@PublicAPI public class SearchOptions extends java.lang.Object implements SearchConstants, java.lang.Cloneable, java.io.Serializable
Modifier and Type | Field and Description |
---|---|
static int |
DEFAULT_TIMEOUT_LIMIT |
protected boolean |
dirty
This flag is set to true whenever any of the options change.
|
protected int |
timeoutLimitMilliseconds
The search on a single target timeouts reaching this number of milliseconds.
|
boolean |
verbose
For debugging purposes.
|
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 |
---|
SearchOptions(int searchType)
Creates a SearchOptions object while setting different search options
according to a predefined search type.
|
Modifier and Type | Method and Description |
---|---|
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.
|
chemaxon.sss.search.options.ChemTermsFilterOption |
getChemTermsFilterOption()
FOR INTERNAL USE ONLY
Returns the chem term filtering options.
|
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
|
MarkushAromaticityHandlingOption |
getMarkushAromHandling()
Gets the Markush aromatic search behavior.
|
java.lang.String |
getOption(java.lang.String name)
Returns option value in string format.
|
java.util.Collection<java.lang.String> |
getOptionNames()
Returns the name of all available options which can be used to set/get option values with
setOption(String, String) and getOption(String) methods. |
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
|
int |
getStereoModel()
Get the stereo model option.
|
int |
getStereoSearchType()
Get the stereo search type option.
|
TargetHomologyMatchingMode |
getTargetHomologyMatchingMode()
Returns the target homology matching mode.
|
int |
getTautomerSearch()
Indicates if tautomers of the query should be enumerated for search.
|
int |
getTimeoutLimitMilliseconds()
The search on a single target timeouts reaching this amount of time.
|
int |
getUndefinedRAtom()
Returns undefined R atom matching behaviour mode.
|
MolComparator[] |
getUserComparators()
Returns the user defined comparators.
|
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 |
isExactQueryAtomMatching()
Returns whether exact matching of query atom information is set.
|
boolean |
isIgnoreAxialStereo()
Retrieves if axial stereo is ignored during searching.
|
boolean |
isIgnoreCumuleneOrRingCisTransStereo()
Retrieves if cumulene cis-trans stereo is ignored during searching.
|
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 |
isPhaseShiftedMatching()
Get option whether phase shifted polymer matches on the original.
|
boolean |
isPolymerMatching()
Get option whether to search consider polymer sgroups during search.
|
boolean |
isReactionUnpairedMapMatching()
Get whether unpaired(orphan or widow) atom maps can match any atom.
|
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 static int |
nonPositiveToInfinite(int value) |
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.io.File file)
Sets the configuration file for Chemical Terms filter.
|
void |
setChemTermsFilterConfig(java.lang.String value)
Sets the configuration string for Chemical Terms filter.
|
void |
setChemTermsFilterOption(chemaxon.sss.search.options.ChemTermsFilterOption chemTermsFilterOption)
FOR INTERNAL USE ONLY.
|
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 |
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 |
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 |
setIgnoreAxialStereo(boolean value)
Sets ignoring axial stereo information during serching.
|
void |
setIgnoreCumuleneOrRingCisTransStereo(boolean value)
Sets ignoring cumulene cis-trans stereo information during serching.
|
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 |
setMarkushAromHandling(MarkushAromaticityHandlingOption value)
Set handling of Markush aromatization information (ambiguous aromatic rings)
during Markush search
|
void |
setMixSgroupMatching(boolean value)
Set options for mixed S-group matching.
|
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 |
setRadicalMatching(int value)
Set the radical matching mode.
|
void |
setReactionUnpairedMapMatching(boolean value)
Set option for matching unpaired(orphan or widow) atom maps to any atom.
|
void |
setRLigandEqualityCheck(boolean value)
Sets whether undefined R-atoms with the same R-group ID should match the same structure.
|
void |
setSSRType(SetOfSmallestRingsOption value)
Sets which type of set of smallest rings to use for property calculations
|
void |
setStereoModel(int value)
Set stereo model option.
|
void |
setStereoSearchType(int value)
Specifies the way stereo information is considered during searching.
|
void |
setTargetHomologyMatchingMode(TargetHomologyMatchingMode mode)
Sets the target homology matching mode option.
|
void |
setTautomerSearch(int value)
Sets if tautomers of the query should be enumerated for search.
|
void |
setThrowExceptionOnTimeout(boolean value)
Sets if search should throw exception upon timeout.
|
void |
setTimeoutLimitMilliseconds(int value)
The search on a single target timeouts reaching this amount of time.
|
void |
setUndefinedRAtom(int value)
Sets the matching behaviour of an undefined R atom in the query.
|
void |
setUndefinedRAtomUserDefined(boolean undefinedRAtomUserDefined)
For internal use only!
|
void |
setVagueBondLevel(int value)
Option for less strict evaluation of query bonds
(e.g.
|
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) |
protected boolean dirty
public boolean verbose
public static final int DEFAULT_TIMEOUT_LIMIT
protected int timeoutLimitMilliseconds
public SearchOptions(int searchType)
Acceptable values:
SearchConstants.SUBSTRUCTURE
(default);SearchConstants.FULL
;SearchConstants.FULL_FRAGMENT
;SearchConstants.DUPLICATE
;SearchConstants.SUPERSTRUCTURE
(no query features allowed);SearchConstants.SIMILARITY
;SearchConstants.NO_SCREEN
; andSearchConstants.NO_ABAS
.searchType
- the predefined search typepublic final boolean isExactQueryAtomMatching()
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.
false
.public void setExactQueryAtomMatching(boolean isExact)
isExactQueryAtomMatching()
.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.
false
except in case of duplicate search.public void setDoubleBondStereoMatchingMode(int value)
value
- The following options can be used: StereoConstants.DBS_MARKED
StereoConstants.DBS_NONE
: No double bond cis/trans is considered.
StereoConstants.DBS_MARKED
: (Default) Double bond cis/trans stereo is checked for double
bonds designated by the stereo search flag only.
StereoConstants.DBS_ALL
: All double bonds are checked for cis/trans stereo matching.
getDoubleBondStereoMatchingMode()
,
Stereochemistry documentationpublic final int getDoubleBondStereoMatchingMode()
chemaxon.struc.StereoConstants.DBS_MARKED
setDoubleBondStereoMatchingMode(int)
,
StereoConstants.DBS_ALL
,
StereoConstants.DBS_MARKED
,
StereoConstants.DBS_NONE
,
Stereochemistry documentationpublic final int getSearchType()
SearchOptions(int)
,
SearchConstants.SUBSTRUCTURE
,
SearchConstants.SUPERSTRUCTURE
,
SearchConstants.FULL
,
SearchConstants.FULL_FRAGMENT
,
SearchConstants.DUPLICATE
,
SearchConstants.SIMILARITY
public final int getHCountMatching()
SearchConstants.HCOUNT_MATCHING_AUTO
.setHCountMatching(int)
,
SearchConstants.HCOUNT_MATCHING_AUTO
,
SearchConstants.HCOUNT_MATCHING_EQUAL
,
SearchConstants.HCOUNT_MATCHING_GREATER_OR_EQUAL
public void setHCountMatching(int value)
value
- possible values:
SearchConstants.HCOUNT_MATCHING_AUTO
.SearchConstants.HCOUNT_MATCHING_AUTO
,
SearchConstants.HCOUNT_MATCHING_EQUAL
,
SearchConstants.HCOUNT_MATCHING_GREATER_OR_EQUAL
public final boolean isVerbose()
true
if debug information is displayed during search.
false
.public void setVerbose(boolean verboseP)
verboseP
- if true more detailed information is sent to the output
false
.public static int getSearchType(java.lang.String searchTypeValue)
SearchConstants
.searchTypeValue
- search type represented as stringpublic void setOptions(java.lang.String optionString)
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!)
