chemaxon.descriptors

Class GenerateMD

java.lang.Object

chemaxon.descriptors.GenerateMD

@PublicAPI
public class GenerateMD
extends java.lang.Object

GenerateMD provides a high level Application Program Interface (API) with comprehensive functionality for the generation of various Molecular Descriptors. The API supports all kinds of inputs and outputs (molecule files, database, desciptor files), and is capable of generating multiple descriptors simultaneously.
Example of typical usage:

      MDParameters cfpConfig = new CFParameters( new File("jchem/examples/config/cfp.xml") );
      MDParameters cfpConfig = new PFParameters( new File("jchem/examples/config/pharma-frag.xml") );
      GenerateMD generator = new GenerateMD( 2 );
      generator.setInput( "molecules.sdf" );
      generator.setSDFileInput( true );
      generator.setDescriptor( 0, "molecules.cfp", "CF", cfpConfig, "" );
      generator.setDescriptor( 1, "molecules.pfp", "PF", pfpConfig, "" );
      generator.init();
      generator.run();
      generator.close();
 

The above example generates two descriptors (a descriptor set) at the same time for every structures read from the input file molecules.sdf. The first component of the descriptor set is a chemical fingerprint which is configured from the parameter file jchem/examples/config/cfp.xml , while the second is a pharmcophore fingerprint configured by the jchem/examples/config/pharma-frag.xml configuration file.
GenerateMD supports the following descriptor types (generatemd -L lists all available built-in descriptor types):

   ECFP fingerprint (ECFP)
   3D Shape descriptor (Shape)
   Chemical Fingerprint (CF)
   Pharmacophore Fingerprint (PF)
   Reaction Fingerprint (RF)
   BCUT descriptors (BCUT)
   Hydrogen bond Donor/Acceptor count (HDon/HAcc)
   octanol-water distribution coefficient (LogD)
   octanol-water partition coefficient (LogP)
   Topological Polar Surface Area (TPSA)
   Mass of molcule (Mass)
   number of Heavy atoms (Heavy)

The chemical and pharmcophore fingerprints generated are written into the files molecules.cfp and molecules.pfp respectively.

This class does not provide methods others than transforming a molecular structure retrieved from the input source into one or more descriptor files or database tables.
GenerateMD also servers as a command line tool for the generation of Molecular Descriptors from batch.
Beside supporting all kinds of MolecularDescriptors implemented by ChemAxon, it is capable of generating arbitarary custom MolecularDescriptors (which are derived from the MolecularDescriptor class) implemented by users or third parties.
GenerateMD accepts various import sources: molecular files in many standard format, and database table (JChem structure tables). MolecularDescriptors generated are stored in file in the case of file input, and in database tables (so called MD tables) when input molecules are retrieved from a structure table. SDfile output stores the descriptors generated in a custom tag. It is also possible to produce MolecularDescriptor files that do not include any structural information only the descriptors in a readable format. Such files allow faster operation than SDfiles in further processing steps (for example in virtual screening).

Since:

JChem 2.0

Author:

Miklos Vargyas, Peter Kovacs (pkovacs84), Adrian Kalaszi

Constructor Summary

Constructors

Constructor and Description
GenerateMD() Creates an empty MolecularDescripotor generator object.
GenerateMD(int descriptorCount) Creates an object for generating the given number of different MolecularDescriptors (a molecular descriptor set, MDSet ) simultaneously.

Method Summary

Modifier and Type	Method and Description
void	addMDConfig(java.lang.String descrName, java.lang.String configName, java.io.File configFile) Adds a new parameter configuration to the descriptor.
void	addMDConfig(java.lang.String descrName, java.lang.String configName, java.lang.String config) Adds a new parameter configuration to the descriptor.
void	close() Closes the generator, all output files or database connection.
void	createMDTable(java.lang.String descrName, java.lang.String className, java.lang.String settings, java.lang.String comment) Creates a database table to store the MolecularDescriptors generated.
void	deleteMDConfig(java.lang.String descrName, java.lang.String configName) Deletes an extension configuration.
void	deleteMDTable(java.lang.String descrName) Deletes a database table that strores molecular descriptors.
int[]	getASSBClusters()
int	getCounter() Gets the number of molecules processed since init() was called.
java.lang.String[]	getMDNames() Gets the names of all descriptor types stored in the database that are associated with the current structure table.
java.lang.String	getStatistics(int di) Gets statistical data on descriptors generated.
void	init() Initialize the generator object.
static void	main(java.lang.String[] args) Command-line entry point to the MolecularDescriptor generator.
void	run() Processes all structures from the input source.
void	setBinaryOutput(boolean binaryOutput) Sets decimal output format.
void	setConnectionHandler(ConnectionHandler connectionHandler) Sets the database connection when both structures and descriptors are stored in a database.
void	setCreateStat(boolean createStat) Toggles create statistics flag.
void	setDecimalOutput(boolean decimalOutput) Sets decimal output format.
void	setDescriptor(int index, java.lang.String name, java.lang.String type, MDParameters params, java.lang.String comment) Sets type, name, parameters and comment for a given descriptor component.
void	setDescriptor(int index, java.lang.String name, java.lang.String type, java.lang.String settings, java.lang.String comment) Sets type, name, parameters and comment for a given descriptor component.
void	setDescriptor(java.lang.String name, java.lang.String type, MDParameters params, java.lang.String comment) Sets type, name, parameters and comment for a given descriptor component.
void	setDescriptor(java.lang.String name, java.lang.String type, java.lang.String settings, java.lang.String comment) Sets the descriptor to be generated.
void	setDescriptors(java.lang.String[] names, java.lang.String[] types, MDParameters[] params, java.lang.String[] comments) Sets type, name, parameters and comment for all components of a molecular descriptor set.
void	setDescriptors(java.lang.String[] names, java.lang.String[] types, java.lang.String[] settings, java.lang.String[] comments) Sets all descriptor components to be generated simultaneously.
void	setGenerateId(int from) Toggles automatic unique structure/descriptor identifier generation mode and sets the value of the first unique identifier.
void	setIdTagName(java.lang.String idTagName) Sets the name of the input SDfile tag which contains unique structure identifiers.
void	setInput(java.io.InputStream input) Sets the input to an already opened molecular structure stream.
void	setInput(java.lang.String inputFileName) Sets the name of the input molecular structure file.
void	setOutputFileName(java.lang.String outputFileName) Sets the name of the output SDfile.
void	setSDfileInput(boolean sdfInput) Toggles input file type.
void	setSDfileOutput(boolean sdfOutput) Toggles SDfile output format.
void	setSelectStatement(java.lang.String whereClause) Sets the optional select statement for fetching molecules from the structure table.
void	setStructureTableName(java.lang.String structureTableName) Sets the name of the structure table to take molecular structures from.
void	setTagName(int index, java.lang.String name) Sets the SDfile tag name for the given descriptor set component.
void	setTagName(java.lang.String name) Sets the SDfile tag name for the only descriptor type generated.
void	setTagNames(java.lang.String[] names) Sets the SDfile tag names for all descriptor set components.
void	setUpdateOnInsert(boolean updateOnInsert) Sets/clears automatic update on insert mode.
void	setValidateDescriptor(java.lang.String activityTagName, double clusteringRadius, java.lang.String metric) Sets parameters for the Activity-seeded Structure-based clustering.
boolean	step() Fetches one structure from the input source and generates descriptors as specified before initialization by the setter methods.
void	updateMDTable(java.lang.String descrName) Systematically regenerates all descriptors.
void	validateDescriptor() Validates a descriptor by the activity-seeded structure-based clustering.

Methods inherited from class java.lang.Object

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

Constructor Detail

GenerateMD

public GenerateMD()

Creates an empty MolecularDescripotor generator object.

GenerateMD

public GenerateMD(int descriptorCount)

Creates an object for generating the given number of different MolecularDescriptors (a molecular descriptor set, MDSet ) simultaneously.

Parameters:

descriptorCount - number of independent descriptor types to be generated

Method Detail

setConnectionHandler

public void setConnectionHandler(ConnectionHandler connectionHandler)
                          throws MDGeneratorException

Sets the database connection when both structures and descriptors are stored in a database.

Parameters:

connectionHandler - valid connection to a database

Throws:

MDGeneratorException - when attempting to call this method after init()

setStructureTableName

public void setStructureTableName(java.lang.String structureTableName)
                           throws MDGeneratorException,
                                  java.sql.SQLException

Sets the name of the structure table to take molecular structures from. Use this when input comes from a database.

Parameters:

structureTableName - name of the database table of input structures

Throws:

MDGeneratorException - when attempting to call this method after init() or when there is no valid database connection; or if descriptor validation option was selected beforehand

java.sql.SQLException - in the case of database management errors

setUpdateOnInsert

public void setUpdateOnInsert(boolean updateOnInsert)

Sets/clears automatic update on insert mode. Auto-update on insert means that the descriptor table is automatically updated when a new structure is inserted into the original structure table.

