chemaxon.sss.search
Class JChemSearchOptions

java.lang.Object
  chemaxon.sss.search.SearchOptions
      chemaxon.sss.search.JChemSearchOptions

All Implemented Interfaces:

SearchConstants, java.io.Serializable, java.lang.Cloneable

public class JChemSearchOptions
extends SearchOptions
implements java.io.Serializable, SearchConstants, java.lang.Cloneable

Class to encapsulate search parameters used by JChemSearch.

Since:

5.0

Author:

pkovacs, Tamas Csizmazia, Vencel Bors

See Also:

Serialized Form

Field Summary

Fields inherited from class chemaxon.sss.search.SearchOptions

dirty, options, verbose

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_SEARCHTYPE, DISSIMILARITY_PROPERTY_NAME, DUPLICATE, FULL, FULL_FRAGMENT, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, HIT_EXCLUDEDQ, HIT_LP, HIT_MULTICENTER, HIT_NON_R, HIT_ORDERING_NONE, HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST, HIT_R, HIT_R_EMPTY_MATCH, HIT_UNMAPABLE, IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, IMPLICIT_H_MATCHING_ENABLED, IMPLICIT_H_MATCHING_IGNORE, ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, MARKUSH_AROM_FINAL_CHECK, MARKUSH_AROM_NO_FINAL_CHECK, MARKUSH_AROM_OFF, MARKUSH_HIT_INNER, MARKUSH_HIT_ORIGINAL, MARKUSH_MCS, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, NO_ABAS, NO_SCREEN, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, SEARCH_MODE_NAMES, SEARCH_OPTIONS_LENGTH, SIMILARITY, STEREO_DIASTEREOMER, STEREO_ENANTIOMER, STEREO_EXACT, STEREO_IGNORE, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, STEREO_SPECIFIC, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_DEFAULT, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, UNDEF_R_MATCHING_ALL, UNDEF_R_MATCHING_GROUP, UNDEF_R_MATCHING_GROUP_H, UNDEF_R_MATCHING_GROUP_H_EMPTY, UNDEF_R_MATCHING_UNDEF_R, VAGUE_BOND_DEFAULT, VAGUE_BOND_LEVEL_HALF, VAGUE_BOND_LEVEL1, VAGUE_BOND_LEVEL2, VAGUE_BOND_LEVEL3, VAGUE_BOND_LEVEL4, VAGUE_BOND_OFF

Constructor Summary

JChemSearchOptions()
Deprecated. As of release 5.5, replaced by JChemSearchOptions(int)

JChemSearchOptions(int searchType)
Creates a JChemSearchOptions object while setting different search options according to a predefined search type.

