chemaxon.reaction
Class SynthesisAlgorithm

java.lang.Object
  chemaxon.reaction.SynthesisAlgorithm

All Implemented Interfaces:

chemaxon.license.Licensable

Direct Known Subclasses:

ExhaustiveAlgorithm, LinearAlgorithm, RandomAlgorithm

Deprecated. Will be removed soon.

public abstract class SynthesisAlgorithm
extends java.lang.Object
implements chemaxon.license.Licensable

Abstract base class for synthesis algorithm implementations. A synthesis algorithm provides the subsequent synthesis steps for the Synthesizer. The set of reactions with reactant and product molecule sets is defined in the SynthesisGraph that is built according to the configuration XML.

Since:

JChem 3.0

Author:

Nora Mate

See Also:

SynthesisGraph

Field Summary

protected org.dom4j.Element	algorithmElement Deprecated. The algorithm element.
protected Evaluator	evaluator Deprecated. Evaluator object.
protected java.lang.String	licenseEnvironment Deprecated.
protected long	logStatTime Deprecated. Log stat time.
protected int	mode Deprecated. The processing mode: Synthesizer.DBMODE, Synthesizer.FILEMODE or Synthesizer.MEMMODE.
protected java.lang.String	name Deprecated. The synthesis name.
protected int	phaseCount Deprecated. The number of phases to be processed.
protected int	rcount Deprecated. The number of reactions processed so far.
static int	RMODE_ALL Deprecated. Reaction processing mode: take all reaction centers.
static int	RMODE_ANY Deprecated. Reaction processing mode: take any of the reaction centers.
static int	RMODE_SINGLE Deprecated. Reaction processing mode: process only if there is one reaction center list.
protected int	scount Deprecated. The number of steps processed so far.
protected int	stepCount Deprecated. The number of steps to be processed.

Constructor Summary

SynthesisAlgorithm()
Deprecated. Default constructor.

Method Summary

protected void	addSets(MoleculeSet[] rsets, MoleculeSet[] psets) Deprecated. Adds reactant and product set IDs for the current step to the set list.
protected static void	clearOriginCode(MolAtom atom) Deprecated. Clears atom origin code (currently stored as atom map).
void	close() Deprecated. Closes the algorithm (writers).
static SynthesisAlgorithm	create(org.dom4j.Element element, chemaxon.reaction.ReactorConfiguration reactorConfig, ConnectionHandler conn, java.lang.String name) Deprecated. Creates the specified synthesis algorithm descendant.
protected MolCondition	createCondition(org.dom4j.Element element) Deprecated.
protected abstract void	fillSetList() Deprecated. Fills the set list with set ID-s with reactant and product sets for each algorithm step.
protected void	flushLog() Deprecated. Flushes log writer.
SynthesisGraph	getGraph() Deprecated. Returns the synthesis graph.
protected static int	getOriginCode(MolAtom atom) Deprecated. Returns atom origin code.
protected static int[]	getOriginCodes(Molecule mol, boolean clear) Deprecated. Returns origin codes in an int[] array according to atom order.
java.lang.String	getSet(int i) Deprecated. Returns the i-th set ID in the list.
java.lang.String[]	getSetIds() Deprecated. Returns the set IDs, each set ID once.
chemaxon.reaction.synthesis.TreeHandler	getTree() Deprecated. Returns the synthesis tree.
protected void	init(org.dom4j.Element algorithmElement, chemaxon.reaction.ReactorConfiguration reactorConfig, ConnectionHandler conn, java.lang.String name) Deprecated. Initializes the algorithm.
boolean	isLicensed() Deprecated. Returns information about the licensing of the product.
protected void	postInit() Deprecated. Initializes the algorithm.
void	restart() Deprecated. Restarts the algorithm.
abstract void	setExcludedIDs(java.lang.String[] ids) Deprecated. Sets phase/step IDs to be excluded.
void	setGraph(SynthesisGraph graph) Deprecated. Sets the synthesis graph.
void	setLicenseEnvironment(java.lang.String env) Deprecated. Every license can have a modifier environment that's tipically an integration environment.
void	setLogging(boolean log) Deprecated. Sets logging.
void	setLogStatTime(long logStatTime) Deprecated. Sets log statistics interval (in minutes).
protected static void	setOriginCode(MolAtom atom, int code) Deprecated. Sets atom origin code.
protected static void	setOriginCodes(Molecule mol, int code) Deprecated. Sets atom codes in the new atoms of the molecule as atom maps: an atom gets the specified new code if its stored origin code is 0 or there is no stored origin code.
protected static void	setOriginCodes(Molecule mol, int[] codes, int code) Deprecated. Sets atom codes in the atoms of the molecule as atom maps: an atom gets the origin code with the corresponding index if it is not 0, gets the specified new code if the origin code is 0.
void	setPhaseCount(int count) Deprecated. Sets the number of phases to be processed (the meaning of a phase depends on the algorithm, default: same as substep).
void	setProgressDisplay(boolean progressDisplay) Deprecated. Sets progress display in status line on System.err.
void	setStepCount(int count) Deprecated. Sets the number of substeps to be processed (the meaning of a substep depends on the algorithm).
boolean	step() Deprecated. Performs the next synthesis phase.
protected void	writeLog(java.lang.String msg) Deprecated. Writes log message if logging is enabled.
protected void	writeLog(java.lang.String msg, Molecule mol) Deprecated. Writes molecule in log if logging is enabled.
protected void	writeLog(java.lang.Throwable e) Deprecated. Logs exception stack trace.
protected void	writeProgress(java.lang.String msg) Deprecated. Writes progress message to status line if progress display is enabled.

