chemaxon.jep

Class Evaluator

java.lang.Object

chemaxon.jep.Evaluator

All Implemented Interfaces:

Serializable

public class Evaluator
extends Object
implements Serializable

Evaluates Chemical Terms expressions. Provides command line interface or creates ChemJEP objects according to configuration. See the documentation for details:

• Chemical Terms Language Reference
• Chemical Terms Reference Tables
• Chemical Terms Evaluator

API usage examples:

1. Evaluate a Chemical Terms expression on molecules and write the results to output:

    // create Evaluator
    Evaluator evaluator = new Evaluator();
   
    // create ChemJEP, compile the Chemical Terms expression
    ChemJEP chemJEP = evaluator.compile("logP()", MolContext.class);
   
    // create context
    MolContext context = new MolContext();
   
    MolImporter importer = new MolImporter("mols.smiles");
    Molecule mol = null;
    while ((mol = importer.read()) != null) {
   
       // set the input molecule
       context.setMolecule(mol);
   
       // get the result by evaluating the expression
       // note: "logP()" expression returns a double, so
       // evaluate_double(ChemContext) method is used
       double result = chemJEP.evaluate_double(context);
   
       // write output
       System.out.println(result);
    }
    importer.close();
    

2. Using a Chemical Terms expression for filtering molecules:

    // create Evaluator
    Evaluator evaluator = new Evaluator();
   
    // create ChemJEP, compile the Chemical Terms expression
    ChemJEP chemJEP = evaluator.compile(
       "mass()<=500 && logP()<=5 && donorCount()<=5 && acceptorCount()<=10",
       MolContext.class);
   
    // create context
    MolContext context = new MolContext();
   
    MolExporter exporter = new MolExporter(System.out, "smiles");
    MolImporter importer = new MolImporter("mols.smiles");
    Molecule mol = null;
    while ((mol = importer.read()) != null) {
   
       // set the input molecule
       context.setMolecule(mol);
   
       // filter molecules that fulfill the previously set
       // Chemical Terms expression (only molecules that
       // fulfill the expression are written to output)
       if(chemJEP.evaluate_boolean(context)) {
           exporter.write(mol);
       }
    }
    importer.close();
    exporter.close();
    

Since:

JChem 2.2, Marvin 5.1

Version:

Marvin 5.4., 07/29/2010

Author:

Nora Mate, Zsolt Mohacsi

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	CONFIG_DIR Default directory for storing configuration files.
static String	DEFAULT_TAG_NAME Default SDFile tag to store the evaluation result.
static String	EVALUATOR_DEFAULTS_FILE Default Function/Plugin settings filename.
static String	EVALUATOR_NAMED_MOLS_FILE Default named molecule set filename.
static String	EVALUATOR_SCRIPT_FILE Initial script filename.

