Package chemaxon.sss.search

Class MolComparator

java.lang.Object

chemaxon.sss.search.MolComparator

@PublicAPI
public class MolComparator
extends Object

Interface for comparing atoms, bonds, etc. against different criteria. Its subclasses are used by the search classes. Methods to be overridden: compareAtoms(int, int), compareBonds(int, int), compareHit(int[], int). The comparison methods in this class are empty convenience methods that always return true. The init and unInit methods should call super method if overridden.

Utility methods to get original query and target atom molecular indexes are: getOrigQueryAtom(int), getOrigTargetAtom(int), getOrigQueryNeighbour(int), getOrigTargetNeighbour(int).

By using MolComparators one can introduce extra matching conditions. Working examples can be found here.

Since:

JChem 3.2

Field Summary

Fields

Modifier and Type	Field	Description
static int	MAYBE_USEFUL	Describes that the MolComparator may be needed with the current search object and the current query, depending on the target.
static int	NOT_USEFUL	Describes that the MolComparator is not needed with the current search object, the current query (and target).
protected Molecule	query
protected chemaxon.sss.search.model.ReadOnlySearchData	querySearchData
protected MolSearchOptions	searchOptions
protected Molecule	target
protected chemaxon.sss.search.model.ReadOnlySearchData	targetSearchData
static int	USEFUL	Describes that the MolComparator should be used with the current search object and the current query, regardless of the target.

Constructor Summary

Constructors

Constructor	Description
MolComparator()

Method Summary

Modifier and Type	Method	Description
boolean	compareAtoms(int a1, int a2)	Compares atoms of indices a1 and a2.
boolean	compareBonds(int b1, int b2)	Compares bonds of indices b1 and b2.
boolean	compareHit(int[] internalHit, int internalHitLength)	Checks a partial hit during the search algorithm.
int	getOrigQueryAtom(int a1)	Converts search internal atom index (in the query) to the original atom index in the query molecule.
int	getOrigQueryAtom1(int bi)	Returns the index of the first atom (atom index in the query molecule) of the given query bond(search internal bond index in the query).
int	getOrigQueryAtom2(int bi)	Returns the index of the second atom (atom index in the query molecule) of the given query bond(search internal bond index in the query).
int	getOrigQueryBond(int bi)	Returns bond index in the query molecule for the given query bond (search internal bond index in the query).
int	getOrigQueryNeighbour(int a)	For a search internal atom index (in the query), returns a neighbour atom index (original atom index in the query molecule).
int	getOrigTargetAtom(int a1)	Converts search internal atom index (in the target) to the original atom index in the target molecule.
int	getOrigTargetAtom1(int bi)	Returns the index of the first atom (atom index in the target molecule) of the given target bond(search internal bond index in the target).
int	getOrigTargetAtom2(int bi)	Returns the index of the second atom (atom index in the target molecule) of the given target bond(search internal bond index in the target).
int	getOrigTargetBond(int bi)	Returns bond index in the target molecule for the given target bond (search internal bond index in the target).
int	getOrigTargetNeighbour(int a)	For a search internal atom index (in the target), returns a neighbour atom index (original atom index in the target molecule).
int	isUsefulForQuery()	Decides based on the query and the search object if the comparator should be used or not.
int	isUsefulForTarget()	Decides based on the query, target and the search object if the comparator should be used or not.
void	setQuery(Molecule q)	Loads the query molecule into this comparator.
void	setQuerySearchData(chemaxon.sss.search.model.ReadOnlySearchData querySearchData)
void	setSearchOptions(MolSearchOptions searchOptions)
void	setTarget(Molecule t)	Loads the target molecule into this comparator.
void	setTargetSearchData(chemaxon.sss.search.model.ReadOnlySearchData targetSearchData)

Methods inherited from class java.lang.Object

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

Field Detail

query

protected Molecule query

target

protected Molecule target

targetSearchData

protected chemaxon.sss.search.model.ReadOnlySearchData targetSearchData

querySearchData

protected chemaxon.sss.search.model.ReadOnlySearchData querySearchData

searchOptions

protected MolSearchOptions searchOptions

USEFUL

public static final int USEFUL

Describes that the MolComparator should be used with the current search object and the current query, regardless of the target.

See Also:

isUsefulForQuery(), Constant Field Values

MAYBE_USEFUL

public static final int MAYBE_USEFUL

Describes that the MolComparator may be needed with the current search object and the current query, depending on the target.

See Also:

isUsefulForQuery(), Constant Field Values

NOT_USEFUL

public static final int NOT_USEFUL

Describes that the MolComparator is not needed with the current search object, the current query (and target).

See Also:

isUsefulForQuery(), Constant Field Values

Constructor Detail

MolComparator

public MolComparator()

Method Detail

setQuery

public void setQuery(Molecule q)

Loads the query molecule into this comparator. the default implementation saves the query into the field 'query'.

Parameters:

q - the query that will be used from now on

setTarget

public void setTarget(Molecule t)

Loads the target molecule into this comparator. the default implementation saves the target into the field 'target'.

Parameters:

t - the query that will be used from now on

setTargetSearchData

public void setTargetSearchData(chemaxon.sss.search.model.ReadOnlySearchData targetSearchData)

setQuerySearchData

public void setQuerySearchData(chemaxon.sss.search.model.ReadOnlySearchData querySearchData)

setSearchOptions

public void setSearchOptions(MolSearchOptions searchOptions)

compareAtoms

public boolean compareAtoms(int a1,
                            int a2)

Compares atoms of indices a1 and a2. Indices are internal search indices, and not refer to the molecule! This method is called during initial match matrix creation.

Parameters:

a1 - atom in query (search internal index)

a2 - atom in target (search internal index)

Returns:

whether query atom a1 matches target atom a2

See Also:

getOrigQueryAtom(int), getOrigTargetAtom(int)

compareBonds

public boolean compareBonds(int b1,
                            int b2)

Compares bonds of indices b1 and b2. It is called during refining.

Parameters:

b1 - bond index in query

b2 - bond index in target

Returns:

whether the two bonds match

getOrigTargetAtom

public int getOrigTargetAtom(int a1)

Converts search internal atom index (in the target) to the original atom index in the target molecule.

Parameters:

a1 - internal target atom index

Returns:

The atom index in the target molecule or -1 if no corresponding atom exists. (e.g. implicit H. In this case, getOrigTargetNeighbour(int) may be helpful.)

getOrigQueryAtom

public int getOrigQueryAtom(int a1)

Converts search internal atom index (in the query) to the original atom index in the query molecule.

Parameters:

a1 - internal query atom index

Returns:

The atom index in the query molecule or -1 if no corresponding atom exists. (e.g. implicit H. In this case, getOrigQueryNeighbour(int) may be helpful.)

getOrigTargetNeighbour

public int getOrigTargetNeighbour(int a)

For a search internal atom index (in the target), returns a neighbour atom index (original atom index in the target molecule).

Parameters:

a - internal target atom index

Returns:

The neighbour atom index in the molecule or -1 if no neighbour atom exists. (e.g. isolated atom)

See Also:

getOrigTargetAtom(int)

getOrigQueryNeighbour

public int getOrigQueryNeighbour(int a)

For a search internal atom index (in the query), returns a neighbour atom index (original atom index in the query molecule).

Parameters:

a - internal query atom index

Returns:

The neighbour atom index in the molecule or -1 if no neighbour atom exists. (e.g. isolated atom)

See Also:

getOrigTargetAtom(int)

compareHit

public boolean compareHit(int[] internalHit,
                          int internalHitLength)

Checks a partial hit during the search algorithm. Useful if the custom matching criteria must use multiple query or target atoms.

