SearchOptions (Marvin API documentation (c) 1998-2020 ChemAxon Ltd.)

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

All Implemented Interfaces:

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

Direct Known Subclasses:

MolSearchOptions
```
@PublicAPI
public class SearchOptions
extends java.lang.Object
implements SearchConstants, java.lang.Cloneable, java.io.Serializable
```
Class to encapsulate common search parameters.

Since:

5.0

Author:

JChem Base team, Szabolcs Csepregi, Tamas Csizmazia, Robert Wagner, Vencel Bors, Nore Mate, Peter Kovacs (pkovacs84)

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`DEFAULT_TIMEOUT_LIMIT`
`protected boolean`	`dirty` This flag is set to true whenever any of the options change.
`protected int`	`timeoutLimitMilliseconds` The search on a single target timeouts reaching this number of milliseconds.
`boolean`	`verbose` For debugging purposes.

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

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

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addUserComparator(MolComparator mc)` Adds the given user-defined comparator to the search.
`boolean`	`areMonomersTransformed()` Obtain monomer transformation information.
`void`	`clearChangesInUserComparators()` Used in initializing searches.
`java.lang.Object`	`clone()` Makes an identical copy of this SearchObject.
`void`	`clonecopy(SearchOptions other)` Copies all search options to other.
`void`	`clonecopyOptions(SearchOptions other)` Copies all search options except search type to other.
`void`	`deleteAllUserComparators()` Deletes all comparator added by the user.
`void`	`deleteUserComparator(MolComparator mc)` Deletes a given user defined comparator if found.
`java.lang.String`	`getAllOptionsAsString()` Returns a string that - describes the state of the options - can be the input of setOptions(String) - contains all options, including those which have their default value (except dissimilarity threshold in case of similarity search)
`java.lang.String`	`getAllOptionsAsString(java.lang.String sep)` Returns a string that - describes the state of the options - can be the input of setOptions(String) - contains all options, including those which have their default value (except dissimilarity threshold in case of similarity search)
`int`	`getAttachedDataMatch()` Returns whether attached data (in data sgroups) should be used when comparing structures.
`java.lang.String`	`getAttachedDataPrefixes()` Returns the prefixes of the names of those data sgroups that will be used during structure comparison or `null` if all data sgroups should be checked.
`protected static boolean`	`getBoolean(java.lang.String value)` Returns value as a boolean flag.
`int`	`getChargeMatching()` Get the charge matching option value
`boolean`	`getCheckSpHyb()` Get the sp-hybridization state option
`java.lang.String`	`getChemTermsFilter()` Gets the Chemical Terms filtering expression
`java.lang.String`	`getChemTermsFilterConfig()` Gets the configuration string for Chemical Terms filter.
`chemaxon.sss.search.options.ChemTermsFilterOption`	`getChemTermsFilterOption()` FOR INTERNAL USE ONLY Returns the chem term filtering options.
`boolean`	`getCompleteHG()` Retrieves the information if only complete structures are matching on target homology groups.
`int`	`getDoubleBondStereoMatchingMode()` Get the double bond stereo matching mode.
`java.lang.String`	`getExactSpecialAtomMatching()` Get the identifiers of those special atoms that should match exactly during structure comparison.
`int`	`getExhaustiveModeLimit()` Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
`int`	`getHCountMatching()` Get the interpretation of H count in the query.
`int`	`getHitOrdering()` Returns the hit ordering type.
`HomologyTranslationOption`	`getHomologyBroadTranslation()` Get target-side homology matching option.
`HomologyTranslationOption`	`getHomologyNarrowTranslation()` Get query-side homology matching option, which homology atoms can match specific atoms.
`int`	`getImplicitHMatching()` Get option for matching implicit and explicit hydrogens
`int`	`getIsotopeMatching()` Get option for matching isotopes
`MarkushAromaticityHandlingOption`	`getMarkushAromHandling()` Gets the Markush aromatic search behavior.
`java.lang.String`	`getOption(java.lang.String name)` Returns option value in string format.
`java.util.Collection<java.lang.String>`	`getOptionNames()` Returns the name of all available options which can be used to set/get option values with `setOption(String, String)` and `getOption(String)` methods.
`int`	`getRadicalMatching()` Get option for radical matching behaviour.
`boolean`	`getRLigandEqualityCheck()` Returns `true` if undefined R-atoms with the same R-group ID should match the same structure.
`int`	`getSearchType()` Returns the currently set global search operation mode.
`static int`	`getSearchType(java.lang.String searchTypeValue)` Decodes the string representation of the search type and returns the predefined constant value defined in `SearchConstants`.
`SetOfSmallestRingsOption`	`getSSRType()` Gets the type of the set of smallest rings to use
`int`	`getStereoModel()` Get the stereo model option.
`int`	`getStereoSearchType()` Get the stereo search type option.
`TargetHomologyMatchingMode`	`getTargetHomologyMatchingMode()` Returns the target homology matching mode.
`int`	`getTautomerSearch()` Indicates if tautomers of the query should be enumerated for search.
`int`	`getTimeoutLimitMilliseconds()` The search on a single target timeouts reaching this amount of time.
`int`	`getUndefinedRAtom()` Returns undefined R atom matching behaviour mode.
`MolComparator[]`	`getUserComparators()` Returns the user defined comparators.
`int`	`getVagueBondLevel()` Getter for vague bond level.
`boolean`	`hasChangesInUserComparators()` Used in initializing searches.
`boolean`	`hasUserComparators()` Gets whether searcher has user defined comparators.
`boolean`	`isBridgingRAllowed()` Returns `true` if different undefined R-atoms can match the same group of atoms.
`boolean`	`isCopolymerMatching()` Specifies whether matching mode is copolymer.
`boolean`	`isDirty()` Returns the dirty flag.
`boolean`	`isEndgroupMatching()` Get whether polymers end groups must match.
`boolean`	`isExactBondMatching()` Indicates whether bond types should match exactly - looking for query bonds target.
`boolean`	`isExactQueryAtomMatching()` Returns whether exact matching of query atom information is set.
`boolean`	`isIgnoreAxialStereo()` Retrieves if axial stereo is ignored during searching.
`boolean`	`isIgnoreCumuleneOrRingCisTransStereo()` Retrieves if cumulene cis-trans stereo is ignored during searching.
`boolean`	`isIgnoreDoubleBondStereo()` Retrieves if double bond stereo is ignored during searching.
`boolean`	`isIgnoreSynAntiStereo()` Retrieves if syn-anti stereo is ignored during searching.
`boolean`	`isIgnoreTetrahedralStereo()` Retrieves if tetrahedral stereo is ignored during searching.
`boolean`	`isKeepQueryOrder()` Get options for rearranging query atoms for better search performance.
`boolean`	`isMixSgroupMatching()` Get option whether search should consider consider COM, MIX and FOR sgroups during search.
`boolean`	`isOrderSensitiveSearch()` Indicates whether the search is order sensitive
`boolean`	`isPhaseShiftedMatching()` Get option whether phase shifted polymer matches on the original.
`boolean`	`isPolymerMatching()` Get option whether to search consider polymer sgroups during search.
`boolean`	`isReactionUnpairedMapMatching()` Get whether unpaired(orphan or widow) atom maps can match any atom.
`boolean`	`isThrowExceptionOnTimeout()` It search should throw exception upon timeout.
`boolean`	`isUndefinedRAtomMatchingGroup()` Gets whether undefined R atom matches group of atoms.
`boolean`	`isValenceMatching()` Get the valence matching option
`boolean`	`isVerbose()` For debugging purposes only.
`protected static int`	`nonPositiveToInfinite(int value)`
`protected java.lang.String`	`returnOptionString(boolean value)`
`void`	`setAttachedDataMatch(int value)` Sets whether attached data (in data sgroups) should be used when comparing structures.
`void`	`setAttachedDataPrefixes(java.lang.String value)` Sets the prefixes of the names of those data sgroups that will be used during structure comparison.
`void`	`setBridgingRAllowed(boolean value)` Sets whether different undefined R-atoms can match the same group of atoms.
`void`	`setChargeMatching(int value)` Set charge matching behaviour.
`void`	`setCheckSpHyb(boolean checkSp)` Sets whether the sp-hybridization state of the atoms should be considered.
`void`	`setChemTermsFilter(java.lang.String value)` Sets the Chemical Terms filtering expression.
`void`	`setChemTermsFilterConfig(java.io.File file)` Sets the configuration file for Chemical Terms filter.
`void`	`setChemTermsFilterConfig(java.lang.String value)` Sets the configuration string for Chemical Terms filter.
`void`	`setChemTermsFilterOption(chemaxon.sss.search.options.ChemTermsFilterOption chemTermsFilterOption)` FOR INTERNAL USE ONLY.
`void`	`setCompleteHG(boolean completeStr)` Sets if only complete structures should match on homology groups.
`void`	`setCopolymerMatching(boolean value)` Adjusts copolymer matching mode.
`void`	`setDirty(boolean v)` Sets or clears the dirty flag.
`void`	`setDoubleBondStereoMatchingMode(int value)` Sets how double bond cis/trans stereo information should match during the search.
`void`	`setEndgroupMatching(boolean value)` Adjusts polymer end group matching.
`void`	`setExactBondMatching(boolean value)` Specifies whether bond types should match exactly - looking for query bonds target.
`void`	`setExactQueryAtomMatching(boolean isExact)` Sets whether exact query atom matching should be used or not.
`void`	`setExactSpecialAtomMatching(java.lang.String value)` Sets the identifiers of those special atoms that should match exactly during structure comparison.
`void`	`setExhaustiveModeLimit(int value)` Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
`void`	`setHCountMatching(int value)` Sets the H count matching mode.
`void`	`setHitOrdering(int value)` Sets the hit ordering type.
`void`	`setHomologyBroadTranslation(HomologyTranslationOption value)` Adjusts for which query atoms broad translation on target homology groups is allowed.
`void`	`setHomologyNarrowTranslation(HomologyTranslationOption value)` Adjusts for which query homology atoms narrow translation on target specific atoms is allowed.
`void`	`setIgnoreAxialStereo(boolean value)` Sets ignoring axial stereo information during serching.
`void`	`setIgnoreCumuleneOrRingCisTransStereo(boolean value)` Sets ignoring cumulene cis-trans stereo information during serching.
`void`	`setIgnoreDoubleBondStereo(boolean value)` Sets ignoring double bond stereo information during serching.
`void`	`setIgnoreSynAntiStereo(boolean value)` Sets ignoring syn-anti stereo information during serching.
`void`	`setIgnoreTetrahedralStereo(boolean value)` Sets ignoring tetrahedral stereo information during serching.
`void`	`setImplicitHMatching(int value)` Set option for matching implicit and explicit hydrogens.
`void`	`setIsotopeMatching(int value)` Set the isotope matching mode.
`void`	`setKeepQueryOrder(boolean value)` Set option for rearranging query atoms to increase search performance.
`void`	`setMarkushAromHandling(MarkushAromaticityHandlingOption value)` Set handling of Markush aromatization information (ambiguous aromatic rings) during Markush search
`void`	`setMixSgroupMatching(boolean value)` Set options for mixed S-group matching.
`void`	`setMonomerTransform(boolean value)` Adjusts if monomers should be transformed to structural repeating units if the monomer is homolopolimerizable.
`void`	`setOption(java.lang.String name, java.lang.String value)` Sets search options.
`void`	`setOptions(java.lang.String optionString)` Sets search options.
`void`	`setOrderSensitiveSearch(boolean value)` Specifies whether the same set of target atoms found in a different order should be considered as a different hit.
`void`	`setPhaseShiftedMatching(boolean value)` Adjusts if the phase shifted polymer should match on the original.
`void`	`setPolymerMatching(boolean value)` Adjust polymer matching.
`void`	`setRadicalMatching(int value)` Set the radical matching mode.
`void`	`setReactionUnpairedMapMatching(boolean value)` Set option for matching unpaired(orphan or widow) atom maps to any atom.
`void`	`setRLigandEqualityCheck(boolean value)` Sets whether undefined R-atoms with the same R-group ID should match the same structure.
`void`	`setSSRType(SetOfSmallestRingsOption value)` Sets which type of set of smallest rings to use for property calculations
`void`	`setStereoModel(int value)` Set stereo model option.
`void`	`setStereoSearchType(int value)` Specifies the way stereo information is considered during searching.
`void`	`setTargetHomologyMatchingMode(TargetHomologyMatchingMode mode)` Sets the target homology matching mode option.
`void`	`setTautomerSearch(int value)` Sets if tautomers of the query should be enumerated for search.
`void`	`setThrowExceptionOnTimeout(boolean value)` Sets if search should throw exception upon timeout.
`void`	`setTimeoutLimitMilliseconds(int value)` The search on a single target timeouts reaching this amount of time.
`void`	`setUndefinedRAtom(int value)` Sets the matching behaviour of an undefined R atom in the query.
`void`	`setUndefinedRAtomUserDefined(boolean undefinedRAtomUserDefined)` For internal use only!
`void`	`setVagueBondLevel(int value)` Option for less strict evaluation of query bonds (e.g.
`void`	`setValenceMatching(boolean value)` Set valence check option.
`void`	`setVerbose(boolean verboseP)` For debugging purposes only.
`java.util.ArrayList<java.lang.String>`	`toList()`
`java.lang.String`	`toString()` Returns a string that - describes the state of the options - can be the input of setOptions(String) - doesn't contain options that have their default value (except dissimilarity threshold in case of similarity search)
`java.lang.String`	`toString(java.lang.String sep)` Returns a string that - describes the state of the options - can be the input of setOptions(String) - doesn't contain options that have their default value (except dissimilarity threshold in case of similarity search)