Method Summary

java.lang.Object	clone() Makes an identical copy of this SearchObject.
void	clonecopy(SearchOptions other) Copies parameters to other.
void	clonecopyOptions(SearchOptions other) Copies all search options except search type to other.
int	getAbsoluteStereo() Get the absolute stereo matching mode.
java.lang.String	getDescriptorConfig() Get the screening configuration string used for descriptor dissimilarity search
java.lang.String	getDescriptorName() Get the name of descriptor used for descriptor similarity search
java.lang.String	getDissimilarityMetric() Get the property dissimilarity metric property.
java.lang.String	getDissimilarityMetricParameters() Get the parameters of the dissimilarity metric.
float	getDissimilarityThreshold() Get the dissimilarity threshold.
java.lang.String	getFilterQuery() Get the filter query property.
java.lang.String	getFormulaSearchQuery() Get the query set for formula search.
int	getFormulaSearchType() Gets the type set for formula search.
chemaxon.sss.search.options.HaltOnErrorOption	getHaltOnError() Get the current error handling behaviour option.
boolean	getMarkushScreeningType(chemaxon.sss.search.options.MarkushScreeningType type) Internal use only!
MatchCountOptions	getMatchCountOptions() Get the match count options.
int	getMaxResultCount() Get the maximum result count.
long	getMaxTime() Get the maximum time option.
java.lang.String	getOption(java.lang.String name) Returns search option value in string format.
protected java.lang.String[]	getOptionNames()
boolean	isCacheRegistrationNeeded() Only for internal use!
boolean	isDissimilarityThresholdExcluded() Get the dissimilarity threshold exclusion option.
boolean	isMarkushScreeningEnabled() Gets whether screening methods are used for Markush search before ABAS step.
boolean	isOptimizeQueries() Get whether query should be optimized.
boolean	isReturnsNonHits() Indicates if an inverse hit list is to be returned.
void	setAbsoluteStereo(int absoluteStereo) Sets the absolute stereo matching mode.
void	setCacheRegistrationNeeded(boolean value) Only for internal use!
void	setDescriptorConfig(java.lang.String descriptorConfig) Sets the screening configuration string used for descriptor dissimilarity search.
void	setDescriptorName(java.lang.String descriptorName) Sets the name of descriptor used for descriptor similarity search
void	setDissimilarityMetric(java.lang.String dissimilarityMetric) Sets the metric to be used during similarity search.
void	setDissimilarityMetricParameters(java.lang.String dissimilarityMetricParam) Sets the parameters of dissimilarity metric to be used during similarity search.
void	setDissimilarityThreshold(float dissimilarityThreshold) Setter for property dissimilarityThreshold.
void	setDissimilarityThresholdExcluded(boolean thresholdExcluded) Setter for property dissimilarityThresholdExcluded.
void	setFilterQuery(java.lang.String filterQuery) Setter for property filterQuery.
void	setFormulaSearchQuery(java.lang.String formulaSearchQuery) Sets the query for the formula search.
void	setFormulaSearchType(int formulaSearchType) Sets the type for the formula search.
void	setHaltOnError(chemaxon.sss.search.options.HaltOnErrorOption value) Set whether search should stop at first error or log the error and continue search if possible.
void	setMarkushScreeningEnabled(boolean value) Set whether to use screening for Markush search before ABAS step.
void	setMarkushScreeningType(chemaxon.sss.search.options.MarkushScreeningType type, boolean enabled) Internal use only!
void	setMarkushScreeningTypes(java.lang.String types) Internal use only!
void	setMatchCountOptions(MatchCountOptions matchCountOptions) Setter for MatchCountOptions
void	setMaxResultCount(int maxResultCount) Setter for property maxResultCount.
void	setMaxTime(long maxTime) Setter for property maxTime.
void	setOptimizeQueries(boolean value) Sets whether the query molecule should be optimized.
void	setOption(java.lang.String name, java.lang.String value) Sets search options.
void	setReturnsNonHits(boolean returnsNonHits) Determines if the inverse of the hit set should be returned.
java.util.ArrayList<java.lang.String>	toList()

Methods inherited from class chemaxon.sss.search.SearchOptions

addUserComparator, areMonomersTransformed, clearChangesInUserComparators, deleteAllUserComparators, deleteUserComparator, getAllOptionsAsString, getAllOptionsAsString, getAttachedDataMatch, getAttachedDataPrefixes, getBoolean, getChargeMatching, getCheckSpHyb, getChemTermsFilter, getChemTermsFilterConfig, getCompleteHG, getDoubleBondStereoMatchingMode, getExactSpecialAtomMatching, getExhaustiveModeLimit, getHCountMatching, getHitOrdering, getHomologyBroadTranslation, getHomologyNarrowTranslation, getImplicitHMatching, getIsotopeMatching, getRadicalMatching, getRLigandEqualityCheck, getSearchType, getSearchType, getSSRType, getStereoModel, getStereoSearchType, getTautomerSearch, getTimeoutLimit, getTimeoutLimitMilliseconds, getUndefinedRAtom, getUserComparators, getVagueBondLevel, hasChangesInUserComparators, hasUserComparators, isBridgingRAllowed, isCopolymerMatching, isDirty, isEndgroupMatching, isExactBondMatching, isExactFragment, isExactQueryAtomMatching, isFullFragment, isIgnoreAlleneStereo, isIgnoreAxialStereo, isIgnoreCTExceptions, isIgnoreDoubleBondStereo, isIgnoreSynAntiStereo, isIgnoreTetrahedralStereo, isKeepQueryOrder, isMixSgroupMatching, isOrderSensitiveSearch, isPerfectSearchType, isPhaseShiftedMatching, isPolymerMatching, isQHomologyHandling, isReactionUnpairedMapMatching, isSubgraphSearch, isSuperstructureSearch, isTautomerDuplicateFiltering, isThrowExceptionOnTimeout, isUndefinedRAtomMatchingGroup, isValenceMatching, isVerbose, returnOptionString, setAttachedDataMatch, setAttachedDataPrefixes, setBridgingRAllowed, setChargeMatching, setCheckSpHyb, setChemTermsFilter, setChemTermsFilterConfig, setCompleteHG, setCopolymerMatching, setDirty, setDoubleBondStereoMatchingMode, setEndgroupMatching, setExactBondMatching, setExactFragment, setExactQueryAtomMatching, setExactSpecialAtomMatching, setExhaustiveModeLimit, setFullFragment, setHCountMatching, setHitOrdering, setHomologyBroadTranslation, setHomologyNarrowTranslation, setIgnoreAlleneStereo, setIgnoreAxialStereo, setIgnoreCTExceptions, setIgnoreDoubleBondStereo, setIgnoreSynAntiStereo, setIgnoreTetrahedralStereo, setImplicitHMatching, setIsotopeMatching, setKeepQueryOrder, setMixSgroupMatching, setMonomerTransform, setOptions, setOrderSensitiveSearch, setPhaseShiftedMatching, setPolymerMatching, setQHomologyHandling, setRadicalMatching, setReactionUnpairedMapMatching, setRLigandEqualityCheck, setSearchType, setSearchType0, setSSRType, setStereoModel, setStereoSearchType, setSubgraphSearch, setSuperstructureSearch, setTautomerDuplicateFiltering, setTautomerSearch, setThrowExceptionOnTimeout, setTimeoutLimit, setTimeoutLimitMilliseconds, setUndefinedRAtom, setVagueBondLevel, setValenceMatching, setVerbose, toString, toString

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

JChemSearchOptions

@Deprecated
public JChemSearchOptions()

Deprecated. As of release 5.5, replaced by JChemSearchOptions(int)

Default constructor for JChemSearchOptions. Initializes the JChemSearchOptions object with search type SearchConstants.DEFAULT_SEARCHTYPE

See Also:

JChemSearchOptions(int)

JChemSearchOptions

public JChemSearchOptions(int searchType)

Creates a JChemSearchOptions object while setting 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 features allowed), SearchConstants.SIMILARITY, SearchConstants.FULL, SearchConstants.DUPLICATE, SearchConstants.FULL_FRAGMENT and SearchConstants.MARKUSH_MCS.

Parameters:

searchType - the predefined search type

Method Detail

setAbsoluteStereo

public void setAbsoluteStereo(int absoluteStereo)

Sets the absolute stereo matching mode.

Parameters:

absoluteStereo - absolute stereo matching mode
Default value is SearchConstants.ABS_STEREO_TABLE_OPTION.

See Also:

SearchConstants.ABS_STEREO_TABLE_OPTION, SearchConstants.ABS_STEREO_CHIRAL_FLAG, SearchConstants.ABS_STEREO_ALWAYS_ON

getAbsoluteStereo

public int getAbsoluteStereo()

Get the absolute stereo matching mode.

Returns:

selected absolute stereo matching mode.
Default value is SearchConstants.ABS_STEREO_TABLE_OPTION.

See Also:

SearchConstants.ABS_STEREO_TABLE_OPTION, SearchConstants.ABS_STEREO_CHIRAL_FLAG, SearchConstants.ABS_STEREO_ALWAYS_ON, setAbsoluteStereo(int)

setFormulaSearchType

public void setFormulaSearchType(int formulaSearchType)

Sets the type for the formula search.

Parameters:

formulaSearchType - Formula search type.
Default value is FormulaSearch.NONE.

See Also:

getFormulaSearchType(), FormulaSearch.NONE, FormulaSearch.EXACT, FormulaSearch.EXACT_SUBFORMULA, FormulaSearch.SUBFORMULA

getFormulaSearchType

public int getFormulaSearchType()

Gets the type set for formula search.

Returns:

formula search type.
Default value is FormulaSearch.NONE.

See Also:

setFormulaSearchType(int), FormulaSearch.NONE, FormulaSearch.EXACT, FormulaSearch.EXACT_SUBFORMULA, FormulaSearch.SUBFORMULA

setFormulaSearchQuery

public void setFormulaSearchQuery(java.lang.String formulaSearchQuery)

Sets the query for the formula search.

Parameters:

formulaSearchQuery - Formula search query. E.g. "C6-8 H-20 N1"
Default value is null.

See Also:

getFormulaSearchQuery(), setFormulaSearchType(int), FormulaSearch

getFormulaSearchQuery

public java.lang.String getFormulaSearchQuery()

Get the query set for formula search.

Returns:

the chemical formula set for the query.
Default value is null.

