Package chemaxon.search.api.options

Class SearchOptions

java.lang.Object

chemaxon.search.api.options.SearchOptions

All Implemented Interfaces:

SearchConstants, Serializable, Cloneable

Direct Known Subclasses:

MolSearchOptions

@PublicApi
public class SearchOptions
extends Object
implements SearchConstants, Cloneable, Serializable

Class to encapsulate common search options.

Since:

5.0

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final 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.search.api.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_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	Description
SearchOptions(int searchType)	Creates a SearchOptions object while setting different search options according to a predefined search type.

Method Summary

Modifier and Type	Method	Description
void	addUserComparator(MolComparator mc)	Adds the given user-defined comparator to the search.
final boolean	areMonomersTransformed()	Obtain monomer transformation information.
final void	clearChangesInUserComparators()	Used in initializing searches.
SearchOptions	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.
protected void	fillOptionList(ArrayList<String> ret, SearchOptions so)	Fills ret with "optionname:optionvalue" pairs.
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)
String	getAllOptionsAsString(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)
final int	getAttachedDataMatch()	Returns whether attached data (in data sgroups) should be used when comparing structures.
final 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(String value)	Returns value as a boolean flag.
final int	getChargeMatching()	Get the charge matching option value
final boolean	getCheckSpHyb()	Get the sp-hybridization state option
final String	getChemTermsFilter()	Gets the Chemical Terms filtering expression
final String	getChemTermsFilterConfig()	Gets the configuration string for Chemical Terms filter.
final int	getDoubleBondStereoMatchingMode()	Get the double bond stereo matching mode.
final String	getExactSpecialAtomMatching()	Get the identifiers of those special atoms that should match exactly during structure comparison.
final int	getExhaustiveModeLimit()	Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
final int	getHCountMatching()	Get the interpretation of H count in the query.
int	getHitOrdering()	Returns the hit ordering type.
final HomologyTranslationOption	getHomologyBroadTranslation()	Get target-side homology matching option.
final HomologyTranslationOption	getHomologyNarrowTranslation()	Get query-side homology matching option, which homology atoms can match specific atoms.
final int	getImplicitHMatching()	Get option for matching implicit and explicit hydrogens
final int	getIsotopeMatching()	Get option for matching isotopes
MarkushAromaticityHandlingOption	getMarkushAromHandling()	Gets the Markush aromatic search behavior.
String	getOption(String name)	Returns option value in string format.
Collection<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.
final int	getRadicalMatching()	Get option for radical matching behavior.
final boolean	getRLigandEqualityCheck()	Returns true if undefined R-atoms with the same R-group ID should match the same structure.
final int	getSearchType()	Returns the currently set global search operation mode.
static int	getSearchType(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
final int	getStereoModel()	Get the stereo model option.
final int	getStereoSearchType()	Get the stereo search type option.
TargetHomologyMatchingMode	getTargetHomologyMatchingMode()	Returns the target homology matching mode.
final 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.
final int	getUndefinedRAtom()	Returns undefined R atom matching behavior mode.
MolComparator[]	getUserComparators()	Returns the user defined comparators.
final int	getVagueBondLevel()	Getter for vague bond level.
final boolean	hasChangesInUserComparators()	Used in initializing searches.
final boolean	hasUserComparators()	Gets whether searcher has user defined comparators.
final boolean	isBridgingRAllowed()	Returns true if different undefined R-atoms can match the same group of atoms.
final boolean	isCopolymerMatching()	Specifies whether matching mode is copolymer.
final boolean	isDirty()	Returns the dirty flag.
final boolean	isEndgroupMatching()	Get whether polymers end groups must match.
final boolean	isExactBondMatching()	Indicates whether bond types should match exactly - looking for query bonds target.
final boolean	isExactQueryAtomMatching()	Returns whether exact matching of query atom information is set.
final boolean	isIgnoreAxialStereo()	Retrieves if axial stereo is ignored during searching.
final boolean	isIgnoreCumuleneOrRingCisTransStereo()	Retrieves if cumulene cis-trans stereo is ignored during searching.
final boolean	isIgnoreDoubleBondStereo()	Retrieves if double bond stereo is ignored during searching.
final boolean	isIgnoreSynAntiStereo()	Retrieves if syn-anti stereo is ignored during searching.
final boolean	isIgnoreTetrahedralStereo()	Retrieves if tetrahedral stereo is ignored during searching.
