Class SRSearcher
- java.lang.Object
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- com.actelion.research.chem.reaction.SRSearcher
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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.
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Constructor Summary
Constructors Constructor Description SRSearcher()
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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).void
stop()
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Method Detail
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setQuery
public void setQuery(byte[] rxncode, byte[] rxnmapping, byte[] rxncoords, long[] reactantFFP, long[] productFFP)
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setReaction
public void setReaction(byte[] rxncode, byte[] rxnmapping, byte[] rxncoords, long[] reactantFFP, long[] productFFP)
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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, then setQuery() merges these into one reactant and one product molecule. If you call setQuery() with the same query reactions multiple times, then for a maximum of performance you should cache merged query reactions and pass these. Merging can be done by getMergedCopy() of the reaction class.- Parameters:
query
-reactantFFP
-productFFP
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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
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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
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setReaction
public void setReaction(Reaction reaction)
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stop
public void stop()
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isQueryInReaction
public boolean isQueryInReaction()
Performs a reaction substructure search with the SSSearcher.cDefaultMatchMode- Returns:
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isQueryInReaction
public boolean isQueryInReaction(int matchMode)
- Parameters:
matchMode
- cDefaultMatchMode or combination of cMatchAtomCharge, cMatchAtomMass, cMatchDBondToDelocalized, cMatchAromDBondToDelocalized- Returns:
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