chemaxon.jchem.db
Class StructureTableOptions

java.lang.Object
  chemaxon.jchem.db.StructureTableOptions

All Implemented Interfaces:

TableTypeConstants

public class StructureTableOptions
extends java.lang.Object
implements TableTypeConstants

Class for storing options for structure table creation.

Since:

JChem 5.0

Author:

Szilard Dorant

Field Summary

boolean	absoluteStereo Specifies if structures should be treated as absolute stereo during database search.
boolean	cartridgeIndexTable For internal use only.
java.util.Map	chemTermColsConfig Map having as keys the names of columns which must be assigned a value (during structure import and update).
boolean	duplicateFiltering Specifies the duplicate filtering option.
java.lang.String	extraColumnDefinitions Definitions of additional columns.
int	fp_numberOfEdges The maximum pattern length.
int	fp_numberOfInts The length of the chemical hashed fingerprint in int size units (bit count / 32).
int	fp_numberOfOnes The number of bits to be set for patterns.
int	mysqlTableType Specifies table engine for MySql.
java.lang.String	name The name of the structure table
java.lang.String	standardizerConfig Custom standardization configuration string (XML or simple action string).
StrucFPConfig	structuralKeyConfig A structural key configuration.
int	structureColumnType Specifies the type of the cd_structure column.
int	tableType Specifies the type of the structure table.
boolean	tautomerDuplicateChecking Specifies if tautomers should be considered during DUPLICATE search, e.g. importing with duplicate checking.
boolean	tautomerSwitchOffAllProtections Specifies if all protections should be switched off in a tautomer duplicate checked table.

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

Constructor Summary

StructureTableOptions()

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

name

public java.lang.String name

The name of the structure table

fp_numberOfInts

public int fp_numberOfInts

The length of the chemical hashed fingerprint in int size units (bit count / 32). The value should be a multiple of 16. The default value is TableTypeConstants.FP_DEFAULT_LENGTH_IN_INTS [TableTypeConstants.TABLE_TYPE_DEFAULT]. More info

fp_numberOfOnes

public int fp_numberOfOnes

The number of bits to be set for patterns. The default value is TableTypeConstants.FP_DEFAULT_BITS_PER_PATTERN [TableTypeConstants.TABLE_TYPE_DEFAULT]. More info

fp_numberOfEdges

public int fp_numberOfEdges

The maximum pattern length. The default value is TableTypeConstants.FP_DEFAULT_PATTERN_LENGTH [TableTypeConstants.TABLE_TYPE_DEFAULT]. More info

standardizerConfig

public java.lang.String standardizerConfig

Custom standardization configuration string (XML or simple action string). If null, default standardization is used.

absoluteStereo

public boolean absoluteStereo

Specifies if structures should be treated as absolute stereo during database search. This overrides the original state of the chiral flag.

structuralKeyConfig

public StrucFPConfig structuralKeyConfig

A structural key configuration.

See Also:

StrucFPConfig

chemTermColsConfig

public java.util.Map chemTermColsConfig

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.

tableType

public int tableType

Specifies the type of the structure table. The following options can be specified:

• TableTypeConstants.TABLE_TYPE_MOLECULES
• TableTypeConstants.TABLE_TYPE_REACTIONS
• TableTypeConstants.TABLE_TYPE_ANY_STRUCTURES
• TableTypeConstants.TABLE_TYPE_MARKUSH_LIBRARIES

The default value is TableTypeConstants.TABLE_TYPE_DEFAULT.

tautomerDuplicateChecking

public 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.
The default value is false.

tautomerSwitchOffAllProtections

public boolean tautomerSwitchOffAllProtections

Specifies if all protections should be switched off in a tautomer duplicate checked table. The default value is false.

extraColumnDefinitions

public java.lang.String extraColumnDefinitions

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.

structureColumnType

public int structureColumnType

Specifies the type of the cd_structure column. The following values are accepted:

• Types.BLOB
• Types.CLOB
• Types.LONGVARBINARY
Specify 0 for the default type.

cartridgeIndexTable

public boolean cartridgeIndexTable

For internal use only.

mysqlTableType

public int mysqlTableType

Specifies table engine for MySql.

See Also:

TableTypeConstants.MYSQL_DEFAULT_TABLE_TYPE, TableTypeConstants.MYSQL_FORCE_INNO_DB, TableTypeConstants.MYSQL_FORCE_MYISAM

duplicateFiltering

public boolean duplicateFiltering

Specifies the duplicate filtering option.

Constructor Detail

StructureTableOptions

public StructureTableOptions()