setOption(String,String)
public void setOrderSensitiveSearch(boolean value)
orderSensitiveSearch
is true
, both cases
are returned, otherwise only one of them (the one found first).value
- set this to true
to get
results in every possible order
false
.public final boolean isOrderSensitiveSearch()
true
if hits are returned in every possible order
false
.setOrderSensitiveSearch(boolean)
public final boolean isExactBondMatching()
public void setExactBondMatching(boolean value)
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".
false
except in case of duplicate search.public void setVagueBondLevel(int value)
value
- the desired vague bond level
SearchConstants.VAGUE_BOND_LEVEL_HALF
.SearchConstants.VAGUE_BOND_OFF
,
SearchConstants.VAGUE_BOND_LEVEL_HALF
,
SearchConstants.VAGUE_BOND_LEVEL1
,
SearchConstants.VAGUE_BOND_LEVEL2
,
SearchConstants.VAGUE_BOND_LEVEL3
,
SearchConstants.VAGUE_BOND_LEVEL4
,
getVagueBondLevel()
,
Vague bond level documenationpublic final int getVagueBondLevel()
SearchConstants.VAGUE_BOND_LEVEL_HALF
.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 documenationpublic void setCompleteHG(boolean completeStr)
completeStr
- if true only complete structures are accepted,
if false all substructures.
true
.getCompleteHG()
public final boolean getCompleteHG()
true
.setCompleteHG(boolean)
public final boolean hasChangesInUserComparators()
true
if there is any changes in user-defined comparators.
After initializing the search, the change flag is cleared.getUserComparators()
,
addUserComparator(MolComparator)
,
deleteUserComparator(MolComparator)
,
deleteAllUserComparators()
,
MolComparator
public final void clearChangesInUserComparators()
public final boolean hasUserComparators()
public void addUserComparator(MolComparator mc)
mc
- user-defined MolComparatorMolComparator
,
getUserComparators()
,
deleteAllUserComparators()
public void deleteUserComparator(MolComparator mc)
mc
- user defined comparator to delete.MolComparator
,
deleteAllUserComparators()
,
addUserComparator(MolComparator)
public void deleteAllUserComparators()
public MolComparator[] getUserComparators()
MolComparator
spublic final boolean isDirty()
setDirty(boolean)
public final void setDirty(boolean v)
v
- new dirty valueisDirty()
public java.lang.Object clone() throws java.lang.CloneNotSupportedException
clone
in class java.lang.Object
java.lang.CloneNotSupportedException
public void clonecopy(SearchOptions other)
other
- search option to overwrite.public void clonecopyOptions(SearchOptions other)
other
- search option object to overwritepublic void setTautomerSearch(int value)
value
- the desired tautomer search behavior
SearchConstants.TAUTOMER_SEARCH_DEFAULT
.SearchConstants.TAUTOMER_SEARCH_DEFAULT
,
SearchConstants.TAUTOMER_SEARCH_OFF
,
SearchConstants.TAUTOMER_SEARCH_ON
,
SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
,
getTautomerSearch()
,
Tautomer search documenationpublic final int getTautomerSearch()
SearchConstants.TAUTOMER_SEARCH_DEFAULT
.SearchConstants.TAUTOMER_SEARCH_DEFAULT
,
SearchConstants.TAUTOMER_SEARCH_OFF
,
SearchConstants.TAUTOMER_SEARCH_ON
,
setTautomerSearch(int)
,
Tautomer search documenationpublic void setOption(java.lang.String name, java.lang.String value)
name
- Name (case insensitive) of search option (e.g. stereoSearch).value
- String form (case insensitive)
of search parameter value (y, M, ef, ...).
getOptionNames()
.getOption(String)
public java.lang.String getOption(java.lang.String name)
name
- Name (case insensitive) of search option (e.g. stereoSearch).
