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

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

Class to encapsulate search parameters used by MolSearch.

Since:

5.0

Author:

pkovacs, Tamas Csizmazia

See Also:

Serialized Form

Field Summary

Fields inherited from class chemaxon.sss.search.SearchOptions

dirty, options, 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, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SIMILARITY_THRESHOLD, DISSIMILARITY, DUPLICATE, EXACT, EXACT_FRAGMENT, EXACT_FRAGMENT_OFF, EXACT_FRAGMENT_ON, FULL, FULL_FRAGMENT, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, HIT_EXCLUDEDQ, HIT_LP, HIT_MULTICENTER, HIT_NON_R, HIT_R, HIT_R_EMPTY_MATCH, HIT_UNMAPABLE, IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, IMPLICIT_H_MATCHING_ENABLED, ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, KEEP_QUERY_ORDER, MARKUSH_AROM_FINAL_CHECK, MARKUSH_AROM_NO_FINAL_CHECK, MARKUSH_AROM_OFF, MARKUSH_DISABLED, MARKUSH_ENABLED, MARKUSH_HIT_INNER, MARKUSH_HIT_ORIGINAL, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, MIX_SGROUP_MATCHING_OFF, MIX_SGROUP_MATCHING_ON, NO_ABAS, NO_SCREEN, OPTION_CHARGE_MATCHING, OPTION_EXACT_FRAGMENT, OPTION_ISOTOPE_MATCHING, OPTION_KEEP_QUERY_ORDER, OPTION_MARKUSH_AROM, OPTION_MARKUSH_ENABLED, OPTION_MARKUSH_HIT, OPTION_MIX_SGROUP_MATCHING, OPTION_RADICAL_MATCHING, OPTION_STEREO_MODEL, OPTION_TAUTOMER_SEARCH, OPTION_VAGUE_BOND, OPTION_VALENCE_MATCHING, PERFECT, R_NODE_PLACEHOLDER, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, REARRANGE_QUERY, SEARCH_MODE_NAMES, SEARCH_OPTIONS_LENGTH, SIMILARITY, STEREO_DIASTEREOMER, STEREO_EXACT, STEREO_IGNORE, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, STEREO_SPECIFIC, SUBSTRUCTURE, SUPERSTRUCTURE, 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, VALENCE_MATCHING_IGNORE, VALENCE_MATCHING_ON

Constructor Summary

MolSearchOptions()

Method Summary

java.lang.Object	clone() Makes an identical copy of this SearchObject.
void	clonecopy(SearchOptions other) Copies parameters to other.
void	deepCopy(SearchOptions other) Deprecated. since 5.0.2 Please use clonecopy(SearchOptions) instead
int	getHitIndexType() Returns the representation on which the the hit indexes are given in case of markush search.
int	getMarkushArom()
java.lang.String	getOption(java.lang.String name) Returns search option value in string format.
protected java.lang.String[]	getOptionNames()
boolean	isDistinctFirstAtomMatching()
boolean	isHitIncludesRNodes() Specifies the result format for R-group queries.
boolean	isMarkushEnabled()
boolean	isMarkushHitSupergraph() Deprecated. since 5.0
boolean	isQueryAbsoluteStereo() Returns whether the chiral flag is ignored or not for the query molecule.
boolean	isSubgraphSearch() Returns whether currently subgraph or complete graph matching is performed.
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	setHitIncludesRNodes(boolean value) Specifies the result format for R-group queries.
void	setHitIndexType(int value)
void	setMarkushArom(int value) Default is MARKUSH_AROM_FINAL_CHECK (consider Markush aromatization during Markush search and check the hit afterwards).
void	setMarkushEnabled(boolean value)
void	setMarkushHitSupergraph(boolean value) Deprecated. use setHitIndexType(int)
void	setOption(int option, int value) Deprecated. Since 5.0 Use setters instead. setHitIndexType(int), setMarkushEnabled(boolean), setMarkushArom(int)
void	setOption(java.lang.String name, java.lang.String value) Sets search options.
void	setQueryAbsoluteStereo(boolean value) Sets whether the chiral flag should be ignored or not for the query molecule.
void	setSubgraphSearch(boolean value) Specifies whether subgraph or complete graph matching should be performed.
void	setTargetAbsoluteStereo(boolean value) Sets whether the chiral flag should be ignored or not for the target molecule.
java.util.ArrayList	toList()

