Class MatchingOptions.Builder
- Direct Known Subclasses:
McsSearchOptions.Builder
- Enclosing class:
- MatchingOptions
MatchingOptions
class.-
Field Summary
Modifier and TypeFieldDescriptionprotected boolean
protected boolean
protected boolean
protected boolean
protected CustomMatcherFactory
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
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Constructor Summary
ModifierConstructorDescriptionprotected
Builder()
Creates a Builder object with the default settings.protected
Builder
(MatchingOptions opts) Creates a Builder object containing the settings of the given search options object. -
Method Summary
Modifier and TypeMethodDescriptionabstract MatchingOptions.Builder
atomMapMatching
(boolean value) Sets whether atom map numbers should be considered in search.abstract MatchingOptions.Builder
atomTypeMatching
(boolean value) Sets whether atom types should be considered in search.abstract MatchingOptions.Builder
bondTypeMatching
(boolean value) Sets whether bond types should be considered in search.abstract MatchingOptions
build()
Creates a search options object with the settings specified by this builder instance.abstract MatchingOptions.Builder
chargeMatching
(boolean value) Sets whether formal charges of atoms should be considered in search.abstract MatchingOptions.Builder
customMatching
(CustomMatcherFactory matcherFactory) Sets the factory to be used to create a custom matcher.abstract MatchingOptions.Builder
exactQueryAtomMatching
(boolean value) Sets whether generic query atoms should be matched only to atoms of exactly the same type.abstract MatchingOptions.Builder
exactQueryBondMatching
(boolean value) Sets whether generic query bonds should be matched only to bonds of exactly the same type.abstract MatchingOptions.Builder
isotopeMatching
(boolean value) Sets whether isotopes of atoms should be considered in search.abstract MatchingOptions.Builder
orderSensitive
(boolean value) Sets whether search is sensitive to the order of the matched atoms and bonds when searching for multiple results.abstract MatchingOptions.Builder
radicalMatching
(boolean value) Sets whether the radical information of atoms should be considered in search.
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Field Details
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atomTypeMatching
protected boolean atomTypeMatching -
bondTypeMatching
protected boolean bondTypeMatching -
chargeMatching
protected boolean chargeMatching -
isotopeMatching
protected boolean isotopeMatching -
radicalMatching
protected boolean radicalMatching -
atomMapMatching
protected boolean atomMapMatching -
exactQueryAtomMatching
protected boolean exactQueryAtomMatching -
exactQueryBondMatching
protected boolean exactQueryBondMatching -
customMatcherFactory
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orderSensitive
protected boolean orderSensitive
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Constructor Details
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Builder
protected 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, i.e., 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, i.e., "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, irrespective 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
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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 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 bonds of exactly the same type- 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 theCustomMatcher
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- Returns:
- this builder
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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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build
Creates a search options object with the settings specified by this builder instance.- Returns:
- the search options object
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