chemaxon.jep
Class Evaluator

java.lang.Object
  chemaxon.jep.Evaluator

public class Evaluator

extends java.lang.Object

Evaluates chemical expressions. Provides command line interface or creates ChemJEP objects according to configuration.

Since:

JChem 2.2

Version:

5.0.1 01/16/2007

Author:

Nora Mate, Zsolt Mohacsi

Field Summary

static java.lang.String	DEFAULT_TAG_NAME Default SDFile tag to store the evaluation result.
static java.lang.String	EVALUATOR_DEFAULTS_FILE Default Function/Plugin settings filename.
static java.lang.String	EVALUATOR_NAMED_MOLS_FILE Default named molecule set filename.
static java.lang.String	EVALUATOR_SCRIPT_FILE Initial script filename.
static java.lang.String	JCHEM_CONFIG_DIR Default directory under jchem directory for storing configuration files.

Constructor Summary

Evaluator()
Default constructor.

Evaluator(org.dom4j.Element element)
Deprecated. for internal use only

Evaluator(org.dom4j.Element element, java.lang.String dir)
Deprecated. for internal use only

Evaluator(org.dom4j.Element element, java.lang.String dir, Standardizer standardizer)
Deprecated. for internal use only

Evaluator(java.io.File file)
Constructor.

Evaluator(java.io.File file, Standardizer standardizer)
Constructor.

Evaluator(java.io.File file, Standardizer standardizer, MolImporter importer, java.lang.String script)
Constructor.

Evaluator(Standardizer standardizer)
Constructor.

Evaluator(java.lang.String configString)
Constructor.

Evaluator(java.lang.String configString, Standardizer standardizer)
Constructor.

Evaluator(java.lang.String configString, Standardizer standardizer, MolImporter importer, java.lang.String script)
Constructor.

Method Summary

ChemJEP	compile(java.lang.String expression) Compiles the expression, creates ChemJEP object.
ChemJEP	compile(java.lang.String expression, java.lang.Class contextClass) Compiles the expression, creates ChemJEP object.
ChemJEP	compile(java.lang.String expression, java.lang.Class contextClass, chemaxon.nfunk.jep.SymbolTable stab) Compiles the expression, creates ChemJEP object.
java.util.Hashtable	getFunctionParameterData() Returns user parameter data for each function.
java.lang.String[]	getPluginIDs() Returns the plugin function IDs from the Plugins section of the configuration XML.
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(java.lang.String[] args) The command line version entry point.
void	runScript(java.lang.String script) Runs a script, variables will be added to the base variable table and can be referenced by chemical expressions.
void	setFingerprintGenerator(chemaxon.sss.screen.CombinedFingerprint cf) Sets the fingerprint generator object (needed for query strings).
void	setVerbose(boolean verbose) Sets verbose mode.
static java.lang.String	toString(java.lang.Object o) Returns String representation of an object using default decimal format with 2 fractional digits.
static java.lang.String	toString(java.lang.Object o, java.text.DecimalFormat df) Returns String representation of an object.
static java.lang.String	toString(java.lang.Object o, int precision) Returns String representation of an object using default decimal format with given number of fractional digits.

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 java.lang.String EVALUATOR_DEFAULTS_FILE

Default Function/Plugin settings filename.

See Also:

Constant Field Values

EVALUATOR_NAMED_MOLS_FILE

public static final java.lang.String EVALUATOR_NAMED_MOLS_FILE

Default named molecule set filename.

See Also:

Constant Field Values

JCHEM_CONFIG_DIR

public static final java.lang.String JCHEM_CONFIG_DIR

Default directory under jchem directory for storing configuration files.

See Also:

Constant Field Values

EVALUATOR_SCRIPT_FILE

public static final java.lang.String EVALUATOR_SCRIPT_FILE

Initial script filename.

See Also:

Constant Field Values

DEFAULT_TAG_NAME

public static final java.lang.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.

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(java.io.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(org.dom4j.Element element)
          throws chemaxon.nfunk.jep.ParseException

Deprecated. for internal use only

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

Parameters:

element - is the configuration root element

Throws:

chemaxon.nfunk.jep.ParseException - on error

Evaluator

public Evaluator(java.lang.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(org.dom4j.Element element,
                 java.lang.String dir)
          throws chemaxon.nfunk.jep.ParseException

Deprecated. for internal use only

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

Parameters:

element - is the configuration root element

dir - is the root directory

Throws:

chemaxon.nfunk.jep.ParseException - on error

Evaluator

public Evaluator(java.io.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

public Evaluator(java.io.File file,
                 Standardizer standardizer,
                 MolImporter importer,
                 java.lang.String script)
          throws chemaxon.nfunk.jep.ParseException

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(org.dom4j.Element element,
                 java.lang.String dir,
                 Standardizer standardizer)
          throws chemaxon.nfunk.jep.ParseException

Deprecated. for internal use only

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

Parameters:

element - is the configuration root element

dir - is the root directory

standardizer - is the standardizer object

Throws:

chemaxon.nfunk.jep.ParseException - on error

Evaluator

public Evaluator(java.lang.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

public Evaluator(java.lang.String configString,
                 Standardizer standardizer,
                 MolImporter importer,
                 java.lang.String script)
          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 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

runScript

public void runScript(java.lang.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

public java.util.Hashtable getFunctionParameterData()
                                             throws chemaxon.nfunk.jep.ParseException

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

public java.lang.String[] getPluginIDs()
                                throws chemaxon.nfunk.jep.ParseException

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

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

setFingerprintGenerator

public void setFingerprintGenerator(chemaxon.sss.screen.CombinedFingerprint cf)

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

Parameters:

cf - 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(java.lang.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(java.lang.String expression,
                       java.lang.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(java.lang.String expression,
                       java.lang.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

public static java.lang.String toString(java.lang.Object o)

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

public static java.lang.String toString(java.lang.Object o,
                                        int precision)

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

public static java.lang.String toString(java.lang.Object o,
                                        java.text.DecimalFormat df)

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(java.lang.String[] args)
                 throws java.lang.Exception

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

Parameters:

args - the command line parameters

Throws:

java.lang.Exception