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

- Field Detail
  - dirty
```
protected boolean dirty
```
    This flag is set to true whenever any of the options change. It can be used by Search objects to check whether options changed since the previous initialization. (They set the dirty flag to false during their own initialization.)
  - verbose
```
public boolean verbose
```
    For debugging purposes. Public, because it does not count for the dirty flag.
  - DEFAULT_TIMEOUT_LIMIT
```
public static final int DEFAULT_TIMEOUT_LIMIT
```
    See Also:
    
    Constant Field Values
  - timeoutLimitMilliseconds
```
protected int timeoutLimitMilliseconds
```
    The search on a single target timeouts reaching this number of milliseconds.
- Constructor Detail
  - SearchOptions
```
public SearchOptions(int searchType)
```
    Creates a SearchOptions object while setting different search options according to a predefined search type. For full explanation see JChem Query Guide.
    Acceptable values:
    - SearchConstants.SUBSTRUCTURE (default);
    - SearchConstants.FULL;
    - SearchConstants.FULL_FRAGMENT;
    - SearchConstants.DUPLICATE;
    - SearchConstants.SUPERSTRUCTURE (no query features allowed);
    - SearchConstants.SIMILARITY;
    - SearchConstants.NO_SCREEN; and
    - SearchConstants.NO_ABAS.
    Parameters:
    
    searchType - the predefined search type
- Method Detail
  - isExactQueryAtomMatching
```
public final boolean isExactQueryAtomMatching()
```
    Returns whether exact matching of query atom information is set. If true, query information (e.g. atom list, any atom, number of hydrogens, aromaticity, etc.) in atoms will not be evaluated, but rather exact matching of these information is required. It is useful for searching in query databases.
    
    Returns:
    
    true if query information (eg atom list, any atom, number of hydrogens, aromaticity, etc) in atoms will not be evaluated, but rather exact matching of these information is required. It is useful for searching in query databases.
    Default value is false.
    
    Since:
    
    JChem 2.2
  - setExactQueryAtomMatching
```
public void setExactQueryAtomMatching(boolean isExact)
```
    Sets whether exact query atom matching should be used or not. See isExactQueryAtomMatching().
    
    Parameters:
    
    isExact - If true, query information (eg atom list, any atom, number of hydrogens, aromaticity, etc) in atoms will not be evaluated, but rather exact matching of these information is required. It is useful for searching in query databases.
    Default value is false except in case of duplicate search.
    
    Since:
    
    JChem 2.2
  - setDoubleBondStereoMatchingMode
```
public void setDoubleBondStereoMatchingMode(int value)
```
    Sets how double bond cis/trans stereo information should match during the search.
    Parameters:
    value - The following options can be used:
    Default value is StereoConstants.DBS_MARKED
    
    StereoConstants.DBS_NONE: No double bond cis/trans is considered.
    StereoConstants.DBS_MARKED: (Default) Double bond cis/trans stereo is checked for double bonds designated by the stereo search flag only.
    StereoConstants.DBS_ALL: All double bonds are checked for cis/trans stereo matching.
    Replaces setStereoCareChecking(boolean)
    Since:
    
    JChem 2.2
    
    See Also:
    
    getDoubleBondStereoMatchingMode(), Stereochemistry documentation
  - getDoubleBondStereoMatchingMode
```
public final int getDoubleBondStereoMatchingMode()
```
    Get the double bond stereo matching mode.
    
    Returns:
    
    the matching mode relating to double bond stereo.
    Default value is chemaxon.struc.StereoConstants.DBS_MARKED
    
    Since:
    
    JChem 2.2
    
    See Also:
    
    setDoubleBondStereoMatchingMode(int), StereoConstants.DBS_ALL, StereoConstants.DBS_MARKED, StereoConstants.DBS_NONE, Stereochemistry documentation
  - getSearchType
```
public final int getSearchType()
```
    Returns the currently set global search operation mode.
    
    Returns:
    
    the search type.
    
    Since:
    
    JChem 3.2
    
    See Also:
    
    SearchOptions(int), SearchConstants.SUBSTRUCTURE, SearchConstants.SUPERSTRUCTURE, SearchConstants.FULL, SearchConstants.FULL_FRAGMENT, SearchConstants.DUPLICATE, SearchConstants.SIMILARITY
  - getHCountMatching
```
public final int getHCountMatching()
```
    Get the interpretation of H count in the query.
    
    Returns:
    
    the H count matching mode. (Default is HCOUNT_MATCHING_AUTO.)
    Default value is SearchConstants.HCOUNT_MATCHING_AUTO.
    
    See Also:
    
    setHCountMatching(int), SearchConstants.HCOUNT_MATCHING_AUTO, SearchConstants.HCOUNT_MATCHING_EQUAL, SearchConstants.HCOUNT_MATCHING_GREATER_OR_EQUAL
  - setHCountMatching
```
public void setHCountMatching(int value)
```
    Sets the H count matching mode.
    
    Parameters:
    
    value - possible values:
    Default value is SearchConstants.HCOUNT_MATCHING_AUTO.
    
    See Also:
    
    SearchConstants.HCOUNT_MATCHING_AUTO, SearchConstants.HCOUNT_MATCHING_EQUAL, SearchConstants.HCOUNT_MATCHING_GREATER_OR_EQUAL
  - isVerbose
```
public final boolean isVerbose()
```
    For debugging purposes only.
    
    Returns:
    
    true if debug information is displayed during search.
    Default value is false.
  - setVerbose
```
public void setVerbose(boolean verboseP)
```
    For debugging purposes only.
    
    Parameters:
    
    verboseP - if true more detailed information is sent to the output
    Default value is false.
  - getSearchType
```
public static int getSearchType(java.lang.String searchTypeValue)
```
    Decodes the string representation of the search type and returns the predefined constant value defined in SearchConstants.
    
    Parameters:
    
    searchTypeValue - search type represented as string
    
    Returns:
    
    the identifier for the given search type
  - setOptions
```
public void setOptions(java.lang.String optionString)
```
    Sets search options.
    Parameters:
    optionString - Can set multiple options. Option names and values (all case insensitive) are defined in JChem Query Guide: summary of search options. Name and value of an option should be separated by ":", and different pairs of names/values by spaces. Instead of spaces an alternative option separator string (even more than 1 character) can be specified at the beginning of optionString by the syntax "sep='separator string' ...". After 'separator string' there must be at least 1 space character!)
    E.g.
    
    setOptions("HCountMatching:E")
    
    setOptions(" hcountmatching:g keepqueryorder:y")
    
    setOptions("sep=*-* hcoUntmatchInG:A*-*KeEpQueryorder:False")
    See Also:
    
    setOption(String,String)
  - setOrderSensitiveSearch
```
public void setOrderSensitiveSearch(boolean value)
```
    Specifies whether the same set of target atoms found in a different order should be considered as a different hit.
    For example the 3-atom query molecule fits 2 positions on the target:
    Hit 1: [1;3;5]
    Hit 2: [5;3;1]
    If orderSensitiveSearch is true, both cases are returned, otherwise only one of them (the one found first).
    
    Parameters:
    
    value - set this to true to get results in every possible order
    Default value is false.
  - isOrderSensitiveSearch
```
public final boolean isOrderSensitiveSearch()
```
    Indicates whether the search is order sensitive
    
    Returns:
    
    true if hits are returned in every possible order
    Default value is false.
    
    See Also:
    
    setOrderSensitiveSearch(boolean)
  - isExactBondMatching
```
public final boolean isExactBondMatching()
```
    Indicates whether bond types should match exactly - looking for query bonds target.
    
    Returns:
    
    true if bond types must match exactly.
    Default value depends on search type.
  - setExactBondMatching
```
public void setExactBondMatching(boolean value)
```
    Specifies whether bond types should match exactly - looking for query bonds target.
    
    Parameters:
    
    value - if set to true, bond types must match exactly. For example "single or double" matches only "single or double", but matches neither "single" or "double".
    Default value is false except in case of duplicate search.
  - setVagueBondLevel
```
public void setVagueBondLevel(int value)
```
    Option for less strict evaluation of query bonds (e.g. ambiguous aromaticity).
    
    Parameters:
    
    value - the desired vague bond level
    Default value is SearchConstants.VAGUE_BOND_LEVEL_HALF.
    
    Since:
    
    JChem 5.0
    
    See Also:
    
    SearchConstants.VAGUE_BOND_OFF, SearchConstants.VAGUE_BOND_LEVEL_HALF, SearchConstants.VAGUE_BOND_LEVEL1, SearchConstants.VAGUE_BOND_LEVEL2, SearchConstants.VAGUE_BOND_LEVEL3, SearchConstants.VAGUE_BOND_LEVEL4, getVagueBondLevel(), Vague bond level documenation
  - getVagueBondLevel
```
public final int getVagueBondLevel()
```
    Getter for vague bond level.
    
    Returns:
    
    the current vague bond level
    Default value is SearchConstants.VAGUE_BOND_LEVEL_HALF.
    
    Since:
    
    JChem 5.0
    
    See Also:
    
    SearchConstants.VAGUE_BOND_LEVEL_HALF, SearchConstants.VAGUE_BOND_LEVEL1, SearchConstants.VAGUE_BOND_LEVEL2, SearchConstants.VAGUE_BOND_LEVEL3, SearchConstants.VAGUE_BOND_LEVEL4, setVagueBondLevel(int), Vague bond level documenation
  - setCompleteHG
```
public void setCompleteHG(boolean completeStr)
```
    Sets if only complete structures should match on homology groups. If set to false than substructures which don't form an entire homology group can also match (e.g. carbon chain on a cycloalkyl).
    
    Parameters:
    
    completeStr - if true only complete structures are accepted, if false all substructures.
    Default value is true.
    
    See Also:
    
    getCompleteHG()
  - getCompleteHG
```
public final boolean getCompleteHG()
```
    Retrieves the information if only complete structures are matching on target homology groups.
    
    Returns:
    
    true if only complete structures are matching, false otherwise.
    Default value is true.
    
    See Also:
    
    setCompleteHG(boolean)
  - hasChangesInUserComparators
```
public final boolean hasChangesInUserComparators()
```
    Used in initializing searches. Specifies whether changes occurred in the user defined comparators.
    
    Returns:
    
    true if there is any changes in user-defined comparators. After initializing the search, the change flag is cleared.
    
    See Also:
    
    getUserComparators(), addUserComparator(MolComparator), deleteUserComparator(MolComparator), deleteAllUserComparators(), MolComparator
  - clearChangesInUserComparators
```
public final void clearChangesInUserComparators()
```
    Used in initializing searches. Clears the change flag of user-defined MolComparators.
    
    See Also:
    
    getUserComparators(), addUserComparator(MolComparator), deleteUserComparator(MolComparator), deleteAllUserComparators(), MolComparator
  - hasUserComparators
```
public final boolean hasUserComparators()
```
    Gets whether searcher has user defined comparators.
    
    Returns:
    
    true, if there is any user-defined MolComparator
  - addUserComparator
```
public void addUserComparator(MolComparator mc)
```
    Adds the given user-defined comparator to the search.
    
    Parameters:
    
    mc - user-defined MolComparator
    
    See Also:
    
    MolComparator, getUserComparators(), deleteAllUserComparators()
  - deleteUserComparator
```
public void deleteUserComparator(MolComparator mc)
```
    Deletes a given user defined comparator if found.
    
