chemaxon.sss.search

Class MolSearchOptions

java.lang.Object

chemaxon.sss.search.SearchOptions

chemaxon.sss.search.MolSearchOptions

All Implemented Interfaces:

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

@PublicAPI
public class MolSearchOptions
extends SearchOptions
implements SearchConstants, java.lang.Cloneable

Class to encapsulate search parameters used by Search implementations(ex: MolSearch).

Since:

5.0

Author:

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

See Also:

Serialized Form

Field Summary

Fields inherited from class chemaxon.sss.search.SearchOptions

DEFAULT_TIMEOUT_LIMIT, dirty, timeoutLimitMilliseconds, verbose

Fields inherited from interface chemaxon.sss.SearchConstants

ABS_STEREO_ALWAYS_ON, ABS_STEREO_CHIRAL_FLAG, ABS_STEREO_TABLE_OPTION, ATTACHED_DATA_MATCH_EXACT, ATTACHED_DATA_MATCH_GENERAL, ATTACHED_DATA_MATCH_IGNORE, ATTACHMENT_ATOM, ATTACHMENT_LABEL, ATTACHMENT_MAP, ATTACHMENT_NONE, ATTACHMENT_POINT, ATTACHMENT_RLABEL, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SEARCHTYPE, DISSIMILARITY_PROPERTY_NAME, DUPLICATE, FULL, FULL_FRAGMENT, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, HIT_EXCLUDEDQ, HIT_LP, HIT_MULTICENTER, HIT_NON_R, HIT_ORDERING_NONE, HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST, HIT_R, HIT_R_EMPTY_MATCH, HIT_UNMAPABLE, IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, IMPLICIT_H_MATCHING_ENABLED, IMPLICIT_H_MATCHING_IGNORE, ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, MARKUSH_HIT_INNER, MARKUSH_HIT_ORIGINAL, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, NO_ABAS, NO_SCREEN, POSITION_ON_0TH_HEAVY_ATOM, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, SEARCH_MODE_NAMES, SEARCH_TYPE_NAMES, SIMILARITY, STEREO_DIASTEREOMER, STEREO_ENANTIOMER, STEREO_EXACT, STEREO_IGNORE, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, STEREO_SPECIFIC, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_DEFAULT, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO, UNDEF_R_MATCHING_ALL, UNDEF_R_MATCHING_GROUP, UNDEF_R_MATCHING_GROUP_H, UNDEF_R_MATCHING_GROUP_H_EMPTY, UNDEF_R_MATCHING_UNDEF_R, VAGUE_BOND_DEFAULT, VAGUE_BOND_LEVEL_HALF, VAGUE_BOND_LEVEL1, VAGUE_BOND_LEVEL2, VAGUE_BOND_LEVEL3, VAGUE_BOND_LEVEL4, VAGUE_BOND_OFF

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
java.lang.Object	clone() Makes an identical copy of this SearchObject.
void	clonecopy(SearchOptions other) Copies parameters to other.
void	clonecopyOptions(SearchOptions other) Copies all search options except search type to other.
int	getHitIndexType() Returns the representation on which the hit indexes are given in case of Markush search.
chemaxon.sss.search.options.TautomerTransformationMode	getTautomerEqualityMode()
boolean	isDistinctFirstAtomMatching() Get option ensuring that upon the findNext() call the first atom must be stepped as well.
boolean	isMarkushEnabled() Specifies whether a target containing Markush features should be treated as a Markush library.
boolean	isQueryAbsoluteStereo() Returns whether the chiral flag is ignored or not for the query molecule.
boolean	isSwitchOffAllProtectsForTDF() Deprecated. Since JChem 5.12, stereo is considered as default in tautomer regions, but SearchOptions.setTautomerSearch(int) with value SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO ignores it.
boolean	isTargetAbsoluteStereo() Returns whether the chiral flag is ignored or not for the target molecule.
void	setDistinctFirstAtomMatching(boolean b) Option ensuring that upon the findNext() call the first atom must be stepped as well.
void	setHitIndexType(int value) Set the representation to use for hit indexes in case of Markush search.
void	setMarkushEnabled(boolean value) Sets whether targets containing Markush features should be treated as Markush libraries
void	setQueryAbsoluteStereo(boolean value) Sets whether the chiral flag should be ignored or not for the query molecule.
void	setSwitchOffAllProtectsForTDF(boolean value) Deprecated. Since JChem 5.12, stereo is considered as default in tautomer regions, but SearchOptions.setTautomerSearch(int) with value SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO ignores it.
void	setTargetAbsoluteStereo(boolean value) Sets whether the chiral flag should be ignored or not for the target molecule.
void	setTautomerEqualityMode(chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode)
java.util.ArrayList<java.lang.String>	toList() Get all search option names.

Methods inherited from class chemaxon.sss.search.SearchOptions

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

Methods inherited from class java.lang.Object

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

Constructor Detail

MolSearchOptions

public MolSearchOptions(int searchType)

Creates a MolSearchOptions 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.FULL, SearchConstants.DUPLICATE and SearchConstants.FULL_FRAGMENT.

Parameters:

searchType - the predefined search type

Method Detail

isQueryAbsoluteStereo

public boolean isQueryAbsoluteStereo()

Returns whether the chiral flag is ignored or not for the query molecule.

Returns:

true, if chiral centers in the query molecule are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
Default value is true.

