chemaxon.sss.search
Class SearchOptions

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

All Implemented Interfaces:

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

Direct Known Subclasses:

JChemSearchOptions, MolSearchOptions

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:

Szabolcs Csepregi Date: 27-Mar-2007, Tamas Csizmazia, Vencel Bors

See Also:

Serialized Form

Field Summary

protected boolean	dirty This flag is set to true whenever any of the options change.
protected int[]	options Field to store various options of the search.
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, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SEARCHTYPE, DISSIMILARITY_PROPERTY_NAME, DUPLICATE, FULL, FULL_FRAGMENT, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, HIT_EXCLUDEDQ, HIT_LP, HIT_MULTICENTER, HIT_NON_R, HIT_ORDERING_NONE, HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST, HIT_R, HIT_R_EMPTY_MATCH, HIT_UNMAPABLE, IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, IMPLICIT_H_MATCHING_ENABLED, IMPLICIT_H_MATCHING_IGNORE, ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, MARKUSH_AROM_FINAL_CHECK, MARKUSH_AROM_NO_FINAL_CHECK, MARKUSH_AROM_OFF, MARKUSH_HIT_INNER, MARKUSH_HIT_ORIGINAL, MARKUSH_MCS, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, NO_ABAS, NO_SCREEN, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, SEARCH_MODE_NAMES, SEARCH_OPTIONS_LENGTH, SIMILARITY, STEREO_DIASTEREOMER, STEREO_ENANTIOMER, STEREO_EXACT, STEREO_IGNORE, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, STEREO_SPECIFIC, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_DEFAULT, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, UNDEF_R_MATCHING_ALL, UNDEF_R_MATCHING_GROUP, UNDEF_R_MATCHING_GROUP_H, UNDEF_R_MATCHING_GROUP_H_EMPTY, UNDEF_R_MATCHING_UNDEF_R, VAGUE_BOND_DEFAULT, VAGUE_BOND_LEVEL_HALF, VAGUE_BOND_LEVEL1, VAGUE_BOND_LEVEL2, VAGUE_BOND_LEVEL3, VAGUE_BOND_LEVEL4, VAGUE_BOND_OFF

Constructor Summary

SearchOptions()
Deprecated. As of relase 5.5, replaced by SearchOptions(int)

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

Method Summary

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.
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
java.lang.String	getOption(java.lang.String name) Returns option value in string format.
protected java.lang.String[]	getOptionNames()
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 Default value is SetOfSmallestRingsOption.SSSR
int	getStereoModel() Get the stereo model option.
int	getStereoSearchType() Get the stereo search type option.
int	getTautomerSearch() Indicates if tautomers of the query should be enumerated for search.
int	getTimeoutLimit() Deprecated. since 5.6 use getTimeoutLimitMilliseconds() instead
int	getTimeoutLimitMilliseconds() The search timeouts reaching this amount of time.
int	getUndefinedRAtom() Returns undefined R atom matching behaviour mode.
MolComparator[]	getUserComparators() Because of efficiency reasons one should check hasUserComparators() before calling this method!
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	isExactFragment() Deprecated. since 5.6, replaced by isFullFragment()
boolean	isExactQueryAtomMatching() Returns whether exact matching of query atom information is set.
boolean	isFullFragment() Get option whether heavy atoms can occur in target besides the returned hit fragments.
boolean	isIgnoreAlleneStereo() Retrieves if allene stereo is ignored during searching.
boolean	isIgnoreAxialStereo() Retrieves if axial stereo is ignored during searching.
boolean	isIgnoreCTExceptions() Get whether only syntactical exceptions are thrown for chemical terms.
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	isPerfectSearchType() Get whether search should match only if query and target are exact matches.
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	isQHomologyHandling() Deprecated. since 5.6, use getHomologyNarrowTranslation()
boolean	isReactionUnpairedMapMatching() Get whether unpaired(orphan or widow) atom maps can match any atom.
boolean	isSubgraphSearch() Returns the subgraph matching option.
boolean	isSuperstructureSearch() True if the current search type is superstructure search.
boolean	isTautomerDuplicateFiltering() Deprecated. since 5.5, replace with getTautomerSearch()
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 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.lang.String value) Sets the configuration string for Chemical Terms filter.
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	setExactFragment(boolean value) Deprecated. since 5.6, replaced by SearchOptions(int)
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	setFullFragment(boolean value) Deprecated. since 5.6, replaced by SearchOptions(int)
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	setIgnoreAlleneStereo(boolean value) Sets ignoring allene stereo information during serching.
void	setIgnoreAxialStereo(boolean value) Sets ignoring axial stereo information during serching.
void	setIgnoreCTExceptions(boolean value) If set true, only syntactical exceptions will be thrown.
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	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	setQHomologyHandling(boolean value) Deprecated. since 5.6, use setHomologyNarrowTranslation(HomologyTranslationOption)
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	setSearchType(int searchType) Deprecated. As of release 5.5, replaced by SearchOptions(int)
protected void	setSearchType0(int searchType) Sets different search options according to a predefined search type.
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	setSubgraphSearch(boolean value) Specifies the matching mode for topology search.
void	setSuperstructureSearch(boolean value) Sets if the current search type is superstructure search.
void	setTautomerDuplicateFiltering(boolean value) Deprecated. As of release 5.5, replaced by setTautomerSearch(int)
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	setTimeoutLimit(int value) Deprecated. since 5.6 use setTimeoutLimitMilliseconds(int) instead
void	setTimeoutLimitMilliseconds(int value) The search timeouts reaching this amount of time.
void	setUndefinedRAtom(int value) Sets the matching behaviour of an undefined R atom in the query.
void	setVagueBondLevel(int value) Option for less strict evaluation of query bonds (e.g. ambiguous aromaticity).
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.

options

protected int[] options

Field to store various options of the search.

Constructor Detail

SearchOptions

@Deprecated
public SearchOptions()

Deprecated. As of relase 5.5, replaced by SearchOptions(int)

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

See Also:

SearchOptions(int)

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.NO_SCREEN, SearchConstants.NO_ABAS, SearchConstants.SUBSTRUCTURE (default), SearchConstants.SUPERSTRUCTURE (no query features allowed), SearchConstants.SIMILARITY, SearchConstants.FULL, SearchConstants.DUPLICATE, SearchConstants.FULL_FRAGMENT and SearchConstants.MARKUSH_MCS.

Parameters:

searchType - the predefined search type

Method Detail

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.

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 chemaxon.struc.StereoConstants.DBS_MARKED

• chemaxon.struc.StereoConstants.DBS_NONE: No double bond cis/trans is considered.
• chemaxon.struc.StereoConstants.DBS_MARKED: (Default) Double bond cis/trans stereo is checked for double bonds designated by the stereo search flag only.
• chemaxon.struc.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

setSearchType

@Deprecated
public void setSearchType(int searchType)

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

Sets different search options according to a predefined search type. For full explanation see JChem Query Guide. Acceptable values: SearchConstants.NO_SCREEN, SearchConstants.NO_ABAS, SearchConstants.SUBSTRUCTURE (default), SearchConstants.SUPERSTRUCTURE (no query features allowed), SearchConstants.SIMILARITY, SearchConstants.FULL, SearchConstants.DUPLICATE, SearchConstants.FULL_FRAGMENT and SearchConstants.MARKUSH_MCS.

WARNING: This method may affect other search settings, therefore if other search options are adjusted, this method should be called first! For affected search options, see links below.

Parameters:

searchType - the predefined search type

See Also:

SearchOptions(int), setExactBondMatching(boolean), setExactQueryAtomMatching(boolean), setSubgraphSearch(boolean)

setSearchType0

protected void setSearchType0(int searchType)

Sets different search options according to a predefined search type. For full explanation see JChem Query Guide. Acceptable values: SearchConstants.NO_SCREEN, SearchConstants.NO_ABAS, SearchConstants.SUBSTRUCTURE (default), SearchConstants.SUPERSTRUCTURE (no query features allowed), SearchConstants.SIMILARITY, SearchConstants.FULL, SearchConstants.DUPLICATE, SearchConstants.FULL_FRAGMENT and SearchConstants.MARKUSH_MCS.

WARNING: This method may affect other search settings, therefore if other search options are adjusted, this method should be called first! For affected search options, see links below.

Parameters:

searchType - the predefined search type

See Also:

setExactBondMatching(boolean), setExactQueryAtomMatching(boolean), setSubgraphSearch(boolean)

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.MARKUSH_MCS, SearchConstants.SIMILARITY

isPerfectSearchType

public final boolean isPerfectSearchType()

Get whether search should match only if query and target are exact matches. Same as duplicate search.

Returns:

whether this search is a DUPLICATE search or not.
Default value depends on search type.

See Also:

SearchConstants.DUPLICATE

isSubgraphSearch

public boolean isSubgraphSearch()

Returns the subgraph matching option.

Returns:

true if substructure search, false if the full molecular graph must match, e.g. full structure search or duplicate match.
Default value depends on search type.

See Also:

setSubgraphSearch(boolean)

setSubgraphSearch

public void setSubgraphSearch(boolean value)

Specifies the matching mode for topology search.
Internal use only. Used when it is important to keep all search option settings, but it is needed to search only for a substructure. Preferred way of usage is through SearchOptions(int) constructor.

Parameters:

value - true for substructure search, false for full structure search matching

See Also:

SearchOptions(int), isSubgraphSearch()

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)

isSuperstructureSearch

public final boolean isSuperstructureSearch()

True if the current search type is superstructure search. This property is usually set indirectly through setSearchType.

Returns:

true in case of superstructure search.
Default value depends on search type.

See Also:

SearchConstants.SUPERSTRUCTURE, setSuperstructureSearch(boolean)

setSuperstructureSearch

public void setSuperstructureSearch(boolean value)

Sets if the current search type is superstructure search. This property is usually set indirectly through setSearchType in case of superstructure search.
Internal use only. Used when it is important to keep all search option settings, but it is needed to search only for a superstructure. Preferred way of usage is through SearchOptions(int) constructor.

Parameters:

value - is true if current search should be superstructure, false otherwise
Default value depends on search type.

See Also:

setSearchType(int), SearchConstants.SUPERSTRUCTURE

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:

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 depends on search type.

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_LEVEL1.

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, 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_LEVEL1.

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 occured 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()

Because of efficiency reasons one should check hasUserComparators() before calling this method!

Returns:

MolComparator[] of 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.

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.

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.

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, 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'.

Useable search parameters:

orderSensitive

tautomer

stereoSearchType

ignoreTetrahedralStereo

ignoreDoubleBondStereo

ignoreAxialStereo

ignoreAlleneStereo

ignoreSynAntiStereo

keepQueryOrder

exactAtomMatching

exactBondMatching

exactQueryAtomMatching

exactRadicalMatching

exactIsotopeMatching

exactChargeMatching

checkSpHyb

doubleBondStereo

HCountMatching

t

implicitHMatching

vagueBond

completeHG

charge

isotope

radical

valence

mix

polymer

endGroupMatching

transformMonomer

markush

stereoModel

undefinedRAtom

bridgingRAllowed

RLigandEqualityCheck

hitOrdering

reactionUnpairedMap

attachedDataMatch

attachedDataPrefixes

exactSpecialAtomMatching

ignoreCTExceptions

exhaustiveModeLimit

timeoutLimit

tdf

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).

Useable search parameters:

orderSensitive

tautomer

stereoSearchType

keepQueryOrder

checkSpHyb

exactBondMatching

exactQueryAtomMatching

doubleBondStereo

HCountMatching

t

implicitHMatching

reactionUnpairedMap

vagueBond

completeHG

charge

isotope

radical

valence

mix

polymer

stereoModel

undefinedRAtom

bridgingRAllowed

RLigandEqualityCheck

hitOrdering

attachedDataMatch

attachedDataPrefixes

exactSpecialAtomMatching

ignoreCTExceptions

exhaustiveModeLimit

timeoutLimit

tdf

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.

isExactFragment

@Deprecated
public final boolean isExactFragment()

Deprecated. since 5.6, replaced by isFullFragment()

Get option whether heavy atoms can occur in target besides the returned hit fragments.

Returns:

true if the query only matches to full(exact) fragments of the target. (No heavy atoms outside the match and each query fragment corresponds to a target fragment.) Same as isFullFragment().
Default value is true.

setExactFragment

@Deprecated
public void setExactFragment(boolean value)

Deprecated. since 5.6, replaced by SearchOptions(int)

Specifies if heavy atoms can occur outside the match. Same as setFullFragment(boolean)

Parameters:

value - true, if the query should only match to full fragments of the target. (No heavy atoms outside the match and each query fragment corresponds to a target fragment.) Same as setFullFragment(boolean).
Default value depends on search type.

isFullFragment

public final boolean isFullFragment()

Get option whether heavy atoms can occur in target besides the returned hit fragments.

Returns:

true if the query only matches to full fragments of the target. (No heavy atoms outside the match and each query fragment corresponds to a target fragment.) Same as isExactFragment().
Default value depends on search type.

setFullFragment

@Deprecated
public void setFullFragment(boolean value)

Deprecated. since 5.6, replaced by SearchOptions(int)

Specifies if heavy atoms can occur outside the match. Same as setExactFragment(boolean)

Parameters:

value - true, if the query should only match to full fragments of the target. (No heavy atoms outside the match and each query fragment corresponds to a target fragment.)
Default value is true.