    Parameters:
    
    mc - user defined comparator to delete.
    
    See Also:
    
    MolComparator, deleteAllUserComparators(), addUserComparator(MolComparator)
  - deleteAllUserComparators
```
public void deleteAllUserComparators()
```
    Deletes all comparator added by the user.
    
    See Also:
    
    MolComparator, addUserComparator(MolComparator), getUserComparators()
  - getUserComparators
```
public MolComparator[] getUserComparators()
```
    Returns the user defined comparators.
    
    Returns:
    
    user-defined MolComparators
  - isDirty
```
public final boolean isDirty()
```
    Returns the dirty flag. Dirty flag usage:
    1. When the search object initializes itself using the actual query, target and options, it clears the dirty flag(sets to false).
    2. When the search options change, the dirty flag is set automatically.
    3. Next time a major operation is done with the search object, it checks the dirty flag of the options. If set, it re-initializes itself.
    Returns:
    
    true if the options are dirty
    
    See Also:
    
    setDirty(boolean)
  - setDirty
```
public final void setDirty(boolean v)
```
    Sets or clears the dirty flag. See the description of isDirty() for its usage.
    
    Parameters:
    
    v - new dirty value
    
    See Also:
    
    isDirty()
  - clone
```
public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException
```
    Makes an identical copy of this SearchObject.
    
    Overrides:
    
    clone in class java.lang.Object
    
    Throws:
    
    java.lang.CloneNotSupportedException
  - clonecopy
```
public void clonecopy(SearchOptions other)
```
    Copies all search options to other. Even the search type.
    
    Parameters:
    
    other - search option to overwrite.
  - clonecopyOptions
```
public void clonecopyOptions(SearchOptions other)
```
    Copies all search options except search type to other.
    
    Parameters:
    
    other - search option object to overwrite
  - setTautomerSearch
```
public void setTautomerSearch(int value)
```
    Sets if tautomers of the query should be enumerated for search.
    
    Parameters:
    
    value - the desired tautomer search behavior
    Default value is SearchConstants.TAUTOMER_SEARCH_DEFAULT.
    
    Since:
    
    JChem 5.4
    
    See Also:
    
    SearchConstants.TAUTOMER_SEARCH_DEFAULT, SearchConstants.TAUTOMER_SEARCH_OFF, SearchConstants.TAUTOMER_SEARCH_ON, SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO, getTautomerSearch(), Tautomer search documenation
  - getTautomerSearch
```
public final int getTautomerSearch()
```
    Indicates if tautomers of the query should be enumerated for search.
    
    Returns:
    
    the current tautomer search behavior
    Default value is SearchConstants.TAUTOMER_SEARCH_DEFAULT.
    
    Since:
    
    JChem 5.4
    
    See Also:
    
    SearchConstants.TAUTOMER_SEARCH_DEFAULT, SearchConstants.TAUTOMER_SEARCH_OFF, SearchConstants.TAUTOMER_SEARCH_ON, setTautomerSearch(int), Tautomer search documenation
  - setOption
```
public void setOption(java.lang.String name,
                      java.lang.String value)
```
    Sets search options.
    
    Parameters:
    
    name - Name (case insensitive) of search option (e.g. stereoSearch).
    
    value - String form (case insensitive) of search parameter value (y, M, ef, ...).
    In case of boolean parameters 'true' is acceptable instead of 'y' and 'false' instead of 'n'. The available options can be obtained by calling getOptionNames().
    
    See Also:
    
    getOption(String)
  - getOption
```
public java.lang.String getOption(java.lang.String name)
```
    Returns option value in string format.
    
    Parameters:
    
    name - Name (case insensitive) of search option (e.g. stereoSearch). For the list of available search options, see setOption(String, String).
    
    Returns:
    
    string value of the given option (true --> y, false --> n, except 'valence', 'polymer' and 'mix': true --> d, false --> i)
    
    See Also:
    
    setOption(String, String)
  - getBoolean
```
protected static boolean getBoolean(java.lang.String value)
```
    Returns value as a boolean flag.
    
    Parameters:
    
    value - String representation of boolean flag.
    
    Returns:
    
    true if value is null, "", "y", "Y"; false if "n" or "N".
    
    Throws:
    
    java.lang.IllegalArgumentException - otherwise.
  - returnOptionString
```
protected java.lang.String returnOptionString(boolean value)
```
  - isKeepQueryOrder
```
public final boolean isKeepQueryOrder()
```
    Get options for rearranging query atoms for better search performance.
    
    Returns:
    
    false if search rearranges query atoms for better search performance
    Default value is false.
  - setKeepQueryOrder
```
public void setKeepQueryOrder(boolean value)
```
    Set option for rearranging query atoms to increase search performance.
    
    Parameters:
    
    value - false, if search should rearrange query atoms for better search performance
    Default value is false.
  - getIsotopeMatching
```
public final int getIsotopeMatching()
```
    Get option for matching isotopes
    
    Returns:
    
    Isotope searching behaviour.
    Default is SearchConstants.ISOTOPE_MATCHING_DEFAULT (isotope query matches only isotope target, nonisotope query matches all)
    
    See Also:
    
    setIsotopeMatching(int), SearchConstants.ISOTOPE_MATCHING_DEFAULT, SearchConstants.ISOTOPE_MATCHING_EXACT, SearchConstants.ISOTOPE_MATCHING_IGNORE, Query features documentation
  - setIsotopeMatching
```
public void setIsotopeMatching(int value)
```
    Set the isotope matching mode.
    
    Parameters:
    
    value - Specifies the isotope searching behavior. Default is SearchConstants.ISOTOPE_MATCHING_DEFAULT (isotope query matches only isotope target, non-isotope query matches all)
    Default is SearchConstants.ISOTOPE_MATCHING_DEFAULT (isotope query matches only isotope target, nonisotope query matches all) with the exception of duplicate search where SearchConstants.ISOTOPE_MATCHING_EXACT is the default.
    
    See Also:
    
    SearchConstants.ISOTOPE_MATCHING_DEFAULT, SearchConstants.ISOTOPE_MATCHING_EXACT, SearchConstants.ISOTOPE_MATCHING_IGNORE, getIsotopeMatching(), Query features documentation
  - getChargeMatching
```
public final int getChargeMatching()
```
    Get the charge matching option value
    
    Returns:
    
    Charge searching behaviour.
    Default is CHARGE_MATCHING_DEFAULT (charged query matches only charged target, noncharged query matches all)
    
    See Also:
    
    setChargeMatching(int), SearchConstants.CHARGE_MATCHING_DEFAULT, SearchConstants.CHARGE_MATCHING_EXACT, SearchConstants.CHARGE_MATCHING_IGNORE, Query features documentation
  - setChargeMatching
```
public void setChargeMatching(int value)
```
    Set charge matching behaviour.
    
    Parameters:
    
    value - Specifies the charge searching behaviour.
    Default value is SearchConstants.CHARGE_MATCHING_DEFAULT (charged query matches only charged target, noncharged query matches all) with the exception of duplicate search where SearchConstants.CHARGE_MATCHING_EXACT is the default.
    
    See Also:
    
    SearchConstants.CHARGE_MATCHING_DEFAULT, SearchConstants.CHARGE_MATCHING_EXACT, SearchConstants.CHARGE_MATCHING_IGNORE, Query features documentation
  - isValenceMatching
```
public final boolean isValenceMatching()
```
    Get the valence matching option
    
    Returns:
    
    true if valence is checked during search.
    Default value is true.
    
    See Also:
    
    setValenceMatching(boolean)
  - setValenceMatching
```
public void setValenceMatching(boolean value)
```
    Set valence check option.
    
    Parameters:
    
    value - true, if valence should be checked during search.
    Default value is true.
    
    See Also:
    
    isValenceMatching()
  - getRadicalMatching
```
public final int getRadicalMatching()
```
    Get option for radical matching behaviour.
    
    Returns:
    
    Radical searching behaviour.
    Default is SearchConstants.RADICAL_MATCHING_DEFAULT (radical query matches only radical target, nonradical query matches all).
    
    See Also:
    
    setRadicalMatching(int), SearchConstants.RADICAL_MATCHING_DEFAULT, SearchConstants.RADICAL_MATCHING_EXACT, SearchConstants.RADICAL_MATCHING_IGNORE, Query features documentation
  - setRadicalMatching
```
public void setRadicalMatching(int value)
```
    Set the radical matching mode.
    