For the list of available search options, see setOption(String, String)
.setOption(String, String)
protected static boolean getBoolean(java.lang.String value)
value
- String representation of boolean flag.java.lang.IllegalArgumentException
- otherwise.protected java.lang.String returnOptionString(boolean value)
public final boolean isKeepQueryOrder()
false
.public void setKeepQueryOrder(boolean value)
value
- false, if search should rearrange query atoms for better
search performance
false
.public final int getIsotopeMatching()
SearchConstants.ISOTOPE_MATCHING_DEFAULT
(isotope query
matches only isotope target, nonisotope query matches all)setIsotopeMatching(int)
,
SearchConstants.ISOTOPE_MATCHING_DEFAULT
,
SearchConstants.ISOTOPE_MATCHING_EXACT
,
SearchConstants.ISOTOPE_MATCHING_IGNORE
,
Query features documentationpublic void setIsotopeMatching(int value)
value
- Specifies the isotope searching behavior.
Default is SearchConstants.ISOTOPE_MATCHING_DEFAULT
(isotope query
matches only isotope target, non-isotope query matches all)
SearchConstants.ISOTOPE_MATCHING_DEFAULT
(isotope query
matches only isotope target, nonisotope query matches all) with the exception of
duplicate search where SearchConstants.ISOTOPE_MATCHING_EXACT
is the default.SearchConstants.ISOTOPE_MATCHING_DEFAULT
,
SearchConstants.ISOTOPE_MATCHING_EXACT
,
SearchConstants.ISOTOPE_MATCHING_IGNORE
,
getIsotopeMatching()
,
Query features documentationpublic final int getChargeMatching()
CHARGE_MATCHING_DEFAULT
(charged query
matches only charged target, noncharged query matches all)setChargeMatching(int)
,
SearchConstants.CHARGE_MATCHING_DEFAULT
,
SearchConstants.CHARGE_MATCHING_EXACT
,
SearchConstants.CHARGE_MATCHING_IGNORE
,
Query features documentationpublic void setChargeMatching(int value)
value
- Specifies the charge searching behaviour.
SearchConstants.CHARGE_MATCHING_DEFAULT
(charged query
matches only charged target, noncharged query matches all) with the exception of
duplicate search where SearchConstants.CHARGE_MATCHING_EXACT
is the default.SearchConstants.CHARGE_MATCHING_DEFAULT
,
SearchConstants.CHARGE_MATCHING_EXACT
,
SearchConstants.CHARGE_MATCHING_IGNORE
,
Query features documentationpublic final boolean isValenceMatching()
true
if valence is checked during search.
true
.setValenceMatching(boolean)
public void setValenceMatching(boolean value)
value
- true, if valence should be checked during search.
true
.isValenceMatching()
public final int getRadicalMatching()
SearchConstants.RADICAL_MATCHING_DEFAULT
(radical query
matches only radical target, nonradical query matches all).setRadicalMatching(int)
,
SearchConstants.RADICAL_MATCHING_DEFAULT
,
SearchConstants.RADICAL_MATCHING_EXACT
,
SearchConstants.RADICAL_MATCHING_IGNORE
,
Query features documentationpublic void setRadicalMatching(int value)
value
- Specifies the radical searching behaviour.
SearchConstants.RADICAL_MATCHING_DEFAULT
(radical query
matches only radical target, nonradical query matches all) with the exception of
duplicate search where SearchConstants.RADICAL_MATCHING_EXACT
is the default.SearchConstants.RADICAL_MATCHING_DEFAULT
,
SearchConstants.RADICAL_MATCHING_EXACT
,
SearchConstants.RADICAL_MATCHING_IGNORE
,
getRadicalMatching()
,
Query features documentationpublic final boolean isMixSgroupMatching()
true
.setMixSgroupMatching(boolean)
public void setMixSgroupMatching(boolean value)
value
- true, if COM, MIX and FOR sgroups should be
considered during search.
true
.isMixSgroupMatching()
public final boolean isPolymerMatching()
true
.setPolymerMatching(boolean)
public void setPolymerMatching(boolean value)
value
- true, if polymer sgroups should be
considered during search.