final boolean	isKeepQueryOrder()	Get options for rearranging query atoms for better search performance.
final boolean	isMixSgroupMatching()	Get option whether search should consider consider COM, MIX and FOR sgroups during search.
final boolean	isOrderSensitiveSearch()	Indicates whether the search is order sensitive
final boolean	isPhaseShiftedMatching()	Get option whether phase shifted polymer matches on the original.
final boolean	isPolymerMatching()	Get option whether to search consider polymer sgroups during search.
final boolean	isReactionUnpairedMapMatching()	Get whether unpaired(orphan or widow) atom maps can match any atom.
final boolean	isThrowExceptionOnTimeout()	Is search should throw exception upon timeout.
final boolean	isUndefinedRAtomMatchingGroup()	Gets whether undefined R atom matches group of atoms.
boolean	isUndefinedRAtomUserDefined()	Fot internal use only! Returns whether the undefined R-atom matching behavior was set externally (user-defined) or else internally as default for a specific query from invalid reference RgroupDecomposition#setQuery(chemaxon.struc.Molecule) .
final boolean	isValenceMatching()	Get the valence matching option
final boolean	isVerbose()	For debugging purposes only.
protected static int	nonPositiveToInfinite(int value)
protected String	returnOptionString(boolean value)
void	setAttachedDataMatch(int value)	Sets whether attached data (in data sgroups) should be used when comparing structures.
void	setAttachedDataPrefixes(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.
final void	setChargeMatching(int value)	Set charge matching behavior.
final void	setCheckSpHyb(boolean checkSp)	Sets whether the sp-hybridization state of the atoms should be considered.
void	setChemTermsFilter(String value)	Sets the Chemical Terms filter expression.
void	setChemTermsFilterConfig(File file)	Sets the configuration file for Chemical Terms filter.
void	setChemTermsFilterConfig(String value)	Sets the configuration string for Chemical Terms filter.
void	setCopolymerMatching(boolean value)	Adjusts copolymer matching mode.
final 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.
final void	setExactBondMatching(boolean value)	Specifies whether bond types should match exactly - looking for query bonds target.
final void	setExactQueryAtomMatching(boolean isExact)	Sets whether exact query atom matching should be used or not.
void	setExactSpecialAtomMatching(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.
final void	setIgnoreAxialStereo(boolean value)	Sets ignoring axial stereo information during serching.
final void	setIgnoreCumuleneOrRingCisTransStereo(boolean value)	Sets ignoring cumulene cis-trans stereo information during serching.
final void	setIgnoreDoubleBondStereo(boolean value)	Sets ignoring double bond stereo information during serching.
final void	setIgnoreSynAntiStereo(boolean value)	Sets ignoring syn-anti stereo information during serching.
final void	setIgnoreTetrahedralStereo(boolean value)	Sets ignoring tetrahedral stereo information during serching.
void	setImplicitHMatching(int value)	Set option for matching implicit and explicit hydrogens.
final 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.
final void	setMonomerTransform(boolean value)	Adjusts if monomers should be transformed to structural repeating units if the monomer is homolopolimerizable.
void	setOption(String name, String value)	Sets search options.
void	setOptions(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.
final 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.
final 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 behavior of an undefined R atom in the query.
void	setUndefinedRAtom(int value, boolean userDefined)	For internal use only! Sets the undefined R-atom matching behavior with a flag denoting whether the value comes from the user (outside) or else from the default R-atom matching setting in invalid reference RgroupDecomposition#setQuery(chemaxon.struc.Molecule) .
void	setUndefinedRAtomUserDefined(boolean undefinedRAtomUserDefined)	For internal use only!
void	setVagueBondLevel(int value)	Option for less strict evaluation of query bonds (e.g.
final void	setValenceMatching(boolean value)	Set valence check option.
void	setVerbose(boolean verboseP)	For debugging purposes only.
ArrayList<String>	toList()	Returns the text representation of this options object as a list of "optionname:optionvalue" strings.
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)
String	toString(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 Details

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 Details

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 Details

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 final 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(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(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 final 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

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 SearchOptions clone()
                    throws CloneNotSupportedException

Makes an identical copy of this SearchObject.

