public class Bingo extends Object
| Constructor and Description |
|---|
Bingo(Indigo indigo,
String location,
String options) |
Bingo(Indigo indigo,
String location,
String type,
String options) |
| Modifier and Type | Method and Description |
|---|---|
static float |
checkResult(Indigo indigo,
float result) |
static int |
checkResult(Indigo indigo,
int result) |
static String |
checkResult(Indigo indigo,
String result) |
void |
close() |
static Bingo |
createDatabaseFile(Indigo indigo,
String location,
String type)
Creates a chemical storage of a specified type in a specified location
|
static Bingo |
createDatabaseFile(Indigo indigo,
String location,
String type,
String options)
Creates a chemical storage of a specified type in a specified location
|
void |
delete(int id)
Delete a record by id
|
void |
dispose() |
BingoObject |
enumerateId()
Execute enumerate id operation
|
protected void |
finalize() |
IndigoObject |
getRecordById(int id)
Returns an IndigoObject for the record with the specified id
|
int |
insert(IndigoObject record)
Insert a structure into the database and returns id of this structure
|
int |
insert(IndigoObject record,
int id)
Inserts a structure under a specified id
|
int |
insertWithExtFP(IndigoObject record,
IndigoObject ext_fp)
Insert a structure into the database and returns id of this structure
|
int |
insertWithExtFP(IndigoObject record,
IndigoObject ext_fp,
int id)
Inserts a structure under a specified id
|
static Bingo |
loadDatabaseFile(Indigo indigo,
String location)
Loads a chemical storage of a specified type from a specified location
|
static Bingo |
loadDatabaseFile(Indigo indigo,
String location,
String options)
Loads a chemical storage of a specified type from a specified location
|
void |
optimize()
Post-process index optimization
|
BingoObject |
searchExact(IndigoObject query)
Perform exact search operation
|
BingoObject |
searchExact(IndigoObject query,
String options)
Perform exact search operation
|
BingoObject |
searchMolFormula(String query)
Perform search by molecular formula
|
BingoObject |
searchMolFormula(String query,
String options)
Perform search by molecular formula
|
BingoObject |
searchSim(IndigoObject query,
float min,
float max)
Execute similarity search operation
|
BingoObject |
searchSim(IndigoObject query,
float min,
float max,
String metric)
Execute similarity search operation
|
BingoObject |
searchSimTopN(IndigoObject query,
int limit,
float minSim)
Execute similarity search for most similar structures (defined by limit)
|
BingoObject |
searchSimTopN(IndigoObject query,
int limit,
float minSim,
String metric)
Execute similarity search for most similar structures (defined by limit)
|
BingoObject |
searchSimTopNWithExtFP(IndigoObject query,
int limit,
float minSim,
IndigoObject extFp)
Execute similarity search for most similar structures with external fingerprint
|
BingoObject |
searchSimTopNWithExtFP(IndigoObject query,
int limit,
float minSim,
IndigoObject extFp,
String metric)
Execute similarity search for most similar structures with external fingerprint
|
BingoObject |
searchSimWithExtFP(IndigoObject query,
float min,
float max,
IndigoObject ext_fp)
Execute similarity search with external fingerprint
|
BingoObject |
searchSimWithExtFP(IndigoObject query,
float min,
float max,
IndigoObject ext_fp,
String metric)
Execute similarity search with external fingerprint
|
BingoObject |
searchSub(IndigoObject query)
Execute substructure search operation
|
BingoObject |
searchSub(IndigoObject query,
String options)
Execute substructure search operation
|
String |
version()
Returns Bingo version
|
public void dispose()
public void close()
public static int checkResult(Indigo indigo, int result)
public static float checkResult(Indigo indigo, float result)
public static Bingo createDatabaseFile(Indigo indigo, String location, String type, String options)
indigo - Indigo instancelocation - Directory with the files locationtype - molecule" or "reaction"options - additional options separated with a semicolon. See the Bingo documentation for more detailpublic static Bingo createDatabaseFile(Indigo indigo, String location, String type)
indigo - Indigo instancelocation - Directory with the files locationtype - molecule" or "reaction"public static Bingo loadDatabaseFile(Indigo indigo, String location, String options)
indigo - Indigo instancelocation - Directory with the files locationoptions - Additional options separated with a semicolon. See the Bingo documentation for more detailspublic static Bingo loadDatabaseFile(Indigo indigo, String location)
indigo - Indigo instancelocation - Directory with the files locationpublic int insert(IndigoObject record)
record - Indigo object with a chemical structure (molecule or reaction)public int insert(IndigoObject record, int id)
record - Indigo object with a chemical structure (molecule or reaction)id - record idpublic int insertWithExtFP(IndigoObject record, IndigoObject ext_fp)
record - Indigo object with a chemical structure (molecule or reaction)ext_fp - Indigo object with a external similarity fingerprint (molecule or reaction)public int insertWithExtFP(IndigoObject record, IndigoObject ext_fp, int id)
record - Indigo object with a chemical structure (molecule or reaction)id - record idext_fp - Indigo object with a external similarity fingerprint (molecule or reaction)public void delete(int id)
id - Record idpublic BingoObject searchSub(IndigoObject query, String options)
query - Indigo query object (molecule or reaction)options - Search optionspublic BingoObject searchSub(IndigoObject query)
query - Indigo query object (molecule or reaction)public BingoObject searchSim(IndigoObject query, float min, float max, String metric)
query - indigo object (molecule or reaction)min - Minimum similarity valuemax - Maximum similarity valuemetric - Default value is "tanimoto"public BingoObject searchSim(IndigoObject query, float min, float max)
query - indigo object (molecule or reaction)min - Minimum similarity valuemax - Maximum similarity valuepublic BingoObject searchSimWithExtFP(IndigoObject query, float min, float max, IndigoObject ext_fp, String metric)
query - indigo object (molecule or reaction)min - Minimum similarity valuemax - Maximum similarity valueext_fp - Indigo object with a external similarity fingerprint (molecule or reaction)metric - Default value is "tanimoto"public BingoObject searchSimWithExtFP(IndigoObject query, float min, float max, IndigoObject ext_fp)
query - indigo object (molecule or reaction)min - Minimum similarity valuemax - Maximum similarity valueext_fp - Indigo object with a external similarity fingerprint (molecule or reaction)public BingoObject searchSimTopN(IndigoObject query, int limit, float minSim, String metric)
query - indigo object (molecule or reaction)limit - Number of structuresminSim - Minimum similarity valuemetric - Default value is "tanimoto"public BingoObject searchSimTopN(IndigoObject query, int limit, float minSim)
query - indigo object (molecule or reaction)limit - Number of structuresminSim - Minimum similarity valuepublic BingoObject searchSimTopNWithExtFP(IndigoObject query, int limit, float minSim, IndigoObject extFp, String metric)
query - indigo object (molecule or reaction)limit - Number of structuresminSim - Minimum similarity valuemetric - Default value is "tanimoto"extFp - Indigo object with a external similarity fingerprint (molecule or reaction)public BingoObject searchSimTopNWithExtFP(IndigoObject query, int limit, float minSim, IndigoObject extFp)
query - indigo object (molecule or reaction)limit - Number of structuresminSim - Minimum similarity valueextFp - Indigo object with a external similarity fingerprint (molecule or reaction)public BingoObject enumerateId()
public BingoObject searchExact(IndigoObject query, String options)
query - indigo object (molecule or reaction)options - search optionspublic BingoObject searchExact(IndigoObject query)
query - indigo object (molecule or reaction)public BingoObject searchMolFormula(String query, String options)
query - string with formula to search. For example, "C22 H23 N3 O2"options - search optionspublic BingoObject searchMolFormula(String query)
query - string with formula to search. For example, "C22 H23 N3 O2"public void optimize()
public IndigoObject getRecordById(int id)
id - record idpublic String version()
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