Package chemaxon.jchem.db
Class StructureTableOptions
- java.lang.Object
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- chemaxon.jchem.db.StructureTableOptions
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- All Implemented Interfaces:
TableTypeConstants
@PublicAPI public class StructureTableOptions extends Object implements TableTypeConstants
Class for storing options for structure table creation.- Since:
- JChem 5.0
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Field Summary
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Fields inherited from interface chemaxon.jchem.db.TableTypeConstants
FP_DEFAULT_BITS_PER_PATTERN, FP_DEFAULT_LENGTH_IN_INTS, FP_DEFAULT_PATTERN_LENGTH, MYSQL_DEFAULT_TABLE_TYPE, MYSQL_FORCE_INNO_DB, MYSQL_FORCE_MYISAM, TABLE_TYPE_ANY_STRUCTURES, TABLE_TYPE_DEFAULT, TABLE_TYPE_EXPLANATIONS, TABLE_TYPE_IS_NOT_SUPPORTED, TABLE_TYPE_MARKUSH_LIBRARIES, TABLE_TYPE_MOLECULES, TABLE_TYPE_NAMES, TABLE_TYPE_QUERY_STRUCTURES, TABLE_TYPE_REACTIONS
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Constructor Summary
Constructors Constructor Description StructureTableOptions(String name)
Creates structure table options with the specified table name and default table type (TableTypeConstants.TABLE_TYPE_DEFAULT
).StructureTableOptions(String name, int tableType)
Creates structure table options with the specified name and table type.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description chemaxon.jchem.base.storage.cache.CacheUpdaterType
getCacheUpdaterType()
Gets the method to update cache.Map<String,String>
getChemTermColsConfig()
Gets a map having as keys the names of columns which are assigned a value (during structure import and update).String
getExtraColumnDefinitions()
Gets the definitions of additional columns.int
getFpNumberOfEdges()
Gets he maximum pattern length.int
getFpNumberOfInts()
Gets the length of the chemical hashed fingerprint.int
getFpNumberOfOnes()
Gets the number of bits set for patterns.int
getMysqlTableType()
Gets the table engine for MySql.String
getName()
Gets the table name.String
getStandardizerConfig()
Gets the standardization configuration string.StrucFPConfig
getStructuralKeyConfig()
Gets the structural key configuration.int
getStructureColumnType()
Gets the type of thecd_structure
column.int
getTableType()
Gets the table name.chemaxon.sss.search.options.TautomerTransformationMode
getTautomerEqualityMode()
boolean
isAbsoluteStereo()
Gets whether the structures should be treated as absolute stereo during database search.boolean
isDuplicateFiltering()
Gets the duplicate filtering option.boolean
isTautomerDuplicateChecking()
Gets whether tautomers are considered during DUPLICATE search.void
setAbsoluteStereo(boolean absoluteStereo)
Specifies if structures should be treated as absolute stereo during database search.void
setCacheUpdaterType(chemaxon.jchem.base.storage.cache.CacheUpdaterType cacheUpdaterType)
Sets the cache update type.void
setChemTermColsConfig(Map<String,String> chemTermColsConfig)
Sets the map having as keys the names of columns which must be assigned a value (during structure import and update).void
setDuplicateFiltering(boolean duplicateFiltering)
Specifies the duplicate filtering option.void
setExtraColumnDefinitions(String extraColumnDefinitions)
Sets the definitions of additional columns.void
setFpNumberOfBonds(int fp_numberOfBonds)
Sets the maximum pattern length.void
setFpNumberOfInts(int fp_numberOfInts)
Sets the length of the chemical hashed fingerprint inint
size units (bit count / 32).void
setFpNumberOfOnes(int fp_numberOfOnes)
Sets the number of bits to be set for patterns.void
setMysqlTableType(int mysqlTableType)
Specifies table engine for MySql.void
setName(String name)
void
setStandardizerConfig(String standardizerConfig)
Sets the standardization configuration string (XML or simple action string).void
setStructuralKeyConfig(StrucFPConfig structuralKeyConfig)
Sets the structural key configuration.void
setStructureColumnType(int structureColumnType)
Sets the structure column type.void
setTableType(int tableType)
void
setTautomerDuplicateChecking(boolean tautomerDuplicateChecking)
Specifies if tautomers should be considered during DUPLICATE search, e.g.void
setTautomerEqualityMode(chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode)
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Constructor Detail
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StructureTableOptions
public StructureTableOptions(String name, int tableType)
Creates structure table options with the specified name and table type.- Parameters:
name
- table nametableType
- table type
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StructureTableOptions
public StructureTableOptions(String name)
Creates structure table options with the specified table name and default table type (TableTypeConstants.TABLE_TYPE_DEFAULT
).- Parameters:
name
- table name
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Method Detail
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getName
public String getName()
Gets the table name.- Returns:
- the table name
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getFpNumberOfInts
public int getFpNumberOfInts()
Gets the length of the chemical hashed fingerprint.- Returns:
- the length of the chemical hashed fingerprint in
int
size units
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getFpNumberOfOnes
public int getFpNumberOfOnes()
Gets the number of bits set for patterns.- Returns:
- the number of bits set for patterns
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getFpNumberOfEdges
public int getFpNumberOfEdges()
Gets he maximum pattern length.- Returns:
- the maximum pattern length
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getStandardizerConfig
public String getStandardizerConfig()
Gets the standardization configuration string.- Returns:
- the standardization configuration string
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isAbsoluteStereo
public boolean isAbsoluteStereo()
Gets whether the structures should be treated as absolute stereo during database search.- Returns:
- structures should be treated as absolute stereo during database search
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getStructuralKeyConfig
public StrucFPConfig getStructuralKeyConfig()
Gets the structural key configuration.- Returns:
- the structural key configuration
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getChemTermColsConfig
public Map<String,String> getChemTermColsConfig()
Gets a map having as keys the names of columns which are assigned a value (during structure import and update). The values assigned to the columns are calculated using the chemical terms expressions contained in the map as values.- Returns:
- a map having as keys the names of columns which are assigned a value
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getTableType
public int getTableType()
Gets the table name.- Returns:
- the table type
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isTautomerDuplicateChecking
public boolean isTautomerDuplicateChecking()
Gets whether tautomers are considered during DUPLICATE search.- Returns:
- returns whether tautomers are considered during DUPLICATE search, e.g. importing with duplicate checking
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getExtraColumnDefinitions
public String getExtraColumnDefinitions()
Gets the definitions of additional columns.- Returns:
- the definitions of additional columns
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getStructureColumnType
public int getStructureColumnType()
Gets the type of thecd_structure
column.- Returns:
- the type of the
cd_structure
column
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getMysqlTableType
public int getMysqlTableType()
Gets the table engine for MySql.- Returns:
- the table engine for MySql.
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isDuplicateFiltering
public boolean isDuplicateFiltering()
Gets the duplicate filtering option.- Returns:
- the duplicate filtering option
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getCacheUpdaterType
public chemaxon.jchem.base.storage.cache.CacheUpdaterType getCacheUpdaterType()
Gets the method to update cache.- Returns:
- the method to update cache
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setFpNumberOfInts
public void setFpNumberOfInts(int fp_numberOfInts)
Sets the length of the chemical hashed fingerprint inint
size units (bit count / 32). The value should be greater than or equal to 8.- Parameters:
fp_numberOfInts
- the chemical hashed fingerprint inint
size units
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setFpNumberOfOnes
public void setFpNumberOfOnes(int fp_numberOfOnes)
Sets the number of bits to be set for patterns.- Parameters:
fp_numberOfOnes
- the number of bits to set
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setFpNumberOfBonds
public void setFpNumberOfBonds(int fp_numberOfBonds)
Sets the maximum pattern length. The value should be between 2 and 10.- Parameters:
fp_numberOfBonds
- maximum pattern length
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setStandardizerConfig
public void setStandardizerConfig(String standardizerConfig)
Sets the standardization configuration string (XML or simple action string).- Parameters:
standardizerConfig
- the standardization configuration string
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setAbsoluteStereo
public void setAbsoluteStereo(boolean absoluteStereo)
Specifies if structures should be treated as absolute stereo during database search. This overrides the original state of the chiral flag.- Parameters:
absoluteStereo
- whether structures should be treated as absolute stereo during database search
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setStructuralKeyConfig
public void setStructuralKeyConfig(StrucFPConfig structuralKeyConfig)
Sets the structural key configuration.- Parameters:
structuralKeyConfig
- the structural key configuration- See Also:
StrucFPConfig
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setChemTermColsConfig
public void setChemTermColsConfig(Map<String,String> chemTermColsConfig)
Sets the map having as keys the names of columns which must be assigned a value (during structure import and update). The values assigned to the columns are calculated using the chemical terms expressions contained in the map as values.- Parameters:
chemTermColsConfig
- the chemical terms expression
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setTautomerDuplicateChecking
public void setTautomerDuplicateChecking(boolean tautomerDuplicateChecking)
Specifies if tautomers should be considered during DUPLICATE search, e.g. importing with duplicate checking.
If set totrue
the import / insert of structures requires some additional CPU time.- Parameters:
tautomerDuplicateChecking
- whether tautomers should be considered during DUPLICATE search or import.
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setExtraColumnDefinitions
public void setExtraColumnDefinitions(String extraColumnDefinitions)
Sets the definitions of additional columns. The syntax of thecolumnDefs
field- starts with a comma
- contains column definitions separated by comma
- see the SQL
CREATE
statement for legal column definitions.
- Parameters:
extraColumnDefinitions
- the definitions of additional columns
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setStructureColumnType
public void setStructureColumnType(int structureColumnType)
Sets the structure column type.- Parameters:
structureColumnType
- the structure column type
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setMysqlTableType
public void setMysqlTableType(int mysqlTableType)
Specifies table engine for MySql.- Parameters:
mysqlTableType
- the mysql table type- See Also:
TableTypeConstants.MYSQL_DEFAULT_TABLE_TYPE
,TableTypeConstants.MYSQL_FORCE_INNO_DB
,TableTypeConstants.MYSQL_FORCE_MYISAM
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setDuplicateFiltering
public void setDuplicateFiltering(boolean duplicateFiltering)
Specifies the duplicate filtering option.- Parameters:
duplicateFiltering
- duplicate filtering option
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setCacheUpdaterType
public void setCacheUpdaterType(chemaxon.jchem.base.storage.cache.CacheUpdaterType cacheUpdaterType)
Sets the cache update type.- Parameters:
cacheUpdaterType
- the method to update cache
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setName
public void setName(String name)
- Parameters:
name
- the name to set
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setTableType
public void setTableType(int tableType)
- Parameters:
tableType
- the tableType to set
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getTautomerEqualityMode
@Beta public chemaxon.sss.search.options.TautomerTransformationMode getTautomerEqualityMode()
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setTautomerEqualityMode
@Beta public void setTautomerEqualityMode(chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode)
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