public abstract static class MatchingOptions.Builder
extends java.lang.Object
MatchingOptions
class.Modifier and Type | Field and Description |
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protected boolean |
atomMapMatching |
protected boolean |
atomTypeMatching |
protected boolean |
bondTypeMatching |
protected boolean |
chargeMatching |
protected CustomMatcherFactory |
customMatcherFactory |
protected boolean |
exactQueryAtomMatching |
protected boolean |
exactQueryBondMatching |
protected boolean |
isotopeMatching |
protected boolean |
orderSensitive |
protected boolean |
radicalMatching |
Constructor and Description |
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Builder()
Creates a Builder object with the default settings.
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Builder(MatchingOptions opts)
Creates a Builder object containing the settings of the given search options object.
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Modifier and Type | Method and Description |
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abstract MatchingOptions.Builder |
atomMapMatching(boolean value)
Sets whether atom map numbers should be considered in search.
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abstract MatchingOptions.Builder |
atomTypeMatching(boolean value)
Sets whether atom types should be considered in search.
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abstract MatchingOptions.Builder |
bondTypeMatching(boolean value)
Sets whether bond types should be considered in search.
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abstract MatchingOptions |
build()
Creates a search options object with the settings specified by this builder instance.
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abstract MatchingOptions.Builder |
chargeMatching(boolean value)
Sets whether formal charges of atoms should be considered in search.
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abstract MatchingOptions.Builder |
customMatching(CustomMatcherFactory matcherFactory)
Sets the factory to be used to create a custom matcher.
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abstract MatchingOptions.Builder |
exactQueryAtomMatching(boolean value)
Sets whether generic query atoms should be matched only to atoms of exactly the same type.
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abstract MatchingOptions.Builder |
exactQueryBondMatching(boolean value)
Sets whether generic query bonds should be matched only to bonds of exactly the same type.
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abstract MatchingOptions.Builder |
isotopeMatching(boolean value)
Sets whether isotopes of atoms should be considered in search.
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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.
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abstract MatchingOptions.Builder |
radicalMatching(boolean value)
Sets whether the radical information of atoms should be considered in search.
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protected boolean atomTypeMatching
protected boolean bondTypeMatching
protected boolean chargeMatching
protected boolean isotopeMatching
protected boolean radicalMatching
protected boolean atomMapMatching
protected boolean exactQueryAtomMatching
protected boolean exactQueryBondMatching
protected CustomMatcherFactory customMatcherFactory
protected boolean orderSensitive
public Builder()
public Builder(MatchingOptions opts)
opts
- the default valuespublic abstract MatchingOptions.Builder atomTypeMatching(boolean value)
value
- specifies whether atom types are checked (true) or ignored (false)public abstract MatchingOptions.Builder bondTypeMatching(boolean value)
value
- specifies whether bond types are checked (true) or ignored (false)public abstract MatchingOptions.Builder chargeMatching(boolean value)
value
- specifies whether charges are checked (true) or ignored (false)public abstract MatchingOptions.Builder isotopeMatching(boolean value)
If atom type matching is disabled, isotopes are also ignored, irrespective of this search option.
value
- specifies whether mass numbers are checked (true) or ignored (false)public abstract MatchingOptions.Builder radicalMatching(boolean value)
value
- specifies whether radicals are checked (true) or ignored (false)public abstract MatchingOptions.Builder atomMapMatching(boolean value)
value
- specifies whether atom map numbers are checked (true) or ignored (false)public abstract MatchingOptions.Builder exactQueryAtomMatching(boolean value)
value
- true if generic query atoms should match only atoms of exactly the same typepublic abstract MatchingOptions.Builder exactQueryBondMatching(boolean value)
value
- true if generic query bonds should match only bonds of exactly the same typepublic abstract MatchingOptions.Builder customMatching(CustomMatcherFactory matcherFactory)
CustomMatcher
created by
the given factory (in addition to the criteria specified by other search options).matcherFactory
- the factory for creating the custom matcher to be usedpublic abstract MatchingOptions.Builder orderSensitive(boolean value)
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.
value
- true if the search should be order sensitivepublic abstract MatchingOptions build()