chemaxon.sss.search
Class SearchOptions

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

All Implemented Interfaces:

java.lang.Cloneable, SearchConstants

Direct Known Subclasses:

JChemSearchOptions, MolSearchOptions

public class SearchOptions

extends java.lang.Object

implements SearchConstants, java.lang.Cloneable

Class to encapsulate common search parameters.

Since:

5.0

Author:

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

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, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SIMILARITY_THRESHOLD, DISSIMILARITY, EXACT, EXACT_FRAGMENT, EXACT_FRAGMENT_OFF, EXACT_FRAGMENT_ON, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, 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_ORIGINAL, MARKUSH_HIT_SUPERGRAPH, 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, REGULAR_SEARCH, SEARCH_MODE_NAMES, SEARCH_OPTIONS_LENGTH, SIMILARITY, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, VAGUE_BOND_DEFAULT, 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.
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)
protected static boolean	getBoolean(java.lang.String value) Returns value as a boolean flag.
int	getChargeMatching()
java.lang.String	getChemTermsFilter() Gets the Chemical Terms filtering expression
java.lang.String	getChemTermsFilterConfig() Gets the configuration string for Chemical Terms filter.
int	getDoubleBondStereoMatchingMode()
int	getHCountMatching()
int	getImplicitHMatching()
int	getIsotopeMatching()
int	getOption(int option) Deprecated. Since 5.0 Please use getters instead. isKeepQueryOrder() isExactFragment() isTautomerSearch() getIsotopeMatching() getChargeMatching() isValenceMatching() getRadicalMatching() getVagueBondLevel() isMixSgroupMatching() getStereoModel() getImplicitHMatching() isReactionUnpairedMapMatching()
java.lang.String	getOption(java.lang.String name) Returns option value in string format.
int[]	getOptions() Deprecated. since 5.0
int	getRadicalMatching()
int	getSearchType() Returns the currently set global search operation mode.
int	getStereoModel()
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	isDirty() Returns the dirty flag.
boolean	isExactBondMatching() Indicates whether bond types should match exacly - looking for query bonds target.
boolean	isExactFragment()
boolean	isExactQueryAtomMatching() Returns whether exact matching of query atom information is set.
boolean	isExactStereoMatching() Returns the exact stereo matching option.
boolean	isKeepQueryOrder()
boolean	isMixSgroupMatching()
boolean	isOrderSensitiveSearch() Indicates whether the search is order sensitive
boolean	isPerfectSearchType()
boolean	isReactionUnpairedMapMatching()
boolean	isStereoSearch() If true, then chirality information is considered during searching, otherwise all stereo information is ignored.
protected boolean	isSubgraphSearch() Returns the subgraph matching option.
boolean	isSuperstructureSearch() True if the current search type is superstructure search.
boolean	isTautomerSearch() Indicates if tautomers of the query should be enumerated for search.
boolean	isValenceMatching()
boolean	isVerbose() For debugging purposes only.
protected java.lang.String	returnOptionString(boolean value)
void	setChargeMatching(int value)
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	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	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	setExactStereoMatching(boolean value) If true, equality is needed in stereochemistry.
void	setHCountMatching(int value) Sets the H count matching mode.
void	setImplicitHMatching(int value)
void	setIsotopeMatching(int value)
void	setKeepQueryOrder(boolean value)
void	setMixSgroupMatching(boolean value)
void	setOption(int option, int value) Deprecated. Since 5.0 Please use setters instead. setKeepQueryOrder(boolean) setExactFragment(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	setRadicalMatching(int value)
void	setReactionUnpairedMapMatching(boolean value)
void	setSearchType(int searchType) Sets different search options according to a predefined search type.
void	setStereoModel(int value)
void	setStereoSearch(boolean value) If true, then chirality information is considered during searching, otherwise all stereo information is ignored.
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	setTautomerSearch(boolean value) Sets if tautomers of the query should be enumerated for search.
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

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 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.EXACT. SearchConstants.PERFECT. SearchConstants.EXACT_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 PERFECT search or not.

isSubgraphSearch

protected boolean isSubgraphSearch()

Returns the subgraph matching option.

Returns:

true if substructure search, false if exact structure search

setSubgraphSearch

protected void setSubgraphSearch(boolean value)

Specifies the matching mode for topology search

Parameters:

value - true for substructure search, false for exact 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)

setExactFragment(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()

isExactFragment()

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 boolean isExactStereoMatching()

Returns the exact stereo matching option. 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 PERFECT search, where it is true. This setting has no effect if stereoSearch == false.

Returns:

the exact-stereo setting

See Also:

isStereoSearch()

setExactStereoMatching

public void setExactStereoMatching(boolean value)

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 PERFECT search, where it is true. This setting has no effect if stereoSearch == false.

Parameters:

value - the exact-stereo setting

See Also:

setStereoSearch(boolean)

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()

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

setStereoSearch

public void setStereoSearch(boolean value)

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

isExactBondMatching

public boolean isExactBondMatching()

Indicates whether bond types should match exacly - 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

Since:

JChem 5.0

See Also:

getVagueBondLevel(), 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_LEVEL1, SearchConstants.VAGUE_BOND_LEVEL2, SearchConstants.VAGUE_BOND_LEVEL3, SearchConstants.VAGUE_BOND_LEVEL4

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 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.

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

exactStereoSearch

stereoSearch

keepQueryOrder

exactAtomMatching

exactQueryAtomMatching

exactRadicalMatching

exactIsotopeMatching

exactChargeMatching

doubleBondStereo

HCountMatching

t

implicitHMatching

vagueBond

charge

isotope

radical

valence

mix

markush

stereoModel

reactionUnpairedMap

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

exactStereoSearch

stereoSearch

keepQueryOrder

doubleBondStereo

HCountMatching

t

implicitHMatching

reactionUnpairedMap

vagueBond

charge

isotope

radical

valence

mix

stereoModel

Returns:

string value of the given option (true --> y, false --> n, except 'valence' 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:

true if search rearranges query atoms for better search performance

setKeepQueryOrder

public void setKeepQueryOrder(boolean value)

Parameters:

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

isExactFragment

public boolean isExactFragment()

Returns:

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

setExactFragment

public void setExactFragment(boolean value)

Parameters:

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

getIsotopeMatching

public 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 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 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).

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

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)

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

Returns:

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

See Also:

setOptions(String), toList()

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()