Package chemaxon.jchem.db

Class MDTableHandler

java.lang.Object
chemaxon.jchem.db.MDTableHandler
@PublicApi public class MDTableHandler extends Object
Class for handling Molecular Descriptor tables.
Since:
JChem 2.0

  • Field Details

  • Constructor Details

    • MDTableHandler

      public MDTableHandler(ConnectionHandler conh, String strucTableName) throws 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:
      SQLException - if an sql error encountered

    • MDTableHandler

      public MDTableHandler(ConnectionHandler conh, String tableName, boolean indexTable) throws 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:
      SQLException - if an sql error encountered

  • Method Details

    • getMDTableName

      public static String getMDTableName(String strucTableName, 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(String descriptorName, String descType, String descSettings, String descComment) throws 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:
      SQLException - if an sql error encountered

    • createMDTable

      public void createMDTable(String descriptorName, String descType, String descSettings, String descComment, boolean updateOnInsert) throws 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:
      SQLException - if an sql error encountered

    • deleteMDTable

      public void deleteMDTable(String descriptorName) throws 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:
      SQLException - if an sql error encountered

    • isMDTableValid

      public boolean isMDTableValid(String descriptorName) throws 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:
      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(String descriptorName) throws 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:
      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(String descriptorName) throws SQLException
      Calculates missing lines in MD table
      Parameters:
      descriptorName - the name of the Molecular Descriptor
      Throws:
      SQLException - if an sql error encountered

    • getMolecularDescriptors

      public String[] getMolecularDescriptors() throws SQLException
      Retrieves the names of MolecularDescriptors assigned to the structure table and stored in the JChem database.
      Returns:
      the descriptor names
      Throws:
      SQLException - if an sql error encountered

    • getMDConfigs

      public String[] getMDConfigs(String descriptorName) throws 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:
      SQLException - if an sql error encountered

    • getMDConfig

      public String getMDConfig(String mdName, String configName) throws 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:
      SQLException - if an sql error encountered

    • setMDConfig

      public void setMDConfig(String mdName, String configName, String config) throws 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:
      SQLException - if an sql error encountered

    • deleteMDConfig

      public void deleteMDConfig(String mdName, String configName) throws SQLException
      Deletes the specified MolecularDescriptor setting
      Parameters:
      mdName - symbolic (user defined) name of the molecular descriptor
      configName - the name of the configuration
      Throws:
      SQLException - if an sql error encountered

    • getMDSettings

      public String getMDSettings(String mdName) throws 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:
      SQLException - if an sql error encountered

    • getMDType

      public String getMDType(String mdName) throws SQLException
      Gets the Type property of the MolecularDescriptor specified by its name.
      Parameters:
      mdName - name of the MolecularDescriptor
      Returns:
      type of the MolecularDescriptor
      Throws:
      SQLException - if an sql error encountered

    • getMDComment

      public String getMDComment(String mdName) throws 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:
      SQLException - if an sql error encountered

    • getMDUpdateOnInsert

      public boolean getMDUpdateOnInsert(String mdName) throws 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:
      SQLException - if an sql error encountered

    • createMDSet

      public MDSet createMDSet(String[] mdNames) throws 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:
      SQLException - if an sql error encountered

    • createMD

      public MolecularDescriptor createMD(String mdName) throws 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:
      SQLException - if an sql error encountered

    • getMDTables

      public String[] getMDTables() throws 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:
      SQLException - if an sql error encountered