    Parameters:
    
    value - Specifies the radical searching behaviour.
    Default is SearchConstants.RADICAL_MATCHING_DEFAULT (radical query matches only radical target, nonradical query matches all) with the exception of duplicate search where SearchConstants.RADICAL_MATCHING_EXACT is the default.
    
    See Also:
    
    SearchConstants.RADICAL_MATCHING_DEFAULT, SearchConstants.RADICAL_MATCHING_EXACT, SearchConstants.RADICAL_MATCHING_IGNORE, getRadicalMatching(), Query features documentation
  - isMixSgroupMatching
```
public final boolean isMixSgroupMatching()
```
    Get option whether search should consider consider COM, MIX and FOR sgroups during search.
    
    Returns:
    
    true if considers COM, MIX and FOR sgroups during search
    Default value is true.
    
    See Also:
    
    setMixSgroupMatching(boolean)
  - setMixSgroupMatching
```
public void setMixSgroupMatching(boolean value)
```
    Set options for mixed S-group matching.
    
    Parameters:
    
    value - true, if COM, MIX and FOR sgroups should be considered during search.
    Default value is true.
    
    See Also:
    
    isMixSgroupMatching()
  - isPolymerMatching
```
public final boolean isPolymerMatching()
```
    Get option whether to search consider polymer sgroups during search.
    
    Returns:
    
    true if considers polymer sgroups during search
    Default value is true.
    
    See Also:
    
    setPolymerMatching(boolean)
  - setPolymerMatching
```
public void setPolymerMatching(boolean value)
```
    Adjust polymer matching.
    
    Parameters:
    
    value - true, if polymer sgroups should be considered during search.
    Default value is true.
    
    See Also:
    
    isPolymerMatching(), Polymer search documentation
  - isEndgroupMatching
```
public final boolean isEndgroupMatching()
```
    Get whether polymers end groups must match.
    
    Returns:
    
    true if polymer end groups must match during search. In this case the star atom can't match on a specified engroup.
    Default value is true.
    
    See Also:
    
    setPolymerMatching(boolean), Polymer search documentation
  - setEndgroupMatching
```
public void setEndgroupMatching(boolean value)
```
    Adjusts polymer end group matching.
    
    Parameters:
    
    value - true, if polymer endgroups should be matched during search. In this case the star atom can't match on a specified engroup.
    Default value is true.
  - areMonomersTransformed
```
public final boolean areMonomersTransformed()
```
    Obtain monomer transformation information.
    
    Returns:
    
    true if monomers (source based representation of polymers) are transformed to sru repeating units if they can be polimerizated.
    Default value is true.
    
    See Also:
    
    setMonomerTransform(boolean), Polymer search documentation
  - setMonomerTransform
```
public void setMonomerTransform(boolean value)
```
    Adjusts if monomers should be transformed to structural repeating units if the monomer is homolopolimerizable.
    
    Parameters:
    
    value - true if monomers should be transformed, false otherwise
    Default value is true.
    
    See Also:
    
    areMonomersTransformed(), Polymer search documentation
  - isPhaseShiftedMatching
```
public final boolean isPhaseShiftedMatching()
```
    Get option whether phase shifted polymer matches on the original.
    
    Returns:
    
    true if the phase-shifted polymers are matching.
    Default value is true.
    
    See Also:
    
    setPhaseShiftedMatching(boolean)
  - setPhaseShiftedMatching
```
public void setPhaseShiftedMatching(boolean value)
```
    Adjusts if the phase shifted polymer should match on the original.
    
    Parameters:
    
    value - true if the phase shifted should be matching false otherwise.
    Default value is true.
    
    See Also:
    
    isPhaseShiftedMatching()
  - isCopolymerMatching
```
public final boolean isCopolymerMatching()
```
    Specifies whether matching mode is copolymer.
    
    Returns:
    
    true if the copolymer matching mode is set.
    Default value is false.
    
    See Also:
    
    setCopolymerMatching(boolean), Polymer search documentation
  - setCopolymerMatching
```
public void setCopolymerMatching(boolean value)
```
    Adjusts copolymer matching mode. If set, then target polymers in copolymers can only be matched by query polymers in copolymers.
    
    Parameters:
    
    value - true if copolymer matching mode should be set, false otherwise. (default false)
    Default value is false
    
    See Also:
    
    isCopolymerMatching(), Polymer search documentation
  - getHomologyNarrowTranslation
```
public final HomologyTranslationOption getHomologyNarrowTranslation()
```
    Get query-side homology matching option, which homology atoms can match specific atoms.
    
    Returns:
    
    see possible values at HomologyTranslationOption.
    Default value is HomologyTranslationOption.MARKED.
    
    See Also:
    
    setHomologyNarrowTranslation(HomologyTranslationOption)
  - setHomologyNarrowTranslation
```
public void setHomologyNarrowTranslation(HomologyTranslationOption value)
```
    Adjusts for which query homology atoms narrow translation on target specific atoms is allowed. If it's allowed for a query homology atom, it may match target specific atoms. If an atom is not marked or all atoms are baned then it can only match the same homology group.
    
    Parameters:
    
    value - For possible values see: HomologyTranslationOption
    Default value is HomologyTranslationOption.MARKED
    
    See Also:
    
    getHomologyNarrowTranslation(), Query features documentation
  - getHomologyBroadTranslation
```
public final HomologyTranslationOption getHomologyBroadTranslation()
```
    Get target-side homology matching option. Which specific atoms can match on homology atoms.
    
    Returns:
    
    see possible values at HomologyTranslationOption.
    Default value is HomologyTranslationOption.MARKED.
    
    See Also:
    
    setHomologyBroadTranslation(HomologyTranslationOption)
  - setHomologyBroadTranslation
```
public void setHomologyBroadTranslation(HomologyTranslationOption value)
```
    Adjusts for which query atoms broad translation on target homology groups is allowed. If it's allowed for a specific query atom, it may match pseudo atoms with homology names on the target side. If an atom is not marked or all atoms are baned then it can match a homology group only if it's a pseudo atom of the same homology group.
    
    Parameters:
    
    value - For possible values see: HomologyTranslationOption
    Default value is HomologyTranslationOption.MARKED
    
    See Also:
    
    getHomologyBroadTranslation()
  - setTargetHomologyMatchingMode
```
public void setTargetHomologyMatchingMode(TargetHomologyMatchingMode mode)
```
    Sets the target homology matching mode option. Only used when homology broad translation is set.
    
    Parameters:
    
    mode - homology matching mode. For possible values, see: TargetHomologyMatchingMode.
    Default value is TargetHomologyMatchingMode.ALL.
    
    See Also:
    
    getTargetHomologyMatchingMode()
  - getTargetHomologyMatchingMode
```
public TargetHomologyMatchingMode getTargetHomologyMatchingMode()
```
    Returns the target homology matching mode. Only used when homology broad translation is set.
    
    Returns:
    
    homology matching mode. For possible return values, see: TargetHomologyMatchingMode.
    Default value is TargetHomologyMatchingMode.ALL.
    
    See Also:
    
    setTargetHomologyMatchingMode(TargetHomologyMatchingMode)
  - setSSRType
```
public void setSSRType(SetOfSmallestRingsOption value)
```
    Sets which type of set of smallest rings to use for property calculations
    
    Parameters:
    
    value - set of smallest rings options to use
    
    See Also:
    
    SetOfSmallestRingsOption, getSSRType()
  - getSSRType
```
public SetOfSmallestRingsOption getSSRType()
```
    Gets the type of the set of smallest rings to use
    Default value is SetOfSmallestRingsOption.SSSR
    
    Returns:
    
    set of smallest rings option
    
    See Also:
    
    SetOfSmallestRingsOption, setSSRType(SetOfSmallestRingsOption)
  - getMarkushAromHandling
```
@Beta
public MarkushAromaticityHandlingOption getMarkushAromHandling()
```
    Gets the Markush aromatic search behavior.
    
    Returns:
    
    behaviour of Markush aromatic search.
    