Parameters:

updateOnInsert - indicates auto-update mode

Since:

JChem 2.3

setSelectStatement

public void setSelectStatement(java.lang.String whereClause)
                        throws MDGeneratorException

Sets the optional select statement for fetching molecules from the structure table.

Parameters:

whereClause - restrict clause without the WHERE statement

Throws:

MDGeneratorException - when attempting to call this method after init() or when there is no valid and alive database connection, or when no structure table name has been set

setInput

public void setInput(java.lang.String inputFileName)
              throws MDGeneratorException,
                     java.io.IOException

Sets the name of the input molecular structure file.

Parameters:

inputFileName - name of the input file

Throws:

MDGeneratorException - when attempting to call this method after init() or when there is already a valid and alive database connection

java.io.IOException - in case of file reading problems.

setInput

public void setInput(java.io.InputStream input)
              throws MDGeneratorException

Sets the input to an already opened molecular structure stream.

Parameters:

input - an input stream

Throws:

MDGeneratorException - when attempting to call this method after init() or when there is already a valid and alive database connection

setSDfileInput

public void setSDfileInput(boolean sdfInput)
                    throws MDGeneratorException

Toggles input file type.

Parameters:

sdfInput - indicates, if input file is an SDfile

Throws:

MDGeneratorException - when attempting to call this method after init() or when no input file has been specified

setOutputFileName

public void setOutputFileName(java.lang.String outputFileName)
                       throws MDGeneratorException

Sets the name of the output SDfile. Note, that if the required output is one or more descriptor file(s), it (they) should not be specified as output file(s), but as descriptor name(s).

Parameters:

outputFileName - name of the output SDfile

Throws:

MDGeneratorException - when attempting to call this method after init() or when there is already a valid and alive database connection

setSDfileOutput

public void setSDfileOutput(boolean sdfOutput)

Toggles SDfile output format.

Parameters:

sdfOutput - indicates if output file is an SDfile

setDecimalOutput

public void setDecimalOutput(boolean decimalOutput)

Sets decimal output format. This file format is recognized by JKlustor tools.

Parameters:

decimalOutput - new value for the option

Since:

JChem 2.0.1

setBinaryOutput

public void setBinaryOutput(boolean binaryOutput)

Sets decimal output format. This file format is recognized by JKlustor tools.

Parameters:

binaryOutput - new value for the option

Since:

JChem 2.3

setIdTagName

public void setIdTagName(java.lang.String idTagName)

Sets the name of the input SDfile tag which contains unique structure identifiers. These identifiers are printed in each line of the decimal output format.

Parameters:

idTagName - SDfile structure identifier tag name

Since:

JChem 2.0.1

setValidateDescriptor

public void setValidateDescriptor(java.lang.String activityTagName,
                                  double clusteringRadius,
                                  java.lang.String metric)
                           throws MDGeneratorException

Sets parameters for the Activity-seeded Structure-based clustering.

Parameters:

activityTagName - name of the SDfile tag storing activity data

clusteringRadius - dissimilarity radius of a cluster around a seed

metric - metric used in clustering

Throws:

MDGeneratorException - when attempting to call this method after init() or when applying this method in multiple descriptor case

Since:

JChem 2.3

setDescriptor

public void setDescriptor(java.lang.String name,
                          java.lang.String type,
                          java.lang.String settings,
                          java.lang.String comment)
                   throws MDGeneratorException

Sets the descriptor to be generated. Use this method when descriptor of one type are generated (that is, the descriptor set has one component only).

Parameters:

name - user given name of the descriptor

type - type name of the descriptor (e.g. ChemicalFingerprint; generatemd -L command lists all available built-in descriptor types)

settings - parameter settings of the descriptor (XML)

comment - optional comment to be stored in database

Throws:

MDGeneratorException - when attempting to call this method after init() or when applying this method in multiple descriptor case

setDescriptor

public void setDescriptor(int index,
                          java.lang.String name,
                          java.lang.String type,
                          java.lang.String settings,
                          java.lang.String comment)
                   throws MDGeneratorException

Sets type, name, parameters and comment for a given descriptor component. Use this method when more than one descriptors are generated at a time (e.g. CF and PF simultaneously).

Parameters:

index - index of the component

name - user given name of the descriptor set component

type - type name of the descriptor (e.g. ChemicalFingerprint; generatemd -L command lists all available built-in descriptor types)

settings - parameter settings for the descriptor (XML)

comment - optional comment to be stored in database

Throws:

MDGeneratorException - when attempting to call this method after init() or when another component's settings were specified with an MDParameters object (rather than a String

setDescriptors

public void setDescriptors(java.lang.String[] names,
                           java.lang.String[] types,
                           java.lang.String[] settings,
                           java.lang.String[] comments)
                    throws MDGeneratorException

Sets all descriptor components to be generated simultaneously.

