@PublicAPI public class MolSearchOptions extends SearchOptions implements SearchConstants, java.lang.Cloneable
Search
implementations(ex: MolSearch).DEFAULT_TIMEOUT_LIMIT, dirty, timeoutLimitMilliseconds, verbose
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 and Description |
---|
MolSearchOptions(int searchType)
Creates a MolSearchOptions object while setting different search options
according to a predefined search type.
|
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.
|
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
public MolSearchOptions(int searchType)
SearchConstants.NO_SCREEN
,
SearchConstants.NO_ABAS
,
SearchConstants.SUBSTRUCTURE
(default),
SearchConstants.SUPERSTRUCTURE
(no query features allowed),
SearchConstants.FULL
,
SearchConstants.DUPLICATE
and
SearchConstants.FULL_FRAGMENT
.
searchType
- the predefined search typepublic boolean isQueryAbsoluteStereo()
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.
true
.setQueryAbsoluteStereo(boolean)
public void setQueryAbsoluteStereo(boolean value)
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.
true
.isQueryAbsoluteStereo()
public boolean isTargetAbsoluteStereo()
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.
true
setTargetAbsoluteStereo(boolean)
public void setTargetAbsoluteStereo(boolean value)
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.
true
.isTargetAbsoluteStereo()
public int getHitIndexType()
SearchConstants.MARKUSH_HIT_ORIGINAL
.setHitIndexType(int)
,
SearchConstants.MARKUSH_HIT_ORIGINAL
,
SearchConstants.MARKUSH_HIT_INNER
public void setHitIndexType(int value)
value
- specifies the representation on which the hit indexes are given
in case of Markush search.
SearchConstants.MARKUSH_HIT_ORIGINAL
.SearchConstants.MARKUSH_HIT_ORIGINAL
,
SearchConstants.MARKUSH_HIT_INNER
,
getHitIndexType()
public boolean isMarkushEnabled()
false
.setMarkushEnabled(boolean)
public void setMarkushEnabled(boolean value)
value
- true, if a target containing Markush features
should be treated as Markush library
false
.isMarkushEnabled()
public void setDistinctFirstAtomMatching(boolean b)
SearchOptions.setKeepQueryOrder(boolean)
is set to true. This must
be set to true, or the first atom can be arbitrary atom.b
- if true the first atom of the query must match on different target atoms
in findAll and findNext searches.
false
.isDistinctFirstAtomMatching()
public boolean isDistinctFirstAtomMatching()
SearchOptions.setKeepQueryOrder(boolean)
is set to true. This must
be set to true, or the first atom can be arbitrary atom.true
if first atom should be different
false
.setDistinctFirstAtomMatching(boolean)
@Deprecated public void setSwitchOffAllProtectsForTDF(boolean value)
SearchOptions.setTautomerSearch(int)
with value
SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
ignores it.value
- true
if all protects should be disabled
during generic tautomer creation.
Default is false
.isSwitchOffAllProtectsForTDF()
@Deprecated public final boolean isSwitchOffAllProtectsForTDF()
SearchOptions.setTautomerSearch(int)
with value
SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
ignores it.true
if protect features should be disabled during generic tautomer
creation false
.setSwitchOffAllProtectsForTDF(boolean)
public java.lang.Object clone() throws java.lang.CloneNotSupportedException
SearchOptions
clone
in class SearchOptions
java.lang.CloneNotSupportedException
public void clonecopy(SearchOptions other)
other
.
It copies
other
is a MolSearchOptions object
clonecopy
in class SearchOptions
other
- search option to overwrite.public void clonecopyOptions(SearchOptions other)
SearchOptions
clonecopyOptions
in class SearchOptions
other
- search option object to overwritepublic java.util.ArrayList<java.lang.String> toList()
toList
in class SearchOptions
SearchOptions.setOptions(String)
,
SearchOptions.toString()
@Beta public chemaxon.sss.search.options.TautomerTransformationMode getTautomerEqualityMode()
@Beta public void setTautomerEqualityMode(chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode)