Package chemaxon.pharmacophore

Class PMapper

java.lang.Object

chemaxon.pharmacophore.PMapper

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicApi
public class PMapper
extends Object
implements chemaxon.license.Licensable

Class for searching for pharmacophore properties in a molecule.

An example for running PharmacophoreMapper:

 String pmConfigFileName; // path to the pharmacophore XML config file
 String stConfigFileName; // path to the molecule standardization config file
 ...
 Standardizer st = new Standardizer(new File(stConfigFileName));
 PMapper pm = new PMapper(new File(pmConfigFileName), st);
 PSymbols symbols = pm.getSymbols();
 ...
 while ( ...  there are more molecules ... ) {
     // getting the next molecule from file or database
     Molecule target = ... ;
     // get the feature ID -> atom index BitSet HashMap
     PMap pmap = pm.createFeatureMap(target);
     // get the feature symbol string
     String result = pmap.toString(symbols);
     System.out.println(result);
 }
 

Since:

JChem 2.0

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DEFAULT_TAG_NAME	Default SDFile tag to store the Pharmacophore Map.

Constructor Summary

Constructors

Constructor	Description
PMapper(File config)	Constructor.
PMapper(File config, Standardizer standardizer)	Constructor.
PMapper(String config)	Constructor.
PMapper(String config, Standardizer standardizer)	Constructor.
PMapper(org.dom4j.Element config)	Constructor.
PMapper(org.dom4j.Element config, Standardizer standardizer)	Constructor.
PMapper(org.dom4j.Element config, Standardizer standardizer, String dir)	Constructor.
PMapper(org.dom4j.Element config, String dir)	Constructor.
PMapper(org.dom4j.Element config, org.dom4j.Element stconfig)	Constructor.
PMapper(org.dom4j.Element config, org.dom4j.Element stconfig, String dir)	Constructor.

Method Summary

Modifier and Type	Method	Description
PMap	createFeatureMap(Molecule target)	Creates the feature ID -> atom index BitSet HashMap for the given target molecule.
String	getID(String symbol)	Returns the ID corresponding to the given symbol.
Molecule	getMolConstant(String id)	Returns the molecule constant corresponding to the given ID.
PSymbols	getSymbols()	Returns the symbol storing object.
boolean	isLicensed()
static void	main(String[] args)	Deprecated, for removal: This API element is subject to removal in a future version. This main method will be removed, CLI interfaces should not be used directly from Java code.
void	setLicenseEnvironment(String env)
void	setVerbose(boolean verbose)	Sets verbose output.

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_TAG_NAME

public static final String DEFAULT_TAG_NAME

Default SDFile tag to store the Pharmacophore Map.

See Also:

• Constant Field Values

Constructor Details

PMapper

public PMapper(File config)
        throws IOException,
chemaxon.nfunk.jep.ParseException

Constructor. Sets the pharmacophore configuration.

Parameters:

config - is the XML config file

Throws:

IOException - on IO error in molecule input

chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error

PMapper

public PMapper(File config,
 Standardizer standardizer)
        throws IOException,
chemaxon.nfunk.jep.ParseException

Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.

Parameters:

config - is the XML config file

standardizer - is the Standardizer object (may be null)

Throws:

IOException - on IO error in molecule input

chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error

IllegalArgumentException - on standardizer configuration error

PMapper

public PMapper(String config)
        throws IOException,
chemaxon.nfunk.jep.ParseException

Constructor. Sets the pharmacophore configuration.

Parameters:

config - is the XML config string

Throws:

IOException - on IO error in molecule input

chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error

IllegalArgumentException - on standardizer configuration error

PMapper

public PMapper(String config,
 Standardizer standardizer)
        throws IOException,
chemaxon.nfunk.jep.ParseException

Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.