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)

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)

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)

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

isQHomologyHandling

@Deprecated
public final boolean isQHomologyHandling()

Deprecated. since 5.6, use getHomologyNarrowTranslation()

Get query side homology matching option.

Returns:

true if the query-side homology matching mode is set.
Default value is true.

See Also:

Query features documentation

setQHomologyHandling

@Deprecated
public void setQHomologyHandling(boolean value)

Deprecated. since 5.6, use setHomologyNarrowTranslation(HomologyTranslationOption)

Adjusts query side homology matching mode. If set, then pseudo atoms with homology names on the query side are handled as homology groups. If false they are handled as pseudo atoms and match only pseudo atoms with the same name.

Parameters:

value - true if homology handling should be set, false otherwise.
Default value is true.

See Also:

Query features 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()

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)

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 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, 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.

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)

setIgnoreAlleneStereo

public final void setIgnoreAlleneStereo(boolean value)

Sets ignoring allene stereo information during serching. This stereo option is not supported for DB searches.

Parameters:

value - the value to set, set true to ignore.
Default value is true.

isIgnoreAlleneStereo

public final boolean isIgnoreAlleneStereo()

Retrieves if allene stereo is ignored during searching.

Returns:

true if ignored.
Default value is true.

See Also:

setIgnoreAlleneStereo(boolean)

setIgnoreAxialStereo

public final void setIgnoreAxialStereo(boolean value)

Sets ignoring axial stereo information during serching. This stereo option is not supported for DB searches.

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.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.

Parameters:

value - 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, getUndefinedRAtom(), Special search types documentation

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

• 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 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)

isIgnoreCTExceptions

public final boolean isIgnoreCTExceptions()

Get whether only syntactical exceptions are thrown for chemical terms.

Returns:

true if Chemical Terms exceptions should be ignored during evalution
Default value is false.

setIgnoreCTExceptions

public void setIgnoreCTExceptions(boolean value)

If set true, only syntactical exceptions will be thrown. Those molecules that return exception during evaluation will be left out from hit list.

Parameters:

value - true if Chemical Terms exceptions should be ignored during evalution
Default value is false.

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()

getTimeoutLimit

@Deprecated
public final int getTimeoutLimit()

Deprecated. since 5.6 use getTimeoutLimitMilliseconds() instead

The search timeouts reaching this number of steps.

Returns:

The timeout step limit.
Default value is 10000000.

See Also:

setTimeoutLimit(int)

setTimeoutLimit

@Deprecated
public void setTimeoutLimit(int value)

Deprecated. since 5.6 use setTimeoutLimitMilliseconds(int) instead

The search timeouts reaching this number of steps. Set it to -1 if you do not want the search to time out.

Parameters:

value - The step limit to set.
Default value is 10000000.

See Also:

getTimeoutLimit()

getTimeoutLimitMilliseconds

public final int getTimeoutLimitMilliseconds()

The search 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 timeouts reaching this amount of time. Set it to -1 if you do not want the search to time out.

Parameters:

value - The time limit to set in milliseconds.
Default value is 120000.

See Also:

getTimeoutLimitMilliseconds()

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()

setTautomerDuplicateFiltering

@Deprecated
public void setTautomerDuplicateFiltering(boolean value)

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

Set option for using the generic tautomers of the target and query when searching.

Parameters:

value - true if generic tautomers of query and target should be used during search. (Effective only in case of duplicate search.)
Default value is false.

See Also:

setTautomerSearch(int), getTautomerSearch(), SearchConstants.TAUTOMER_SEARCH_ON, SearchConstants.TAUTOMER_SEARCH_OFF, SearchConstants.TAUTOMER_SEARCH_DEFAULT

isTautomerDuplicateFiltering

@Deprecated
public final boolean isTautomerDuplicateFiltering()

Deprecated. since 5.5, replace with getTautomerSearch()

Get whether search should use tautomer duplicate filtering.

Returns:

true if generic tautomers of query and target should be used during search. (Effective only in case of duplicate search.)
Default value is false.

See Also:

setTautomerSearch(int), getTautomerSearch(), SearchConstants.TAUTOMER_SEARCH_ON, SearchConstants.TAUTOMER_SEARCH_OFF, SearchConstants.TAUTOMER_SEARCH_DEFAULT

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

protected java.lang.String[] getOptionNames()