JChemSearchOptions (JChem Base API documentation (c) 1998-2017 ChemAxon Ltd.)

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

All Implemented Interfaces:

SearchConstants, Serializable, Cloneable
```
public class JChemSearchOptions
extends SearchOptions
implements Serializable, SearchConstants, Cloneable
```
Class to encapsulate search parameters used by JChemSearch.

Since:

5.0

Author:

JChem Base team, Peter Kovacs (pkovacs), Tamas Csizmazia, Edvard Buki, Vencel Bors, Robert Wagner

See Also:

Serialized Form

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

Constructor Summary

Constructors
Constructor and Description
`JChemSearchOptions(int searchType)` Creates a JChemSearchOptions object while setting different search options according to a predefined search type.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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.
`String`	`getDescriptorConfig()` Get the screening configuration string used for descriptor dissimilarity search.
`String`	`getDescriptorName()` Get the name of descriptor used for descriptor similarity search
`String`	`getDissimilarityMetric()` Get the property dissimilarity metric property.
`String`	`getDissimilarityMetricParameters()` Get the parameters of the dissimilarity metric.
`float`	`getDissimilarityThreshold()` Get the dissimilarity threshold.
`String`	`getFilterQuery()` Get the filter query property.
`String`	`getFormulaSearchQuery()` Get the query set for formula search.
`int`	`getFormulaSearchType()` Gets the type set for formula search.
`HaltOnErrorOption`	`getHaltOnError()` Get the current error handling behaviour option.
`boolean`	`getMarkushScreeningType(chemaxon.sss.search.options.MarkushScreeningType type)` Internal use only! Gets whether a given Markush screening is enabled or disabled
`MatchCountOptions`	`getMatchCountOptions()` Get the match count options.
`int`	`getMaxResultCount()` Get the maximum result count.
`int`	`getTimeoutLimitMilliseconds()` The search on a single target timeouts reaching this amount of time.
`int`	`getTotalSearchTimeoutLimitMilliseconds()` The total search on a database table timeouts reaching this amount of time.
`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(String descriptorConfig)` Sets the screening configuration string used for descriptor dissimilarity search.
`void`	`setDescriptorName(String descriptorName)` Sets the name of descriptor used for descriptor similarity search
`void`	`setDissimilarityMetric(String dissimilarityMetric)` Sets the metric to be used during similarity search.
`void`	`setDissimilarityMetricParameters(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(String filterQuery)` Setter for property filterQuery.
`void`	`setFormulaSearchQuery(String formulaSearchQuery)` Sets the query for the formula search.
`void`	`setFormulaSearchType(int formulaSearchType)` Sets the type for the formula search.
`void`	`setHaltOnError(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! Sets the use of a given Markush screening options.
`void`	`setMarkushScreeningTypes(String types)` Internal use only! Enables all Markush screening options represented by the given option string.
`void`	`setMatchCountOptions(MatchCountOptions matchCountOptions)` Setter for MatchCountOptions
`void`	`setMaxResultCount(int maxResultCount)` Sets the maximum number of molecules returned by the search.
`void`	`setOptimizeQueries(boolean value)` Sets whether the query molecule should be optimized.
`void`	`setReturnsNonHits(boolean returnsNonHits)` Determines if the inverse of the hit set should be returned.
`void`	`setTotalSearchTimeoutLimitMilliseconds(int value)` The total search on a database timeouts reaching this amount of time.
`ArrayList<String>`	`toList()`