See Also:

setFormulaSearchQuery(String), setFormulaSearchType(int), FormulaSearch

getFilterQuery

public java.lang.String getFilterQuery()

Get the filter query property.

Returns:

Value of property filterQuery.
Default value is null.

See Also:

setFilterQuery(String)

setFilterQuery

public void setFilterQuery(java.lang.String filterQuery)

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

    searcOptions.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 JChemSearch.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.
Default value is null.

Since:

JChem 2.3

See Also:

getFilterQuery()

setDissimilarityThreshold

public void setDissimilarityThreshold(float dissimilarityThreshold)

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

Parameters:

dissimilarityThreshold - value of the dissimilarity threshold.
Default value is 0.3.

See Also:

getDissimilarityThreshold()

getDissimilarityThreshold

public float getDissimilarityThreshold()

Get the dissimilarity threshold.

Returns:

Value of property dissimilarityThreshold.
Default value is 0.3.

See Also:

setDissimilarityThreshold(float)

setDissimilarityThresholdExcluded

public void setDissimilarityThresholdExcluded(boolean thresholdExcluded)

Setter for property dissimilarityThresholdExcluded. Determines whether dissimilarity values equaling the threshold value are considered hits or not.

Parameters:

thresholdExcluded - If true, only dissimilarity values less than the threshold value are considered hits. If false, dissimilarity values equaling the threshold value are also considered hits. (Defaults to false.)
Default value is false.

See Also:

isDissimilarityThresholdExcluded()

isDissimilarityThresholdExcluded

public boolean isDissimilarityThresholdExcluded()

Get the dissimilarity threshold exclusion option.

Returns:

the value of the dissimilarity threshold exclusion.
Default value is false.

See Also:

setDissimilarityThresholdExcluded(boolean)

getMaxTime

public long getMaxTime()

Get the maximum time option.

Returns:

maximum time set in milliseconds.
Default value is 0.

See Also:

setMaxTime(long)

setMaxTime

public void setMaxTime(long maxTime)

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.

Parameters:

maxTime - New value of property maxTime.
Default value is 0.

See Also:

getMaxTime()

getMaxResultCount

public int getMaxResultCount()

Get the maximum result count.

Returns:

number of maximum results.
Default value is 0.

See Also:

setMaxResultCount(int)

setMaxResultCount

public void setMaxResultCount(int maxResultCount)
                       throws java.lang.IllegalArgumentException

Setter for property maxResultCount. Limits the number of molecules returned by the search to maxResultCount". If maxResultCount is 0, then there is no limit.

NOTE:

• For non-similarity search the search will stop after the maximum result count is reached. This can save time when there would be too many results.
• For SIMILARITY searches the search will run completely and give back the n most similar results. In this case this option does not mean speedup. The setMaxTime option is recommended instead of maxResultCount, if the goal is saving search time.

Parameters:

maxResultCount - New value of property maxResultCount.
Default value is 0.
An IllegalArgumentException is thrown if maxResultCount was negative number.

Throws:

java.lang.IllegalArgumentException

See Also:

getMaxResultCount()

setReturnsNonHits

public void setReturnsNonHits(boolean returnsNonHits)

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

Parameters:

returnsNonHits - set to true to get non-hit structures. Default is false.
Default value is false.

See Also:

isReturnsNonHits()

isReturnsNonHits

public boolean isReturnsNonHits()

Indicates if an inverse hit list is to be returned.

Returns:

true if inverse hit list it to be returned.
Default value is false.

See Also:

setReturnsNonHits(boolean)

setDissimilarityMetric

public void setDissimilarityMetric(java.lang.String dissimilarityMetric)

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. For reaction tables see @link ReactionFingerprint. For molecule and any tables the default metrics can be replaced by the metrics described in SimilarityCalculatorFactory.create(String).
Default value is null.

See Also:

JChemSearch.getDissimilarityMetrics(chemaxon.util.ConnectionHandler, String), getDissimilarityMetric(), setDissimilarityThreshold(float), getDissimilarityThreshold(), SimilarityCalculatorFactory.create(String), ReactionFingerprint

getDissimilarityMetric

public java.lang.String getDissimilarityMetric()

Get the property dissimilarity metric property.

Returns:

value of dissimilarityMetric
Default value is null.

See Also:

setDissimilarityMetric(String), setDissimilarityThreshold(float), getDissimilarityThreshold()

setDissimilarityMetricParameters

public void setDissimilarityMetricParameters(java.lang.String dissimilarityMetricParam)

Sets the parameters of dissimilarity metric to be used during similarity search.

