MaxCommonSubstructure (JChem Base API documentation (c) 1998-2021 ChemAxon Ltd.)

java.lang.Object
- com.chemaxon.search.mcs.MaxCommonSubstructure

All Implemented Interfaces:

chemaxon.license.Licensable

Direct Known Subclasses:

BuildupMcs, MaxCliqueMcs
```
@PublicAPI
public abstract class MaxCommonSubstructure
extends java.lang.Object
implements chemaxon.license.Licensable
```
Abstract base class of the algorithms for finding the maximum common substructure (MCS) of two molecules. More precisely, these algorithms find the maximum common edge subgraph (MCES) of the input structures. For more information, see the user's guide.
An instance of the default MCS algorithm implementation can be created using newInstance() or newInstance(McsSearchOptions). The provided MCS algorithms are powerful heuristic methods, which typically find large common substructures in a short time. However, they do not always provide the exact optimal result due to the complexity of the MCS problem (especially for large molecules). Furthermore, as the algorithms perform randomized search, different results might be obtained for equivalent molecule representations.
Warning: MCS algorithms do not perform transformations on the input molecules, so you should be aware of aromatization (and other standardization actions) before using them.
Features: Query and target structures basically play the same role in MCS search except for query features: a query molecule may contain generic query atoms (A, Q, M, X, list atom, not list atom, etc.) and query bonds (any, single or double, etc.), but query properties (e.g., valence, hydrogen count) are ignored. If exact query atom/bond matching is set to true, then generic atoms and bonds are allowed in both molecules, but they are matched in exact manner. Reactions are also supported, but Markush structures are not.
Typical usage:
```
 MaxCommonSubstructure mcs = MaxCommonSubstructure.newInstance();
 mcs.setMolecules(queryMol, targetMol);
 McsSearchResult result = mcs.find();
 System.out.println("Atoms in MCS: " + result.getAtomCount());
 System.out.println("Bonds in MCS: " + result.getBondCount());
 System.out.println("MCS molecule: " + MolExporter.exportToFormat(result.getAsMolecule(), "smiles"));
 
```
Author:

Peter Kovacs (pkovacs84), Peter Englert

Field Summary

Fields
Modifier and Type	Field and Description
`static long`	`DEFAULT_RANDOM_SEED` Default random seed.
`protected static java.util.logging.Logger`	`LOG` Logger object.
`protected Molecule`	`queryMol` Query molecule (it is neither cloned nor modified).
`protected long`	`randomSeed` Random seed (0 means using the current time).
`protected SearchMode`	`searchMode` Search mode.
`protected McsSearchOptions`	`searchOpts` Search options.
`protected Molecule`	`targetMol` Target molecule (it is neither cloned nor modified).
`protected long`	`timeLimit` Time limit in milliseconds (-1 means disabled).

Constructor Summary

Constructors
Modifier Constructor and Description

protected MaxCommonSubstructure(McsSearchOptions searchOpts)

Constructors
Modifier	Constructor and Description
`protected`	`MaxCommonSubstructure(McsSearchOptions searchOpts)`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`float`	`calculateSimilarityUpperBound()` Calculates an upper bound on the similarity of the query and target molecules with respect to the specified search options.
`int`	`calculateUpperBound()` Calculates an upper bound on the number of bonds the maximum common substructure may contain with respect to the specified search options.
`McsSearchResult`	`find()` Performs MCS search according to the specified options.
`protected abstract McsSearchResult`	`findMcs(com.chemaxon.search.sss.Matcher matcher)` Finds the MCS and all related data (fragments and mappings).
`Molecule`	`getQuery()` Gets the query structure.
`long`	`getRandomSeed()` Gets the random seed value.
`SearchMode`	`getSearchMode()` Gets the current search mode.
`McsSearchOptions`	`getSearchOptions()` Returns the search options used by this instance.
`Molecule`	`getTarget()` Gets the target structure.
`long`	`getTimeLimit()` Gets the maximum allowed MCS search time in milliseconds.
`boolean`	`hasNextResult()` Returns whether there are more results available.
`boolean`	`isLicensed()` Returns information about the licensing of the product.
`static MaxCommonSubstructure`	`newInstance()` Creates a new instance of MCS search algorithm using the default search options.
`static MaxCommonSubstructure`	`newInstance(McsSearchOptions searchOpts)` Creates a new instance of MCS search algorithm using the given search options.
`McsSearchResult`	`nextResult()` Finds the next MCS search result according to the specified options.
`void`	`setLicenseEnvironment(java.lang.String env)` Sets the license environment.
`void`	`setMolecules(Molecule query, Molecule target)` Sets the two molecular structures to be matched.
`void`	`setQuery(Molecule query)` Sets the query structure.
`void`	`setRandomSeed(long seed)` Sets the random seed value.
`void`	`setSearchMode(SearchMode mode)` Sets the search mode that controls the running time and the accuracy of the algorithm.
`void`	`setTarget(Molecule target)` Sets the target structure.
`void`	`setTimeLimit(long maxMilliseconds)` Sets the maximum allowed time for MCS search.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - DEFAULT_RANDOM_SEED
```
public static final long DEFAULT_RANDOM_SEED
```
    Default random seed.
    