Methods inherited from class java.lang.Object

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

Field Detail

RMODE_ANY

public static final int RMODE_ANY

Deprecated.

Reaction processing mode: take any of the reaction centers.

See Also:

Constant Field Values

RMODE_SINGLE

public static final int RMODE_SINGLE

Deprecated.

Reaction processing mode: process only if there is one reaction center list.

See Also:

Constant Field Values

RMODE_ALL

public static final int RMODE_ALL

Deprecated.

Reaction processing mode: take all reaction centers.

See Also:

Constant Field Values

name

protected java.lang.String name

Deprecated.

The synthesis name.

mode

protected int mode

Deprecated.

The processing mode: Synthesizer.DBMODE, Synthesizer.FILEMODE or Synthesizer.MEMMODE.

algorithmElement

protected org.dom4j.Element algorithmElement

Deprecated.

The algorithm element.

evaluator

protected Evaluator evaluator

Deprecated.

Evaluator object.

rcount

protected int rcount

Deprecated.

The number of reactions processed so far.

scount

protected int scount

Deprecated.

The number of steps processed so far.

stepCount

protected int stepCount

Deprecated.

The number of steps to be processed.

phaseCount

protected int phaseCount

Deprecated.

The number of phases to be processed.

logStatTime

protected long logStatTime

Deprecated.

Log stat time.

licenseEnvironment

protected java.lang.String licenseEnvironment

Deprecated.

Constructor Detail

SynthesisAlgorithm

public SynthesisAlgorithm()

Deprecated.

Default constructor.

Method Detail

create

public static SynthesisAlgorithm create(org.dom4j.Element element,
                                        chemaxon.reaction.ReactorConfiguration reactorConfig,
                                        ConnectionHandler conn,
                                        java.lang.String name)
                                 throws ReactionException

Deprecated.

Creates the specified synthesis algorithm descendant.

Parameters:

element - is the configuration DOM element

reactorConfig - is the reactor configuration object

conn - is the db connection handler, or null if memory based synthesis

name - is the synthesis name

Throws:

ReactionException - on error

restart

public void restart()

Deprecated.

Restarts the algorithm.

init

protected void init(org.dom4j.Element algorithmElement,
                    chemaxon.reaction.ReactorConfiguration reactorConfig,
                    ConnectionHandler conn,
                    java.lang.String name)
             throws ReactionException

Deprecated.

Initializes the algorithm. The default implementation creates the synthesis tree.

Parameters:

algorithmElement - is the configuration DOM element

reactorConfig - is the reactor configuration object

conn - is the db connection handler, or null if memory based synthesis

name - is the synthesis name

Throws:

ReactionException - on error

postInit

protected void postInit()
                 throws ReactionException

Deprecated.

Initializes the algorithm. Called after the synthesis graph is set and the set list is filled. The default implementation does nothing.

Throws:

ReactionException - on error

createCondition

protected final MolCondition createCondition(org.dom4j.Element element)
                                      throws ReactionException

Deprecated.

Throws:

ReactionException

setProgressDisplay

public void setProgressDisplay(boolean progressDisplay)

Deprecated.

Sets progress display in status line on System.err.

Parameters:

progressDisplay - is true is progress count is to be displayed in status line

Since:

JChem 3.1

setStepCount

public void setStepCount(int count)

Deprecated.

Sets the number of substeps to be processed (the meaning of a substep depends on the algorithm). Default: Integer.MAX_VALUE, all substeps are processed.

Parameters:

count - is the number of steps to be processed

setPhaseCount

public void setPhaseCount(int count)

Deprecated.

Sets the number of phases to be processed (the meaning of a phase depends on the algorithm, default: same as substep). Default: Integer.MAX_VALUE, all phases are processed.

Parameters:

count - is the number of phases to be processed

setOriginCode

protected static final void setOriginCode(MolAtom atom,
                                          int code)
                                   throws ReactionException

Deprecated.

Sets atom origin code. Currently uses the atom map for this purpose.

Parameters:

atom - is the atom object

code - is the origin code

Throws:

ReactionException - if the code exceeds the max atom map (1023)

getOriginCode

protected static final int getOriginCode(MolAtom atom)

Deprecated.

Returns atom origin code. Currently the atom map stores the origin code.

Parameters:

atom - is the atom object

Returns:

the atom origin code

clearOriginCode

protected static final void clearOriginCode(MolAtom atom)

Deprecated.

Clears atom origin code (currently stored as atom map). To be called before the molecule is exported.

Parameters:

atom - is the atom object

setOriginCodes

protected static void setOriginCodes(Molecule mol,
                                     int[] codes,
                                     int code)
                              throws ReactionException

Deprecated.

Sets atom codes in the atoms of the molecule as atom maps: an atom gets the origin code with the corresponding index if it is not 0, gets the specified new code if the origin code is 0.

Parameters:

mol - is the molceule

codes - is the origin code array (one code for each atom)

code - is the atom code for new atoms (with origin code 0)

Throws:

ReactionException - if code is out of range (greater than 1023)

setOriginCodes

protected static void setOriginCodes(Molecule mol,
                                     int code)
                              throws ReactionException

Deprecated.

Sets atom codes in the new atoms of the molecule as atom maps: an atom gets the specified new code if its stored origin code is 0 or there is no stored origin code.

Parameters:

mol - is the molceule

code - is the atom code for new atoms (with origin code 0)

Throws:

ReactionException - if code is out of range (greater than 1023)

getOriginCodes

protected static int[] getOriginCodes(Molecule mol,
                                      boolean clear)

Deprecated.

Returns origin codes in an int[] array according to atom order. Clears origin codes if required.

Parameters:

mol - is the molecule

clear - is true if origin codes should be cleared

Returns:

the origin codes

addSets

protected final void addSets(MoleculeSet[] rsets,
                             MoleculeSet[] psets)

Deprecated.

Adds reactant and product set IDs for the current step to the set list.

Parameters:

rsets - is the reactant set array

psets - is the product set array

getSet

public java.lang.String getSet(int i)

Deprecated.

Returns the i-th set ID in the list.

Parameters:

i - is the set index in the list

Returns:

the set ID

getSetIds

public java.lang.String[] getSetIds()

Deprecated.

Returns the set IDs, each set ID once.

Returns:

the set IDs

setGraph

public void setGraph(SynthesisGraph graph)

Deprecated.

Sets the synthesis graph.

Parameters:

graph - is the synthesis graph

getGraph

public final SynthesisGraph getGraph()

Deprecated.

Returns the synthesis graph.

Returns:

the synthesis graph

getTree

public final chemaxon.reaction.synthesis.TreeHandler getTree()

Deprecated.

Returns the synthesis tree.

Returns:

the synthesis tree

close

public void close()
           throws ReactionException

Deprecated.

Closes the algorithm (writers).

Throws:

ReactionException - on error

setLogging

public void setLogging(boolean log)
                throws java.io.IOException

Deprecated.

Sets logging. Log file: <synthesis name>.log Currently log messages are written only in case of RandomAlgorithm, database mode.

Parameters:

log - is true if logging enabled

Throws:

java.io.IOException

Since:

JChem 3.1

setLogStatTime

public void setLogStatTime(long logStatTime)
                    throws java.io.IOException

Deprecated.

Sets log statistics interval (in minutes). If set, various log events are summerized in the statistics file: <synthesis name>.log.stat If not set (i.e., set to -1), no log statistics is written. Currently implemented only in RandomAlgorithm, database mode.

Parameters:

logStatTime - the log statistics interval (in minutes)

Throws:

java.io.IOException

Since:

JChem 3.1

writeLog

protected void writeLog(java.lang.String msg)

Deprecated.

Writes log message if logging is enabled.

Parameters:

msg - is the log message

writeLog

protected void writeLog(java.lang.String msg,
                        Molecule mol)

Deprecated.

Writes molecule in log if logging is enabled.

Parameters:

msg - is the log message

mol - is the molecule

writeLog

protected void writeLog(java.lang.Throwable e)

Deprecated.

Logs exception stack trace.

Parameters:

e - is the throwable object

writeProgress

protected void writeProgress(java.lang.String msg)

Deprecated.

Writes progress message to status line if progress display is enabled.

Parameters:

msg - is the progress message

Since:

JChem 3.1

flushLog

protected void flushLog()

Deprecated.

Flushes log writer.

setExcludedIDs

public abstract void setExcludedIDs(java.lang.String[] ids)

Deprecated.

Sets phase/step IDs to be excluded.

Parameters:

ids - the phase/step IDs to be excluded

step

public boolean step()
             throws ReactionException

Deprecated.

Performs the next synthesis phase. The default implementation calls postInit() if needed.

Returns:

true if there are more phases, false if end of synthesis

Throws:

ReactionException - on error

fillSetList

protected abstract void fillSetList()
                             throws ReactionException

Deprecated.

Fills the set list with set ID-s with reactant and product sets for each algorithm step. Used for coloring atoms by origin code.

Throws:

ReactionException - on error

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.String env)

Deprecated.

Description copied from interface: chemaxon.license.Licensable

Every license can have a modifier environment that's tipically an integration environment. All being Licensable should be prepared to store and show a set environment to the LicenseHandler. Example implementation:

 private String licenseEnvironment = "";
 public void setLicenseEnvironment(String env) {
     licenseEnvironment = env;
 }
 

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable

Parameters:

env - environment String to be stored and passed to the LicenseHandler in the isLicensed method

isLicensed

public boolean isLicensed()

Deprecated.

Description copied from interface: chemaxon.license.Licensable

Returns information about the licensing of the product. Example implementation: return LicenseHandler.getInstance().isLicensed( LicenseHandler.MY_IDENTIFIER, licenseEnvironment );

Specified by:

isLicensed in interface chemaxon.license.Licensable

Returns:

true if the product is correctly licensed