chemaxon.jchem.db

Class MDTableHandler

java.lang.Object

chemaxon.jchem.db.MDTableHandler

@PublicAPI
public class MDTableHandler
extends java.lang.Object

Class for handling Molecular Descriptor tables.

Since:

JChem 2.0

Author:

JChem Base team, Szilard Dorant, Peter Kovacs (pkovacs84)

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	MD_PROPERTY_COMMENT
static java.lang.String	MD_PROPERTY_CONF_PREFIX
static java.lang.String	MD_PROPERTY_SETTINGS
static java.lang.String	MD_PROPERTY_TYPE
static java.lang.String	MD_PROPERTY_UPDATE

Constructor Summary

Constructors

Constructor and Description
MDTableHandler(ConnectionHandler conh, java.lang.String strucTableName) Creates a new instance of MDTableHandler
MDTableHandler(ConnectionHandler conh, java.lang.String tableName, boolean indexTable) Internally used.

Method Summary

Modifier and Type	Method and Description
MolecularDescriptor	createMD(java.lang.String mdName) Creates an MolecularDescriptor based on settings stored in the database
MDSet	createMDSet(java.lang.String[] mdNames) Creates an MDSet based on settings stored in the database
void	createMDTable(java.lang.String descriptorName, java.lang.String descType, java.lang.String descSettings, java.lang.String descComment) Creates a Molecular Descriptor Table.
void	createMDTable(java.lang.String descriptorName, java.lang.String descType, java.lang.String descSettings, java.lang.String descComment, boolean updateOnInsert) Creates a Molecular Descriptor Table.
void	deleteMDConfig(java.lang.String mdName, java.lang.String configName) Deletes the specified MolecularDescriptor setting
void	deleteMDTable(java.lang.String descriptorName) Deletes a Molecular Descriptor Table.
java.lang.String	getMDComment(java.lang.String mdName) Gets the value of the Comment property of the MolecularDescriptor specified by its name from the property table of the JChem database.
java.lang.String	getMDConfig(java.lang.String mdName, java.lang.String configName) Retrieves the value of the specified MolecularDescriptor configuration
java.lang.String[]	getMDConfigs(java.lang.String descriptorName) Retrieves the names of stored configurations associated with a certain Molecular Descriptor
java.lang.String	getMDSettings(java.lang.String mdName) Gets the value of the Settings property of the MolecularDescriptor specified by its name from the property table of the JChem database.
static java.lang.String	getMDTableName(java.lang.String strucTableName, java.lang.String descriptorName) Generates table name for storing Molecular Descriptors
java.lang.String[]	getMDTables() Retrieves the names of Molecular Descriptor tables assigned to the structure table and stored in the JChem database.
java.lang.String	getMDType(java.lang.String mdName) Gets the Type property of the MolecularDescriptor specified by its name.
boolean	getMDUpdateOnInsert(java.lang.String mdName) Gets the value of the UpdateOnInsert property of the MolecularDescriptor specified by its name from the property table of the JChem database.
java.lang.String[]	getMolecularDescriptors() Retrieves the names of MolecularDescriptors assigned to the structure table and stored in the JChem database.
void	incRegenerateDescriptorTable(java.lang.String descriptorName) Calculates missing lines in MD table
boolean	isMDTableValid(java.lang.String descriptorName) Tests, if a given MD table is valid or not.
boolean	isMDTableValidByAllIDs(java.lang.String descriptorName) Tests, whether a given MD table is valid.
void	setMDConfig(java.lang.String mdName, java.lang.String configName, java.lang.String config) Sets the value of the specified MolecularDescriptor configuration

Methods inherited from class java.lang.Object

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

Field Detail

MD_PROPERTY_TYPE

public static final java.lang.String MD_PROPERTY_TYPE

See Also:

Constant Field Values

MD_PROPERTY_SETTINGS

public static final java.lang.String MD_PROPERTY_SETTINGS

See Also:

Constant Field Values

MD_PROPERTY_COMMENT

public static final java.lang.String MD_PROPERTY_COMMENT

See Also:

Constant Field Values

MD_PROPERTY_UPDATE

public static final java.lang.String MD_PROPERTY_UPDATE

See Also:

Constant Field Values

MD_PROPERTY_CONF_PREFIX

public static final java.lang.String MD_PROPERTY_CONF_PREFIX

See Also:

Constant Field Values

Constructor Detail

MDTableHandler

public MDTableHandler(ConnectionHandler conh,
                      java.lang.String strucTableName)
               throws java.sql.SQLException

Creates a new instance of MDTableHandler

Parameters:

conh - ConnectionHanlder opened to the database

strucTableName - the name of the structure table, the Molecular Descriptors were created using these structures

Throws:

java.sql.SQLException - if an sql error encountered

MDTableHandler

public MDTableHandler(ConnectionHandler conh,
                      java.lang.String tableName,
                      boolean indexTable)
               throws java.sql.SQLException

Internally used. Creates a new instance of MDTableHandler

Parameters:

conh - ConnectionHanlder opened to the database

tableName - the name of the structure table

indexTable - strucTableName is an index table

Throws:

java.sql.SQLException - if an sql error encountered

Method Detail

getMDTableName

public static java.lang.String getMDTableName(java.lang.String strucTableName,
                                              java.lang.String descriptorName)

Generates table name for storing Molecular Descriptors

Parameters:

strucTableName - the name of the structure table

descriptorName - the name of the descriptor

Returns:

the MD table name generated according to conventions

createMDTable

public void createMDTable(java.lang.String descriptorName,
                          java.lang.String descType,
                          java.lang.String descSettings,
                          java.lang.String descComment)
                   throws java.sql.SQLException

Creates a Molecular Descriptor Table. Creates table named "<strucTableName>_MD_<descriptorName>", and stores creation parameters in the property table

Parameters:

descriptorName - the name of the Molecular Descriptor

descType - the type of the descriptor as a fully qualified class name

descSettings - the descriptor settings to be used for descriptor generation

descComment - a comment text for the descriptor table

Throws:

java.sql.SQLException - if an sql error encountered

createMDTable

public void createMDTable(java.lang.String descriptorName,
                          java.lang.String descType,
                          java.lang.String descSettings,
                          java.lang.String descComment,
                          boolean updateOnInsert)
                   throws java.sql.SQLException

Creates a Molecular Descriptor Table. Creates table named "<strucTableName>_MD_<descriptorName>", and stores creation parameters in the property table

Parameters:

descriptorName - the name of the Molecular Descriptor

descType - the type of the descriptor as a fully qualified class name

descSettings - the descriptor settings to be used for descriptor generation

descComment - a comment text for the descriptor table

updateOnInsert - if set to true, the descriptors will be automatically added for inserted structures. The default setting is false.

Throws:

java.sql.SQLException - if an sql error encountered

deleteMDTable

public void deleteMDTable(java.lang.String descriptorName)
                   throws java.sql.SQLException

Deletes a Molecular Descriptor Table. Deletes table named "<strucTableName>_MD_<descriptorName>". Also removes entry from the property table

Parameters:

descriptorName - the name of the Molecular Descriptor

Throws:

java.sql.SQLException - if an sql error encountered

isMDTableValid

public boolean isMDTableValid(java.lang.String descriptorName)
                       throws java.sql.SQLException

Tests, if a given MD table is valid or not.
Only tests, whether the maximum value of cd_id is bigger in the structure table than in the MD table (invalid) , or equal (valid)

Parameters:

descriptorName - the name of the Molecular Descriptor

Returns:

true if every row has a pair in the two tables
false if the structure table contains rows not listed in the MD table (import occurred after generation, regeneration is necessary)

Throws:

java.sql.SQLException - in case of database error, or if there are rows in the MD table that are not represented in the structure table (this shouldn't occur)

isMDTableValidByAllIDs

public boolean isMDTableValidByAllIDs(java.lang.String descriptorName)
                               throws java.sql.SQLException

Tests, whether a given MD table is valid.
Checks if every row in structure table has a pair in the MD table. (this may take some time)

Parameters:

descriptorName - the name of the Molecular Descriptor

Returns:

true if every row has a pair in the two tables
false if the structure table contains rows not listed in the MD table (import occurred after generation, regeneration is necessary)

Throws:

java.sql.SQLException - in case of database error, or if there are rows in the MD table that are not represented in the structure table (this shouldn't occur)

incRegenerateDescriptorTable

public void incRegenerateDescriptorTable(java.lang.String descriptorName)
                                  throws java.sql.SQLException

Calculates missing lines in MD table

Parameters:

descriptorName - the name of the Molecular Descriptor

Throws:

java.sql.SQLException - if an sql error encountered

getMolecularDescriptors

public java.lang.String[] getMolecularDescriptors()
                                           throws java.sql.SQLException

Retrieves the names of MolecularDescriptors assigned to the structure table and stored in the JChem database.

Returns:

the descriptor names

Throws:

java.sql.SQLException - if an sql error encountered

getMDConfigs

public java.lang.String[] getMDConfigs(java.lang.String descriptorName)
                                throws java.sql.SQLException

Retrieves the names of stored configurations associated with a certain Molecular Descriptor

Parameters:

descriptorName - the name of the molecular descriptor

Returns:

the names of the configurations

Throws:

java.sql.SQLException - if an sql error encountered

getMDConfig

public java.lang.String getMDConfig(java.lang.String mdName,
                                    java.lang.String configName)
                             throws java.sql.SQLException

Retrieves the value of the specified MolecularDescriptor configuration

Parameters:

mdName - symbolic (user defined) name of the molecular descriptor

configName - the name of the configuration

Returns:

the retrieved configuration string

Throws:

java.sql.SQLException - if an sql error encountered

setMDConfig

public void setMDConfig(java.lang.String mdName,
                        java.lang.String configName,
                        java.lang.String config)
                 throws java.sql.SQLException

Sets the value of the specified MolecularDescriptor configuration

Parameters:

mdName - symbolic (user defined) name of the molecular descriptor

configName - the name of the configuration

config - the configuration string

Throws:

java.sql.SQLException - if an sql error encountered

deleteMDConfig

public void deleteMDConfig(java.lang.String mdName,
                           java.lang.String configName)
                    throws java.sql.SQLException

Deletes the specified MolecularDescriptor setting

Parameters:

mdName - symbolic (user defined) name of the molecular descriptor

configName - the name of the configuration

Throws:

java.sql.SQLException - if an sql error encountered

getMDSettings

public java.lang.String getMDSettings(java.lang.String mdName)
                               throws java.sql.SQLException

Gets the value of the Settings property of the MolecularDescriptor specified by its name from the property table of the JChem database.

Parameters:

mdName - name of the MolecularDescriptor

Returns:

the value of the Settings property

Throws:

java.sql.SQLException - if an sql error encountered

getMDType

public java.lang.String getMDType(java.lang.String mdName)
                           throws java.sql.SQLException

Gets the Type property of the MolecularDescriptor specified by its name.

Parameters:

mdName - name of the MolecularDescriptor

Returns:

type of the MolecularDescriptor

Throws:

java.sql.SQLException - if an sql error encountered

getMDComment

public java.lang.String getMDComment(java.lang.String mdName)
                              throws java.sql.SQLException

Gets the value of the Comment property of the MolecularDescriptor specified by its name from the property table of the JChem database.

Parameters:

mdName - name of the MolecularDescriptor

Returns:

optional comment given by the user when the descriptor was created and stored

Throws:

java.sql.SQLException - if an sql error encountered

getMDUpdateOnInsert

public boolean getMDUpdateOnInsert(java.lang.String mdName)
                            throws java.sql.SQLException

Gets the value of the UpdateOnInsert property of the MolecularDescriptor specified by its name from the property table of the JChem database.

Parameters:

mdName - name of the MolecularDescriptor

Returns:

true if the descriptor should be updated on insert.

Throws:

java.sql.SQLException - if an sql error encountered

createMDSet

public MDSet createMDSet(java.lang.String[] mdNames)
                  throws java.sql.SQLException

Creates an MDSet based on settings stored in the database

Parameters:

mdNames - the names of the Molecular Descriptors

Returns:

the generated MDSet, contains descriptors initialized with their stored settings

Throws:

java.sql.SQLException - if an sql error encountered

createMD

public MolecularDescriptor createMD(java.lang.String mdName)
                             throws java.sql.SQLException

Creates an MolecularDescriptor based on settings stored in the database

Parameters:

mdName - the name of the Molecular Descriptor

Returns:

the generated descriptor, initialized with its stored settings

Throws:

java.sql.SQLException - if an sql error encountered

getMDTables

public java.lang.String[] getMDTables()
                               throws java.sql.SQLException

Retrieves the names of Molecular Descriptor tables assigned to the structure table and stored in the JChem database.

Returns:

the names of the descriptor tables

Throws:

java.sql.SQLException - if an sql error encountered