    See Also:
    
    Constant Field Values
  - randomSeed
```
protected long randomSeed
```
    Random seed (0 means using the current time).
  - searchMode
```
protected SearchMode searchMode
```
    Search mode.
  - timeLimit
```
protected long timeLimit
```
    Time limit in milliseconds (-1 means disabled).
  - queryMol
```
protected Molecule queryMol
```
    Query molecule (it is neither cloned nor modified).
  - targetMol
```
protected Molecule targetMol
```
    Target molecule (it is neither cloned nor modified).
  - searchOpts
```
protected final McsSearchOptions searchOpts
```
    Search options.
  - LOG
```
protected static final java.util.logging.Logger LOG
```
    Logger object.
- Constructor Detail
  - MaxCommonSubstructure
```
protected MaxCommonSubstructure(McsSearchOptions searchOpts)
```
- Method Detail
  - newInstance
```
public static MaxCommonSubstructure newInstance()
```
    Creates a new instance of MCS search algorithm using the default search options.
    MaxCliqueMcs implementation is used, which turned out to be the most efficient and robust according to our benchmark tests.
    
    Returns:
    
    a new instance of the default algorithm implementation
    
    See Also:
    
    newInstance(McsSearchOptions)
  - newInstance
```
public static MaxCommonSubstructure newInstance(McsSearchOptions searchOpts)
```
    Creates a new instance of MCS search algorithm using the given search options.
    MaxCliqueMcs implementation is used, which turned out to be the most efficient and robust according to our benchmark tests.
    
    Parameters:
    
    searchOpts - the search options (not null)
    
    Returns:
    
    a new instance of the default algorithm implementation
  - isLicensed
```
public final boolean isLicensed()
```
    Returns information about the licensing of the product.
    
    Specified by:
    
    isLicensed in interface chemaxon.license.Licensable
    
    Returns:
    
    true if the product is correctly licensed
  - setLicenseEnvironment
```
public final void setLicenseEnvironment(java.lang.String env)
```
    Sets the license environment.
    
    Specified by:
    
    setLicenseEnvironment in interface chemaxon.license.Licensable
  - setMolecules
```
public final void setMolecules(Molecule query,
                               Molecule target)
```
    Sets the two molecular structures to be matched.
    
    Parameters:
    
    query - query molecule (not null)
    
    target - target molecule (not null)
  - setQuery
```
public final void setQuery(Molecule query)
```
    Sets the query structure.
    
    Parameters:
    
    query - query molecule (not null)
  - setTarget
```
public final void setTarget(Molecule target)
```
    Sets the target structure.
    
    Parameters:
    
    target - target molecule (not null)
  - getQuery
```
public final Molecule getQuery()
```
    Gets the query structure.
    
    Returns:
    
    the query molecule
  - getTarget
```
public final Molecule getTarget()
```
    Gets the target structure.
    
    Returns:
    
    the target molecule
  - getSearchOptions
```
public final McsSearchOptions getSearchOptions()
```
    Returns the search options used by this instance. For more information, see McsSearchOptions.
    
    Returns:
    
    search options (not null)
  - setSearchMode
```
public final void setSearchMode(SearchMode mode)
```
    Sets the search mode that controls the running time and the accuracy of the algorithm. The default option is SearchMode.NORMAL. For more information, see SearchMode.
    
    Parameters:
    
    mode - search mode (not null)
  - getSearchMode
```
public final SearchMode getSearchMode()
```
    Gets the current search mode. For more information, see SearchMode.
    
    Returns:
    
    current search mode (not null)
  - setTimeLimit
```
public final void setTimeLimit(long maxMilliseconds)
```
    Sets the maximum allowed time for MCS search. If the given limit is exceeded, the search process terminates with the best result obtained so far. When searching for multiple results (without changing the input molecules), the time limit is applied only to the first call of nextResult() (or hasNextResult()).
    This is an optional limit, which is set to 1 minute by default. You can use a negative parameter value to disable it.
    If the search process seems to be too slow, consider using FAST search mode instead of decreasing the time limit (see setSearchMode(SearchMode)).
    