Parameters:

names - user given names of the descriptor set components

types - type names of the descriptors (e.g. ChemicalFingerprint; generatemd -L command lists all available built-in descriptor types)

settings - parameter settings for the descriptors (XML)

comments - optional comments to be stored in database

Throws:

MDGeneratorException - when attempting to call this method after init()

setDescriptor

public void setDescriptor(java.lang.String name,
                          java.lang.String type,
                          MDParameters params,
                          java.lang.String comment)
                   throws MDGeneratorException

Sets type, name, parameters and comment for a given descriptor component. Use this method when only one descriptor type is generated.

Parameters:

name - user given name of the descriptor

type - type name of the descriptor (e.g. ChemicalFingerprint; generatemd -L command lists all available built-in descriptor types)

params - parameter settings for the descriptor (e.g. CFParameters)

comment - optional comment to be stored in database

Throws:

MDGeneratorException - when attempting to call this method after init() or when applying this method in multiple descriptor case

setDescriptor

public void setDescriptor(int index,
                          java.lang.String name,
                          java.lang.String type,
                          MDParameters params,
                          java.lang.String comment)
                   throws MDGeneratorException

Sets type, name, parameters and comment for a given descriptor component. Use this method when more than one descriptors are generated at a time and they are not specified all in one go.

Parameters:

index - index of the component to be specified

name - user given name of the descriptor

type - type name of the descriptor (e.g. ChemicalFingerprint; generatemd -L command lists all available built-in descriptor types)

params - parameter settings of the descriptor (e.g. CFParameters)

comment - optional comment to be stored indatabase only

Throws:

MDGeneratorException - when attempting to call this method after init() or when a previously set component was specified with a String parameter setting

setDescriptors

public void setDescriptors(java.lang.String[] names,
                           java.lang.String[] types,
                           MDParameters[] params,
                           java.lang.String[] comments)
                    throws MDGeneratorException

Sets type, name, parameters and comment for all components of a molecular descriptor set.

Parameters:

names - user given names of the descriptor components

types - type names of the descriptors (e.g. ChemicalFingerprint; generatemd -L command lists all available built-in descriptor types)

params - parameter settings for the descriptor components (e.g. CFParameters)

comments - optional comments to be stored in database

Throws:

MDGeneratorException - when attempting to call this method after init()

setTagName

public void setTagName(java.lang.String name)
                throws MDGeneratorException

Sets the SDfile tag name for the only descriptor type generated.

Parameters:

name - SDfile tag name

Throws:

MDGeneratorException - when attempting to call this method after init() or when applying this method in multiple descriptor case

setTagName

public void setTagName(int index,
                       java.lang.String name)
                throws MDGeneratorException

Sets the SDfile tag name for the given descriptor set component.

Parameters:

index - index of the component

name - SDfile tag name

Throws:

MDGeneratorException - when attempting to call this method after init()

setTagNames

public void setTagNames(java.lang.String[] names)
                 throws MDGeneratorException

Sets the SDfile tag names for all descriptor set components.

Parameters:

names - SDfile tag names

Throws:

MDGeneratorException - when attempting to call this method after init()

setGenerateId

public void setGenerateId(int from)
                   throws MDGeneratorException

Toggles automatic unique structure/descriptor identifier generation mode and sets the value of the first unique identifier.

Parameters:

from - the value of the first id to be generated

Throws:

MDGeneratorException - when attempting to call this method after init() or when attempting to generate ID-s for database structures

setCreateStat

public void setCreateStat(boolean createStat)

Toggles create statistics flag.

Parameters:

createStat - new value for the create statistics flag

init

public void init()
          throws MDGeneratorException

Initialize the generator object. Call this method only after all features, modes and parameters have been set by the setter methods.

Throws:

MDGeneratorException - when attempting to initialize once again, all input/output (file creation and writing) and all database (SQL) exceptions are re-thrown

step

public boolean step()
             throws MDGeneratorException

Fetches one structure from the input source and generates descriptors as specified before initialization by the setter methods.

Returns:

true if a structure was successfully processed

Throws:

MDGeneratorException - when not yet initialized or failure to read input or write output

getCounter

public int getCounter()
               throws MDGeneratorException

Gets the number of molecules processed since init() was called.

