public static final class McsSearchOptions.Builder extends MatchingOptions.Builder
McsSearchOptions
class.atomMapMatching, atomTypeMatching, bondTypeMatching, chargeMatching, customMatcherFactory, exactQueryAtomMatching, exactQueryBondMatching, isotopeMatching, orderSensitive, radicalMatching
Constructor and Description |
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Builder()
Creates a Builder object with the default settings.
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Builder(McsSearchOptions 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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McsSearchOptions.Builder |
atomMapMatching(boolean value)
Sets whether atom map numbers should be considered in search.
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McsSearchOptions.Builder |
atomTypeMatching(boolean value)
Sets whether atom types should be considered in search.
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McsSearchOptions.Builder |
bondTypeMatching(boolean value)
Sets whether bond types should be considered in search.
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McsSearchOptions |
build()
Creates a search options object with the settings specified by this builder instance.
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McsSearchOptions.Builder |
chargeMatching(boolean value)
Sets whether formal charges of atoms should be considered in search.
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McsSearchOptions.Builder |
connectedMode(boolean connected)
Sets whether the common substructures should be connected or they can consist of multiple fragments.
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McsSearchOptions.Builder |
customMatching(CustomMatcherFactory matcherFactory)
Sets the factory to be used to create a custom matcher.
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McsSearchOptions.Builder |
exactQueryAtomMatching(boolean value)
Sets whether generic query atoms should be matched only to atoms of exactly the same type.
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McsSearchOptions.Builder |
exactQueryBondMatching(boolean value)
Sets whether generic query bonds should be matched only to bonds of exactly the same type.
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McsSearchOptions.Builder |
isotopeMatching(boolean value)
Sets whether isotopes of atoms should be considered in search.
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McsSearchOptions.Builder |
maxConsideredRingSize(int value)
Sets the maximum size of rings considered for ring matching purposes.
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McsSearchOptions.Builder |
minFragmentSize(int bondCount)
Sets the minimum required size of the fragments of MCS.
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McsSearchOptions.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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McsSearchOptions.Builder |
radicalMatching(boolean value)
Sets whether the radical information of atoms should be considered in search.
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McsSearchOptions.Builder |
ringHandlingMode(RingHandlingMode value)
Sets how rings should be handled during the search.
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public Builder()
public Builder(McsSearchOptions opts)
opts
- the default valuespublic McsSearchOptions.Builder atomTypeMatching(boolean value)
MatchingOptions.Builder
atomTypeMatching
in class MatchingOptions.Builder
value
- specifies whether atom types are checked (true) or ignored (false)public McsSearchOptions.Builder bondTypeMatching(boolean value)
MatchingOptions.Builder
bondTypeMatching
in class MatchingOptions.Builder
value
- specifies whether bond types are checked (true) or ignored (false)public McsSearchOptions.Builder chargeMatching(boolean value)
MatchingOptions.Builder
chargeMatching
in class MatchingOptions.Builder
value
- specifies whether charges are checked (true) or ignored (false)public McsSearchOptions.Builder isotopeMatching(boolean value)
MatchingOptions.Builder
If atom type matching is disabled, isotopes are also ignored, irrespective of this search option.
isotopeMatching
in class MatchingOptions.Builder
value
- specifies whether mass numbers are checked (true) or ignored (false)public McsSearchOptions.Builder radicalMatching(boolean value)
MatchingOptions.Builder
radicalMatching
in class MatchingOptions.Builder
value
- specifies whether radicals are checked (true) or ignored (false)public McsSearchOptions.Builder atomMapMatching(boolean value)
MatchingOptions.Builder
atomMapMatching
in class MatchingOptions.Builder
value
- specifies whether atom map numbers are checked (true) or ignored (false)public McsSearchOptions.Builder exactQueryAtomMatching(boolean value)
MatchingOptions.Builder
exactQueryAtomMatching
in class MatchingOptions.Builder
value
- true if generic query atoms should match only atoms of exactly the same typepublic McsSearchOptions.Builder exactQueryBondMatching(boolean value)
MatchingOptions.Builder
exactQueryBondMatching
in class MatchingOptions.Builder
value
- true if generic query bonds should match only bonds of exactly the same typepublic McsSearchOptions.Builder ringHandlingMode(RingHandlingMode value)
RingHandlingMode
for more information.value
- ring handling mode (not null)maxConsideredRingSize(int)
public McsSearchOptions.Builder maxConsideredRingSize(int value)
value
- the maximum considered ring sizeringHandlingMode(RingHandlingMode)
public McsSearchOptions.Builder connectedMode(boolean connected)
connected
- specifies if connected common substructures should be found (true) or disconnected
substructures are also allowed (false)minFragmentSize(int)
public McsSearchOptions.Builder minFragmentSize(int bondCount)
bondCount
- minimum required bond count in additional fragments (except for the largest one)connectedMode(boolean)
public McsSearchOptions.Builder orderSensitive(boolean value)
MatchingOptions.Builder
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.
orderSensitive
in class MatchingOptions.Builder
value
- true if the search should be order sensitivepublic McsSearchOptions.Builder customMatching(CustomMatcherFactory matcherFactory)
MatchingOptions.Builder
CustomMatcher
created by
the given factory (in addition to the criteria specified by other search options).customMatching
in class MatchingOptions.Builder
matcherFactory
- the factory for creating the custom matcher to be usedpublic McsSearchOptions build()
MatchingOptions.Builder
build
in class MatchingOptions.Builder