com.chemaxon.search.mcs

Class McsSearchOptions.Builder

java.lang.Object

com.chemaxon.search.MatchingOptions.Builder

com.chemaxon.search.mcs.McsSearchOptions.Builder

Enclosing class:

McsSearchOptions

public static final class McsSearchOptions.Builder
extends MatchingOptions.Builder

Builder class for creating immutable instances of the enclosing McsSearchOptions class.

Field Summary

Fields inherited from class com.chemaxon.search.MatchingOptions.Builder

atomMapMatching, atomTypeMatching, bondTypeMatching, chargeMatching, customMatcherFactory, exactQueryAtomMatching, exactQueryBondMatching, isotopeMatching, orderSensitive, radicalMatching

Constructor Summary

Constructors

Constructor and Description
Builder() 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 Type	Method and Description
McsSearchOptions.Builder	atomMapMatching(boolean value) Sets whether atom map numbers should be considered in search.
McsSearchOptions.Builder	atomTypeMatching(boolean value) Sets whether atom types should be considered in search.
McsSearchOptions.Builder	bondTypeMatching(boolean value) Sets whether bond types should be considered in search.
McsSearchOptions	build() Creates a search options object with the settings specified by this builder instance.
McsSearchOptions.Builder	chargeMatching(boolean value) Sets whether formal charges of atoms should be considered in search.
McsSearchOptions.Builder	connectedMode(boolean connected) Sets whether the common substructures should be connected or they can consist of multiple fragments.
McsSearchOptions.Builder	customMatching(CustomMatcherFactory matcherFactory) Sets the factory to be used to create a custom matcher.
McsSearchOptions.Builder	exactQueryAtomMatching(boolean value) Sets whether generic query atoms should be matched only to atoms of exactly the same type.
McsSearchOptions.Builder	exactQueryBondMatching(boolean value) Sets whether generic query bonds should be matched only to bonds of exactly the same type.
McsSearchOptions.Builder	isotopeMatching(boolean value) Sets whether isotopes of atoms should be considered in search.
McsSearchOptions.Builder	maxConsideredRingSize(int value) Sets the maximum size of rings considered for ring matching purposes.
McsSearchOptions.Builder	minFragmentSize(int bondCount) Sets the minimum required size of the fragments of MCS.
McsSearchOptions.Builder	orderSensitive(boolean value) Sets whether search is sensitive to the order of the matched atoms and bonds when searching for multiple results.
McsSearchOptions.Builder	radicalMatching(boolean value) Sets whether the radical information of atoms should be considered in search.
McsSearchOptions.Builder	ringHandlingMode(RingHandlingMode value) Sets how rings should be handled during the search.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Builder

public Builder()

Creates a Builder object with the default settings.

Builder

public Builder(McsSearchOptions opts)

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

Method Detail

atomTypeMatching

public McsSearchOptions.Builder atomTypeMatching(boolean value)

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 class MatchingOptions.Builder

Parameters:

value - specifies whether atom types are checked (true) or ignored (false)

Returns:

this builder

bondTypeMatching

public McsSearchOptions.Builder bondTypeMatching(boolean value)

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 class MatchingOptions.Builder

Parameters:

value - specifies whether bond types are checked (true) or ignored (false)

Returns:

this builder

chargeMatching

public McsSearchOptions.Builder chargeMatching(boolean value)

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 class MatchingOptions.Builder

Parameters:

value - specifies whether charges are checked (true) or ignored (false)

Returns:

this builder

isotopeMatching

public McsSearchOptions.Builder isotopeMatching(boolean value)

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 class MatchingOptions.Builder

Parameters:

value - specifies whether mass numbers are checked (true) or ignored (false)

Returns:

this builder

radicalMatching

public McsSearchOptions.Builder radicalMatching(boolean value)

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 class MatchingOptions.Builder

Parameters:

value - specifies whether radicals are checked (true) or ignored (false)

Returns:

this builder

atomMapMatching

public McsSearchOptions.Builder atomMapMatching(boolean value)

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 class MatchingOptions.Builder

Parameters:

value - specifies whether atom map numbers are checked (true) or ignored (false)

Returns:

this builder

exactQueryAtomMatching

public McsSearchOptions.Builder exactQueryAtomMatching(boolean value)

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 class MatchingOptions.Builder

Parameters:

value - true if generic query atoms should match only atoms of exactly the same type

Returns:

this builder

exactQueryBondMatching

public McsSearchOptions.Builder exactQueryBondMatching(boolean value)

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 class MatchingOptions.Builder

Parameters:

value - true if generic query bonds should match only bonds of exactly the same type

Returns:

this builder

ringHandlingMode

public McsSearchOptions.Builder ringHandlingMode(RingHandlingMode value)

Sets how rings should be handled during the search. See RingHandlingMode for more information.

Parameters:

value - ring handling mode (not null)

Returns:

this builder

See Also:

maxConsideredRingSize(int)

maxConsideredRingSize

public McsSearchOptions.Builder maxConsideredRingSize(int value)

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:

ringHandlingMode(RingHandlingMode)

connectedMode

public McsSearchOptions.Builder connectedMode(boolean connected)

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:

minFragmentSize(int)

minFragmentSize

public McsSearchOptions.Builder minFragmentSize(int bondCount)

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:

connectedMode(boolean)

orderSensitive

public McsSearchOptions.Builder orderSensitive(boolean value)

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 class MatchingOptions.Builder

Parameters:

value - true if the search should be order sensitive

Returns:

this builder

customMatching

public McsSearchOptions.Builder customMatching(CustomMatcherFactory matcherFactory)

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 the CustomMatcher created by the given factory (in addition to the criteria specified by other search options).

Specified by:

customMatching in class MatchingOptions.Builder

Parameters:

matcherFactory - the factory for creating the custom matcher to be used

Returns:

this builder

build

public McsSearchOptions build()

Description copied from class: MatchingOptions.Builder

Creates a search options object with the settings specified by this builder instance.

Specified by:

build in class MatchingOptions.Builder

Returns:

the search options object