com.chemaxon.search.mcs

Class McsSearchOptions

java.lang.Object

com.chemaxon.search.MatchingOptions

com.chemaxon.search.mcs.McsSearchOptions

@PublicAPI
public final class McsSearchOptions
extends MatchingOptions

Options class for MaxCommonSubstructure (MCS) search. Instances of this class are immutable, they can be created using the McsSearchOptions.Builder nested class. For example,

 McsSearchOptions searchOpts = new McsSearchOptions.Builder().chargeMatching(true).build();
 

There are various options for specifying when the atoms and bonds of the two molecules can be matched with each other. By default, only atom and bond types are considered, but other properties can also be taken into account optionally (e.g. charge, isotope, radical).

MCS algorithms can search for connected and disconnected common substructures as well. The latter one is the default, which means that the common substructures could consist of more than one fragment. A minimum required size can be specified for these fragments, but the largest fragment is kept regardless of the specified minimum size.

Author:

Peter Englert, Peter Kovacs (pkovacs84)

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	McsSearchOptions.Builder Builder class for creating immutable instances of the enclosing McsSearchOptions class.

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_MAX_CONSIDERED_RING_SIZE Default value for McsSearchOptions.Builder.maxConsideredRingSize(int).

Method Summary

Modifier and Type	Method and Description
static McsSearchOptions	getDefault() Returns the default search options object.
int	getMaxConsideredRingSize() Gets the maximum size of rings considered during search for the specified ring handling mode.
int	getMinFragmentSize() Gets the minimum required size of the fragments of the common substructures.
RingHandlingMode	getRingHandlingMode() Gets the ring handling mode specified.
boolean	isConnectedMode() Gets whether the common substructures should be connected or they can consist of multiple fragments.

Methods inherited from class com.chemaxon.search.MatchingOptions

getCustomMatching, isAtomMapMatching, isAtomTypeMatching, isBondTypeMatching, isChargeMatching, isExactQueryAtomMatching, isExactQueryBondMatching, isIsotopeMatching, isOrderSensitiveSearch, isRadicalMatching

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MAX_CONSIDERED_RING_SIZE

public static final int DEFAULT_MAX_CONSIDERED_RING_SIZE

Default value for McsSearchOptions.Builder.maxConsideredRingSize(int).

See Also:

Constant Field Values

Method Detail

getDefault

public static McsSearchOptions getDefault()

Returns the default search options object. It is the same as new SearchOptions.Builder().build(), but it does not create a new object, it returns the same immutable McsSearchOptions instance for each call.

Returns:

the default search options

getRingHandlingMode

public RingHandlingMode getRingHandlingMode()

Gets the ring handling mode specified.

Returns:

the ring handling mode (not null)

getMaxConsideredRingSize

public int getMaxConsideredRingSize()

Gets the maximum size of rings considered during search for the specified ring handling mode.

Returns:

the maximum considered ring size

See Also:

RingHandlingMode

isConnectedMode

public boolean isConnectedMode()

Gets whether the common substructures should be connected or they can consist of multiple fragments. See McsSearchOptions.Builder.connectedMode(boolean).

Returns:

true if the search is for a connected common substructure

getMinFragmentSize

public int getMinFragmentSize()

Gets the minimum required size of the fragments of the common substructures. Fragments having less bonds than this limit are ignored, except for one largest fragment found. See McsSearchOptions.Builder.minFragmentSize(int).

Returns:

minimum required bond count in additional fragments (except for the largest one)