Returns:

number of structures processed

Throws:

MDGeneratorException - when not yet initialized

getASSBClusters

public int[] getASSBClusters()

run

public void run()
         throws MDGeneratorException

Processes all structures from the input source. Structure from the input are retrieved one-by-one and all descriptors types set earlier (by the set methods) are generated and stored in the specified output.

Throws:

MDGeneratorException - not yet initialized or failed to read input or write output

getStatistics

public java.lang.String getStatistics(int di)

Gets statistical data on descriptors generated.

Parameters:

di - descriptor component index

Returns:

statistics in a formatted string

Since:

JChem 2.1

validateDescriptor

public void validateDescriptor()

Validates a descriptor by the activity-seeded structure-based clustering.

close

public void close()
           throws MDGeneratorException

Closes the generator, all output files or database connection.

Throws:

MDGeneratorException - when not yet initialized or failed to close output files

createMDTable

public void createMDTable(java.lang.String descrName,
                          java.lang.String className,
                          java.lang.String settings,
                          java.lang.String comment)
                   throws MDGeneratorException

Creates a database table to store the MolecularDescriptors generated. There is no need to call this method directly if descriptors are generated with methods offered by this class, for advanced usage only.
The corresponding structure table's name should be set by setStructureTableName( String ) prior to calling this function.

Parameters:

descrName - symbolic name of the descriptor, given by the user

className - name of the class implementing the descriptor

settings - parameter string

comment - optional comment

Throws:

MDGeneratorException - when there is no valid database connection or an SQL error occurred

deleteMDTable

public void deleteMDTable(java.lang.String descrName)
                   throws MDGeneratorException,
                          java.sql.SQLException

Deletes a database table that strores molecular descriptors. All raws, the table and all corresponding administrative information is lost irreversibly.

Parameters:

descrName - name of the descriptor (as given by the user when created)

Throws:

MDGeneratorException - when there is no valid database

java.sql.SQLException - any database error

updateMDTable

public void updateMDTable(java.lang.String descrName)
                   throws MDGeneratorException,
                          java.sql.SQLException

Systematically regenerates all descriptors. Call this method, when new structures are added to the structure table.

Parameters:

descrName - name of the descriptor (as given by the user when created)

Throws:

MDGeneratorException - when there is no valid database

java.sql.SQLException - any database error

addMDConfig

public void addMDConfig(java.lang.String descrName,
                        java.lang.String configName,
                        java.lang.String config)
                 throws MDGeneratorException,
                        java.sql.SQLException

Adds a new parameter configuration to the descriptor. Such extra configurations, often called as 'screening configurations' can extend or overwrite parameter settings stored in the time of creation. A typical example is adding new dissimilarity metrics optimized for a new active compound family to the existing set of metrics.

Parameters:

descrName - name of the descriptor (as given by the user when created)

configName - symbolic name given by the user to help the identification of the extension configuration

config - extra configuration settings

Throws:

MDGeneratorException - when there is no valid database or an existing configuration is attempted to be redefined

java.sql.SQLException - any database error

addMDConfig

public void addMDConfig(java.lang.String descrName,
                        java.lang.String configName,
                        java.io.File configFile)
                 throws java.sql.SQLException,
                        java.io.IOException,
                        MDGeneratorException

Adds a new parameter configuration to the descriptor. Such extra configurations, often called as 'screening configurations' can extend or overwrite parameter settings stored in the time of creation. A typical example is adding new dissimilarity metrics optimized for a new active compound family to the existing set of metrics.

Parameters:

descrName - name of the descriptor (as given by the user when created)

configName - symbolic name given by the user to help the identification of the extension configuration

configFile - file of extra configuration settings

Throws:

MDGeneratorException - when there is no valid database or an existing configuration is attempted to be redefined

java.sql.SQLException - any database error

java.io.IOException - in case of file reading problems.

deleteMDConfig

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

Deletes an extension configuration.

Parameters:

descrName - name of the descriptor (as given by the user when created)

configName - symbolic name given by the user to help the identification of the extension configuration

Throws:

MDGeneratorException - when there is no valid database

java.sql.SQLException - any database error

getMDNames

public java.lang.String[] getMDNames()
                              throws MDGeneratorException,
                                     java.sql.SQLException

Gets the names of all descriptor types stored in the database that are associated with the current structure table.

Returns:

molecular descriptors' names

Throws:

MDGeneratorException - when there is no valid database

java.sql.SQLException - any database error

main

public static void main(java.lang.String[] args)

Command-line entry point to the MolecularDescriptor generator.

Parameters:

args - the command line arguments