Parameters:

config - is the XML config string

standardizer - is the Standardizer object (may be null)

Throws:

IOException - on IO error in molecule input

chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error

IllegalArgumentException - on standardizer configuration error

PMapper

public PMapper(org.dom4j.Element config,
 String dir)
        throws IOException,
chemaxon.nfunk.jep.ParseException

Constructor. Sets the pharmacophore configuration.

Parameters:

config - is the XML config root node

dir - is the root directory

Throws:

IOException - on IO error in molecule input

chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error

PMapper

public PMapper(org.dom4j.Element config)
        throws IOException,
chemaxon.nfunk.jep.ParseException

Constructor. Sets the pharmacophore configuration.

Parameters:

config - is the XML config root node

Throws:

IOException - on IO error in molecule input

chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error

PMapper

public PMapper(org.dom4j.Element config,
 Standardizer standardizer,
 String dir)
        throws IOException,
chemaxon.nfunk.jep.ParseException

Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.

Parameters:

config - is the XML config root node

standardizer - is the Standardizer object (may be null)

dir - is the root directory

Throws:

IOException - on IO error in molecule input

chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error

PMapper

public PMapper(org.dom4j.Element config,
 Standardizer standardizer)
        throws IOException,
chemaxon.nfunk.jep.ParseException

Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.

Parameters:

config - is the XML config root node

standardizer - is the Standardizer object (may be null)

Throws:

IOException - on IO error in molecule input

chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error

PMapper

public PMapper(org.dom4j.Element config,
 org.dom4j.Element stconfig,
 String dir)
        throws IOException,
chemaxon.nfunk.jep.ParseException

Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.

Parameters:

config - is the XML config root node

stconfig - is the standardizer config root node

dir - is the root directory

Throws:

IOException - on IO error in molecule input

chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error

IllegalArgumentException - if the standardizer object creation fails

PMapper

public PMapper(org.dom4j.Element config,
 org.dom4j.Element stconfig)
        throws IOException,
chemaxon.nfunk.jep.ParseException

Constructor. Sets the pharmacophore configuration and the standardizer object used to standardize the molecules before pharmacophore property search.

Parameters:

config - is the XML config root node

stconfig - is the standardizer config root node

Throws:

IOException - on IO error in molecule input

chemaxon.nfunk.jep.ParseException - on DOM parse error or configuration error

IllegalArgumentException - if the standardizer object creation fails

Method Details

setVerbose

public void setVerbose(boolean verbose)

Sets verbose output.

Parameters:

verbose - is true if verbose output

getMolConstant

public Molecule getMolConstant(String id)

Returns the molecule constant corresponding to the given ID.

Parameters:

id - is the molecule ID

Returns:

the molecule constant with the given ID or null if no such molecule

getSymbols

public PSymbols getSymbols()

Returns the symbol storing object.

Returns:

the symbol storing object

getID

public String getID(String symbol)

Returns the ID corresponding to the given symbol.

Parameters:

symbol - is the feature symbol

Returns:

the ID corresponding to the given symbol

createFeatureMap

public PMap createFeatureMap(Molecule target)
                      throws SearchException,
chemaxon.nfunk.jep.ParseException,
LicenseException

Creates the feature ID -> atom index BitSet HashMap for the given target molecule. The i-th bit in the BitSet is 1 if the i-th atom has the feature, 0 otherwise.

Parameters:

target - is the target molecule

Returns:

the feature ID -> atom index BitSet HashMap

Throws:

SearchException - if the standardization fails

chemaxon.nfunk.jep.ParseException - if the feature expression cannot be evaluated

LicenseException - if no license found

setLicenseEnvironment

public void setLicenseEnvironment(String env)

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable

isLicensed

public boolean isLicensed()

Specified by:

isLicensed in interface chemaxon.license.Licensable

main

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JAN_01_2025)
public static void main(String[] args)
                 throws Exception

Deprecated, for removal: This API element is subject to removal in a future version.

This main method will be removed, CLI interfaces should not be used directly from Java code.

The command line version entry point. Parameter parsing, initialization then start.

Parameters:

args - the command line parameters

Throws:

Exception