    Since:
    
    6.2
    
    See Also:
    
    MarkushAromaticityHandlingOption, setMarkushAromHandling(MarkushAromaticityHandlingOption)
  - setMarkushAromHandling
```
@Beta
public void setMarkushAromHandling(MarkushAromaticityHandlingOption value)
```
    Set handling of Markush aromatization information (ambiguous aromatic rings) during Markush search
    
    Parameters:
    
    value - the desired Markush aromatic search option
    
    Since:
    
    6.2
    
    See Also:
    
    MarkushAromaticityHandlingOption, getMarkushAromHandling()
  - getStereoModel
```
public final int getStereoModel()
```
    Get the stereo model option.
    
    Returns:
    
    Used stereo model. Default is STEREO_MODEL_COMPREHENSIVE for substructure and supertructure searches and STEREO_MODEL_GLOBAL otherwise.
    
    See Also:
    
    SearchConstants.STEREO_MODEL_LOCAL, SearchConstants.STEREO_MODEL_COMPREHENSIVE, SearchConstants.STEREO_MODEL_GLOBAL, SearchConstants.STEREO_MODEL_DEFAULT, Stereo Model documentation
  - setStereoModel
```
public void setStereoModel(int value)
```
    Set stereo model option.
    
    Parameters:
    
    value - Specifies the used stereo model. Default is SearchConstants.STEREO_MODEL_DEFAULT, whose actual behavior depends on the search type and, in case of database search, the type of the structure table. For substructure and superstructure searches, it equals to SearchConstants.STEREO_MODEL_COMPREHENSIVE, while for other searches, it usually equals to SearchConstants.STEREO_MODEL_GLOBAL.
    
    See Also:
    
    SearchConstants.STEREO_MODEL_LOCAL, SearchConstants.STEREO_MODEL_COMPREHENSIVE, SearchConstants.STEREO_MODEL_GLOBAL, SearchConstants.STEREO_MODEL_DEFAULT, getStereoModel(), Stereo Model documentation
  - setStereoSearchType
```
public final void setStereoSearchType(int value)
```
    Specifies the way stereo information is considered during searching. (setStereoModel(int) specifies the model for calculating the stereo information.)
    
    Parameters:
    
    value - Specifies the stereo mode.
    Default value is SearchConstants.STEREO_SPECIFIC with the exception of duplicate search where SearchConstants.STEREO_EXACT is the default.
    
    See Also:
    
    SearchConstants.STEREO_SPECIFIC, SearchConstants.STEREO_IGNORE, SearchConstants.STEREO_EXACT, SearchConstants.STEREO_DIASTEREOMER, SearchConstants.STEREO_ENANTIOMER, getStereoSearchType(), Stereochemistry documentation
  - getStereoSearchType
```
public final int getStereoSearchType()
```
    Get the stereo search type option.
    
    Returns:
    
    Specifies the stereo search type.
    Default is SearchConstants.STEREO_SPECIFIC.
    
    See Also:
    
    SearchConstants.STEREO_SPECIFIC, SearchConstants.STEREO_IGNORE, SearchConstants.STEREO_EXACT, SearchConstants.STEREO_DIASTEREOMER, SearchConstants.STEREO_ENANTIOMER, setStereoSearchType(int), Stereochemistry documentation
  - setIgnoreTetrahedralStereo
```
public final void setIgnoreTetrahedralStereo(boolean value)
```
    Sets ignoring tetrahedral stereo information during serching. If this option is set tetrahedral stereo information is ignored and setStereoSearchType(int) only specifies double bond stereo matching.
    
    Parameters:
    
    value - the value to set, set true to ignore.
    Default value is false.
  - isIgnoreTetrahedralStereo
```
public final boolean isIgnoreTetrahedralStereo()
```
    Retrieves if tetrahedral stereo is ignored during searching.
    
    Returns:
    
    true if ignored.
    Default value is false.
    
    See Also:
    
    setIgnoreTetrahedralStereo(boolean)
  - setIgnoreDoubleBondStereo
```
public final void setIgnoreDoubleBondStereo(boolean value)
```
    Sets ignoring double bond stereo information during serching. If this option is set double bond stereo information is ignored and setStereoSearchType(int) only specifies tetrahedral stereo matching.
    
    Parameters:
    
    value - the value to set, set true to ignore.
    Default value is false.
  - isIgnoreDoubleBondStereo
```
public final boolean isIgnoreDoubleBondStereo()
```
    Retrieves if double bond stereo is ignored during searching.
    
    Returns:
    
    true if ignored.
    Default value is false.
    
    See Also:
    
    setIgnoreDoubleBondStereo(boolean)
  - setIgnoreCumuleneOrRingCisTransStereo
```
public final void setIgnoreCumuleneOrRingCisTransStereo(boolean value)
```
    Sets ignoring cumulene cis-trans stereo information during serching.
    
    Parameters:
    
    value - the value to set, set true to ignore.
    Default value is true.
  - isIgnoreCumuleneOrRingCisTransStereo
```
public final boolean isIgnoreCumuleneOrRingCisTransStereo()
```
    Retrieves if cumulene cis-trans stereo is ignored during searching.
    
    Returns:
    
    true if ignored.
    Default value is true.
    
    See Also:
    
    setIgnoreCumuleneOrRingCisTransStereo(boolean)
  - setIgnoreAxialStereo
```
public final void setIgnoreAxialStereo(boolean value)
```
    Sets ignoring axial stereo information during serching.
    
    Parameters:
    
    value - the value to set, set true to ignore.
    Default value is true.
  - isIgnoreAxialStereo
```
public final boolean isIgnoreAxialStereo()
```
    Retrieves if axial stereo is ignored during searching.
    
    Returns:
    
    true if ignored.
    Default value is true.
    
    See Also:
    
    setIgnoreAxialStereo(boolean)
  - setIgnoreSynAntiStereo
```
public final void setIgnoreSynAntiStereo(boolean value)
```
    Sets ignoring syn-anti stereo information during serching.
    
    Parameters:
    
    value - the value to set, set true to ignore.
    Default value is true.
  - isIgnoreSynAntiStereo
```
public final boolean isIgnoreSynAntiStereo()
```
    Retrieves if syn-anti stereo is ignored during searching.
    
    Returns:
    
    true if ignored.
    Default value is true.
    
    See Also:
    
    setIgnoreSynAntiStereo(boolean)
  - getCheckSpHyb
```
public final boolean getCheckSpHyb()
```
    Get the sp-hybridization state option
    
    Returns:
    
    true if sp-hybridization state of the atoms is considered,
    Default value is false.
    
    See Also:
    
    setCheckSpHyb(boolean), MoleculeGraph.calcHybridization(), Search options documenation
  - setCheckSpHyb
```
public void setCheckSpHyb(boolean checkSp)
```
    Sets whether the sp-hybridization state of the atoms should be considered.
    
    Parameters:
    
    checkSp - If true the sp-hybridization state is checked.
    Default value is false.
    
    Since:
    
    5.1
    
    See Also:
    
    getCheckSpHyb(), MoleculeGraph.calcHybridization(), Search options documenation
  - getImplicitHMatching
```
public final int getImplicitHMatching()
```
    Get option for matching implicit and explicit hydrogens
    
    Returns:
    
    Matching behaviour between explicit and implicit hydrogens.
    Default is SearchConstants.IMPLICIT_H_MATCHING_DEFAULT (matching depends on the circumstances of search)
    
    See Also:
    
    SearchConstants.IMPLICIT_H_MATCHING_DEFAULT, SearchConstants.IMPLICIT_H_MATCHING_DISABLED, SearchConstants.IMPLICIT_H_MATCHING_ENABLED, Search options documentation
  - setImplicitHMatching
```
public void setImplicitHMatching(int value)
```
    Set option for matching implicit and explicit hydrogens.
    
    Parameters:
    
    value - Specifies matching bahaviour between explicit and implicit hydrogens.
    Default is SearchConstants.IMPLICIT_H_MATCHING_DEFAULT (matching depends on the circumstances of search)
    
    See Also:
    
    SearchConstants.IMPLICIT_H_MATCHING_DEFAULT, SearchConstants.IMPLICIT_H_MATCHING_DISABLED, SearchConstants.IMPLICIT_H_MATCHING_ENABLED, SearchConstants.IMPLICIT_H_MATCHING_IGNORE, Implicit H matching documentation
  - isReactionUnpairedMapMatching
```
public final boolean isReactionUnpairedMapMatching()
```
    Get whether unpaired(orphan or widow) atom maps can match any atom.
    
    Returns:
    
    true if in reaction search unpaired (orphan and widow) atom maps can match any atom map.
    Default value is true.
    