Methods inherited from class chemaxon.sss.search.SearchOptions
addUserComparator, areMonomersTransformed, clearChangesInUserComparators, deleteAllUserComparators, deleteUserComparator, getAllOptionsAsString, getAllOptionsAsString, getAttachedDataMatch, getAttachedDataPrefixes, getBoolean, getChargeMatching, getCheckSpHyb, getChemTermsFilter, getChemTermsFilterConfig, getChemTermsFilterOption, getCompleteHG, getDoubleBondStereoMatchingMode, getExactSpecialAtomMatching, getExhaustiveModeLimit, getHCountMatching, getHitOrdering, getHomologyBroadTranslation, getHomologyNarrowTranslation, getImplicitHMatching, getIsotopeMatching, getMarkushAromHandling, getOption, getOptionNames, getRadicalMatching, getRLigandEqualityCheck, getSearchType, getSearchType, getSSRType, getStereoModel, getStereoSearchType, getTargetHomologyMatchingMode, getTautomerSearch, getUndefinedRAtom, getUserComparators, getVagueBondLevel, hasChangesInUserComparators, hasUserComparators, isBridgingRAllowed, isCopolymerMatching, isDirty, isEndgroupMatching, isExactBondMatching, isExactQueryAtomMatching, isIgnoreAxialStereo, isIgnoreCumuleneOrRingCisTransStereo, isIgnoreDoubleBondStereo, isIgnoreSynAntiStereo, isIgnoreTetrahedralStereo, isKeepQueryOrder, isMixSgroupMatching, isOrderSensitiveSearch, isPhaseShiftedMatching, isPolymerMatching, isReactionUnpairedMapMatching, isThrowExceptionOnTimeout, isUndefinedRAtomMatchingGroup, isValenceMatching, isVerbose, nonPositiveToInfinite, returnOptionString, setAttachedDataMatch, setAttachedDataPrefixes, setBridgingRAllowed, setChargeMatching, setCheckSpHyb, setChemTermsFilter, setChemTermsFilterConfig, setChemTermsFilterConfig, setChemTermsFilterOption, setCompleteHG, setCopolymerMatching, setDirty, setDoubleBondStereoMatchingMode, setEndgroupMatching, setExactBondMatching, setExactQueryAtomMatching, setExactSpecialAtomMatching, setExhaustiveModeLimit, setHCountMatching, setHitOrdering, setHomologyBroadTranslation, setHomologyNarrowTranslation, setIgnoreAxialStereo, setIgnoreCumuleneOrRingCisTransStereo, setIgnoreDoubleBondStereo, setIgnoreSynAntiStereo, setIgnoreTetrahedralStereo, setImplicitHMatching, setIsotopeMatching, setKeepQueryOrder, setMarkushAromHandling, setMixSgroupMatching, setMonomerTransform, setOption, setOptions, setOrderSensitiveSearch, setPhaseShiftedMatching, setPolymerMatching, setRadicalMatching, setReactionUnpairedMapMatching, setRLigandEqualityCheck, setSSRType, setStereoModel, setStereoSearchType, setTargetHomologyMatchingMode, setTautomerSearch, setThrowExceptionOnTimeout, setTimeoutLimitMilliseconds, setUndefinedRAtom, setUndefinedRAtomUserDefined, setVagueBondLevel, setValenceMatching, setVerbose, toString, toString

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

- Constructor Detail
  - 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 and SearchConstants.FULL_FRAGMENT.
    
    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(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 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 String getFilterQuery()
```
    Get the filter query property.
    
    Returns:
    
    Value of property filterQuery.
    Default value is null.
    
    See Also:
    
    setFilterQuery(String)
  - setFilterQuery
```
public void setFilterQuery(String filterQuery)
```
    Setter for property filterQuery. SQL query for filtering. The result should contain the cd_id values. Example:
```
    searchOptions.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)
  - 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 IllegalArgumentException
```
    Sets the maximum number of molecules returned by the search. If the given parameter is 0, then there is no limit.
    NOTE:
    - In case of non-similarity search, the search process will be stopped when the maximum result count is reached. This can save time when there would be too many results.
    - In case of similarity searches, the full search is performed and the maxResultCount most similar results will be given back. In this case this option does not mean speedup.
    Parameters:
    
    maxResultCount - New value of property maxResultCount. Default value is 0, i.e. there is no limit.
    
    Throws:
    
    IllegalArgumentException - if maxResultCount was negative number.
    
    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(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 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 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(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 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(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 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(String descriptorName)
```
    Sets the name of descriptor used for descriptor similarity search
    
    Parameters:
    
    descriptorName - the descriptor identifier used for similarity 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 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!
    
