Package chemaxon.sss.search
Class MolSearchOptions
- java.lang.Object
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- chemaxon.sss.search.SearchOptions
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- chemaxon.sss.search.MolSearchOptions
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- All Implemented Interfaces:
SearchConstants
,Serializable
,Cloneable
@PublicAPI public class MolSearchOptions extends SearchOptions implements SearchConstants, Cloneable
Class to encapsulate search parameters used bySearch
implementations(ex: MolSearch).- Since:
- 5.0
- See Also:
- Serialized Form
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Field Summary
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Fields inherited from class chemaxon.sss.search.SearchOptions
DEFAULT_TIMEOUT_LIMIT, dirty, timeoutLimitMilliseconds, verbose
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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
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Constructor Summary
Constructors Constructor Description MolSearchOptions(int searchType)
Creates a MolSearchOptions object while setting different search options according to a predefined search type.
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description Object
clone()
Makes an identical copy of this SearchObject.void
clonecopy(SearchOptions other)
Copies parameters toother
.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, butSearchOptions.setTautomerSearch(int)
with valueSearchConstants.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 librariesvoid
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, butSearchOptions.setTautomerSearch(int)
with valueSearchConstants.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)
ArrayList<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
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Constructor Detail
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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
andSearchConstants.FULL_FRAGMENT
.- Parameters:
searchType
- the predefined search type
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Method Detail
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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 istrue
.- See Also:
setQueryAbsoluteStereo(boolean)
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setQueryAbsoluteStereo
public void setQueryAbsoluteStereo(boolean value)
Sets whether the chiral flag should be ignored or not for the query molecule.- Parameters:
value
- iftrue
, 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 istrue
.- See Also:
isQueryAbsoluteStereo()
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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 istrue
- See Also:
setTargetAbsoluteStereo(boolean)
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setTargetAbsoluteStereo
public void setTargetAbsoluteStereo(boolean value)
Sets whether the chiral flag should be ignored or not for the target molecule.- Parameters:
value
- iftrue
, 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 istrue
.- See Also:
isTargetAbsoluteStereo()
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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 isSearchConstants.MARKUSH_HIT_ORIGINAL
. - See Also:
setHitIndexType(int)
,SearchConstants.MARKUSH_HIT_ORIGINAL
,SearchConstants.MARKUSH_HIT_INNER
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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 isSearchConstants.MARKUSH_HIT_ORIGINAL
.- See Also:
SearchConstants.MARKUSH_HIT_ORIGINAL
,SearchConstants.MARKUSH_HIT_INNER
,getHitIndexType()
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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 isfalse
. - Since:
- 5.0
- See Also:
setMarkushEnabled(boolean)
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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 isfalse
.- Since:
- 5.0
- See Also:
isMarkushEnabled()
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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 theSearchOptions.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 isfalse
.- See Also:
isDistinctFirstAtomMatching()
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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 theSearchOptions.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 isfalse
.- See Also:
setDistinctFirstAtomMatching(boolean)
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setSwitchOffAllProtectsForTDF
@Deprecated public void setSwitchOffAllProtectsForTDF(boolean value)
Deprecated.Since JChem 5.12, stereo is considered as default in tautomer regions, butSearchOptions.setTautomerSearch(int)
with valueSearchConstants.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 isfalse
.- See Also:
isSwitchOffAllProtectsForTDF()
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isSwitchOffAllProtectsForTDF
@Deprecated public final boolean isSwitchOffAllProtectsForTDF()
Deprecated.Since JChem 5.12, stereo is considered as default in tautomer regions, butSearchOptions.setTautomerSearch(int)
with valueSearchConstants.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 isfalse
.- See Also:
setSwitchOffAllProtectsForTDF(boolean)
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clone
public Object clone() throws CloneNotSupportedException
Description copied from class:SearchOptions
Makes an identical copy of this SearchObject.- Overrides:
clone
in classSearchOptions
- Throws:
CloneNotSupportedException
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clonecopy
public void clonecopy(SearchOptions other)
Copies parameters toother
. It copies
- all parameters ifother
is a MolSearchOptions object
- only the parameters defined in SearchOptions if it is a SearchOptions or JchemSearchOptions object- Overrides:
clonecopy
in classSearchOptions
- Parameters:
other
- search option to overwrite.
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clonecopyOptions
public void clonecopyOptions(SearchOptions other)
Description copied from class:SearchOptions
Copies all search options except search type to other.- Overrides:
clonecopyOptions
in classSearchOptions
- Parameters:
other
- search option object to overwrite
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toList
public ArrayList<String> toList()
Get all search option names.- Overrides:
toList
in classSearchOptions
- Returns:
- a list containing all search option names
- See Also:
SearchOptions.setOptions(String)
,SearchOptions.toString()
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getTautomerEqualityMode
@Beta public chemaxon.sss.search.options.TautomerTransformationMode getTautomerEqualityMode()
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setTautomerEqualityMode
@Beta public void setTautomerEqualityMode(chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode)
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