Class McsSearchOptions.Builder
- Enclosing class:
- McsSearchOptions
McsSearchOptions
class.-
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
(McsCustomMatcherFactory 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
Sets whether atom types should be considered in search. By default, the atom types are checked For example, a carbon atom does not match to an oxygen atom.- Parameters:
value
- specifies whether atom types are checked (true) or ignored (false)- Returns:
- this builder
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bondTypeMatching
Sets whether bond types should be considered in search. By default, the bond types are checked. For example, "CC" does not match to "C=C".- Parameters:
value
- specifies whether bond types are checked (true) or ignored (false)- Returns:
- this builder
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chargeMatching
Sets whether formal charges of atoms should be considered in search. By default, charges are ignored.- Parameters:
value
- specifies whether charges are checked (true) or ignored (false)- Returns:
- this builder
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isotopeMatching
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, independently of this search option.
- Parameters:
value
- specifies whether mass numbers are checked (true) or ignored (false)- Returns:
- this builder
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radicalMatching
Sets whether the radical information of atoms should be considered in search. By default, radicals are ignored.- Parameters:
value
- specifies whether radicals are checked (true) or ignored (false)- Returns:
- this builder
-
atomMapMatching
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.- Parameters:
value
- specifies whether atom map numbers are checked (true) or ignored (false)- Returns:
- this builder
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exactQueryAtomMatching
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.- Parameters:
value
- true if generic query atoms should match only to atoms of exactly the same type- Returns:
- this builder
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exactQueryBondMatching
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.- Parameters:
value
- true if generic query bonds should match only to 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
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.
- Parameters:
value
- true if the search should be order-sensitive- Returns:
- this builder
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customMatching
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 theMcsCustomMatcher
created by the given factory, in addition to the criteria specified by other search options.- Parameters:
matcherFactory
- the factory for creating the custom matcher to be used (can be null)- Returns:
- this builder
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build
Creates a search options object with the settings specified by this builder instance.- Returns:
- the search options object
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