Class McsSearchOptions.Builder
- Enclosing class:
- McsSearchOptions
McsSearchOptions
class.-
Field Summary
Fields inherited from class com.chemaxon.search.MatchingOptions.Builder
atomMapMatching, atomTypeMatching, bondTypeMatching, chargeMatching, customMatcherFactory, exactQueryAtomMatching, exactQueryBondMatching, isotopeMatching, orderSensitive, radicalMatching
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Constructor Summary
ConstructorDescriptionBuilder()
Creates a Builder object with the default settings.Builder
(McsSearchOptions opts) Creates a Builder object containing the settings of the given search options object. -
Method Summary
Modifier and TypeMethodDescriptionatomMapMatching
(boolean value) Sets whether atom map numbers should be considered in search.atomTypeMatching
(boolean value) Sets whether atom types should be considered in search.bondTypeMatching
(boolean value) Sets whether bond types should be considered in search.build()
Creates a search options object with the settings specified by this builder instance.chargeMatching
(boolean value) Sets whether formal charges of atoms should be considered in search.connectedMode
(boolean connected) Sets whether the common substructures should be connected or they can consist of multiple fragments.customMatching
(CustomMatcherFactory matcherFactory) Sets the factory to be used to create a custom matcher.exactQueryAtomMatching
(boolean value) Sets whether generic query atoms should be matched only to atoms of exactly the same type.exactQueryBondMatching
(boolean value) Sets whether generic query bonds should be matched only to bonds of exactly the same type.isotopeMatching
(boolean value) Sets whether isotopes of atoms should be considered in search.maxConsideredRingSize
(int value) Sets the maximum size of rings considered for ring matching purposes.minFragmentSize
(int bondCount) Sets the minimum required size of the fragments of MCS.orderSensitive
(boolean value) Sets whether search is sensitive to the order of the matched atoms and bonds when searching for multiple results.radicalMatching
(boolean value) Sets whether the radical information of atoms should be considered in search.ringHandlingMode
(RingHandlingMode value) Sets how rings should be handled during the search.
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Constructor Details
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Builder
public Builder()Creates a Builder object with the default settings. -
Builder
Creates a Builder object containing the settings of the given search options object. Useful if only a few options need to be changed, compared to an existing search options object.- Parameters:
opts
- the default values
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Method Details
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atomTypeMatching
Description copied from class:MatchingOptions.Builder
Sets whether atom types should be considered in search. By default, the atom types are checked, i.e., a carbon atom does not match to an oxygen atom.- Specified by:
atomTypeMatching
in classMatchingOptions.Builder
- Parameters:
value
- specifies whether atom types are checked (true) or ignored (false)- Returns:
- this builder
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bondTypeMatching
Description copied from class:MatchingOptions.Builder
Sets whether bond types should be considered in search. By default, the bond types are checked, i.e., "CC" does not match to "C=C".- Specified by:
bondTypeMatching
in classMatchingOptions.Builder
- Parameters:
value
- specifies whether bond types are checked (true) or ignored (false)- Returns:
- this builder
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chargeMatching
Description copied from class:MatchingOptions.Builder
Sets whether formal charges of atoms should be considered in search. By default, charges are ignored.- Specified by:
chargeMatching
in classMatchingOptions.Builder
- Parameters:
value
- specifies whether charges are checked (true) or ignored (false)- Returns:
- this builder
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isotopeMatching
Description copied from class:MatchingOptions.Builder
Sets whether isotopes of atoms should be considered in search. By default, mass numbers are ignored, so isotopes of the same element match each other.If atom type matching is disabled, isotopes are also ignored, irrespective of this search option.
- Specified by:
isotopeMatching
in classMatchingOptions.Builder
- Parameters:
value
- specifies whether mass numbers are checked (true) or ignored (false)- Returns:
- this builder
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radicalMatching
Description copied from class:MatchingOptions.Builder
Sets whether the radical information of atoms should be considered in search. By default, radicals are ignored.- Specified by:
radicalMatching
in classMatchingOptions.Builder
- Parameters:
value
- specifies whether radicals are checked (true) or ignored (false)- Returns:
- this builder
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atomMapMatching
Description copied from class:MatchingOptions.Builder
Sets whether atom map numbers should be considered in search. If set to true, two atoms with different map numbers do not match each other. By default, it is set to false.- Specified by:
atomMapMatching
in classMatchingOptions.Builder
- Parameters:
value
- specifies whether atom map numbers are checked (true) or ignored (false)- Returns:
- this builder
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exactQueryAtomMatching
Description copied from class:MatchingOptions.Builder
Sets whether generic query atoms should be matched only to atoms of exactly the same type. If set to true, generic atoms are not considered as query features. For example, an "any" atom matches only to another "any" atom. By default, it is set to false.- Specified by:
exactQueryAtomMatching
in classMatchingOptions.Builder
- Parameters:
value
- true if generic query atoms should match only atoms of exactly the same type- Returns:
- this builder
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exactQueryBondMatching
Description copied from class:MatchingOptions.Builder
Sets whether generic query bonds should be matched only to bonds of exactly the same type. If set to true, generic bonds are not considered as query features. For example, an "any" bond matches only to another "any" bond. By default, it is set to false.- Specified by:
exactQueryBondMatching
in classMatchingOptions.Builder
- Parameters:
value
- true if generic query bonds should match only bonds of exactly the same type- Returns:
- this builder
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ringHandlingMode
Sets how rings should be handled during the search. SeeRingHandlingMode
for more information.- Parameters:
value
- ring handling mode (not null)- Returns:
- this builder
- See Also:
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maxConsideredRingSize
Sets the maximum size of rings considered for ring matching purposes. The default value is 8. (A ring of 9 or more atoms is considered a macrocycle.)- Parameters:
value
- the maximum considered ring size- Returns:
- this builder
- See Also:
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connectedMode
Sets whether the common substructures should be connected or they can consist of multiple fragments.- Parameters:
connected
- specifies if connected common substructures should be found (true) or disconnected substructures are also allowed (false)- Returns:
- this builder
- See Also:
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minFragmentSize
Sets the minimum required size of the fragments of MCS. Fragments having less bonds than this limit are ignored, except for one largest fragment found. The default value is 1 (that is, all fragments are kept).- Parameters:
bondCount
- minimum required bond count in additional fragments (except for the largest one)- Returns:
- this builder
- See Also:
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orderSensitive
Description copied from class:MatchingOptions.Builder
Sets whether search is sensitive to the order of the matched atoms and bonds when searching for multiple results.By default, this option is set to false. It means that two search results are considered to be different only when they cover different atoms or bonds of the query or the target. In contrast, order sensitive search differentiates two results with the same set of mapped atoms and bonds in both molecules if the actual mappings are different.
For example, if the query molecule is "CNC" and target molecule is "CNCNC", then order sensitive search provides four different mappings of the query to the target, while order insensitive (default) search provides only two of these hits (that cover different parts of the target molecule).
Warning: Order sensitive search may produce orders of magnitude more hits as it also deals with the internal symmetry of the molecules.
- Specified by:
orderSensitive
in classMatchingOptions.Builder
- Parameters:
value
- true if the search should be order sensitive- Returns:
- this builder
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customMatching
Description copied from class:MatchingOptions.Builder
Sets the factory to be used to create a custom matcher. During search, two atom or bonds may be matched only if they are accepted by the corresponding method of theCustomMatcher
created by the given factory (in addition to the criteria specified by other search options).- Specified by:
customMatching
in classMatchingOptions.Builder
- Parameters:
matcherFactory
- the factory for creating the custom matcher to be used- Returns:
- this builder
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build
Description copied from class:MatchingOptions.Builder
Creates a search options object with the settings specified by this builder instance.- Specified by:
build
in classMatchingOptions.Builder
- Returns:
- the search options object
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