true
.isPolymerMatching()
,
Polymer search documentationpublic final boolean isEndgroupMatching()
true
if polymer end groups must match during search. In
this case the star atom can't match on a specified engroup.
true
.setPolymerMatching(boolean)
,
Polymer search documentationpublic void setEndgroupMatching(boolean value)
value
- true, if polymer endgroups should be
matched during search. In this case the star atom
can't match on a specified engroup.
true
.public final boolean areMonomersTransformed()
true
.setMonomerTransform(boolean)
,
Polymer search documentationpublic void setMonomerTransform(boolean value)
value
- true if monomers should be transformed, false otherwise
true
.areMonomersTransformed()
,
Polymer search documentationpublic final boolean isPhaseShiftedMatching()
true
.setPhaseShiftedMatching(boolean)
public void setPhaseShiftedMatching(boolean value)
value
- true if the phase shifted should be matching
false otherwise.
true
.isPhaseShiftedMatching()
public final boolean isCopolymerMatching()
false
.setCopolymerMatching(boolean)
,
Polymer search documentationpublic void setCopolymerMatching(boolean value)
value
- true if copolymer matching mode should be set,
false otherwise. (default false)
false
isCopolymerMatching()
,
Polymer search documentationpublic final HomologyTranslationOption getHomologyNarrowTranslation()
HomologyTranslationOption
.
HomologyTranslationOption.MARKED
.setHomologyNarrowTranslation(HomologyTranslationOption)
public void setHomologyNarrowTranslation(HomologyTranslationOption value)
value
- For possible values see: HomologyTranslationOption
HomologyTranslationOption.MARKED
getHomologyNarrowTranslation()
,
Query features documentationpublic final HomologyTranslationOption getHomologyBroadTranslation()
HomologyTranslationOption
.
HomologyTranslationOption.MARKED
.setHomologyBroadTranslation(HomologyTranslationOption)
public void setHomologyBroadTranslation(HomologyTranslationOption value)
value
- For possible values see: HomologyTranslationOption
HomologyTranslationOption.MARKED
getHomologyBroadTranslation()
public void setTargetHomologyMatchingMode(TargetHomologyMatchingMode mode)
mode
- homology matching mode. For possible values, see: TargetHomologyMatchingMode
.
TargetHomologyMatchingMode.ALL
.getTargetHomologyMatchingMode()
public TargetHomologyMatchingMode getTargetHomologyMatchingMode()
TargetHomologyMatchingMode
.
TargetHomologyMatchingMode.ALL
.setTargetHomologyMatchingMode(TargetHomologyMatchingMode)
public void setSSRType(SetOfSmallestRingsOption value)
value
- set of smallest rings options to useSetOfSmallestRingsOption
,
getSSRType()
public SetOfSmallestRingsOption getSSRType()
Default value is SetOfSmallestRingsOption.SSSR
SetOfSmallestRingsOption
,
setSSRType(SetOfSmallestRingsOption)
@Beta public MarkushAromaticityHandlingOption getMarkushAromHandling()
MarkushAromaticityHandlingOption
,
setMarkushAromHandling(MarkushAromaticityHandlingOption)
@Beta public void setMarkushAromHandling(MarkushAromaticityHandlingOption value)
value
- the desired Markush aromatic search optionMarkushAromaticityHandlingOption
,
getMarkushAromHandling()
public final int getStereoModel()
SearchConstants.STEREO_MODEL_LOCAL
,
SearchConstants.STEREO_MODEL_COMPREHENSIVE
,
SearchConstants.STEREO_MODEL_GLOBAL
,
SearchConstants.STEREO_MODEL_DEFAULT
,
Stereo Model documentationpublic void setStereoModel(int value)
value
- Specifies the used stereo model. Default is SearchConstants.STEREO_MODEL_DEFAULT
, whose
actual behavior depends on the search type and, in case of database search, the type of the structure
table. For substructure and superstructure searches, it equals to
SearchConstants.STEREO_MODEL_COMPREHENSIVE
, while for other searches, it usually equals to
SearchConstants.STEREO_MODEL_GLOBAL
.SearchConstants.STEREO_MODEL_LOCAL
,
SearchConstants.STEREO_MODEL_COMPREHENSIVE
,
SearchConstants.STEREO_MODEL_GLOBAL
,
SearchConstants.STEREO_MODEL_DEFAULT
,
getStereoModel()
,
Stereo Model documentationpublic final void setStereoSearchType(int value)
setStereoModel(int)
specifies the model for calculating the
stereo information.)value
- Specifies the stereo mode.