    See Also:
    
    setReactionUnpairedMapMatching(boolean), Reaction search documentation
  - setReactionUnpairedMapMatching
```
public void setReactionUnpairedMapMatching(boolean value)
```
    Set option for matching unpaired(orphan or widow) atom maps to any atom.
    
    Parameters:
    
    value - true, if in reaction search unpaired (orphan and widow) atom maps can match any atom map.
    Default value is true.
    
    See Also:
    
    isReactionUnpairedMapMatching(), Reaction search documentation
  - setChemTermsFilter
```
public void setChemTermsFilter(java.lang.String value)
```
    Sets the Chemical Terms filtering expression.
    
    Parameters:
    
    value - the chemical terms filter expression
    Default value is null.
    
    See Also:
    
    getChemTermsFilter(), Chemical terms documentation
  - getChemTermsFilter
```
public final java.lang.String getChemTermsFilter()
```
    Gets the Chemical Terms filtering expression
    
    Returns:
    
    chemical filter expression
    Default value is null.
    
    See Also:
    
    setChemTermsFilter(String), Chemical terms documentation
  - setChemTermsFilterConfig
```
public void setChemTermsFilterConfig(java.io.File file)
                              throws java.io.IOException
```
    Sets the configuration file for Chemical Terms filter.
    
    Parameters:
    
    file - the configuration file. Set to null for default configuration.
    Default value is null.
    
    Throws:
    
    java.io.IOException - if the supplied file can't be read with the default charset.
    
    Since:
    
    JChem 6.0
    
    See Also:
    
    getChemTermsFilterConfig(), Chemical terms documentation
  - setChemTermsFilterConfig
```
public void setChemTermsFilterConfig(java.lang.String value)
```
    Sets the configuration string for Chemical Terms filter.
    
    Parameters:
    
    value - the configuration string. Set to null for default configuration.
    Default value is null.
    
    See Also:
    
    getChemTermsFilterConfig(), Chemical terms documentation
  - getChemTermsFilterConfig
```
public final java.lang.String getChemTermsFilterConfig()
```
    Gets the configuration string for Chemical Terms filter.
    
    Returns:
    
    the configuration string
    Default value is null.
    
    See Also:
    
    setChemTermsFilterConfig(String), Chemical terms documentation
  - setUndefinedRAtom
```
public void setUndefinedRAtom(int value)
```
    Sets the matching behaviour of an undefined R atom in the query.
    
    Possible values for search:
    Possible values for RGroupDecomposition:
    - SearchConstants.UNDEF_R_MATCHING_GROUP
    - SearchConstants.UNDEF_R_MATCHING_GROUP_H (default for queries with explicit undefined R-atom)
    - SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY (default for queries without explicit undefined R-atom)
    Parameters:
    
    value - Matching mode value.
    
    See Also:
    
    getUndefinedRAtom(), Special search types documentation
  - setUndefinedRAtomUserDefined
```
public void setUndefinedRAtomUserDefined(boolean undefinedRAtomUserDefined)
```
    For internal use only!
    
    Parameters:
    
    undefinedRAtomUserDefined - the new value.
  - getUndefinedRAtom
```
public final int getUndefinedRAtom()
```
    Returns undefined R atom matching behaviour mode.
    
    Returns:
    
    Matching mode value.
    Default is SearchConstants.UNDEF_R_MATCHING_GROUP.
    
    See Also:
    
    SearchConstants.UNDEF_R_MATCHING_ALL, SearchConstants.UNDEF_R_MATCHING_UNDEF_R, SearchConstants.UNDEF_R_MATCHING_GROUP, SearchConstants.UNDEF_R_MATCHING_GROUP_H, SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY, setUndefinedRAtom(int), Special search types documentation
  - isUndefinedRAtomMatchingGroup
```
public final boolean isUndefinedRAtomMatchingGroup()
```
    Gets whether undefined R atom matches group of atoms. This is the case when getUndefinedRAtom() is
    Returns:
    
    true if undefined R atom matches group
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    setUndefinedRAtom(int), getUndefinedRAtom()
  - setBridgingRAllowed
```
public void setBridgingRAllowed(boolean value)
```
    Sets whether different undefined R-atoms can match the same group of atoms. This parameter is only used if R atom matching behaviour (setUndefinedRAtom(int)) is set to group matching:
    SearchConstants.UNDEF_R_MATCHING_GROUP or
    SearchConstants.UNDEF_R_MATCHING_GROUP_H or SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY.
    
    Parameters:
    
    value - true if different undefined R-atoms can match the same group of atoms
    Default value is false.
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    setUndefinedRAtom(int)
  - isBridgingRAllowed
```
public final boolean isBridgingRAllowed()
```
    Returns true if different undefined R-atoms can match the same group of atoms. This parameter is only used if R atom matching behaviour.
    
    Returns:
    
    true if different undefined R-atoms can match the same group of atoms
    Default value is false.
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    SearchConstants.UNDEF_R_MATCHING_GROUP, SearchConstants.UNDEF_R_MATCHING_GROUP_H, SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY, setBridgingRAllowed(boolean)
  - setRLigandEqualityCheck
```
public void setRLigandEqualityCheck(boolean value)
```
    Sets whether undefined R-atoms with the same R-group ID should match the same structure. This parameter is only used if R atom matching behaviour
    
    Parameters:
    
    value - true if undefined R-atoms with the same R-group ID should match the same structure
    Default value is true.
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    setUndefinedRAtom(int), SearchConstants.UNDEF_R_MATCHING_GROUP, SearchConstants.UNDEF_R_MATCHING_GROUP_H, SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY, getRLigandEqualityCheck(), Special search types documentation
  - getRLigandEqualityCheck
```
public final boolean getRLigandEqualityCheck()
```
    Returns true if undefined R-atoms with the same R-group ID should match the same structure. This parameter is only used if R atom matching behaviour
    
    Returns:
    
    true if undefined R-atoms with the same R-group ID should match the same structure
    Default value is true.
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    SearchConstants.UNDEF_R_MATCHING_GROUP, SearchConstants.UNDEF_R_MATCHING_GROUP_H, SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY, setRLigandEqualityCheck(boolean), Special search types documentation
  - setHitOrdering
```
public void setHitOrdering(int value)
```
    Sets the hit ordering type.
    
    Parameters:
    
    value - hit ordering type value.
    Default value is SearchConstants.HIT_ORDERING_NONE.
    
    Since:
    
    JChem 5.4
    
    See Also:
    
    SearchConstants.HIT_ORDERING_NONE, SearchConstants.HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST, getHitOrdering()
  - getHitOrdering
```
public int getHitOrdering()
```
    Returns the hit ordering type.
    
    Returns:
    
    the hit ordering type.
    Default value is SearchConstants.HIT_ORDERING_NONE.
    
    Since:
    
    JChem 5.4
    
    See Also:
    
    SearchConstants.HIT_ORDERING_NONE, SearchConstants.HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST, setHitOrdering(int)
  - setAttachedDataMatch
```
public void setAttachedDataMatch(int value)
```
    Sets whether attached data (in data sgroups) should be used when comparing structures.
    
    Parameters:
    
    value - attach data match type
    Default value is SearchConstants.ATTACHED_DATA_MATCH_IGNORE (no attached data used)
    
    See Also:
    
    getAttachedDataMatch(), SearchConstants.ATTACHED_DATA_MATCH_IGNORE, SearchConstants.ATTACHED_DATA_MATCH_GENERAL, SearchConstants.ATTACHED_DATA_MATCH_EXACT, Query features documentation
  - getAttachedDataMatch
```
public final int getAttachedDataMatch()
```
    Returns whether attached data (in data sgroups) should be used when comparing structures.
    
    Returns:
    
    value of attached data match type
    Default value is SearchConstants.ATTACHED_DATA_MATCH_IGNORE (no attached data used)
    
    See Also:
    
    setAttachedDataMatch(int), SearchConstants.ATTACHED_DATA_MATCH_IGNORE, SearchConstants.ATTACHED_DATA_MATCH_GENERAL, SearchConstants.ATTACHED_DATA_MATCH_EXACT, Query features documentation
  - setAttachedDataPrefixes
```
public void setAttachedDataPrefixes(java.lang.String value)
```
    Sets the prefixes of the names of those data sgroups that will be used during structure comparison. The value is used only when attached data is not ignored
    Prefixes are case insensitive.
    
    Parameters:
    
    value - comma separated list of name prefixes, e.g. "weight,atomcount"
    Default value is null (all data sgroups will be checked).
    
    See Also:
    
    setAttachedDataMatch(int), getAttachedDataPrefixes(), Query features documentation
  - getAttachedDataPrefixes
```
public final java.lang.String getAttachedDataPrefixes()
```
    Returns the prefixes of the names of those data sgroups that will be used during structure comparison or null if all data sgroups should be checked.
    
    Returns:
    
    comma separated list of name prefixes or null
    Default value is null (all data sgroups will be checked).
    
    See Also:
    
    setAttachedDataPrefixes(String), Query features documentation
  - setExactSpecialAtomMatching
```
public void setExactSpecialAtomMatching(java.lang.String value)
```
    Sets the identifiers of those special atoms that should match exactly during structure comparison.
    Identifiers are case insensitive.
    Available identifiers are generic query atoms (A, AH, Q, ...) (see this page ) and pseudo atom aliases (see this page ).
    
    Parameters:
    
    value - comma separated list of identifiers
    Default value is "" (all data sgroups will be checked). e.g. "A,G18,*,Resin"
  - getExactSpecialAtomMatching
```
public final java.lang.String getExactSpecialAtomMatching()
```
    Get the identifiers of those special atoms that should match exactly during structure comparison.
    
    Returns:
    
    comma separated list of identifiers
    Default value is "" (all data sgroups will be checked). e.g. "A,G18,*,Resin"
    
    See Also:
    
    setExactSpecialAtomMatching(String)
  - getExhaustiveModeLimit
```
public final int getExhaustiveModeLimit()
```
    Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
    
    Returns:
    
    The limit value.
    Default value is -1.
    
    See Also:
    
    setExhaustiveModeLimit(int)
  - setExhaustiveModeLimit
```
public void setExhaustiveModeLimit(int value)
```
    Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
    
    Parameters:
    
    value - Set it to -1 if you do not want to switch to exhaustive mode. Set it to 0 if you want to use exhaustive mode only.
    Default value is -1.
    
    See Also:
    
    getExhaustiveModeLimit()
  - getTimeoutLimitMilliseconds
```
public int getTimeoutLimitMilliseconds()
```
    The search on a single target timeouts reaching this amount of time.
    
    Returns:
    
    The timeout limit in milliseconds.
    Default value is 120000 .
    
    See Also:
    
    setTimeoutLimitMilliseconds(int)
  - setTimeoutLimitMilliseconds
```
public void setTimeoutLimitMilliseconds(int value)
```
    The search on a single target timeouts reaching this amount of time. Set it to a negative value if you do not want the search to time out.
    
    Parameters:
    
    value - The time limit to set in milliseconds. Negative values are treated as Integer.MAX_VALUE.
    Default value is 120000.
    
    See Also:
    
    getTimeoutLimitMilliseconds()
  - nonPositiveToInfinite
```
protected static int nonPositiveToInfinite(int value)
```
  - isThrowExceptionOnTimeout
```
public final boolean isThrowExceptionOnTimeout()
```
    It search should throw exception upon timeout.
    
    Returns:
    
    true if it throws exception.
    Default value is false.
    
    See Also:
    
    setThrowExceptionOnTimeout(boolean)
  - setThrowExceptionOnTimeout
```
public void setThrowExceptionOnTimeout(boolean value)
```
    Sets if search should throw exception upon timeout. If set to false, search returns as if there were no hits.
    
    Parameters:
    
    value - true if exception should be thrown.
    Default value is false.
    
    See Also:
    
    isThrowExceptionOnTimeout()
  - getChemTermsFilterOption
```
@Beta
public chemaxon.sss.search.options.ChemTermsFilterOption getChemTermsFilterOption()
```
    FOR INTERNAL USE ONLY Returns the chem term filtering options.
    
    Returns:
    
    the chemTermOption
  - setChemTermsFilterOption
```
@Beta
public void setChemTermsFilterOption(chemaxon.sss.search.options.ChemTermsFilterOption chemTermsFilterOption)
```
    FOR INTERNAL USE ONLY. Sets the chem term filtering options
    
    Parameters:
    
    chemTermsFilterOption - the chemTermOption to set
    
    Throws:
    
    java.lang.NullPointerException - in case chemTermsFilterOption is null
  - toString
```
public java.lang.String toString()
```
    Returns a string that
    - describes the state of the options
    - can be the input of setOptions(String)
    - doesn't contain options that have their default value (except dissimilarity threshold in case of similarity search)
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    a string in format "optionname1:optionvalue1 optionname2:optionvalue2 ..."
    
    See Also:
    
    setOptions(String), toList()
  - toString
```
public java.lang.String toString(java.lang.String sep)
```
    Returns a string that
    - describes the state of the options
    - can be the input of setOptions(String)
    - doesn't contain options that have their default value (except dissimilarity threshold in case of similarity search)
    
    Parameters:
    
    sep - the separator string between options
    
    Returns:
    
    a string in format "optionname1:optionvalue1 optionname2:optionvalue2 ..."
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    setOptions(String), toList()
  - getAllOptionsAsString
```
public java.lang.String getAllOptionsAsString()
```
    Returns a string that
    - describes the state of the options
    - can be the input of setOptions(String)
    - contains all options, including those which have their default value (except dissimilarity threshold in case of similarity search)
    
    Returns:
    
    a string in format "optionname1:optionvalue1 optionname2:optionvalue2 ..."
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    getAllOptionsAsString(String), setOptions(String), toString()
  - getAllOptionsAsString
```
public java.lang.String getAllOptionsAsString(java.lang.String sep)
```
    Returns a string that
    - describes the state of the options
    - can be the input of setOptions(String)
    - contains all options, including those which have their default value (except dissimilarity threshold in case of similarity search)
    
    Parameters:
    
    sep - is the separator
    
    Returns:
    
    a string in format "sep=$$ optionname1:optionvalue1$$optionname2:optionvalue2$$...", where $$ is the separator
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    getAllOptionsAsString(), setOptions(String), toString()
  - toList
```
public java.util.ArrayList<java.lang.String> toList()
```
    Returns:
    
    An arraylist that contains strings of format "optionname:optionvalue". Doesn't contain options that have their default value.
    
    See Also:
    
    setOptions(String), toString()
  - getOptionNames
```
public java.util.Collection<java.lang.String> getOptionNames()
```
    Returns the name of all available options which can be used to set/get option values with setOption(String, String) and getOption(String) methods.
    
    Returns:
    
    Collection of available option names

Class SearchOptions

Field Summary

Fields inherited from interface chemaxon.sss.SearchConstants

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

dirty

verbose

DEFAULT_TIMEOUT_LIMIT

timeoutLimitMilliseconds

Constructor Detail

SearchOptions

Method Detail

isExactQueryAtomMatching

setExactQueryAtomMatching

setDoubleBondStereoMatchingMode

getDoubleBondStereoMatchingMode

getSearchType

getHCountMatching

setHCountMatching

isVerbose

setVerbose

getSearchType

setOptions

setOrderSensitiveSearch

isOrderSensitiveSearch

isExactBondMatching

setExactBondMatching

setVagueBondLevel

getVagueBondLevel

setCompleteHG

getCompleteHG

hasChangesInUserComparators

clearChangesInUserComparators

hasUserComparators

addUserComparator

deleteUserComparator

deleteAllUserComparators

getUserComparators

isDirty

setDirty

clone

clonecopy

clonecopyOptions

setTautomerSearch

getTautomerSearch

setOption

getOption

getBoolean

returnOptionString

isKeepQueryOrder

setKeepQueryOrder

getIsotopeMatching

setIsotopeMatching

getChargeMatching

setChargeMatching

isValenceMatching

setValenceMatching

getRadicalMatching

setRadicalMatching

isMixSgroupMatching

setMixSgroupMatching

isPolymerMatching

setPolymerMatching

isEndgroupMatching

setEndgroupMatching

areMonomersTransformed

setMonomerTransform

isPhaseShiftedMatching

setPhaseShiftedMatching

isCopolymerMatching

setCopolymerMatching

getHomologyNarrowTranslation

setHomologyNarrowTranslation

getHomologyBroadTranslation

setHomologyBroadTranslation

setTargetHomologyMatchingMode

getTargetHomologyMatchingMode

setSSRType