See Also:

setQueryAbsoluteStereo(boolean)

setQueryAbsoluteStereo

public void setQueryAbsoluteStereo(boolean value)

Sets whether the chiral flag should be ignored or not for the query molecule.

Parameters:

value - if true, chiral centers in the query molecule are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
Default value is true.

See Also:

isQueryAbsoluteStereo()

isTargetAbsoluteStereo

public boolean isTargetAbsoluteStereo()

Returns whether the chiral flag is ignored or not for the target molecule.

Returns:

true, if chiral centers in the target molecule are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
Default value is true

See Also:

setTargetAbsoluteStereo(boolean)

setTargetAbsoluteStereo

public void setTargetAbsoluteStereo(boolean value)

Sets whether the chiral flag should be ignored or not for the target molecule.

Parameters:

value - if true, chiral centers in the target molecule are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
Default value is true.

See Also:

isTargetAbsoluteStereo()

getHitIndexType

public int getHitIndexType()

Returns the representation on which the hit indexes are given in case of Markush search.

Returns:

of which representation the hit indexes are.
Default value is SearchConstants.MARKUSH_HIT_ORIGINAL.

See Also:

setHitIndexType(int), SearchConstants.MARKUSH_HIT_ORIGINAL, SearchConstants.MARKUSH_HIT_INNER

setHitIndexType

public void setHitIndexType(int value)

Set the representation to use for hit indexes in case of Markush search.

Parameters:

value - specifies the representation on which the hit indexes are given in case of Markush search.
Default value is SearchConstants.MARKUSH_HIT_ORIGINAL.

See Also:

SearchConstants.MARKUSH_HIT_ORIGINAL, SearchConstants.MARKUSH_HIT_INNER, getHitIndexType()

isMarkushEnabled

public boolean isMarkushEnabled()

Specifies whether a target containing Markush features should be treated as a Markush library.

Returns:

true, if a target should be treated as a Markush library when it contains Markush features
Default value is false.

Since:

5.0

See Also:

setMarkushEnabled(boolean)

setMarkushEnabled

public void setMarkushEnabled(boolean value)

Sets whether targets containing Markush features should be treated as Markush libraries

Parameters:

value - true, if a target containing Markush features should be treated as Markush library
Default value is false.

Since:

5.0

See Also:

isMarkushEnabled()

setDistinctFirstAtomMatching

public void setDistinctFirstAtomMatching(boolean b)

Option ensuring that upon the findNext() call the first atom must be stepped as well. Option is considered only in case of searching a recursive SMARTS query.
The search-internal first atom is ensured to be the original first atom only if the SearchOptions.setKeepQueryOrder(boolean) is set to true. This must be set to true, or the first atom can be arbitrary atom.

Parameters:

b - if true the first atom of the query must match on different target atoms in findAll and findNext searches.
Default value is false.

See Also:

isDistinctFirstAtomMatching()

isDistinctFirstAtomMatching

public boolean isDistinctFirstAtomMatching()

Get option ensuring that upon the findNext() call the first atom must be stepped as well. Option is considered only in case of searching a recursive SMARTS query.
The search-internal first atom is ensured to be the original first atom only if the SearchOptions.setKeepQueryOrder(boolean) is set to true. This must be set to true, or the first atom can be arbitrary atom.

Returns:

true if first atom should be different
Default value is false.

See Also:

setDistinctFirstAtomMatching(boolean)

setSwitchOffAllProtectsForTDF

@Deprecated
public void setSwitchOffAllProtectsForTDF(boolean value)

Deprecated. Since JChem 5.12, stereo is considered as default in tautomer regions, but SearchOptions.setTautomerSearch(int) with value SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO ignores it.

Sets the switch off all protects for generic tautomer creation. Considered only when tautomer search is on.

Parameters:

value - true if all protects should be disabled during generic tautomer creation. Default is false.

See Also:

isSwitchOffAllProtectsForTDF()

isSwitchOffAllProtectsForTDF

@Deprecated
public final boolean isSwitchOffAllProtectsForTDF()

Deprecated. Since JChem 5.12, stereo is considered as default in tautomer regions, but SearchOptions.setTautomerSearch(int) with value SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO ignores it.

Specifies whether all protects are switched off during generic tautomer creation. Considered only when tautomer search is on.

Returns:

true if protect features should be disabled during generic tautomer creation
Default is false.

See Also:

setSwitchOffAllProtectsForTDF(boolean)

clone

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

Description copied from class: SearchOptions

Makes an identical copy of this SearchObject.

Overrides:

clone in class SearchOptions

Throws:

java.lang.CloneNotSupportedException

clonecopy

public void clonecopy(SearchOptions other)

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

Overrides:

clonecopy in class SearchOptions

Parameters:

other - search option to overwrite.

clonecopyOptions

public void clonecopyOptions(SearchOptions other)

Description copied from class: SearchOptions

Copies all search options except search type to other.

Overrides:

clonecopyOptions in class SearchOptions

Parameters:

other - search option object to overwrite

toList

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

Get all search option names.

Overrides:

toList in class SearchOptions

Returns:

a list containing all search option names

See Also:

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

getTautomerEqualityMode

@Beta
public chemaxon.sss.search.options.TautomerTransformationMode getTautomerEqualityMode()

setTautomerEqualityMode

@Beta
public void setTautomerEqualityMode(chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode)