chemaxon.reaction
Class Standardizer

java.lang.Object
  chemaxon.reaction.Standardizer

All Implemented Interfaces:

Standardizer, java.io.Serializable

public class Standardizer
extends java.lang.Object
implements java.io.Serializable, Standardizer

Performs the standardization actions determined by the xml config file. This class can be used from command-line or from the API.
See the documentation for details:

• User's Guide
• Configuration
• Developer's Guide

API usage examples:

1. A simple example:

    Standardizer st = new Standardizer(new File("standardize.xml"));
    st.standardize(mol);
    

2. A more complex example with importing molecules, standardization with a final clean action to arrange changed atoms, storing standardization information in molecule properties and finally exporting the molecules in SDF format:

    // create Standardizer with XML configuration file
    Standardizer standardizer = new Standardizer(new File("config.xml"));
   
    // set final clean action to arranged changed atoms
    standardizer.setFinalClean();
   
    MolExporter exporter = new MolExporter(System.out, "sdf");
    MolImporter importer = new MolImporter("mols.sdf");
    Molecule mol = null;
    while ((mol = importer.read()) != null) {
   
        // standardize molecule
        standardizer.standardize(mol);
   
        // get applied task indexes
        int[] inds = standardizer.getAppliedTaskIndexes();
   
        // get applied task IDs
        String[] ids = standardizer.getAppliedTaskIDs();
   
        // store applied task indexes and IDs in molecule properties
        String indsprop = "";
        for (int i=0; i < inds.length; ++i) {
              indsprop += inds[i] + " ";
        }
        String idsprop = "";
        for (int i=0; i < ids.length; ++i) {
              idsprop += ids[i] + " ";
        }
        mol.setProperty("TASK_INDEXES", indsprop);
        mol.setProperty("TASK_IDS", idsprop);
   
        // write output
        exporter.write(mol);
    }
    importer.close();
    exporter.close();
    

Since:

JChem 2.0

Version:

JChem 5.1.2, 09/11/2008

Author:

Nora Mate, Zsolt Mohacsi

See Also:

Serialized Form

Field Summary

static java.lang.String	FINAL_CLEAN_ID Final clean task ID.
static java.lang.String	GROUP_QUERY Query group: "query".
static java.lang.String	GROUP_TARGET Target group: "target".
static java.util.HashSet	SET_TARGET Target group set: contains only "target".

Constructor Summary

Standardizer(org.dom4j.Element configElement)
Constructor.

Standardizer(org.dom4j.Element configElement, java.lang.String dir)
Constructor.

Standardizer(java.io.File file)
Constructor.

Standardizer(java.io.InputStream is)
Constructor.

Standardizer(java.lang.String str)
Constructor.

Method Summary

void	clearInactiveTasks() Clears the inactive tasks list.
java.lang.String[]	getActiveGroups() Deprecated. Not used anymore.
java.lang.String[]	getAppliedTaskIDs() Returns the IDs of tasks applied to the last input molecule.
int[]	getAppliedTaskIndexes() Returns the indexes of tasks applied to the last input molecule.
int[]	getNewToOld() Returns the new -> old atom index mapping.
int[]	getOldToNew() Returns the old -> new atom index mapping.
boolean	getOptionalTasksEnabled() Deprecated. as of JChem 3.2, replaced by getActiveGroups()
boolean	isLastTaskClean() Returns true if last task is clean or there are no tasks (final clean not needed before output to file).
boolean	isLicensed()
static void	main(java.lang.String[] args) Command line entry point.
void	setActiveGroup(java.lang.String group) Deprecated. Not used anymore. Practical examples may use setInactiveTasks(String)
void	setActiveGroups(java.lang.String[] groups) Deprecated. Not used anymore.
void	setAtomIndexQuery(boolean atomIndexQuery) Sets whether atom index query is possible.
void	setCleanTemplates(Molecule[] templates) Sets the default clean templates.
void	setFinalClean() Sets final clean task: original molecule dimension, partial, optional.
void	setFinalClean(int dim) Sets final clean task: partial, target-only.
void	setFinalClean(int dim, boolean partial) Sets final clean task: target-only.
void	setFinalClean(int dim, boolean partial, java.util.HashSet groups) Sets final clean task.
void	setInactiveTasks(java.lang.String str) Adds the Standardizer tasks specified in the str parameter to the inactive tasks list.
void	setLicenseEnvironment(java.lang.String env)
void	setOptionalTasksEnabled(boolean optionals) Deprecated. as of JChem 3.2, replaced by setActiveGroups(java.lang.String[]) and setActiveGroup(java.lang.String) which in turn were replaced by setInactiveTasks(String) as of 5.0
Molecule	standardize(Molecule mol) Standardization for one input molecule: performs the standardization actions according to the XML configuration.
void	standardize(Molecule[] mols) Standardization for more input molecules: performs the standardization reactions.

Methods inherited from class java.lang.Object

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

Field Detail

GROUP_QUERY

public static final java.lang.String GROUP_QUERY

Query group: "query".

See Also:

Constant Field Values

GROUP_TARGET

public static final java.lang.String GROUP_TARGET

Target group: "target".

See Also:

Constant Field Values

SET_TARGET

public static java.util.HashSet SET_TARGET

Target group set: contains only "target".

FINAL_CLEAN_ID

public static final java.lang.String FINAL_CLEAN_ID

Final clean task ID.

See Also:

Constant Field Values

Constructor Detail

Standardizer

public Standardizer(java.lang.String str)
             throws StandardizerException

Constructor. Configuration is given as XML string or simple config string. A simple config string is a sequence of item strings, separated by "..". The order of the item strings determines the order of the corresponding actions. An item string is either a reaction SMARTS string or an action keyword. An action keyword is one of the following:

• aromatize (aromatize in Daylight style, general)
• aromatize:b (aromatize in ChemAxon style, basic)
• dearomatize
• addexplicitH (formerly: hydrogenize) (converts implicit H-s to explicit)
• removeexplicitH[:lonely:isotope:charged:radical:mapped:wedged] (formerly: dehydrogenize) (converts explicit H-s to implicit, except for lonely, isotope, charged, radical, mapped and wedged H-s; if some of these are specified in a ':'-separated list then the given H types are are also converted)
• clean (partial clean)
• clean:full (full clean)
• clean:tb, clean: