Class SRSearcher
- java.lang.Object
-
- com.actelion.research.chem.reaction.SRSearcher
-
public class SRSearcher extends java.lang.Object
The SRSearcher class handles reaction-sub-structure searches. Correctly, the class should be named SuperReactionSearcher, because it is rather a search for super reactions for a given query reaction. The query reaction may also be called transformation and may contain atom or bond based query features.
-
-
Constructor Summary
Constructors Constructor Description SRSearcher()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
isQueryInReaction()
Performs a reaction substructure search with the SSSearcher.cDefaultMatchModeboolean
isQueryInReaction(int matchMode)
void
setQuery(byte[] rxncode, byte[] rxnmapping, byte[] rxncoords, long[] reactantFFP, long[] productFFP)
void
setQuery(Reaction query)
This defines the query reaction (or transformation).void
setQuery(Reaction query, long[] reactantFFP, long[] productFFP)
This defines the query reaction (or transformation).void
setReaction(byte[] rxncode, byte[] rxnmapping, byte[] rxncoords, long[] reactantFFP, long[] productFFP)
void
setReaction(Reaction reaction)
void
setReaction(Reaction reaction, long[] reactantFFP, long[] productFFP)
This defines the query reaction (or transformation).
-
-
-
Method Detail
-
setQuery
public void setQuery(byte[] rxncode, byte[] rxnmapping, byte[] rxncoords, long[] reactantFFP, long[] productFFP)
-
setReaction
public void setReaction(byte[] rxncode, byte[] rxnmapping, byte[] rxncoords, long[] reactantFFP, long[] productFFP)
-
setQuery
public void setQuery(Reaction query, long[] reactantFFP, long[] productFFP)
This defines the query reaction (or transformation). Typically, this method is called once, while setReaction() is called many times, if a reaction collection is searched for hits. For acceleration through ffp based pre-screening, you should use this method to supply query ffps. If the query reaction contains multiple reactants or multiple products, these are merged into one molecule each. Thus, for a maximum of performance you may avoid this step by parsing a reaction that contains one reactant and one product only.- Parameters:
query
-reactantFFP
-productFFP
-
-
setReaction
public void setReaction(Reaction reaction, long[] reactantFFP, long[] productFFP)
This defines the query reaction (or transformation). Typically, this method is called once, while setReaction() is called many times, if a reaction collection is searched for hits. For acceleration through ffp based pre-screening, you should use this method to supply query ffps. If the query reaction contains multiple reactants or multiple products, these are merged into one molecule each. Thus, for a maximum of performance you may avoid this step by parsing a reaction that contains one reactant and one product only.- Parameters:
reaction
-reactantFFP
-productFFP
-
-
setQuery
public void setQuery(Reaction query)
This defines the query reaction (or transformation). Typically, this method is called once, while setReaction() is called many times, if a reaction collection is searched for hits. If the query reaction contains multiple reactants or multiple products, these are merged into one molecule each. Thus, for a maximum of performance you may avoid this step by parsing a reaction that contains one reactant and one product only.- Parameters:
query
-
-
setReaction
public void setReaction(Reaction reaction)
-
isQueryInReaction
public boolean isQueryInReaction()
Performs a reaction substructure search with the SSSearcher.cDefaultMatchMode- Returns:
-
isQueryInReaction
public boolean isQueryInReaction(int matchMode)
- Parameters:
matchMode
- cDefaultMatchMode or combination of cMatchAtomCharge, cMatchAtomMass, cMatchDBondToDelocalized, cMatchAromDBondToDelocalized- Returns:
-
-