    Parameters:
    
    value - new value for cacheRegistration
  - isCacheRegistrationNeeded
```
public boolean isCacheRegistrationNeeded()
```
    Only for internal use!
    
    Returns:
    
    current value
  - 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(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(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 HaltOnErrorOption getHaltOnError()
```
    Get the current error handling behaviour option.
    
    Returns:
    
    the option set for error handling behaviour
    
    See Also:
    
    HaltOnErrorOption, setHaltOnError(HaltOnErrorOption)
  - clone
```
public Object clone()
             throws CloneNotSupportedException
```
    Makes an identical copy of this SearchObject.
    
    Overrides:
    
    clone in class SearchOptions
    
    Throws:
    
    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
  - getTimeoutLimitMilliseconds
```
public int getTimeoutLimitMilliseconds()
```
    The search on a single target timeouts reaching this amount of time. If the total timeout limit is less than the single search timeout limit, this function returns with the total timeout limit.
    
    Overrides:
    
    getTimeoutLimitMilliseconds in class SearchOptions
    
    Returns:
    
    The timeout limit in milliseconds.
    Default value is
    
    See Also:
    
    SearchOptions.getTimeoutLimitMilliseconds(), SearchOptions.setTimeoutLimitMilliseconds(int), setTotalSearchTimeoutLimitMilliseconds(int)
  - getTotalSearchTimeoutLimitMilliseconds
```
public final int getTotalSearchTimeoutLimitMilliseconds()
```
    The total search on a database table timeouts reaching this amount of time.
    
    Returns:
    
    The timeout limit in milliseconds.
    
    See Also:
    
    setTotalSearchTimeoutLimitMilliseconds(int), getTimeoutLimitMilliseconds()
  - setTotalSearchTimeoutLimitMilliseconds
```
public void setTotalSearchTimeoutLimitMilliseconds(int value)
```
    The total search on a database timeouts reaching this amount of time. Set it to a negative value if you do not want to the search time out. Note: if SearchOptions.setTimeoutLimitMilliseconds(int) is set the search still can time out.
    If the search is running in asynchronous mode, JChemSearch.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:
    
    value - The time limit to set in milliseconds. Negative values are treated as Integer.MAX_VALUE.
    
    See Also:
    
    getTotalSearchTimeoutLimitMilliseconds(), SearchOptions.setTimeoutLimitMilliseconds(int)
  - toList
```
public ArrayList<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()

Class JChemSearchOptions

Field Summary

Fields inherited from class chemaxon.sss.search.SearchOptions

Fields inherited from interface chemaxon.sss.SearchConstants

Constructor Summary

Method Summary

Methods inherited from class chemaxon.sss.search.SearchOptions

Methods inherited from class java.lang.Object

Constructor Detail

JChemSearchOptions

Method Detail

setAbsoluteStereo

getAbsoluteStereo

setFormulaSearchType

getFormulaSearchType

setFormulaSearchQuery

getFormulaSearchQuery

getFilterQuery

setFilterQuery

setDissimilarityThreshold

getDissimilarityThreshold

setDissimilarityThresholdExcluded

isDissimilarityThresholdExcluded

getMaxResultCount

setMaxResultCount

setReturnsNonHits

isReturnsNonHits

setDissimilarityMetric

getDissimilarityMetric

setDissimilarityMetricParameters

getDissimilarityMetricParameters

setDescriptorConfig

getDescriptorConfig

setDescriptorName

getDescriptorName

setMatchCountOptions

getMatchCountOptions

isOptimizeQueries

setOptimizeQueries

setCacheRegistrationNeeded

isCacheRegistrationNeeded

setMarkushScreeningEnabled

isMarkushScreeningEnabled

setMarkushScreeningType

setMarkushScreeningTypes

getMarkushScreeningType

setHaltOnError

getHaltOnError

clone

clonecopy

clonecopyOptions

getTimeoutLimitMilliseconds

getTotalSearchTimeoutLimitMilliseconds

setTotalSearchTimeoutLimitMilliseconds

toList