Parameters:

dissimilarityMetricParam - parameters of the dissimilarity metric e.g. for Tversky: "0.3,0.7" or equivalenly: "queryWeight=0.3,targetWeight=0.7" Specify empty string for no parameters or default parameter. For molecule and any tables the available metrics are the ones described in SimilarityCalculatorFactory.create(String).
Default value is null.

See Also:

getDissimilarityMetricParameters(), JChemSearch.getDissimilarityMetrics(chemaxon.util.ConnectionHandler, String), getDissimilarityMetric(), setDissimilarityThreshold(float), getDissimilarityThreshold(), SimilarityCalculatorFactory.create(String), ReactionFingerprint

getDissimilarityMetricParameters

public java.lang.String getDissimilarityMetricParameters()

Get the parameters of the dissimilarity metric.

Returns:

dissimilarity metric parameters
Default value is null.

See Also:

setDissimilarityMetricParameters(String), setDissimilarityMetric(String), setDissimilarityThreshold(float), getDissimilarityThreshold()

setDescriptorConfig

public void setDescriptorConfig(java.lang.String descriptorConfig)

Sets the screening configuration string used for descriptor dissimilarity search.

Parameters:

descriptorConfig - the configuration string used for dissimilarity search calculation. Default value: null (means default configuration)
Default value is null.

See Also:

getDescriptorConfig(), MDTableHandler.getMDConfig(String, String), setDescriptorName(String), getDescriptorName()

getDescriptorConfig

public java.lang.String getDescriptorConfig()

Get the screening configuration string used for descriptor dissimilarity search

Returns:

the screening configuration string
Default value is null.

See Also:

setDescriptorConfig(String), setDescriptorName(String), getDescriptorName()

setDescriptorName

public void setDescriptorName(java.lang.String descriptorName)

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.
Default value is null.

Since:

JChem 2.0

See Also:

getDescriptorName(), setDescriptorConfig(String), getDescriptorConfig()

getDescriptorName

public java.lang.String getDescriptorName()

Get the name of descriptor used for descriptor similarity search

Returns:

the name of the descriptor
Default value is null.

See Also:

setDescriptorName(String), setDescriptorConfig(String), getDescriptorConfig()

setMatchCountOptions

public void setMatchCountOptions(MatchCountOptions matchCountOptions)

Setter for MatchCountOptions

Parameters:

matchCountOptions - a predefined MatchCountOptions object

See Also:

getMatchCountOptions()

getMatchCountOptions

public MatchCountOptions getMatchCountOptions()

Get the match count options.

Returns:

the matchCountOptions

See Also:

MatchCountOptions, setMatchCountOptions(MatchCountOptions)

isOptimizeQueries

public boolean isOptimizeQueries()

Get whether query should be optimized. (certain atomlists and bondlists are enumerated)

Returns:

true if the query molecule should be optimized
Default value is true.

See Also:

setOptimizeQueries(boolean)

setOptimizeQueries

public void setOptimizeQueries(boolean value)

Sets whether the query molecule should be optimized. (certain atomlists and bondlists are enumerated)

Parameters:

value - true if the query molecule should be optimized.
Default value is true.

See Also:

isOptimizeQueries()

setCacheRegistrationNeeded

public void setCacheRegistrationNeeded(boolean value)

Only for internal use!

isCacheRegistrationNeeded

public boolean isCacheRegistrationNeeded()

Only for internal use!

setMarkushScreeningEnabled

public void setMarkushScreeningEnabled(boolean value)

Set whether to use screening for Markush search before ABAS step. If set to true all known screening methods are enabled, if set to false all known screening methods are disabled.
By default all known Markush screening methods are enabled.

Parameters:

value - markush screening should be used or not.
Default value is true.

See Also:

isMarkushScreeningEnabled(), setMarkushScreeningType(MarkushScreeningType, boolean), MarkushScreeningType

isMarkushScreeningEnabled

public boolean isMarkushScreeningEnabled()

Gets whether screening methods are used for Markush search before ABAS step.

Returns:

true if screening is used, false otherwise.

