Class ReactionSearchSpecification
- java.lang.Object
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- com.actelion.research.chem.reaction.ReactionSearchSpecification
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- All Implemented Interfaces:
java.io.Serializable
public class ReactionSearchSpecification extends java.lang.Object implements java.io.Serializable
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static int
TYPE_EXACT_NO_STEREO
static int
TYPE_EXACT_STRICT
static int
TYPE_NO_REACTION
static int
TYPE_RETRON
static int
TYPE_SIMILARITY
static int
TYPE_SUBREACTION
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Constructor Summary
Constructors Constructor Description ReactionSearchSpecification(int searchType, java.lang.String[] query, long[][] reactionDescriptor, long[][] reactantDescriptor, long[][] productDescriptor)
Creates a complete specification for a reaction substructure search with one or more query generic reactions.ReactionSearchSpecification(int searchType, java.lang.String[] query, long[][] reactionDescriptor, long[][] reactantDescriptor, long[][] productDescriptor, float reactionCenterSimilarity, float peripherySimilarity)
Creates a complete specification for a reaction similarity search with one or more query reactions.ReactionSearchSpecification(java.lang.String[] query, long[][] retronDescriptor)
Creates a complete specification for a retron search with one or more query retron substructures.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getEncodedQuery(int index)
Returns the (or one of the) query structures encodes as idcode.float
getPeripherySimilarity()
long[]
getProductDescriptor(int index)
long[]
getReactantDescriptor(int index)
float
getReactionCenterSimilarity()
int
getReactionCount()
Returns the search type as integer including mode flags.long[]
getReactionDescriptor(int index)
long[]
getRetronDescriptor(int index)
boolean
isExactSearch()
An exact search is a comparison of idcodes of standardized molecules with full stereo features.boolean
isNoReactionSearch()
boolean
isNoStereoSearch()
A noStereo search is a hash code comparison from encoding stereo depleted structures.boolean
isRetronSearch()
boolean
isSimilaritySearch()
boolean
isSubreactionSearch()
void
removeDescriptors()
java.lang.String
toString()
java.lang.String
validate()
Checks, whether this specification is correctly defining a search.
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Field Detail
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TYPE_NO_REACTION
public static final int TYPE_NO_REACTION
- See Also:
- Constant Field Values
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TYPE_SUBREACTION
public static final int TYPE_SUBREACTION
- See Also:
- Constant Field Values
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TYPE_SIMILARITY
public static final int TYPE_SIMILARITY
- See Also:
- Constant Field Values
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TYPE_RETRON
public static final int TYPE_RETRON
- See Also:
- Constant Field Values
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TYPE_EXACT_STRICT
public static final int TYPE_EXACT_STRICT
- See Also:
- Constant Field Values
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TYPE_EXACT_NO_STEREO
public static final int TYPE_EXACT_NO_STEREO
- See Also:
- Constant Field Values
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Constructor Detail
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ReactionSearchSpecification
public ReactionSearchSpecification(int searchType, java.lang.String[] query, long[][] reactionDescriptor, long[][] reactantDescriptor, long[][] productDescriptor, float reactionCenterSimilarity, float peripherySimilarity)
Creates a complete specification for a reaction similarity search with one or more query reactions.- Parameters:
searchType
- one of TYPE_...query
- list of encoded query reactionsreactionDescriptor
- null or query reaction descriptorsreactantDescriptor
- null or reactant FFP512 descriptorsproductDescriptor
- null or product FFP512 descriptorsreactionCenterSimilarity
- in case of TYPE_SIMILARITYperipherySimilarity
- in case of TYPE_SIMILARITY
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ReactionSearchSpecification
public ReactionSearchSpecification(int searchType, java.lang.String[] query, long[][] reactionDescriptor, long[][] reactantDescriptor, long[][] productDescriptor)
Creates a complete specification for a reaction substructure search with one or more query generic reactions.- Parameters:
searchType
- one of TYPE_...query
- list of encoded query reactionsreactionDescriptor
- null or query reaction descriptorsreactantDescriptor
- null or reactant FFP512 descriptorsproductDescriptor
- null or product FFP512 descriptors
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ReactionSearchSpecification
public ReactionSearchSpecification(java.lang.String[] query, long[][] retronDescriptor)
Creates a complete specification for a retron search with one or more query retron substructures.- Parameters:
query
- list of encoded retron structuresretronDescriptor
- null or product FFP512 descriptors
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Method Detail
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getReactionCount
public int getReactionCount()
Returns the search type as integer including mode flags. In case of TYPE_SIMILARITY use getDescriptorShortName() and getSimilarityThreshold() for a full search specification.- Returns:
- one of TYPE_... and possibly MODE_LARGEST_FRAGMENT_ONLY public int getSearchType() { return mSearchType; }
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getEncodedQuery
public java.lang.String getEncodedQuery(int index)
Returns the (or one of the) query structures encodes as idcode.- Parameters:
index
-- Returns:
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getReactionDescriptor
public long[] getReactionDescriptor(int index)
- Parameters:
index
-- Returns:
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getReactantDescriptor
public long[] getReactantDescriptor(int index)
- Parameters:
index
-- Returns:
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getProductDescriptor
public long[] getProductDescriptor(int index)
- Parameters:
index
-- Returns:
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getRetronDescriptor
public long[] getRetronDescriptor(int index)
- Parameters:
index
-- Returns:
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isSimilaritySearch
public boolean isSimilaritySearch()
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isNoReactionSearch
public boolean isNoReactionSearch()
- Returns:
- whether this search does not include a structure search component is uses exclusively external criteria
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isSubreactionSearch
public boolean isSubreactionSearch()
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isRetronSearch
public boolean isRetronSearch()
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isExactSearch
public boolean isExactSearch()
An exact search is a comparison of idcodes of standardized molecules with full stereo features.- Returns:
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isNoStereoSearch
public boolean isNoStereoSearch()
A noStereo search is a hash code comparison from encoding stereo depleted structures.- Returns:
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removeDescriptors
public void removeDescriptors()
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getReactionCenterSimilarity
public float getReactionCenterSimilarity()
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getPeripherySimilarity
public float getPeripherySimilarity()
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validate
public java.lang.String validate()
Checks, whether this specification is correctly defining a search. If something is missing or inconsistent, an error message describing the problem is returned.- Returns:
- null or error message
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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