Package ambit2.db.search.structure

Class Summary

Class	Description
AbstractStructureQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition>
ChemicalByQueryFolder	Retrieves chemicals from set of datasets, defined in the query table restricted by sessions.title
FingerprintsByStatus
FreeTextQuery	select idchemical,metric from ( (select idchemical,2 as metric from properties join property_values using(idproperty) join property_string using(idvalue_string) join structure using(idstructure) where name like "MA%" and value like "Reaction%" ) union (select idchemical,2 as metric from properties join property_values using(idproperty) join property_string using(idvalue_string) join structure using(idstructure) where value like "MA%" and name like "Reaction%" ) union (select idchemical,1 as metric from properties join property_values using(idproperty) join structure using(idstructure) where name like "MA%") union (select idchemical,1 as metric from property_values join property_string using(idvalue_string) join structure using(idstructure) where value like "MA%") union (select idchemical,1 as metric from properties join property_values using(idproperty) join structure using(idstructure) where name like "Reaction%") union (select idchemical,1 as metric from property_values join property_string using(idvalue_string) join structure using(idstructure) where value like "Reaction%") ) a
MissingFingerprintsQuery
MissingInChIsQuery
NumberQuery<F>
ProcessorMissingDescriptorsQuery	Creates a query to retrieve structures without given list of descriptors
QueryAtomEnvironment	Similarity via atom environment matrix /query/similarity?search=c1ccccc1O&threshold=0.5&mode=ae
QueryByIdentifierWithStructureFallback	Calls findByProperty stored procedure
QueryCombinedStructure
QueryComplement	Complement of the scope query
QueryDataset	src_dataset.name = ?
QueryDatasetByID
QueryDistance	Distance between two atoms, provided as symbols.
QueryExactStructure	Deprecated Convert to InChI and use QueryStructure
QueryField	Search for a structure with property with given name and value
QueryFieldAbstract<T,C extends net.idea.modbcum.i.IQueryCondition,NC extends net.idea.modbcum.i.IQueryCondition>
QueryFieldMultiple
QueryFieldNumeric
QueryFunctionalGroups
QueryLookupStructure	This is a wrapper around QueryStructure , allowing to use IStructureRecord as a parameter
QueryMissingDescriptor	reads structures, for each there are / or there are not (depending on getCondition) descriptors with given idname and reference title.
QueryMissingDistances	Reads structures without precalculated pairwise atom distances from the database.
QueryMissingProperty
QueryPrescreenBitSet	First bitset is from structural keys, second from fingerprints
QuerySimilarity<F,T,C extends net.idea.modbcum.i.IQueryCondition>
QuerySimilarityBitset	Tanimoto similarity of BitSet.
QuerySimilarityStructure
QuerySMARTS	Select structures by querying fungroups table by smarts
QueryStoredResults
QueryStoredResultsByName	Retrieve structure collections from query table by name and folder (sessions table)
QueryStructure	Search for smiles, inchi, formula
QueryStructureByID	Selects a structure by idstructure
QueryStructureByQuality
QueryStructureByQualityPairLabel
QueryStructureByValueQuality
QueryStructureType
QueryStrucType
ScopeQuery	A convenience class for a query used to restrict the scope of other queries

Enum Summary

Enum	Description
AbstractStructureQuery.FIELD_NAMES
QueryAtomEnvironment.q_modifier
SCOPE