chemaxon.sss.search
Class SearchOptions

java.lang.Object
  chemaxon.sss.search.SearchOptions

All Implemented Interfaces:

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

Direct Known Subclasses:

JChemSearchOptions, MolSearchOptions

public class SearchOptions
extends java.lang.Object
implements SearchConstants, java.lang.Cloneable, java.io.Serializable

Class to encapsulate common search parameters.

Since:

5.0

Author:

Szabolcs Csepregi Date: 27-Mar-2007, Tamas Csizmazia

See Also:

Serialized Form

Field Summary

protected boolean	dirty This flag is set to true whenever any of the options change.
protected int[]	options Field to store various options of the search.
boolean	verbose For debugging purposes.

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

SearchOptions()

Method Summary

void	addUserComparator(MolComparator mc) Adds the given user-defined comparator to the search.
boolean	areMonomersTransformed()
void	clearChangesInUserComparators() Used in initializing searches.
java.lang.Object	clone() Makes an identical copy of this SearchObject.
void	clonecopy(SearchOptions other) Copies all parameters to the other object.
protected void	deepCopy(SearchOptions toOther) Deprecated. since 5.0.2 Please use clonecopy(SearchOptions) instead
void	deleteAllUserComparators()
void	deleteUserComparator(MolComparator mc)
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()
boolean	getCheckSpHyb() Returns true if sp-hybridization state of the atoms should be considered, false otherwise
java.lang.String	getChemTermsFilter() Gets the Chemical Terms filtering expression
java.lang.String	getChemTermsFilterConfig() Gets the configuration string for Chemical Terms filter.
boolean	getCompleteHG() Retrieves the information if only complete structures are matching on target homology groups.
int	getDoubleBondStereoMatchingMode()
java.lang.String	getExactSpecialAtomMatching() Returns 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()
int	getImplicitHMatching()
int	getIsotopeMatching()
int	getOption(int option) Deprecated. Since 5.0 Please use getters instead. isKeepQueryOrder() isFullFragment() isTautomerSearch() getIsotopeMatching() getChargeMatching() isValenceMatching() getRadicalMatching() getVagueBondLevel() isMixSgroupMatching() getStereoModel() getImplicitHMatching() isReactionUnpairedMapMatching()
java.lang.String	getOption(java.lang.String name) Returns option value in string format.
protected java.lang.String[]	getOptionNames()
int[]	getOptions() Deprecated. since 5.0
int	getRadicalMatching()
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.
int	getStereoModel()
int	getStereoSearchType()
int	getTimeoutLimit() The search timeouts reaching this number of steps.
int	getUndefinedRAtom() Returns undefined R atom matching behaviour mode.
MolComparator[]	getUserComparators() Because of efficiency reasons one should check hasUserComparators() before calling this method!
int	getVagueBondLevel() Getter for vague bond level.
boolean	hasChangesInUserComparators() Used in initializing searches.
boolean	hasUserComparators()
boolean	isBridgingRAllowed() Returns true if different undefined R-atoms can match the same group of atoms.
boolean	isCopolymerMatching()
boolean	isDiastereomerMatching() Deprecated. Please use getStereoSearchType() instead.
boolean	isDirty() Returns the dirty flag.
boolean	isEndgroupMatching()
boolean	isExactBondMatching() Indicates whether bond types should match exactly - looking for query bonds target.
boolean	isExactFragment()
boolean	isExactQueryAtomMatching() Returns whether exact matching of query atom information is set.
boolean	isExactStereoMatching() Deprecated. Please use getStereoSearchType() instead.
boolean	isFullFragment()
boolean	isIgnoreCTExceptions()
boolean	isKeepQueryOrder()
boolean	isMixSgroupMatching()
boolean	isOrderSensitiveSearch() Indicates whether the search is order sensitive
boolean	isPerfectSearchType()
boolean	isPhaseShiftedMatching()
boolean	isPolymerMatching()
boolean	isQHomologyHandling()
boolean	isReactionUnpairedMapMatching()
boolean	isStereoSearch() Deprecated. Please use getStereoSearchType() instead.
protected boolean	isSubgraphSearch() Returns the subgraph matching option.
boolean	isSuperstructureSearch() True if the current search type is superstructure search.
boolean	isTautomerDuplicateFiltering()
boolean	isTautomerSearch() Indicates if tautomers of the query should be enumerated for search.
boolean	isUndefinedRAtomMatchingGroup() Returns whether undefined R atom matches group of atoms.
boolean	isValenceMatching()
boolean	isVerbose() For debugging purposes only.
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)
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.lang.String value) Sets the configuration string for Chemical Terms filter.
void	setCompleteHG(boolean completeStr) Sets if only complete structures should match on homology groups.
void	setCopolymerMatching(boolean value) Adjusts copolymer matching mode.
void	setDiastereomerMatching(boolean value) Deprecated. Please use setStereoSearchType(STEREO_DIASTEREOMER) and setStereoSearchType(STEREO_SPECIFIC) instead.
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 exacly - looking for query bonds target.
void	setExactFragment(boolean value)
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	setExactStereoMatching(boolean value) Deprecated. Please use setStereoSearchType(STEREO_EXACT) and setStereoSearchType(STEREO_SPECIFIC) instead.
void	setExhaustiveModeLimit(int value) Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.
void	setFullFragment(boolean value)
void	setHCountMatching(int value) Sets the H count matching mode.
void	setIgnoreCTExceptions(boolean value) If set true, only syntactical exceptions will be thrown.
void	setImplicitHMatching(int value)
void	setIsotopeMatching(int value)
void	setKeepQueryOrder(boolean value)
void	setMixSgroupMatching(boolean value)
void	setMonomerTransform(boolean value) Adjusts if monomers should be transformed to structural repeating units if the monomer is homolopolimerizable.
void	setOption(int option, int value) Deprecated. Since 5.0 Please use setters instead. setKeepQueryOrder(boolean) setFullFragment(boolean) setTautomerSearch(boolean) setIsotopeMatching(int) setChargeMatching(int) setValenceMatching(boolean) setRadicalMatching(int) setVagueBondLevel(int) setMixSgroupMatching(boolean) setStereoModel(int) setImplicitHMatching(int) setReactionUnpairedMapMatching(boolean)
void	setOption(java.lang.String name, java.lang.String value) Sets search options.
void	setOptions(int[] newOptions) Deprecated. since 5.0
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	setQHomologyHandling(boolean value) Adjusts query side homology matching mode.
void	setRadicalMatching(int value)
void	setReactionUnpairedMapMatching(boolean value)
void	setRLigandEqualityCheck(boolean value) Sets whether undefined R-atoms with the same R-group ID should match the same structure.
void	setSearchType(int searchType) Sets different search options according to a predefined search type.
void	setStereoModel(int value)
void	setStereoSearch(boolean value) Deprecated. Please use setStereoSearchType(STEREO_SPECIFIC) and setStereoSearchType(STEREO_IGNORE) instead.
void	setStereoSearchType(int value) Specifies the way stereo information is considered during searching.
protected void	setSubgraphSearch(boolean value) Specifies the matching mode for topology search
void	setSuperstructureSearch(boolean value) Sets if the current search type is superstructure search.
void	setTautomerDuplicateFiltering(boolean value)
void	setTautomerSearch(boolean value) Sets if tautomers of the query should be enumerated for search.
void	setTimeoutLimit(int value) The search timeouts reaching this number of steps.
void	setUndefinedRAtom(int value) Sets the matching behaviour of an undefined R atom in the query.
void	setVagueBondLevel(int value) Option for less strict evaluation of query bonds (e.g. ambiguious aromaticity).
void	setValenceMatching(boolean value)
void	setVerbose(boolean verboseP) For debugging purposes only.
java.util.ArrayList	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)

Methods inherited from class java.lang.Object

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

Field Detail

dirty

protected boolean dirty

This flag is set to true whenever any of the options change. It can be used by Search objects to check whether options changed since the previous initialization. (They set the dirty flag to false during their own initialization.)

verbose

public boolean verbose

For debugging purposes. Public, because it does not count for the dirty flag.

options

protected int[] options

Field to store various options of the search.

Constructor Detail

SearchOptions

public SearchOptions()

Method Detail

isExactQueryAtomMatching

public final boolean isExactQueryAtomMatching()

Returns whether exact matching of query atom information is set. If true, query information (e.g. 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. Default is false.

Since:

JChem 2.2

setExactQueryAtomMatching

public void setExactQueryAtomMatching(boolean isExact)

Sets whether exact query atom matching should be used or not. See Search.isExactQueryAtomMatching.

Since:

JChem 2.2

setDoubleBondStereoMatchingMode

public void setDoubleBondStereoMatchingMode(int value)

Sets how double bond cis/trans stereo information should match during the search.

Parameters:

value - The following options can be used:

• chemaxon.struc.StereoConstants.DBS_NONE: No double bond cis/trans is considered.
• chemaxon.struc.StereoConstants.DBS_MARKED: (Default) Double bond cis/trans stereo is checked for double bonds designated by the stereo search flag only.
• chemaxon.struc.StereoConstants.DBS_ALL: All double bonds are checked for cis/trans stereo matching.

Replaces setStereoCareChecking(boolean)

Since:

JChem 2.2

getDoubleBondStereoMatchingMode

public int getDoubleBondStereoMatchingMode()

Returns:

the matching mode relating to double bond stereo.

Since:

JChem 2.2

See Also:

setDoubleBondStereoMatchingMode(int)

setSearchType

public void setSearchType(int searchType)

Sets 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.SIMILARITY, and SearchConstants.FULL. SearchConstants.DUPLICATE. SearchConstants.FULL_FRAGMENT.

WARNING: This method may affect other search settings, therefore if other search options are adjusted, this method should be called first! For affected search options, see links below.

Parameters:

searchType - the predefined search type

See Also:

setExactBondMatching(boolean), setExactQueryAtomMatching(boolean), setExactStereoMatching(boolean), setStereoSearch(boolean), setSubgraphSearch(boolean), setOption(int, int), SearchConstants.OPTION_CHARGE_MATCHING, SearchConstants.OPTION_ISOTOPE_MATCHING, SearchConstants.OPTION_RADICAL_MATCHING, SearchConstants.OPTION_VALENCE_MATCHING

getSearchType

public int getSearchType()

Returns the currently set global search operation mode.

Returns:

The last set value.

Since:

JChem 3.2

See Also:

setSearchType(int)

isPerfectSearchType

public boolean isPerfectSearchType()

Returns:

whether this search is a DUPLICATE search or not.

isSubgraphSearch

protected boolean isSubgraphSearch()

Returns the subgraph matching option.

Returns:

true if substructure search, false if the full molecular graph must match, e.g. full structure search or duplicate match.

setSubgraphSearch

protected void setSubgraphSearch(boolean value)

Specifies the matching mode for topology search

Parameters:

value - true for substructure search, false for full structure search matching

getHCountMatching

public int getHCountMatching()

Returns:

the H count matching mode. (Default is HCOUNT_MATCHING_AUTO.)

See Also:

setHCountMatching(int), SearchConstants.HCOUNT_MATCHING_AUTO, SearchConstants.HCOUNT_MATCHING_EQUAL, SearchConstants.HCOUNT_MATCHING_GREATER_OR_EQUAL

setHCountMatching

public void setHCountMatching(int value)

Sets the H count matching mode. Default is HCOUNT_MATCHING_AUTO.

Parameters:

value - possible values:

See Also:

SearchConstants.HCOUNT_MATCHING_AUTO, SearchConstants.HCOUNT_MATCHING_EQUAL, SearchConstants.HCOUNT_MATCHING_GREATER_OR_EQUAL

isVerbose

public boolean isVerbose()

For debugging purposes only.

setVerbose

public void setVerbose(boolean verboseP)

For debugging purposes only.

setOption

public void setOption(int option,
                      int value)

Deprecated. Since 5.0 Please use setters instead.

setKeepQueryOrder(boolean)

setFullFragment(boolean)

setTautomerSearch(boolean)

setIsotopeMatching(int)

setChargeMatching(int)

setValenceMatching(boolean)

setRadicalMatching(int)

setVagueBondLevel(int)

setMixSgroupMatching(boolean)

setStereoModel(int)

setImplicitHMatching(int)

setReactionUnpairedMapMatching(boolean)

Sets search options.

Parameters:

option - Option identifier to be set.

value - Value of option to be set.

See Also:

SearchConstants.OPTION_KEEP_QUERY_ORDER, SearchConstants.OPTION_EXACT_FRAGMENT, SearchConstants.OPTION_TAUTOMER_SEARCH, SearchConstants.OPTION_ISOTOPE_MATCHING, SearchConstants.OPTION_CHARGE_MATCHING, SearchConstants.OPTION_VALENCE_MATCHING, SearchConstants.OPTION_RADICAL_MATCHING, SearchConstants.OPTION_VAGUE_BOND, SearchConstants.OPTION_MIX_SGROUP_MATCHING, SearchConstants.OPTION_STEREO_MODEL

getOption

public final int getOption(int option)

Deprecated. Since 5.0 Please use getters instead.

isKeepQueryOrder()

isFullFragment()

isTautomerSearch()

getIsotopeMatching()

getChargeMatching()

isValenceMatching()

getRadicalMatching()

getVagueBondLevel()

isMixSgroupMatching()

getStereoModel()

getImplicitHMatching()

isReactionUnpairedMapMatching()

Gets a search option.

Parameters:

option - Option identifier to be asked for.

Returns:

the setting of the given option

See Also:

SearchConstants.OPTION_KEEP_QUERY_ORDER, SearchConstants.OPTION_EXACT_FRAGMENT, SearchConstants.OPTION_TAUTOMER_SEARCH, SearchConstants.OPTION_ISOTOPE_MATCHING, SearchConstants.OPTION_CHARGE_MATCHING, SearchConstants.OPTION_VALENCE_MATCHING, SearchConstants.OPTION_RADICAL_MATCHING, SearchConstants.OPTION_VAGUE_BOND, SearchConstants.OPTION_MIX_SGROUP_MATCHING, SearchConstants.OPTION_STEREO_MODEL

setOptions

public void setOptions(int[] newOptions)

Deprecated. since 5.0

Rapidly sets all needed search options.

Parameters:

newOptions - Option array to copy.

getOptions

public int[] getOptions()

Deprecated. since 5.0

Gets all needed search options.

setOptions

public void setOptions(java.lang.String optionString)

Sets search options.

Parameters:

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!)
E.g.

setOptions("HCountMatching:E")

setOptions(" hcountmatching:g keepqueryorder:y")

setOptions("sep=*-* hcoUntmatchInG:A*-*KeEpQueryorder:False")

See Also:

setOption(String,String)

isSuperstructureSearch

public boolean isSuperstructureSearch()

True if the current search type is superstructure search. This property is usually set indirectly through setSearchType.

See Also:

setSearchType(int), SearchConstants.SUPERSTRUCTURE, setSuperstructureSearch(boolean)

setSuperstructureSearch

public void setSuperstructureSearch(boolean value)

Sets if the current search type is superstructure search. This property is usually set indirectly through setSearchType in case of superstructure search.

See Also:

setSearchType(int), SearchConstants.SUPERSTRUCTURE

isExactStereoMatching

public final boolean isExactStereoMatching()

Deprecated. Please use getStereoSearchType() instead.

Returns whether exact stereo matching stereo search type is set. If true, equality is needed in stereochemistry. ("All stereo info is exactly the same.") It mainly has an effect when the query has no stereo information: it only matches non-stereo target. Similarly, a query with a wiggly tetrahedral center will only match wiggly tetrahedral center, and not specific R and S configurations. If false, non-stereo query matches both nonstereo and stereo target.

By default, this is false for all search types except for DUPLICATE search, where it is true.

Returns:

the exact-stereo setting

See Also:

isStereoSearch()

setExactStereoMatching

public void setExactStereoMatching(boolean value)

Deprecated. Please use setStereoSearchType(STEREO_EXACT) and setStereoSearchType(STEREO_SPECIFIC) instead.

If true, equality is needed in stereochemistry. ("All stereo info is exactly the same.") It mainly has an effect when the query has no stereo information: it only matches non-stereo target. Similarly, a query with a wiggly tetrahedral center will only match wiggly tetrahedral center, and not specific R and S configurations. If false, non-stereo query matches both nonstereo and stereo target.

By default, this setting is false for all search types except for DUPLICATE search, where it is true.

Parameters:

value - the exact-stereo setting

See Also:

setStereoSearch(boolean), setStereoSearchType(int)

isDiastereomerMatching

public boolean isDiastereomerMatching()

Deprecated. Please use getStereoSearchType() instead.

Returns the diastereomer matching option. If true the diastereomers targets of a given query structure are also matched. This mean that it is only required that if a query atom has stereo information, the target atom should have as well but the two configurations are treated the same. If exactStereoMatching is true (see isExactStereoMatching() then this option has no effect. By default this setting is false for all search types.

Returns:

diastereomer matching is true or not

setDiastereomerMatching

public void setDiastereomerMatching(boolean value)

Deprecated. Please use setStereoSearchType(STEREO_DIASTEREOMER) and setStereoSearchType(STEREO_SPECIFIC) instead.

If true sets the stereo search type option to diastereomer search, else STEREO_SPECIFIC is set.

Parameters:

value -

See Also:

isDiastereomerMatching(), setStereoSearchType(int)

setOrderSensitiveSearch

public void setOrderSensitiveSearch(boolean value)

Specifies whether the same set of target atoms found in a different order should be considered as a different hit.
For example the 3-atom query molecule fits 2 positions on the target:
Hit 1: [1;3;5]
Hit 2: [5;3;1]
If orderSensitiveSearch is true, both cases are returned, otherwise only one of them (the one found first).

Parameters:

value - set this to true to get results in every possible order

isOrderSensitiveSearch

public boolean isOrderSensitiveSearch()

Indicates whether the search is order sensitive

Returns:

if hits are returned in every possible order

See Also:

setOrderSensitiveSearch(boolean)

isStereoSearch

public boolean isStereoSearch()

Deprecated. Please use getStereoSearchType() instead.

If true, then chirality information is considered during searching, otherwise all stereo information is ignored. (Default: true)

setStereoSearch

public void setStereoSearch(boolean value)

Deprecated. Please use setStereoSearchType(STEREO_SPECIFIC) and setStereoSearchType(STEREO_IGNORE) instead.

If true, then chirality information is considered during searching, otherwise all stereo information is ignored. (Default: true)

See Also:

setStereoSearchType(int)

isExactBondMatching

public final boolean isExactBondMatching()

Indicates whether bond types should match exactly - looking for query bonds target.

Returns:

true if bond types must match exactly. Default value is false

setExactBondMatching

public void setExactBondMatching(boolean value)

Specifies whether bond types should match exacly - looking for query bonds target.

Parameters:

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". Default value is false

setVagueBondLevel

public void setVagueBondLevel(int value)

Option for less strict evaluation of query bonds (e.g. ambiguious aromaticity). Default value is VAGUE_BOND_LEVEL1

Parameters:

value - the desired vague bond level

Since:

JChem 5.0

See Also:

getVagueBondLevel(), SearchConstants.VAGUE_BOND_LEVEL_HALF, SearchConstants.VAGUE_BOND_LEVEL1, SearchConstants.VAGUE_BOND_LEVEL2, SearchConstants.VAGUE_BOND_LEVEL3, SearchConstants.VAGUE_BOND_LEVEL4

getVagueBondLevel

public int getVagueBondLevel()

Getter for vague bond level.

Returns:

the current vague bond level

Since:

JChem 5.0

See Also:

setVagueBondLevel(int), SearchConstants.VAGUE_BOND_LEVEL_HALF, SearchConstants.VAGUE_BOND_LEVEL1, SearchConstants.VAGUE_BOND_LEVEL2, SearchConstants.VAGUE_BOND_LEVEL3, SearchConstants.VAGUE_BOND_LEVEL4

setCompleteHG

public void setCompleteHG(boolean completeStr)

Sets if only complete structures should match on homology groups. If set to false than substructures which don't form an entire homology group can also match (e.g. carbon chain on a cycloalkyl).

Parameters:

completeStr - if true only complete structures are accepted, if false all substructures.

See Also:

getCompleteHG()

getCompleteHG

public boolean getCompleteHG()

Retrieves the information if only complete structures are matching on target homology groups.

Returns:

true if only complete structures are matching, false otherwise.

See Also:

setCompleteHG(boolean)

hasChangesInUserComparators

public boolean hasChangesInUserComparators()

Used in initializing searches. Returns true, if there is any changes in user-defined comparators. After initializing the search, the change flag is cleared.

Returns:

the value of the change flag of user-defined MolComparators.

clearChangesInUserComparators

public void clearChangesInUserComparators()

Used in initializing searches. Clears the change flag of user-defined MolComparators.

hasUserComparators

public final boolean hasUserComparators()

Returns:

true, if there is any user-defined MOlComparator

addUserComparator

public void addUserComparator(MolComparator mc)

Adds the given user-defined comparator to the search.

Parameters:

mc - user-defined MolComparator

deleteUserComparator

public void deleteUserComparator(MolComparator mc)

deleteAllUserComparators

public void deleteAllUserComparators()

getUserComparators

public MolComparator[] getUserComparators()

Because of efficiency reasons one should check hasUserComparators() before calling this method!

Returns:

MolComparator[] of user-defined MolComparators

isDirty

public boolean isDirty()

Returns the dirty flag. Dirty flag usage:

1. When the search object initializes itself using the actual query, target and options, it clears the dirty flag(sets to false).
2. When the search options change, the dirty flag is set automatically.
3. Next time a major operation is done with the search object, it checks the dirty flag of the options. If set, it re-initializes itself.

See Also:

setDirty(boolean)

setDirty

public void setDirty(boolean v)

Sets or clears the dirty flag. See the description of isDirty() for its usage.

See Also:

isDirty()

clone

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

Makes an identical copy of this SearchObject.

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

clonecopy

public void clonecopy(SearchOptions other)

Copies all parameters to the other object.

deepCopy

protected void deepCopy(SearchOptions toOther)

Deprecated. since 5.0.2 Please use clonecopy(SearchOptions) instead

Copies the complex data structures only from this to toOther.

setTautomerSearch

public void setTautomerSearch(boolean value)

Sets if tautomers of the query should be enumerated for search. Default is false.

Parameters:

value - set to true to enable enumeration of the tautomers of the query for search. The default is false.

See Also:

SearchConstants.OPTION_TAUTOMER_SEARCH

isTautomerSearch

public boolean isTautomerSearch()

Indicates if tautomers of the query should be enumerated for search. Default is false.

Returns:

wheather tautomers of the query are enumerated for search.

See Also:

setTautomerSearch(boolean), SearchConstants.OPTION_TAUTOMER_SEARCH

setOption

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

Sets search options.

Parameters:

name - Name (case insensitive) of search option (e.g. stereoSearch).

value - String form (case insensitive) of search parameter value (y, M, ef, ...).
In case of boolean parameters 'true' is acceptable instead of 'y' and 'false' instead of 'n'.

Useable search parameters:

orderSensitive

tautomer

stereoSearchType

keepQueryOrder

exactAtomMatching

exactBondMatching

exactQueryAtomMatching

exactRadicalMatching

exactIsotopeMatching

exactChargeMatching

checkSpHyb

doubleBondStereo

HCountMatching

t

implicitHMatching

vagueBond

completeHG

charge

isotope

radical

valence

mix

polymer

endGroupMatching

transformMonomer

markush

stereoModel

undefinedRAtom

bridgingRAllowed

RLigandEqualityCheck

reactionUnpairedMap

attachedDataMatch

attachedDataPrefixes

exactSpecialAtomMatching

ignoreCTExceptions

exhaustiveModeLimit

timeoutLimit

tdf

See Also:

getOption(String)

getOption

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

Returns option value in string format.

Parameters:

name - Name (case insensitive) of search option (e.g. stereoSearch).

Useable search parameters:

orderSensitive

tautomer

stereoSearchType

keepQueryOrder

checkSpHyb

exactBondMatching

exactQueryAtomMatching

doubleBondStereo

HCountMatching

t

implicitHMatching

reactionUnpairedMap

vagueBond

completeHG

charge

isotope

radical

valence

mix

polymer

stereoModel

undefinedRAtom

bridgingRAllowed

RLigandEqualityCheck

attachedDataMatch

attachedDataPrefixes

exactSpecialAtomMatching

ignoreCTExceptions

exhaustiveModeLimit

timeoutLimit

tdf

Returns:

string value of the given option (true --> y, false --> n, except 'valence', 'polymer' and 'mix': true --> d, false --> i)

See Also:

setOption(String, String)

getBoolean

protected static boolean getBoolean(java.lang.String value)

Returns value as a boolean flag.

Parameters:

value - String representation of boolean flag.

Returns:

true if value is null, "", "y", "Y"; false if "n" or "N".

Throws:

java.lang.IllegalArgumentException - otherwise.

returnOptionString

protected java.lang.String returnOptionString(boolean value)

isKeepQueryOrder

public boolean isKeepQueryOrder()

Returns:

false if search rearranges query atoms for better search performance

setKeepQueryOrder

public void setKeepQueryOrder(boolean value)

Parameters:

value - false, if search should rearrange query atoms for better search performance

isExactFragment

public boolean isExactFragment()

Returns:

true if the query only matches to full(exact) fragments of the target. (No heavy atoms outside the match and each query fragment corresponds to a target fragment.) Same as isFullFragment().

setExactFragment

public void setExactFragment(boolean value)

Parameters:

value - true, if the query should only match to full fragments of the target. (No heavy atoms outside the match and each query fragment corresponds to a target fragment.) Same as setFullFragment(boolean).

isFullFragment

public final boolean isFullFragment()

Returns:

true if the query only matches to full fragments of the target. (No heavy atoms outside the match and each query fragment corresponds to a target fragment.) Same as isExactFragment().

setFullFragment

public void setFullFragment(boolean value)

Parameters:

value - true, if the query should only match to full fragments of the target. (No heavy atoms outside the match and each query fragment corresponds to a target fragment.) Same as setExactFragment(boolean)

getIsotopeMatching

public final int getIsotopeMatching()

Returns:

Isotope searching behaviour. Default is ISOTOPE_MATCHING_DEFAULT (isotope query matches only isotope target, nonisotope query matches all)

See Also:

SearchConstants.ISOTOPE_MATCHING_DEFAULT, SearchConstants.ISOTOPE_MATCHING_EXACT, SearchConstants.ISOTOPE_MATCHING_IGNORE

setIsotopeMatching

public void setIsotopeMatching(int value)

Parameters:

value - Specifies the isotope searching behaviour. Default is ISOTOPE_MATCHING_DEFAULT (isotope query matches only isotope target, nonisotope query matches all)

See Also:

SearchConstants.ISOTOPE_MATCHING_DEFAULT, SearchConstants.ISOTOPE_MATCHING_EXACT, SearchConstants.ISOTOPE_MATCHING_IGNORE

getChargeMatching

public final int getChargeMatching()

Returns:

Charge searching behaviour. Default is CHARGE_MATCHING_DEFAULT (charged query matches only charged target, noncharged query matches all)

See Also:

SearchConstants.CHARGE_MATCHING_DEFAULT, SearchConstants.CHARGE_MATCHING_EXACT, SearchConstants.CHARGE_MATCHING_IGNORE

setChargeMatching

public void setChargeMatching(int value)

Parameters:

value - Specifies the charge searching behaviour. Default is CHARGE_MATCHING_DEFAULT (charged query matches only charged target, noncharged query matches all)

See Also:

SearchConstants.CHARGE_MATCHING_DEFAULT, SearchConstants.CHARGE_MATCHING_EXACT, SearchConstants.CHARGE_MATCHING_IGNORE

isValenceMatching

public boolean isValenceMatching()

Returns:

true if valence is checked during search. Default value is true.

setValenceMatching

public void setValenceMatching(boolean value)

Parameters:

value - true, if valence should be checked during search. Default value is true.

getRadicalMatching

public final int getRadicalMatching()

Returns:

Radical searching behaviour. Default is RADICAL_MATCHING_DEFAULT (radical query matches only radical target, nonradical query matches all)

See Also:

SearchConstants.RADICAL_MATCHING_DEFAULT, SearchConstants.RADICAL_MATCHING_EXACT, SearchConstants.RADICAL_MATCHING_IGNORE

setRadicalMatching

public void setRadicalMatching(int value)

Parameters:

value - Specifies the radical searching behaviour. Default is RADICAL_MATCHING_DEFAULT (radical query matches only radical target, nonradical query matches all)

See Also:

SearchConstants.RADICAL_MATCHING_DEFAULT, SearchConstants.RADICAL_MATCHING_EXACT, SearchConstants.RADICAL_MATCHING_IGNORE

isMixSgroupMatching

public boolean isMixSgroupMatching()

Returns:

true if considers COM, MIX and FOR sgroups during search Default value is true.

setMixSgroupMatching

public void setMixSgroupMatching(boolean value)

Parameters:

value - true, if COM, MIX and FOR sgroups should be considered during search. Default value is true).

isPolymerMatching

public boolean isPolymerMatching()

Returns:

true if considers polymer sgroups during search Default value is true.

See Also:

setPolymerMatching(boolean)

setPolymerMatching

public void setPolymerMatching(boolean value)

Adjust polymer matching.

Parameters:

value - true, if polymer sgroups should be considered during search. (Default value is true).

See Also:

isPolymerMatching()

isEndgroupMatching

public boolean isEndgroupMatching()

Returns:

true if polymer end groups must match during search. In this case the star atom can't match on a specified engroup. Default value is true.

setEndgroupMatching

public void setEndgroupMatching(boolean value)

Adjusts polymer end group matching.

Parameters:

value - true, if polymer endgroups should be matched during search. In this case the star atom can't match on a specified engroup. (Default value is true).

areMonomersTransformed

public boolean areMonomersTransformed()

Returns:

true if monomers (source based representation of polymers) are transformed to sru repeating units if they can be polimerizated.

See Also:

setMonomerTransform(boolean)

setMonomerTransform

public void setMonomerTransform(boolean value)

Adjusts if monomers should be transformed to structural repeating units if the monomer is homolopolimerizable.

Parameters:

value - true if monomers should be transformed, false otherwise

See Also:

areMonomersTransformed()

isPhaseShiftedMatching

public boolean isPhaseShiftedMatching()

Returns:

true if the phase-shifted polymers are matching.

See Also:

setPhaseShiftedMatching(boolean)

setPhaseShiftedMatching

public void setPhaseShiftedMatching(boolean value)

Adjusts if the phase shifted polymer should match on the original.

Parameters:

value - true if the phase shifted should be matching false otherwise. (default true)

See Also:

isPhaseShiftedMatching()

isCopolymerMatching

public boolean isCopolymerMatching()

Returns:

true if the copolymer matching mode is set.

See Also:

setCopolymerMatching(boolean)

setCopolymerMatching

public void setCopolymerMatching(boolean value)

Adjusts copolymer matching mode. If set, then target polymers in copolymers can only be matched by query polymers in copolymers.

Parameters:

value - true if copolymer matching mode should be set, false otherwise. (default false)

See Also:

isCopolymerMatching()

isQHomologyHandling

public boolean isQHomologyHandling()

Returns:

true if the query-side homology matching mode is set.

See Also:

setQHomologyHandling(boolean)

setQHomologyHandling

public void setQHomologyHandling(boolean value)

Adjusts query side homology matching mode. If set, then pseudo atoms with homology names on the query side are handled as homology groups. If false they are handled as pseudo atoms and match only pseudo atoms with the same name.

Parameters:

value - true if homology handling should be set, false otherwise. (default true)

See Also:

isQHomologyHandling()

getStereoModel

public int getStereoModel()

Returns:

Used stereo model. Default is STEREO_MODEL_LOCAL (it may change in the future!)

See Also:

SearchConstants.STEREO_MODEL_LOCAL, SearchConstants.STEREO_MODEL_COMPREHENSIVE, SearchConstants.STEREO_MODEL_GLOBAL, SearchConstants.STEREO_MODEL_DEFAULT

setStereoModel

public void setStereoModel(int value)

Parameters:

value - Specifies the used stereo model. Default is STEREO_MODEL_LOCAL (it may change in the future!)

