MolComparator (JChem Base API documentation (c) 1998-2019 ChemAxon Ltd.)

java.lang.Object
- chemaxon.sss.search.MolComparator

```
@PublicAPI
public class MolComparator
extends java.lang.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

Author:

Szabolcs Csepregi Date: Dec 12, 2005

Field Summary

Fields
Modifier and Type	Field and 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 and Description

MolComparator()

Constructors
Constructor and Description
`MolComparator()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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

Class MolComparator

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

query

target

targetSearchData

querySearchData

searchOptions

USEFUL

MAYBE_USEFUL

NOT_USEFUL

Constructor Detail

MolComparator

Method Detail

setQuery

setTarget

setTargetSearchData

setQuerySearchData

setSearchOptions

compareAtoms

compareBonds

getOrigTargetAtom

getOrigQueryAtom

getOrigTargetNeighbour

getOrigQueryNeighbour

compareHit

isUsefulForQuery

isUsefulForTarget

getOrigQueryAtom1

getOrigQueryAtom2

getOrigTargetAtom1

getOrigTargetAtom2

getOrigQueryBond

getOrigTargetBond