Methods inherited from class chemaxon.sss.search.SearchOptions

addUserComparator, areMonomersTransformed, clearChangesInUserComparators, deleteAllUserComparators, deleteUserComparator, getAllOptionsAsString, getAllOptionsAsString, getAttachedDataMatch, getAttachedDataPrefixes, getBoolean, getChargeMatching, getCheckSpHyb, getChemTermsFilter, getChemTermsFilterConfig, getCompleteHG, getDoubleBondStereoMatchingMode, getExactSpecialAtomMatching, getExhaustiveModeLimit, getHCountMatching, getImplicitHMatching, getIsotopeMatching, getOption, getOptions, getRadicalMatching, getRLigandEqualityCheck, getSearchType, getStereoModel, getStereoSearchType, getTimeoutLimit, getUndefinedRAtom, getUserComparators, getVagueBondLevel, hasChangesInUserComparators, hasUserComparators, isBridgingRAllowed, isCopolymerMatching, isDiastereomerMatching, isDirty, isEndgroupMatching, isExactBondMatching, isExactFragment, isExactQueryAtomMatching, isExactStereoMatching, isFullFragment, isIgnoreCTExceptions, isKeepQueryOrder, isMixSgroupMatching, isOrderSensitiveSearch, isPerfectSearchType, isPhaseShiftedMatching, isPolymerMatching, isQHomologyHandling, isReactionUnpairedMapMatching, isStereoSearch, isSuperstructureSearch, isTautomerDuplicateFiltering, isTautomerSearch, isUndefinedRAtomMatchingGroup, isValenceMatching, isVerbose, returnOptionString, setAttachedDataMatch, setAttachedDataPrefixes, setBridgingRAllowed, setChargeMatching, setCheckSpHyb, setChemTermsFilter, setChemTermsFilterConfig, setCompleteHG, setCopolymerMatching, setDiastereomerMatching, setDirty, setDoubleBondStereoMatchingMode, setEndgroupMatching, setExactBondMatching, setExactFragment, setExactQueryAtomMatching, setExactSpecialAtomMatching, setExactStereoMatching, setExhaustiveModeLimit, setFullFragment, setHCountMatching, setIgnoreCTExceptions, setImplicitHMatching, setIsotopeMatching, setKeepQueryOrder, setMixSgroupMatching, setMonomerTransform, setOptions, setOptions, setOrderSensitiveSearch, setPhaseShiftedMatching, setPolymerMatching, setQHomologyHandling, setRadicalMatching, setReactionUnpairedMapMatching, setRLigandEqualityCheck, setSearchType, setStereoModel, setStereoSearch, setStereoSearchType, setSuperstructureSearch, setTautomerDuplicateFiltering, setTautomerSearch, setTimeoutLimit, setUndefinedRAtom, 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()

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.

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.

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.

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.

isHitIncludesRNodes

public boolean isHitIncludesRNodes()

Specifies the result format for R-group queries. If false, the hits will contain only the matching atom indexes for non-R-group atoms in the root structure, in order (default). In this case the hit list contains less indexes, than the number of nodes in the root structure.
If set to true, the hit list will contain placeholders for the R-nodes with the value of SearchConstants.R_NODE_PLACEHOLDER, thus maintaining root indexes in the result.

setHitIncludesRNodes

public void setHitIncludesRNodes(boolean value)

Specifies the result format for R-group queries.

Parameters:

value - if set to false, the hits will contain only the matching atom indexes for non-R-group atoms in the root structure, in order (default). In this case the hit list contains less indexes, than the number of nodes in the root structure.
If set to true, the hit list will contain placeholders for the R-nodes with the value of SearchConstants.R_NODE_PLACEHOLDER, thus maintaining root indexes in the result.

isSubgraphSearch

public boolean isSubgraphSearch()

Returns whether currently subgraph or complete graph matching is performed.

Overrides:

isSubgraphSearch in class SearchOptions

Returns:

true for substructure and full fragment search, false for full structure search and duplicate search.

setSubgraphSearch

public void setSubgraphSearch(boolean value)

Specifies whether subgraph or complete graph matching should be performed.

Overrides:

setSubgraphSearch in class SearchOptions

Parameters:

value - true for substructure and full fragment search, false for full structure search and duplicate search.

isMarkushHitSupergraph

public boolean isMarkushHitSupergraph()

Deprecated. since 5.0

Returns:

true, if search returns hit indices of the inner, compiled representation of a Markush target (instead of the original Markush target).

getHitIndexType

public int getHitIndexType()

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

Returns:

of which representation the hit indexes are.

See Also:

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

setMarkushHitSupergraph

public void setMarkushHitSupergraph(boolean value)

Deprecated. use setHitIndexType(int)

Parameters:

value - true, if search should return hit indices of the inner, compiled representation of a Markush target if false the search will return hit indexes of the original Markush target. (instead of the original Markush target).

setHitIndexType

public void setHitIndexType(int value)

Parameters:

value - specifies the representation on which the hit indexes are given in case of markush search. Possible values:
SearchConstants.MARKUSH_HIT_ORIGINAL (default)
SearchConstants.MARKUSH_HIT_INNER

isMarkushEnabled

public boolean isMarkushEnabled()

Returns:

true, if a target containing Markush features should be treated as Markush library since 5.0

setMarkushEnabled

public void setMarkushEnabled(boolean value)

Parameters:

value - true, if a target containing Markush features should be treated as Markush library

Since:

5.0

getMarkushArom

public int getMarkushArom()

Returns:

Behaviour of Markush aromatic search.

Since:

5.0

See Also:

SearchConstants.MARKUSH_AROM_FINAL_CHECK, SearchConstants.MARKUSH_AROM_NO_FINAL_CHECK, SearchConstants.MARKUSH_AROM_OFF

setMarkushArom

public void setMarkushArom(int value)

Default is MARKUSH_AROM_FINAL_CHECK (consider Markush aromatization during Markush search and check the hit afterwards).

Parameters:

value - the desired Markush aromatic search option

Since:

5.0

See Also:

SearchConstants.MARKUSH_AROM_FINAL_CHECK, SearchConstants.MARKUSH_AROM_NO_FINAL_CHECK, SearchConstants.MARKUSH_AROM_OFF

setDistinctFirstAtomMatching

public void setDistinctFirstAtomMatching(boolean b)

Option ensuring that upon the findNext() call the first atom must be stepped as well. 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.

isDistinctFirstAtomMatching

public boolean isDistinctFirstAtomMatching()

See Also:

setDistinctFirstAtomMatching(boolean)

setOption

public void setOption(int option,
                      int value)

Deprecated. Since 5.0 Use setters instead. setHitIndexType(int), setMarkushEnabled(boolean), setMarkushArom(int)

Sets search options.

Overrides:

setOption in class SearchOptions

Parameters:

option - Option identifier to be set.

value - Value of option to be set.

See Also:

SearchConstants.OPTION_MARKUSH_HIT, SearchConstants.OPTION_MARKUSH_ENABLED, SearchConstants.OPTION_MARKUSH_AROM

setOption

public void setOption(java.lang.String name,
                      java.lang.String value)

Sets search options.

Overrides:

setOption in class SearchOptions

Parameters:

name - Option name to be set. Useable options:

queryAbsoluteStereo

targetAbsoluteStereo

markush

hitIndexType

value - String value of option to be set.

See Also:

SearchOptions.setOption(String, String), getOption(String)

getOption

public java.lang.String getOption(java.lang.String name)

Returns search option value in string format.

Overrides:

getOption in class SearchOptions

Parameters:

name - Option name to get. Useable options:

queryAbsoluteStereo

targetAbsoluteStereo

markush

hitIndexType

Returns:

String value of option

See Also:

SearchOptions.getOption(String), setOption(String, String)

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

deepCopy

public void deepCopy(SearchOptions other)

Deprecated. since 5.0.2 Please use clonecopy(SearchOptions) instead

Copies the complex data structures only from this to toOther.

Overrides:

deepCopy in class SearchOptions

toList

public java.util.ArrayList toList()

Overrides:

toList in class SearchOptions

Returns:

An arraylist that contains strings of format "optionname:optionvalue". Doesn't contain options that have their default value.

See Also:

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

getOptionNames

protected java.lang.String[] getOptionNames()

Overrides:

getOptionNames in class SearchOptions