Package chemaxon.jchem.db

Class StructureTableOptions

java.lang.Object
chemaxon.jchem.db.StructureTableOptions
All Implemented Interfaces:
TableTypeConstants
@PublicApi public class StructureTableOptions extends Object implements TableTypeConstants
Class for storing options for structure table creation.
Since:
JChem 5.0

  • Constructor Details

    • StructureTableOptions

      public StructureTableOptions(String name, int tableType)
      Creates structure table options with the specified name and table type.
      Parameters:
      name - table name
      tableType - table type

    • 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

  • Method Details

    • getName

      public String getName()
      Gets the table name.
      Returns:
      the table name

    • getFpNumberOfInts

      public int getFpNumberOfInts()
      Gets the length of the chemical hashed fingerprint.
      Returns:
      the length of the chemical hashed fingerprint in int size units

    • getFpNumberOfOnes

      public int getFpNumberOfOnes()
      Gets the number of bits set for patterns.
      Returns:
      the number of bits set for patterns

    • getFpNumberOfEdges

      public int getFpNumberOfEdges()
      Gets he maximum pattern length.
      Returns:
      the maximum pattern length

    • getStandardizerConfig

      public String getStandardizerConfig()
      Gets the standardization configuration string.
      Returns:
      the standardization configuration string

    • 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

    • getStructuralKeyConfig

      public StrucFPConfig getStructuralKeyConfig()
      Gets the structural key configuration.
      Returns:
      the structural key configuration

    • 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

    • getTableType

      public int getTableType()
      Gets the table name.
      Returns:
      the table type

    • 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

    • getExtraColumnDefinitions

      public String getExtraColumnDefinitions()
      Gets the definitions of additional columns.
      Returns:
      the definitions of additional columns

    • getStructureColumnType

      public int getStructureColumnType()
      Gets the type of the cd_structure column.
      Returns:
      the type of the cd_structure column

    • getMysqlTableType

      public int getMysqlTableType()
      Gets the table engine for MySql.
      Returns:
      the table engine for MySql.

    • isDuplicateFiltering

      public boolean isDuplicateFiltering()
      Gets the duplicate filtering option.
      Returns:
      the duplicate filtering option

    • getCacheUpdaterType

      @Beta public chemaxon.jchem.base.storage.cache.CacheUpdaterType getCacheUpdaterType()
      Internal use only.

    • setFpNumberOfInts

      public void setFpNumberOfInts(int fp_numberOfInts)
      Sets the length of the chemical hashed fingerprint in int size units (bit count / 32). The value should be greater than or equal to 8.
      Parameters:
      fp_numberOfInts - the chemical hashed fingerprint in int size units

    • 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

    • 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

    • setStandardizerConfig

      public void setStandardizerConfig(String standardizerConfig)
      Sets the standardization configuration string (XML or simple action string).
      Parameters:
      standardizerConfig - the standardization configuration string

    • 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

    • setStructuralKeyConfig

      public void setStructuralKeyConfig(StrucFPConfig structuralKeyConfig)
      Sets the structural key configuration.
      Parameters:
      structuralKeyConfig - the structural key configuration
      See Also:

    • 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

    • setTautomerDuplicateChecking

      public void setTautomerDuplicateChecking(boolean tautomerDuplicateChecking)
      Specifies if tautomers should be considered during DUPLICATE search, e.g. importing with duplicate checking.
      If set to true the import / insert of structures requires some additional CPU time.
      Parameters:
      tautomerDuplicateChecking - whether tautomers should be considered during DUPLICATE search or import.

    • setExtraColumnDefinitions

      public void setExtraColumnDefinitions(String extraColumnDefinitions)
      Sets the definitions of additional columns. The syntax of the columnDefs 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

    • setStructureColumnType

      public void setStructureColumnType(int structureColumnType)
      Sets the structure column type.
      Parameters:
      structureColumnType - the structure column type

    • setMysqlTableType

      public void setMysqlTableType(int mysqlTableType)
      Specifies table engine for MySql.
      Parameters:
      mysqlTableType - the mysql table type
      See Also:

    • setDuplicateFiltering

      public void setDuplicateFiltering(boolean duplicateFiltering)
      Specifies the duplicate filtering option.
      Parameters:
      duplicateFiltering - duplicate filtering option

    • setCacheUpdaterType

      @Beta public void setCacheUpdaterType(chemaxon.jchem.base.storage.cache.CacheUpdaterType cacheUpdaterType)
      Internal use only.

    • setName

      public void setName(String name)
      Parameters:
      name - the name to set

    • setTableType

      public void setTableType(int tableType)
      Parameters:
      tableType - the tableType to set

    • getTautomerEqualityMode

      @Beta public TautomerEqualityMode getTautomerEqualityMode()
      Internal use only.

    • setTautomerEqualityMode

      @Beta public void setTautomerEqualityMode(TautomerEqualityMode tautomerEqualityMode)
      Internal use only.