SearchConstants.STEREO_SPECIFIC
with the exception
of duplicate search where SearchConstants.STEREO_EXACT
is the default.SearchConstants.STEREO_SPECIFIC
,
SearchConstants.STEREO_IGNORE
,
SearchConstants.STEREO_EXACT
,
SearchConstants.STEREO_DIASTEREOMER
,
SearchConstants.STEREO_ENANTIOMER
,
getStereoSearchType()
,
Stereochemistry documentationpublic final int getStereoSearchType()
SearchConstants.STEREO_SPECIFIC
.SearchConstants.STEREO_SPECIFIC
,
SearchConstants.STEREO_IGNORE
,
SearchConstants.STEREO_EXACT
,
SearchConstants.STEREO_DIASTEREOMER
,
SearchConstants.STEREO_ENANTIOMER
,
setStereoSearchType(int)
,
Stereochemistry documentationpublic final void setIgnoreTetrahedralStereo(boolean value)
setStereoSearchType(int)
only specifies double bond
stereo matching.value
- the value to set, set true to ignore.
false
.public final boolean isIgnoreTetrahedralStereo()
false
.setIgnoreTetrahedralStereo(boolean)
public final void setIgnoreDoubleBondStereo(boolean value)
setStereoSearchType(int)
only specifies tetrahedral
stereo matching.value
- the value to set, set true to ignore.
false
.public final boolean isIgnoreDoubleBondStereo()
false
.setIgnoreDoubleBondStereo(boolean)
public final void setIgnoreCumuleneOrRingCisTransStereo(boolean value)
value
- the value to set, set true to ignore. true
.public final boolean isIgnoreCumuleneOrRingCisTransStereo()
true
.setIgnoreCumuleneOrRingCisTransStereo(boolean)
public final void setIgnoreAxialStereo(boolean value)
value
- the value to set, set true to ignore. true
.public final boolean isIgnoreAxialStereo()
true
.setIgnoreAxialStereo(boolean)
public final void setIgnoreSynAntiStereo(boolean value)
value
- the value to set, set true to ignore. true
.public final boolean isIgnoreSynAntiStereo()
true
.setIgnoreSynAntiStereo(boolean)
public final boolean getCheckSpHyb()
true
if sp-hybridization state of the atoms is considered,
false
.setCheckSpHyb(boolean)
,
MoleculeGraph.calcHybridization()
,
Search options documenationpublic void setCheckSpHyb(boolean checkSp)
checkSp
- If true the sp-hybridization state is checked.
false
.getCheckSpHyb()
,
MoleculeGraph.calcHybridization()
,
Search options documenationpublic final int getImplicitHMatching()
SearchConstants.IMPLICIT_H_MATCHING_DEFAULT
(matching depends on
the circumstances of search)SearchConstants.IMPLICIT_H_MATCHING_DEFAULT
,
SearchConstants.IMPLICIT_H_MATCHING_DISABLED
,
SearchConstants.IMPLICIT_H_MATCHING_ENABLED
,
Search options documentationpublic void setImplicitHMatching(int value)
value
- Specifies matching bahaviour between
explicit and implicit hydrogens.
SearchConstants.IMPLICIT_H_MATCHING_DEFAULT
(matching depends on
the circumstances of search)SearchConstants.IMPLICIT_H_MATCHING_DEFAULT
,
SearchConstants.IMPLICIT_H_MATCHING_DISABLED
,
SearchConstants.IMPLICIT_H_MATCHING_ENABLED
,
SearchConstants.IMPLICIT_H_MATCHING_IGNORE
,
Implicit H matching documentationpublic final boolean isReactionUnpairedMapMatching()
true
.setReactionUnpairedMapMatching(boolean)
,
Reaction search documentationpublic void setReactionUnpairedMapMatching(boolean value)
value
- true, if in reaction search unpaired (orphan and widow)
atom maps can match any atom map.
true
.isReactionUnpairedMapMatching()
,
Reaction search documentationpublic void setChemTermsFilter(java.lang.String value)
value
- the chemical terms filter expression
null
.getChemTermsFilter()
,
Chemical terms documentationpublic final java.lang.String getChemTermsFilter()
null
.setChemTermsFilter(String)
,
Chemical terms documentationpublic void setChemTermsFilterConfig(java.io.File file) throws java.io.IOException
file
- the configuration file. Set to
null
for default configuration.
null
.java.io.IOException
- if the supplied file can't be read with the default charset.getChemTermsFilterConfig()
,
Chemical terms documentationpublic void setChemTermsFilterConfig(java.lang.String value)
value
- the configuration string. Set to
null
for default configuration.
null
.getChemTermsFilterConfig()
,
Chemical terms documentationpublic final java.lang.String getChemTermsFilterConfig()
null
.setChemTermsFilterConfig(String)
,
Chemical terms documentationpublic void setUndefinedRAtom(int value)
Sets the matching behaviour of an undefined R atom in the query.
Possible values for search:
SearchConstants.UNDEF_R_MATCHING_ALL
SearchConstants.UNDEF_R_MATCHING_UNDEF_R
SearchConstants.UNDEF_R_MATCHING_GROUP
(default)SearchConstants.UNDEF_R_MATCHING_GROUP_H
SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY
Possible values for RGroupDecomposition:
SearchConstants.UNDEF_R_MATCHING_GROUP
SearchConstants.UNDEF_R_MATCHING_GROUP_H
(default for queries with explicit undefined R-atom)SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY
(default for queries without explicit undefined R-atom)value
- Matching mode value.getUndefinedRAtom()
,
Special search types documentationpublic void setUndefinedRAtomUserDefined(boolean undefinedRAtomUserDefined)
undefinedRAtomUserDefined
- the new value.public final int getUndefinedRAtom()
SearchConstants.UNDEF_R_MATCHING_GROUP
.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 documentationpublic final boolean isUndefinedRAtomMatchingGroup()
getUndefinedRAtom()
is
true
if undefined R atom matches groupsetUndefinedRAtom(int)
,
getUndefinedRAtom()
public void setBridgingRAllowed(boolean value)
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
.value
- true
if different undefined R-atoms can match
the same group of atoms
false
.setUndefinedRAtom(int)
public final boolean isBridgingRAllowed()
true
if different undefined R-atoms can match the same group of atoms.
This parameter is only used if R atom matching behaviour.true
if different undefined R-atoms can match the same group of atoms
false
.SearchConstants.UNDEF_R_MATCHING_GROUP
,
SearchConstants.UNDEF_R_MATCHING_GROUP_H
,
SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY
,
setBridgingRAllowed(boolean)
public void setRLigandEqualityCheck(boolean value)
value
- true
if undefined R-atoms with the same R-group ID should match
the same structure
true
.setUndefinedRAtom(int)
,
SearchConstants.UNDEF_R_MATCHING_GROUP
,
SearchConstants.UNDEF_R_MATCHING_GROUP_H
,
SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY
,
getRLigandEqualityCheck()
,
Special search types documentationpublic final boolean getRLigandEqualityCheck()
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 behaviourtrue
if undefined R-atoms with the same R-group ID
should match the same structure
true
.SearchConstants.UNDEF_R_MATCHING_GROUP
,
SearchConstants.UNDEF_R_MATCHING_GROUP_H
,
SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY
,
setRLigandEqualityCheck(boolean)
,
Special search types documentationpublic void setHitOrdering(int value)
value
- hit ordering type value.
