Package chemaxon.descriptors

Class MDDBReader

java.lang.Object

chemaxon.descriptors.MDReader

chemaxon.descriptors.MDDBReader

@PublicAPI
public class MDDBReader
extends MDReader

Class for reading MolecularDescriptors from a database. Capable of generating MolecularDescriptors on-the-fly from molecules if required.

Since:

JChem 2.0

Field Summary

Fields inherited from class chemaxon.descriptors.MDReader

cloneResult, firstId, generateDescriptor, generateId, id, idTagName, lastReadMolecule, mdSet, takeTags

Constructor Summary

Constructors

Constructor	Description
MDDBReader(ConnectionHandler ch, String strucTableName, MDSet mdSet, String sqlCondition)	Deprecated. since 2.3 Use MDDBReader(java.lang.String, chemaxon.util.ConnectionHandler, chemaxon.descriptors.MDSet, java.lang.String) instead.
MDDBReader(ConnectionHandler ch, String strucTableName, String[] mdNames, String sqlCondition)	Deprecated. since 2.3 Use MDDBReader(java.lang.String, chemaxon.util.ConnectionHandler, java.lang.String[], java.lang.String) instead.
MDDBReader(String strucTableName, ConnectionHandler ch, MDSet mdSet, String query)	Constructs a new MDDBReader object.
MDDBReader(String strucTableName, ConnectionHandler ch, String[] mdNames, String query)	Constructs a new MDDBReader object.
MDDBReader(String strucTableName, ConnectionHandler ch, String[] mdNames, String query, int[] filterIDList, int[] filterIDNotList, boolean indexTable)	Constructs a new MDDBReader object.

Method Summary

Modifier and Type	Method	Description
void	close()	Closes down the descriptor stream.
int	getLastID()	Gets the cd_id that belongs to the last processed descriptor from the structure table
MDSet	getMDSet()	Gets the molecular descriptor set.
Molecule	getMolecule()	Gets the molecule that belongs to the last processed descriptor from the structure table
MDSet	next()	Fetches the next element form the stream or returns null when there are no more accessible data.
void	reset()	Initializes the MolecularDescriptor stream.

Methods inherited from class chemaxon.descriptors.MDReader

createMDSetComponent, getCloneResult, setCloneResult, setFirstId, setGenerateId, setIdTagName, setTakeTag

Methods inherited from class java.lang.Object

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

Constructor Detail

MDDBReader

@Deprecated
public MDDBReader(ConnectionHandler ch,
                  String strucTableName,
                  MDSet mdSet,
                  String sqlCondition)

Deprecated.

since 2.3 Use MDDBReader(java.lang.String, chemaxon.util.ConnectionHandler, chemaxon.descriptors.MDSet, java.lang.String) instead.

Constructs a new MDDBReader object. Using this constructor the descriptors will be generated on-the-fly.

Parameters:

ch - a ConnectionHandler with an open connection to the database

strucTableName - name of the structure table

mdSet - the contains the appropriate descriptors

sqlCondition - a condition to be used in an SQL where clause (e.g: "cd_id > 1000"). If null, then all rows are retrieved.

MDDBReader

public MDDBReader(String strucTableName,
                  ConnectionHandler ch,
                  MDSet mdSet,
                  String query)

Constructs a new MDDBReader object. Using this constructor the descriptors will be generated on-the-fly.

Parameters:

ch - a ConnectionHandler with an open connection to the database

strucTableName - name of the structure table

mdSet - the contains the appropriate descriptors

query - SQL query for filtering. It should contain the cd_id values. Example "select cd_id from mystructures where cd_id > 1000"). If null, then all rows are retrieved.

MDDBReader

@Deprecated
public MDDBReader(ConnectionHandler ch,
                  String strucTableName,
                  String[] mdNames,
                  String sqlCondition)

Deprecated.

since 2.3 Use MDDBReader(java.lang.String, chemaxon.util.ConnectionHandler, java.lang.String[], java.lang.String) instead.

Constructs a new MDDBReader object. Using this constructor the descriptors will be read from database

Parameters:

ch - a ConnectionHandler with an open connection to the database

strucTableName - name of the structure table

mdNames - the names of the descriptors stored in the database

sqlCondition - a condition to be used in an SQL where clause (e.g: "cd_id > 1000").If null or empty string all rows are retrieved.

MDDBReader

public MDDBReader(String strucTableName,
                  ConnectionHandler ch,
                  String[] mdNames,
                  String query)

Constructs a new MDDBReader object. Using this constructor the descriptors will be read from database

Parameters:

ch - a ConnectionHandler with an open connection to the database

strucTableName - name of the structure table

mdNames - the names of the descriptors stored in the database

query - SQL query for filtering. It should contain the cd_id values. Example "select cd_id from mystructures where cd_id > 1000"). If null, then all rows are retrieved.

MDDBReader

public MDDBReader(String strucTableName,
                  ConnectionHandler ch,
                  String[] mdNames,
                  String query,
                  int[] filterIDList,
                  int[] filterIDNotList,
                  boolean indexTable)

Constructs a new MDDBReader object. Using this constructor the descriptors will be read from database

Parameters:

ch - a ConnectionHandler with an open connection to the database

strucTableName - name of the structure table

mdNames - the names of the descriptors stored in the database

query - SQL query for filtering. It should contain the cd_id values. Example "select cd_id from mystructures where cd_id > 1000"). If null, then all rows are retrieved.

filterIDList - a cd_id list to filter with. No filtering if null.

filterIDNotList - excluded cd_id list

indexTable - true if used from cartridge

Since:

JChem 3.1

Method Detail

getMDSet

public MDSet getMDSet()

Gets the molecular descriptor set. This method is provided in order to allow the used intervene into descriptor generation (for instance by overriding parameter settings).

Overrides:

getMDSet in class MDReader

Returns:

the MDSet object

reset

public void reset()
           throws MDReaderException

Initializes the MolecularDescriptor stream. If the stream is not empty the consequent call to next() returns the first element.

Overrides:

reset in class MDReader

Throws:

MDReaderException - when failed to reset the reader

next

public MDSet next()
           throws MDReaderException

Fetches the next element form the stream or returns null when there are no more accessible data. Also initializes the stream, if necessary.

Specified by:

next in class MDReader

Returns:

null if couldn't read descriptor or no more descriptors to read

Throws:

MDReaderException - when failed reading the next descriptor set

getMolecule

public Molecule getMolecule()
                     throws MDReaderException

Gets the molecule that belongs to the last processed descriptor from the structure table

Overrides:

getMolecule in class MDReader

Returns:

the requested molecule, or null if not found

Throws:

MDReaderException - when failed reading the next descriptor set

getLastID

public int getLastID()

Gets the cd_id that belongs to the last processed descriptor from the structure table

Returns:

the ID, or -1 if not found

close

public void close()
           throws MDReaderException

Closes down the descriptor stream. After this, no more operation is permitted on the stream.
NOTE: Doesn't close the database connection specified in the ConnectionHandler.

Specified by:

close in class MDReader

Throws:

MDReaderException - when failed to close the input stream