See Also:

setMarkushScreeningEnabled(boolean), setMarkushScreeningType(MarkushScreeningType, boolean), getMarkushScreeningType(MarkushScreeningType)

setMarkushScreeningType

public void setMarkushScreeningType(chemaxon.sss.search.options.MarkushScreeningType type,
                                    boolean enabled)

Internal use only!
Sets the use of a given Markush screening options. Enables or disables its usage while performing Markush table searches

Parameters:

type - Markush screening option enabled or disabled

enabled - true to enable screening option, false to disable screening option

See Also:

setMarkushScreeningEnabled(boolean), getMarkushScreeningType(MarkushScreeningType), MarkushScreeningType

setMarkushScreeningTypes

public void setMarkushScreeningTypes(java.lang.String types)

Internal use only!
Enables all Markush screening options represented by the given option string.

Parameters:

types - Markush screening options to enable separated by a comma. If null (default), all screening options are enabled. If empty string, no methods are enabled.

getMarkushScreeningType

public boolean getMarkushScreeningType(chemaxon.sss.search.options.MarkushScreeningType type)

Internal use only!
Gets whether a given Markush screening is enabled or disabled

Parameters:

type - Markush screening option to check

Returns:

true if screening is enabled, false if screening method is disabled

See Also:

getMarkushScreeningType(MarkushScreeningType), MarkushScreeningType

setHaltOnError

public void setHaltOnError(chemaxon.sss.search.options.HaltOnErrorOption value)

Set whether search should stop at first error or log the error and continue search if possible.

Parameters:

value - stop at first error or not.
Default value is HaltOnErrorOption.DEFAULT

See Also:

HaltOnErrorOption, getHaltOnError()

getHaltOnError

public chemaxon.sss.search.options.HaltOnErrorOption getHaltOnError()

Get the current error handling behaviour option.

Returns:

the option set for error handling behaviour

See Also:

HaltOnErrorOption, setHaltOnError(HaltOnErrorOption)

setOption

public void setOption(java.lang.String name,
                      java.lang.String value)

Sets search options.

Overrides:

setOption in class SearchOptions

Parameters:

name - Name (case insensitive) of search option (e.g. absoluteStereo).

value - String form (case insensitive) of search parameter value (y, T, false...).
In case of boolean parameters 'true' is acceptable instead of 'y' and 'false' instead of 'n'.

Useable search parameters are all the acceptable values of SearchOptions.setOption(String, String) plus the following ones:

absoluteStereo

expression

maxTime

maxResults or maxHitCount

optimizeQueries

dissimilarityThreshold or simThreshold

orderSensitive

dissimilarityMetric

dissimilarityMetricParameters

returnNonHits

filterQuery

descriptorConfig

descriptorName

matchCountOptions

markushFPScreening

markushScreening

haltOnError

See Also:

getOption(String), SearchOptions.setOption(String, String)

getOption

public java.lang.String getOption(java.lang.String name)

Returns search option value in string format.

Overrides:

getOption in class SearchOptions

Parameters:

name - Name (case insensitive) of search option (e.g. stereoSearch).

Useable search parameters are all the acceptable values of SearchOptions.getOption(String) plus the following ones:

absoluteStereo

expression

maxTime

maxResults or maxHitCount

optimizeQueries

dissimilarityThreshold or simThreshold

orderSensitive

dissimilarityMetric

dissimilarityMetricParameters

returnNonHits

filterQuery

descriptorConfig

descriptorName

matchCountOptions

Returns:

string value of the given option (true --> y, false --> n)

See Also:

setOption(String, String), SearchOptions.getOption(String)

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Makes an identical copy of this SearchObject.

Overrides:

clone in class SearchOptions

Throws:

java.lang.CloneNotSupportedException

clonecopy

public void clonecopy(SearchOptions other)

Copies parameters to other. It copies
- all parameters if other is a JchemSearchOptions object
- only the parameters defined in SearchOptions if it is a SearchOptions or MolSearchOptions object

Overrides:

clonecopy in class SearchOptions

Parameters:

other - search option to overwrite.

clonecopyOptions

public void clonecopyOptions(SearchOptions other)

Description copied from class: SearchOptions

Copies all search options except search type to other.

Overrides:

clonecopyOptions in class SearchOptions

Parameters:

other - search option object to overwrite

toList

public java.util.ArrayList<java.lang.String> toList()

Overrides:

toList in class SearchOptions

Returns:

An arraylist that contains strings of format "optionname:optionvalue". Doesn't contain options that have their default value.

See Also:

SearchOptions.setOptions(String), SearchOptions.toString()

getOptionNames

protected java.lang.String[] getOptionNames()

Overrides:

getOptionNames in class SearchOptions