Parameters:

internalHit - the current hit vector from the associated search object that contains atom indices of internal search representation. Strictly read only! The values of this array are incremented by 1 because of algorithmic reasons. This vector may contain only a partial match, so possibly not all query atoms have associated matchings.
You can get original atom indexes by using getOrigQueryAtom(int) (from array indexes) and getOrigTargetAtom(int) (from array values - do not forget to call a decreased value: getOrigTargetAtom(internalHit[i]-1) ).
For efficiency reasons, an array longer than necessary is returned, parameter internalHitLength contains the effective length of the array.
The search algorithm is incremental, so for the call history of this method a (partial) hit vector is preceded by its shorter prefixes of size at least 2. (This means that for a partial hit vector [1, 5, 2, 3], hit vectors [1, 5] and [1, 5, 2] have already been checked.)

internalHitLength - the effective length of internalHit.

Returns:

true if the partial hit describes a correct query-target correspondence.

See Also:

getOrigQueryAtom(int), getOrigTargetAtom(int)

isUsefulForQuery

public int isUsefulForQuery()

Decides based on the query and the search object if the comparator should be used or not. Override to save execution time of the search. If MAYBE_USEFUL is returned by this method, isUsefulForTarget is also called.

Returns:

USEFUL (default), MAYBE_USEFUL or NOT_USEFUL.

See Also:

USEFUL, MAYBE_USEFUL, NOT_USEFUL, isUsefulForTarget()

isUsefulForTarget

public int isUsefulForTarget()

Decides based on the query, target and the search object if the comparator should be used or not. Override to save execution time of the search. It is only used after isUsefulForQuery returned MAYBE_USEFUL

Returns:

USEFUL (default) or NOT_USEFUL.

See Also:

USEFUL, MAYBE_USEFUL, NOT_USEFUL, isUsefulForQuery()

getOrigQueryAtom1

public int getOrigQueryAtom1(int bi)

Returns the index of the first atom (atom index in the query molecule) of the given query bond(search internal bond index in the query).

Parameters:

bi - internal query bond index

Returns:

The atom index in the query molecule or -1 if no corresponding atom exists. (e.g. implicit H.)

Since:

JChem 3.2.3

getOrigQueryAtom2

public int getOrigQueryAtom2(int bi)

Returns the index of the second atom (atom index in the query molecule) of the given query bond(search internal bond index in the query).

Parameters:

bi - internal query bond index

Returns:

The atom index in the query molecule or -1 if no corresponding atom exists. (e.g. implicit H.)

Since:

JChem 3.2.3

getOrigTargetAtom1

public int getOrigTargetAtom1(int bi)

Returns the index of the first atom (atom index in the target molecule) of the given target bond(search internal bond index in the target).

Parameters:

bi - internal target bond index

Returns:

The atom index in the target molecule or -1 if no corresponding atom exists. (e.g. implicit H.)

Since:

JChem 3.2.3

getOrigTargetAtom2

public int getOrigTargetAtom2(int bi)

Returns the index of the second atom (atom index in the target molecule) of the given target bond(search internal bond index in the target).

Parameters:

bi - internal target bond index

Returns:

The atom index in the target molecule or -1 if no corresponding atom exists. (e.g. implicit H.)

Since:

JChem 3.2.3

getOrigQueryBond

public int getOrigQueryBond(int bi)

Returns bond index in the query molecule for the given query bond (search internal bond index in the query).

Parameters:

bi - internal query bond index

Returns:

The bond index in the query molecule or -1 if no corresponding atom exists. (e.g. relating to an implicit H.)

Since:

JChem 3.2.3

getOrigTargetBond

public int getOrigTargetBond(int bi)

Returns bond index in the target molecule for the given target bond (search internal bond index in the target).

Parameters:

bi - internal target bond index

Returns:

The bond index in the target molecule or -1 if no corresponding atom exists. (e.g. relating to an implicit H.)

Since:

JChem 3.2.3