See Also:

SearchConstants.STEREO_MODEL_LOCAL, SearchConstants.STEREO_MODEL_COMPREHENSIVE, SearchConstants.STEREO_MODEL_GLOBAL, SearchConstants.STEREO_MODEL_DEFAULT

setStereoSearchType

public void setStereoSearchType(int value)

Specifies the way stereo information is considered during searching. (setStereoModel(int) specifies the model for calculating the stereo information.)

Parameters:

value - Specifies the stereo mode. Accepted values: SearchConstants.STEREO_SPECIFIC SearchConstants.STEREO_IGNORE SearchConstants.STEREO_EXACT SearchConstants.STEREO_DIASTEREOMER

getStereoSearchType

public final int getStereoSearchType()

Returns:

Specifies the stereo search type. Default is STEREO_SPECIFIC.

See Also:

SearchConstants.STEREO_SPECIFIC, SearchConstants.STEREO_IGNORE, SearchConstants.STEREO_EXACT, SearchConstants.STEREO_DIASTEREOMER, setStereoSearchType(int)

getCheckSpHyb

public final boolean getCheckSpHyb()

Returns true if sp-hybridization state of the atoms should be considered, false otherwise

Returns:

true if sp-hybridization state of the atoms is considered,

See Also:

setCheckSpHyb(boolean), MoleculeGraph.calcHybridization()

setCheckSpHyb

public void setCheckSpHyb(boolean checkSp)

Sets whether the sp-hybridization state of the atoms should be considered.

Parameters:

checkSp - If true the sp-hybridization state is checked.

Since:

5.1

See Also:

getCheckSpHyb(), MoleculeGraph.calcHybridization()

getImplicitHMatching

public int getImplicitHMatching()

Returns:

Matching behaviour between explicit and implicit hydrogens. Default is IMPLICIT_H_MATCHING_DEFAULT (matching depends on the circumstances of search)

See Also:

SearchConstants.IMPLICIT_H_MATCHING_DEFAULT, SearchConstants.IMPLICIT_H_MATCHING_DISABLED, SearchConstants.IMPLICIT_H_MATCHING_ENABLED

setImplicitHMatching

public void setImplicitHMatching(int value)

Parameters:

value - Specifies matching bahaviour between explicit and implicit hydrogens. Default is IMPLICIT_H_MATCHING_DEFAULT (matching depends on the circumstances of search)

See Also:

SearchConstants.IMPLICIT_H_MATCHING_DEFAULT, SearchConstants.IMPLICIT_H_MATCHING_DISABLED, SearchConstants.IMPLICIT_H_MATCHING_ENABLED

isReactionUnpairedMapMatching

public boolean isReactionUnpairedMapMatching()

Returns:

true if in reaction search unpaired (orphan and widow) atom maps can match any atom map. Default value is true.

setReactionUnpairedMapMatching

public void setReactionUnpairedMapMatching(boolean value)

Parameters:

value - true, if in reaction search unpaired (orphan and widow) atom maps can match any atom map. Default value is true.

setChemTermsFilter

public void setChemTermsFilter(java.lang.String value)

Sets the Chemical Terms filtering expression.

See Also:

getChemTermsFilter()

getChemTermsFilter

public java.lang.String getChemTermsFilter()

Gets the Chemical Terms filtering expression

See Also:

setChemTermsFilter(String)

setChemTermsFilterConfig

public void setChemTermsFilterConfig(java.lang.String value)

Sets the configuration string for Chemical Terms filter.

Parameters:

value - the configuration string. Set to null for default configuration.

See Also:

getChemTermsFilterConfig()

getChemTermsFilterConfig

public java.lang.String getChemTermsFilterConfig()

Gets the configuration string for Chemical Terms filter.

Returns:

the configuration string

See Also:

setChemTermsFilterConfig(String)

setUndefinedRAtom

public void setUndefinedRAtom(int value)

Sets the matching behaviour of an undefined R atom in the query. Default is SearchConstants.UNDEF_R_MATCHING_GROUP.

Parameters:

value - Matching mode value.

See Also:

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, getUndefinedRAtom()

getUndefinedRAtom

public int getUndefinedRAtom()

Returns undefined R atom matching behaviour mode.

Returns:

Matching mode value.

See Also:

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)

isUndefinedRAtomMatchingGroup

public boolean isUndefinedRAtomMatchingGroup()

Returns whether undefined R atom matches group of atoms. This is the case when getUndefinedRAtom() returns SearchConstants.UNDEF_R_MATCHING_GROUP, SearchConstants.UNDEF_R_MATCHING_GROUP_H or SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY.

Returns:

true if undefined R atom matches group

Since:

JChem 5.3

setBridgingRAllowed

public void setBridgingRAllowed(boolean value)

Sets whether different undefined R-atoms can match the same group of atoms. This parameter is only used if R atom matching behaviour (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. Default: false.

Parameters:

value - true if different undefined R-atoms can match the same group of atoms

Since:

JChem 5.3

See Also:

setUndefinedRAtom(int)

isBridgingRAllowed

public boolean isBridgingRAllowed()

Returns true if different undefined R-atoms can match the same group of atoms. This parameter is only used if R atom matching behaviour (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.

Returns:

true if different undefined R-atoms can match the same group of atoms

Since:

JChem 5.3

See Also:

setBridgingRAllowed(boolean)

setRLigandEqualityCheck

public void setRLigandEqualityCheck(boolean value)

Sets whether undefined R-atoms with the same R-group ID should match the same structure. This parameter is only used if R atom matching behaviour (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. Default: false.

Parameters:

value - true if undefined R-atoms with the same R-group ID should match the same structure

Since:

JChem 5.3

See Also:

setUndefinedRAtom(int)

getRLigandEqualityCheck

public boolean getRLigandEqualityCheck()

Returns 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 behaviour (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.

Returns:

true if undefined R-atoms with the same R-group ID should match the same structure

Since:

JChem 5.3

See Also:

setRLigandEqualityCheck(boolean)

setAttachedDataMatch

public void setAttachedDataMatch(int value)

Sets whether attached data (in data sgroups) should be used when comparing structures. Default value is SearchConstants.ATTACHED_DATA_MATCH_IGNORE (no attached data used)

Parameters:

value -

See Also:

getAttachedDataMatch(), SearchConstants.ATTACHED_DATA_MATCH_IGNORE, SearchConstants.ATTACHED_DATA_MATCH_GENERAL, SearchConstants.ATTACHED_DATA_MATCH_EXACT

getAttachedDataMatch

public int getAttachedDataMatch()

Returns whether attached data (in data sgroups) should be used when comparing structures.

Returns:

value of attached data match type

See Also:

setAttachedDataMatch(int), SearchConstants.ATTACHED_DATA_MATCH_IGNORE, SearchConstants.ATTACHED_DATA_MATCH_GENERAL, SearchConstants.ATTACHED_DATA_MATCH_EXACT

setAttachedDataPrefixes

public void setAttachedDataPrefixes(java.lang.String value)

Sets the prefixes of the names of those data sgroups that will be used during structure comparison.
Default value is null (all data sgroups will be checked). The value is used only when attached data is not ignored (see setAttachedDataMatch(int)).
Prefixes are case insensitive.

Parameters:

value - comma separated list of name prefixes, e.g. "weight,atomcount"

getAttachedDataPrefixes

public 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.

Returns:

comma separated list of name prefixes or null

setExactSpecialAtomMatching

public void setExactSpecialAtomMatching(java.lang.String value)

Sets the identifiers of those special atoms that should match exactly during structure comparison.
Default value is "" (all data sgroups will be checked).
Identifiers are case insensitive.
Available identifiers are generic query atoms (A, AH, Q, ...) (see this page ) and pseudo atom aliases (see this page ).

Parameters:

value - comma separated list of identifiers e.g. "A,G18,*,Resin"

getExactSpecialAtomMatching

public java.lang.String getExactSpecialAtomMatching()

Returns the identifiers of those special atoms that should match exactly during structure comparison.

Returns:

comma separated list of identifiers

isIgnoreCTExceptions

public boolean isIgnoreCTExceptions()

Returns:

true if Chemical Terms exceptions should be ignored during evalution

setIgnoreCTExceptions

public void setIgnoreCTExceptions(boolean value)

If set true, only syntactical exceptions will be thrown. Those molecules that return exception during evaluation will be left out from hit list. Default value is false.

Parameters:

value - true if Chemical Terms exceptions should be ignored during evalution

getExhaustiveModeLimit

public int getExhaustiveModeLimit()

Upon reaching this number of steps, the search switches to exhaustive mode from fast mode.

Returns:

The limit value.

See Also:

setExhaustiveModeLimit(int)

setExhaustiveModeLimit

public void setExhaustiveModeLimit(int value)

Upon reaching this number of steps, the search switches to exhaustive mode from fast mode. Default value is one million.

Parameters:

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.

getTimeoutLimit

public int getTimeoutLimit()

The search timeouts reaching this number of steps.

Returns:

The timeout step limit.

See Also:

setTimeoutLimit(int)

setTimeoutLimit

public void setTimeoutLimit(int value)

The search timeouts reaching this number of steps. Set it to -1 if you do not want the search to time out. Default value is ten million.

Parameters:

value - The step limit to set.

setTautomerDuplicateFiltering

public void setTautomerDuplicateFiltering(boolean value)

Parameters:

value - true if generic tautomers of query and target should be used during search. (Effective only in case of duplicate search.) Default is false.

isTautomerDuplicateFiltering

public boolean isTautomerDuplicateFiltering()

Returns:

true if generic tautomers of query and target should be used during search. (Effective only in case of duplicate search.)

toString

public 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)

Overrides:

toString in class java.lang.Object

Returns:

a string in format "optionname1:optionvalue1 optionname2:optionvalue2 ..."

See Also:

setOptions(String), toList()

toString

public 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)

Parameters:

sep - the separator string between options

Returns:

a string in format "optionname1:optionvalue1 optionname2:optionvalue2 ..."

Since:

JChem 5.3

See Also:

setOptions(String), toList()

getAllOptionsAsString

public 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)

Returns:

a string in format "optionname1:optionvalue1 optionname2:optionvalue2 ..."

Since:

JChem 5.3

See Also:

getAllOptionsAsString(String), setOptions(String), toString()

getAllOptionsAsString

public 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)

Parameters:

sep - is the separator

Returns:

a string in format "sep=$$ optionname1:optionvalue1$$optionname2:optionvalue2$$...", where $$ is the separator

Since:

JChem 5.3

See Also:

getAllOptionsAsString(), setOptions(String), toString()

toList

public java.util.ArrayList toList()

Returns:

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

See Also:

setOptions(String), toString()

getOptionNames

protected java.lang.String[] getOptionNames()