Constructor Summary

Constructors

Constructor and Description
Evaluator() Default constructor.
Evaluator(File file) Constructor.
Evaluator(File file, Standardizer standardizer) Constructor.
Evaluator(File file, Standardizer standardizer, MolImporter importer, String script) Deprecated.
Evaluator(Standardizer standardizer) Constructor.
Evaluator(String configString) Constructor.
Evaluator(String configString, Standardizer standardizer) Constructor.
Evaluator(String configString, Standardizer standardizer, MolImporter importer, String script) Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
ChemJEP	compile(String expression) Compiles the expression, creates ChemJEP object.
ChemJEP	compile(String expression, Class contextClass) Compiles the expression, creates ChemJEP object.
ChemJEP	compile(String expression, Class contextClass, chemaxon.nfunk.jep.SymbolTable stab) Compiles the expression, creates ChemJEP object.
Hashtable<String,String>	getFunctionalGroupDisplayMolTable() Returns a hashtable containing |functional group name| -> |displayable molecule representation|.
Hashtable<String,chemaxon.jep.CTFunctionData>	getFunctionData() Returns information about Chemical Terms functions wrapped in chemaxon.jep.CTFunctionData objects.
Hashtable<String,chemaxon.jep.CTFunctionData>	getFunctionData(boolean addServices) Returns information about Chemical Terms functions wrapped in chemaxon.jep.CTFunctionData objects.
Hashtable	getFunctionParameterData() Deprecated. use getFunctionData()
String[]	getPluginIDs() Deprecated. use getFunctionData()
String	getServicesConfigurationPath() Returns the custom services configuration path.
chemaxon.nfunk.jep.SymbolTable	getSymbolTable() Returns the symbol table of predefined constants (molecules, molecule sets and other constants defined in the built-in and the user-defined jep.script).
static void	main(String[] args) The command line version entry point.
void	runScript(String script) Runs a script, variables will be added to the base variable table and can be referenced by chemical expressions.
void	setFingerprintGenerator(FingerprintGenerator fg) Sets the fingerprint generator object (needed for query strings).
void	setLicenseEnvironment(String env) For internal usage only.
void	setServicesConfigurationPath(String servicesConfigurationPath) Sets the custom services configuration path.
void	setVerbose(boolean verbose) Sets verbose mode.
static String	toString(Object o) Deprecated. For internal use only.
static String	toString(Object o, DecimalFormat df) Deprecated. For internal use only.
static String	toString(Object o, int precision) Deprecated. For internal use only.

Methods inherited from class java.lang.Object

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

Field Detail

EVALUATOR_DEFAULTS_FILE

public static final String EVALUATOR_DEFAULTS_FILE

Default Function/Plugin settings filename.

See Also:

Constant Field Values

EVALUATOR_NAMED_MOLS_FILE

public static final String EVALUATOR_NAMED_MOLS_FILE

Default named molecule set filename.

See Also:

Constant Field Values

CONFIG_DIR

public static final String CONFIG_DIR

Default directory for storing configuration files.

See Also:

Constant Field Values

EVALUATOR_SCRIPT_FILE

public static final String EVALUATOR_SCRIPT_FILE

Initial script filename.

See Also:

Constant Field Values

DEFAULT_TAG_NAME

public static final String DEFAULT_TAG_NAME

Default SDFile tag to store the evaluation result.

See Also:

Constant Field Values

Constructor Detail

Evaluator

public Evaluator()
          throws chemaxon.nfunk.jep.ParseException

Default constructor.

Throws:

chemaxon.nfunk.jep.ParseException

Evaluator

public Evaluator(Standardizer standardizer)
          throws chemaxon.nfunk.jep.ParseException

Constructor. Loads default configuration with standardizer, loads default named molecule sets and runs default initial scripts.

Parameters:

standardizer - is the standardizer object

Throws:

chemaxon.nfunk.jep.ParseException - on error

Since:

JChem 3.1.4

Evaluator

public Evaluator(File file)
          throws chemaxon.nfunk.jep.ParseException

Constructor. Loads default configuration and configuration from specified file, loads default named molecule sets and runs default initial scripts.

Parameters:

file - is the XML configuration file

Throws:

chemaxon.nfunk.jep.ParseException - on error

Evaluator

public Evaluator(String configString)
          throws chemaxon.nfunk.jep.ParseException

Constructor. Loads default configuration and configuration from specified XML configuration string, loads default named molecule sets and runs default initial scripts.

Parameters:

configString - is the XML configuration string

Throws:

chemaxon.nfunk.jep.ParseException - on error

Since:

JChem 5.0

Evaluator

public Evaluator(File file,
         Standardizer standardizer)
          throws chemaxon.nfunk.jep.ParseException

Constructor. Loads default configuration and configuration from specified file with standardizer. Loads also default named molecule sets and runs default initial scripts.

Parameters:

file - is the XML configuration file

standardizer - is the standardizer object

Throws:

chemaxon.nfunk.jep.ParseException - on error

Evaluator

@Deprecated
public Evaluator(File file,
                    Standardizer standardizer,
                    MolImporter importer,
                    String script)
          throws chemaxon.nfunk.jep.ParseException

Deprecated.

Constructor. Loads default configuration and configuration from specified file with standardizer. Loads also default named molecule sets and named molecule sets from the specified importer. Runs initial scripts.

Parameters:

file - is the XML configuration file

standardizer - is the standardizer object

importer - is the MolImporter object used for loading named molecule sets (if null, then default molecule sets are loaded)

script - is the initial script (Chemical Terms expression; if null, then default initial scripts are run)

Throws:

chemaxon.nfunk.jep.ParseException - on error

Since:

JChem 5.0

Evaluator

public Evaluator(String configString,
         Standardizer standardizer)
          throws chemaxon.nfunk.jep.ParseException

Constructor. Loads default configuration and configuration from specified XML configuration string with standardizer. Loads also default named molecule sets and runs default initial scripts.

Parameters:

configString - is the XML configuration string

standardizer - is the standardizer object

Throws:

chemaxon.nfunk.jep.ParseException - on error

Since:

JChem 5.0

Evaluator

@Deprecated
public Evaluator(String configString,
                    Standardizer standardizer,
                    MolImporter importer,
                    String script)
          throws chemaxon.nfunk.jep.ParseException

Deprecated.

Constructor. Loads default configuration and configuration from specified XML configuration string with standardizer. Loads also default named molecule sets and named molecule sets from the specified importer. Runs initial scripts.

Parameters:

configString - is the XML configuration string

standardizer - is the standardizer object

importer - is the MolImporter object used for loading named molecule sets (if null, then default molecule sets are loaded)

script - is the initial script (Chemical Terms expression; if null, then default initial scripts are run)

Throws:

chemaxon.nfunk.jep.ParseException - on error

Since:

JChem 5.0

Method Detail

setLicenseEnvironment

public void setLicenseEnvironment(String env)

For internal usage only.

Parameters:

env - the license environment

runScript

public void runScript(String script)
               throws chemaxon.nfunk.jep.ParseException

Runs a script, variables will be added to the base variable table and can be referenced by chemical expressions.

Parameters:

script - is the script (Chemical Terms expression)

Throws:

chemaxon.nfunk.jep.ParseException - on error

Since:

JChem 3.2

getFunctionParameterData

@Deprecated
public Hashtable getFunctionParameterData()
                                   throws chemaxon.nfunk.jep.ParseException

Deprecated. use getFunctionData()

Returns user parameter data for each function. The table is built according to the UserParam sections of the configuration XML. The keys are the function IDs, the values are the corresponding parameter record arrays:

 <function ID> -> UserParam[]
 

Returns:

the user parameter data for each function

Throws:

chemaxon.nfunk.jep.ParseException - on configuration error

Since:

JChem 3.2

getPluginIDs

@Deprecated
public String[] getPluginIDs()
                      throws chemaxon.nfunk.jep.ParseException

Deprecated. use getFunctionData()

Returns the plugin function IDs from the Plugins section of the configuration XML.

Returns:

the plugin function IDs

Throws:

chemaxon.nfunk.jep.ParseException - on configuration error

Since:

JChem 3.2

getFunctionData

public Hashtable<String,chemaxon.jep.CTFunctionData> getFunctionData()
                                                              throws chemaxon.nfunk.jep.ParseException

Returns information about Chemical Terms functions wrapped in chemaxon.jep.CTFunctionData objects. The keys are the function IDs, the values are the corresponding chemaxon.jep.CTFunctionData objects.

 <function ID> -> CTFunctionData
 

For internal use only.

Returns:

table containing CTFunctionData for each Chemical Terms function

Throws:

chemaxon.nfunk.jep.ParseException - on configuration error

Since:

JChem 5.2

getFunctionData

public Hashtable<String,chemaxon.jep.CTFunctionData> getFunctionData(boolean addServices)
                                                              throws chemaxon.nfunk.jep.ParseException

Returns information about Chemical Terms functions wrapped in chemaxon.jep.CTFunctionData objects. The keys are the function IDs, the values are the corresponding chemaxon.jep.CTFunctionData objects.

 <function ID> -> CTFunctionData
 

For internal use only.

Parameters:

addServices - if true then services data will be added as function data

Returns:

table containing CTFunctionData for each Chemical Terms function

Throws:

chemaxon.nfunk.jep.ParseException - on configuration error

Since:

JChem 5.6

getServicesConfigurationPath

public String getServicesConfigurationPath()

Returns the custom services configuration path.

Returns:

the custom services configuration path or null if using marvin's default lookup

Since:

5.10

setServicesConfigurationPath

public void setServicesConfigurationPath(String servicesConfigurationPath)

Sets the custom services configuration path.

Parameters:

servicesConfigurationPath - the new file path or URL. Set null to use marvin's default lookup

Since:

5.10

getSymbolTable

public chemaxon.nfunk.jep.SymbolTable getSymbolTable()

Returns the symbol table of predefined constants (molecules, molecule sets and other constants defined in the built-in and the user-defined jep.script).

Returns:

the symbol table of predefined constants

Since:

JChem 3.2

getFunctionalGroupDisplayMolTable

public Hashtable<String,String> getFunctionalGroupDisplayMolTable()

Returns a hashtable containing |functional group name| -> |displayable molecule representation|.

Returns:

the |functional group name| -> |displayable molecule representation| table

Since:

Marvin 5.4

setFingerprintGenerator

public void setFingerprintGenerator(FingerprintGenerator fg)

Sets the fingerprint generator object (needed for query strings).

Parameters:

fg - is the fingerprint generator object

setVerbose

public void setVerbose(boolean verbose)

Sets verbose mode.

Parameters:

verbose - is true if verbose mode

compile

public ChemJEP compile(String expression)
                throws chemaxon.nfunk.jep.ParseException

Compiles the expression, creates ChemJEP object. Call ChemJEP.evaluate(ChemContext) to evaluate the expression.

Parameters:

expression - is the expression string

Returns:

the created ChemJEP object

Throws:

chemaxon.nfunk.jep.ParseException - on compile error

compile

public ChemJEP compile(String expression,
              Class contextClass)
                throws chemaxon.nfunk.jep.ParseException

Compiles the expression, creates ChemJEP object. Call ChemJEP.evaluate(ChemContext) to evaluate the expression.

Parameters:

expression - is the expression string

contextClass - is the evaluation context class object

Returns:

the created ChemJEP object

Throws:

chemaxon.nfunk.jep.ParseException - on compile error

compile

public ChemJEP compile(String expression,
              Class contextClass,
              chemaxon.nfunk.jep.SymbolTable stab)
                throws chemaxon.nfunk.jep.ParseException

Compiles the expression, creates ChemJEP object. Call ChemJEP.evaluate(ChemContext) to evaluate the expression.

Parameters:

expression - is the expression string

contextClass - is the evaluation context class object

stab - is the vaiable table, null if the default varibale table should be used

Returns:

the created ChemJEP object

Throws:

chemaxon.nfunk.jep.ParseException - on compile error

toString

@Deprecated
public static String toString(Object o)

Deprecated. For internal use only.

Returns String representation of an object using default decimal format with 2 fractional digits.

Parameters:

o - is the object

Returns:

the string representation of the object

toString

@Deprecated
public static String toString(Object o,
                         int precision)

Deprecated. For internal use only.

Returns String representation of an object using default decimal format with given number of fractional digits.

Parameters:

o - is the object

precision - is the number of fractional digits

Returns:

the string representation of the object

toString

@Deprecated
public static String toString(Object o,
                         DecimalFormat df)

Deprecated. For internal use only.

Returns String representation of an object.

Parameters:

o - is the object

df - is the real-number formatter

Returns:

the string representation of the object

main

public static void main(String[] args)
                 throws Exception

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

Parameters:

args - the command line parameters

Throws:

Exception