Overrides:

clone in class Object

Throws:

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(String name,
 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 String getOption(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(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:

IllegalArgumentException - otherwise.

returnOptionString

protected 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 behavior.
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 final 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 behavior.
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 final void setChargeMatching(int value)

Set charge matching behavior.

Parameters:

value - Specifies the charge searching behavior.
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 final 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 behavior.

Returns:

Radical searching behavior.
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 final void setRadicalMatching(int value)

Set the radical matching mode.

Parameters:

value - Specifies the radical searching behavior.
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

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)

setMonomerTransform

public final 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

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.ALL.

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.ALL.

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.NONE.

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.NONE.

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:

behavior 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 final 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 behavior 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(String value)

Sets the Chemical Terms filter expression.

Parameters:

value - the Chemical Terms filter expression
Default value is null.

See Also:

• getChemTermsFilter()
• Chemical Terms documentation

getChemTermsFilter

public final 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(File file)
                              throws 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:

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(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 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 behavior of an undefined R atom in the query.

Possible values for search:

• SearchConstants.UNDEF_R_MATCHING_ALL
• SearchConstants.UNDEF_R_MATCHING_UNDEF_R
• SearchConstants.UNDEF_R_MATCHING_GROUP (default)
• SearchConstants.UNDEF_R_MATCHING_GROUP_H
• SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY

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

setUndefinedRAtom

public void setUndefinedRAtom(int value,
 boolean userDefined)

For internal use only! Sets the undefined R-atom matching behavior with a flag denoting whether the value comes from the user (outside) or else from the default R-atom matching setting in

invalid reference

RgroupDecomposition#setQuery(chemaxon.struc.Molecule)

.

Parameters:

value - Matching mode value.

userDefined - true if (outside) user setting, false if called from RgroupDecomposition when setting the default behavior for the query

isUndefinedRAtomUserDefined

public boolean isUndefinedRAtomUserDefined()

Fot internal use only! Returns whether the undefined R-atom matching behavior was set externally (user-defined) or else internally as default for a specific query from

invalid reference

RgroupDecomposition#setQuery(chemaxon.struc.Molecule)

.

Returns:

true if the undefined R-atom matching behavior was set externally, false if internally from RgroupDecomposition

See Also:

• setUndefinedRAtom(int value, boolean userDefined)

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 behavior 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

• SearchConstants.UNDEF_R_MATCHING_GROUP
• SearchConstants.UNDEF_R_MATCHING_GROUP_H
• SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY

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 behavior (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 behavior (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.

Returns:

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)
• 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 behavior (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 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)
• 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 behavior (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.

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:

• setUndefinedRAtom(int)
• 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(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 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(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 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()

Is 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()

toString

public 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 Object

Returns:

a string in format "optionname1:optionvalue1 optionname2:optionvalue2 ..."

See Also:

• setOptions(String)
• toList()

toString

public String toString(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 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 String getAllOptionsAsString(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 ArrayList<String> toList()

Returns the text representation of this options object as a list of "optionname:optionvalue" strings. Only those options are listed that have non-default values.

Returns:

a list containing the non-default options as "optionname:optionvalue" pairs

getOptionNames

public Collection<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

fillOptionList

protected void fillOptionList(ArrayList<String> ret,
 SearchOptions so)

Fills ret with "optionname:optionvalue" pairs. optionname is a property of SearchOptions class and optionvalue is not a default value (except dissimilarity threshold in case of similarity search)