    Parameters:
    
    maxMilliseconds - maximum running time in milliseconds (negative value means disabled)
  - getTimeLimit
```
public final long getTimeLimit()
```
    Gets the maximum allowed MCS search time in milliseconds. If no such limit is specified, this method returns -1. For more information, see setTimeLimit().
    
    Returns:
    
    maximum running time in milliseconds or -1 if no such limit is specified
  - setRandomSeed
```
public final void setRandomSeed(long seed)
```
    Sets the random seed value. 0 means using the current time.
    
    Parameters:
    
    seed - random seed
  - getRandomSeed
```
public final long getRandomSeed()
```
    Gets the random seed value. 0 means using the current time.
    
    Returns:
    
    seed random seed
  - find
```
public final McsSearchResult find()
```
    Performs MCS search according to the specified options. This method returns a valid result object even if the MCS is empty or the search time limit is reached.
    If multiple MCS results are desired, use hasNextResult() and nextResult().
    
    Returns:
    
    the McsSearchResult object containing the found common substructure
    
    Throws:
    
    java.lang.IllegalStateException - if the input molecules are not set before calling this method or the method is called more than once for the same input molecules
    
    java.util.concurrent.CancellationException - if the thread has been interrupted
  - hasNextResult
```
public final boolean hasNextResult()
```
    Returns whether there are more results available. See nextResult().
    
    Returns:
    
    true if nextResult() can be called to obtain a new McsSearchResult object
    
    Throws:
    
    java.lang.IllegalStateException - if the input molecules are not set before calling this method
    
    java.util.concurrent.CancellationException - if the thread has been interrupted
  - nextResult
```
public final McsSearchResult nextResult()
```
    Finds the next MCS search result according to the specified options. The first call to this method always returns a valid result object, even if the MCS is empty or the search time limit is reached.
    If multiple search results are desired, this method can be called repeatedly. The results typically correspond to equivalent common substructures but with different mappings. (See McsSearchResult for more information.) When this method is called multiple times, hasNextResult() should be called first to avoid exception.
    The search state is reset after a call to setQuery(Molecule), setTarget(Molecule) or setMolecules(Molecule, Molecule).
    
    Returns:
    
    the McsSearchResult object containing the found common substructure
    
    Throws:
    
    java.lang.IllegalStateException - if the input molecules are not set before the first call to this method or there are no more results to return
    
    java.util.concurrent.CancellationException - if the thread has been interrupted
  - calculateUpperBound
```
public final int calculateUpperBound()
```
    Calculates an upper bound on the number of bonds the maximum common substructure may contain with respect to the specified search options. The returned value is an upper bound on McsSearchResult.getBondCount().
    As this method is much faster than executing the MCS algorithm (find()), it can be used for pre-filtering.
    
    Returns:
    
    an upper bound on the size (bond count) of the MCS
    
    Throws:
    
    java.lang.IllegalStateException - if the input molecules are not set
    
    java.util.concurrent.CancellationException - if the thread has been interrupted
  - calculateSimilarityUpperBound
```
public final float calculateSimilarityUpperBound()
```
    Calculates an upper bound on the similarity of the query and target molecules with respect to the specified search options. The returned value is an upper bound on McsSearchResult.getSimilarity().
    As this method is much faster than executing the MCS algorithm (find()), it can be used for pre-filtering.
    
    Returns:
    
    an upper bound on the (MCS based) similarity of the query and the target
    
    Throws:
    
    java.lang.IllegalStateException - if the input molecules are not set
    
    java.util.concurrent.CancellationException - if the thread has been interrupted
  - findMcs
```
protected abstract McsSearchResult findMcs(com.chemaxon.search.sss.Matcher matcher)
```
    Finds the MCS and all related data (fragments and mappings). Deriving classes must implement this method to calculate an (approximate) maximum common substructure.
    This method is called from find(), nextResult(), and hasNextResult() with a properly initialized matcher object.
    
    Parameters:
    
    matcher - the matcher object, which also contains the preprocessed query and target molecules

Class MaxCommonSubstructure

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_RANDOM_SEED

randomSeed

searchMode

timeLimit

queryMol

targetMol

searchOpts

LOG

Constructor Detail

MaxCommonSubstructure

Method Detail

newInstance

newInstance

isLicensed

setLicenseEnvironment

setMolecules

setQuery

setTarget

getQuery

getTarget

getSearchOptions

setSearchMode

getSearchMode

setTimeLimit

getTimeLimit

setRandomSeed

getRandomSeed

find

hasNextResult

nextResult

calculateUpperBound

calculateSimilarityUpperBound

findMcs