license can have a modifier environment that's tipically an integration environment.
void	setMatchCountBetween(int hitLimitLow, boolean isLowerLimitIncluded, int hitLimitHigh, boolean isHigherLimitIncluded) Deprecated. since JChem 5.0 use chemaxon.sss.search.JChemSearchOptions#setMatchCountOption(MatchCountOptions) instead
void	setMatchCountInRelation(java.lang.String relation, int hitLimit) Deprecated. since JChem 5.0 use chemaxon.sss.search.JChemSearchOptions#setMatchCountOption(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	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:

• setExactChargeMatching(boolean)
• setExactIsotopeMatching(boolean)
• setExactQueryAtomMatching(boolean)
• setExactRadicalMatching(boolean)
• setExactStereoMatching(boolean)
• setStereoSearch(boolean)

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:

• SearchConstants.OPTION_KEEP_QUERY_ORDER
• SearchConstants.OPTION_EXACT_FRAGMENT
• SearchConstants.OPTION_TAUTOMER_SEARCH
• SearchConstants.OPTION_ISOTOPE_MATCHING
• SearchConstants.OPTION_CHARGE_MATCHING
• SearchConstants.OPTION_VALENCE_MATCHING
• SearchConstants.OPTION_RADICAL_MATCHING
• SearchConstants.OPTION_VAGUE_BOND
• SearchConstants.OPTION_MIX_SGROUP_MATCHING
• SearchConstants.OPTION_STEREO_MODEL

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:

• SearchConstants.OPTION_KEEP_QUERY_ORDER
• SearchConstants.OPTION_EXACT_FRAGMENT
• SearchConstants.OPTION_TAUTOMER_SEARCH
• SearchConstants.OPTION_ISOTOPE_MATCHING
• SearchConstants.OPTION_CHARGE_MATCHING
• SearchConstants.OPTION_VALENCE_MATCHING
• SearchConstants.OPTION_RADICAL_MATCHING
• SearchConstants.OPTION_VAGUE_BOND
• SearchConstants.OPTION_MIX_SGROUP_MATCHING
• SearchConstants.OPTION_STEREO_MODEL

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 JChemSearchOptions.getFilterQuery() 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 JChemSearchOptions.getFilterQuery() instead.

Getter for property deleteFilterTableWhenReady.

Returns:

Value of property deleteFilterTableWhenReady.

setDeleteFilterTableWhenReady

public void setDeleteFilterTableWhenReady(boolean deleteFilterTableWhenReady)

Deprecated. since 2.3. Please use JChemSearchOptions.getFilterQuery() 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 ste