SearchConstants.HIT_ORDERING_NONE
.SearchConstants.HIT_ORDERING_NONE
,
SearchConstants.HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
,
getHitOrdering()
public int getHitOrdering()
SearchConstants.HIT_ORDERING_NONE
.SearchConstants.HIT_ORDERING_NONE
,
SearchConstants.HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
,
setHitOrdering(int)
public void setAttachedDataMatch(int value)
value
- attach data match type
SearchConstants.ATTACHED_DATA_MATCH_IGNORE
(no attached data used)getAttachedDataMatch()
,
SearchConstants.ATTACHED_DATA_MATCH_IGNORE
,
SearchConstants.ATTACHED_DATA_MATCH_GENERAL
,
SearchConstants.ATTACHED_DATA_MATCH_EXACT
,
Query features documentationpublic final int getAttachedDataMatch()
SearchConstants.ATTACHED_DATA_MATCH_IGNORE
(no attached data used)setAttachedDataMatch(int)
,
SearchConstants.ATTACHED_DATA_MATCH_IGNORE
,
SearchConstants.ATTACHED_DATA_MATCH_GENERAL
,
SearchConstants.ATTACHED_DATA_MATCH_EXACT
,
Query features documentationpublic void setAttachedDataPrefixes(java.lang.String value)
value
- comma separated list of name prefixes,
e.g. "weight,atomcount"
null
(all data sgroups will be checked).setAttachedDataMatch(int)
,
getAttachedDataPrefixes()
,
Query features documentationpublic final java.lang.String getAttachedDataPrefixes()
null
if all data sgroups should be checked.null
null
(all data sgroups will be checked).setAttachedDataPrefixes(String)
,
Query features documentationpublic void setExactSpecialAtomMatching(java.lang.String value)
value
- comma separated list of identifiers
""
(all data sgroups will be checked).
e.g. "A,G18,*,Resin"public final java.lang.String getExactSpecialAtomMatching()
""
(all data sgroups will be checked).
e.g. "A,G18,*,Resin"setExactSpecialAtomMatching(String)
public final int getExhaustiveModeLimit()
-1
.setExhaustiveModeLimit(int)
public void setExhaustiveModeLimit(int value)
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.
-1
.getExhaustiveModeLimit()
public int getTimeoutLimitMilliseconds()
setTimeoutLimitMilliseconds(int)
public void setTimeoutLimitMilliseconds(int value)
value
- The time limit to set in milliseconds. Negative values are treated as Integer.MAX_VALUE
.
getTimeoutLimitMilliseconds()
protected static int nonPositiveToInfinite(int value)
public final boolean isThrowExceptionOnTimeout()
false
.setThrowExceptionOnTimeout(boolean)
public void setThrowExceptionOnTimeout(boolean value)
value
- true if exception should be thrown.
false
.isThrowExceptionOnTimeout()
@Beta public chemaxon.sss.search.options.ChemTermsFilterOption getChemTermsFilterOption()
@Beta public void setChemTermsFilterOption(chemaxon.sss.search.options.ChemTermsFilterOption chemTermsFilterOption)
chemTermsFilterOption
- the chemTermOption to setjava.lang.NullPointerException
- in case chemTermsFilterOption
is nullpublic java.lang.String toString()
toString
in class java.lang.Object
setOptions(String)
,
toList()
public java.lang.String toString(java.lang.String sep)
sep
- the separator string between optionssetOptions(String)
,
toList()
public java.lang.String getAllOptionsAsString()
getAllOptionsAsString(String)
,
setOptions(String)
,
toString()
public java.lang.String getAllOptionsAsString(java.lang.String sep)
sep
- is the separatorgetAllOptionsAsString()
,
setOptions(String)
,
toString()
public java.util.ArrayList<java.lang.String> toList()
setOptions(String)
,
toString()
public java.util.Collection<java.lang.String> getOptionNames()
setOption(String, String)
and getOption(String)
methods.