chemaxon.marvin.calculations
Class StereoisomerPlugin

java.lang.Object
  chemaxon.marvin.plugin.CalculatorPlugin
      chemaxon.marvin.calculations.StereoisomerPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

public class StereoisomerPlugin
extends CalculatorPlugin

Plugin class for stereoisomer calculation. * Data types:

• "structure"
• "structures"
• "count"

API usage example:

    // read input molecule
    MolImporter mi = new MolImporter("test.mol");
    Molecule mol = mi.read();
    mi.close();

    // create plugin
    StereoisomerPlugin plugin = new StereoisomerPlugin();

    // set target molecule
    plugin.setMolecule(mol);
    
    // set parameters for calculation
    plugin.setStereoisomerismType(StereoisomerPlugin.TETRAHEDRAL);  
    plugin.setMaxNumberOfStereoisomers(2048);     // if not set all stereoisomers are generated

    // run the calculation
    plugin.run();

    // get results
    Molecule[] stereoisomers = plugin.getStereoisomers();
    int stereoisomerCount = plugin.getStereoisomerCount();
    Molecule m;
    for (int i = 0; i < stereoisomerCount; ++i) {
        m = stereoisomers[i];   // same as m = plugin.getStereoisomer(i);
        // do something with molecule ...
    }

    // do something with the results ...
 

Note: Stereoisomer plugin does not handle enhanced stereo information. Enhanced stereo information is cleared before generating the stereoisomers.

For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.

Since:

Marvin 4.1 03/07/2006

Version:

5.7, 04/26/2011

Author:

Zsolt Mohacsi

Nested Class Summary

Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin

CalculatorPlugin.HydrogenData

Field Summary

static int	BOTH
static int	DOUBLE_BOND
static int	TETRAHEDRAL

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, EPSILON, explicitHydrogens, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, KEEP_HYDROGENS, keepHydrogens, licenseEnvironment, MOLECULE, MOLECULES, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED, TRUE

Constructor Summary

StereoisomerPlugin()

Method Summary

void	checkMolecule(Molecule mol) Checks the input molecule.
int	chiralCenterCount() Calculates the number of tetrahedral stereogenic centers.
java.lang.String	getProductName() Returns the product identifier of the plugin as given by LicenseManager.
java.lang.Object	getResult(java.lang.Object type, int index) Returns the result item for the specified key and index.
java.lang.String	getResultAsString(java.lang.Object type, int index, java.lang.Object result) Returns the specified result in String format.
int	getResultCount(java.lang.Object type) Returns the number of result items for the given result key.
int	getResultDomain(java.lang.Object type) Returns the calculation domain.
chemaxon.marvin.plugin.PluginMDocSource	getResultSource() Returns the result as a document source object.
java.lang.Object[]	getResultTypes() Returns the result types.
Molecule	getStereoisomer(int index) Returns a stereoisomer.
int	getStereoisomerCount() Returns the number of different stereoisomers.
Molecule[]	getStereoisomers() Returns the stereoisomers in a Molecule[] array.
java.lang.String	getTypeString(java.lang.Object type) Returns a string representation of the given type.
java.lang.String	getWarningMessage() Returns a warning message if there are no stereoisomers, null otherwise.
boolean	handlesMultiFragmentMolecules() Returns true if the plugin handles multifragment molecules, false otherwise.
boolean	isChiralCenter(int a) Determines if an atom can be a tetrahedral stereogenic center.
boolean	isIn3D() Returns true if structures are returned in 3D.
boolean	run() Runs the plugin.
void	setCheck3DStereo(boolean c) Sets the 3D stereo conformation checking of the structure.
void	setIn3D(boolean b) Sets to display the molecule in 3D.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setMaxNumberOfStereoisomers(int n) Sets the maxinum number of stereoisomers to be generated.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	setProgressMonitor(chemaxon.common.util.MProgressMonitor pmon) Sets a progress monitor to be used in run() to display progress status.
void	setProtectDoubleBondStereo(boolean protect) Sets double bond stereo protection: if true then the stereo configuration of double bonds with preset stereo information will not be changed.
void	setProtectTetrahedralStereo(boolean protect) Sets the protection of tetrahedral stereo centers: if true then stereo configuration of tetrahedral stereo centers with preset stereo information will not be changed.
void	setStereoisomerismType(int itype) Sets which type of stereoiseomers should be generated.
void	standardize(Molecule mol) Clears enhanced stereo information.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecule, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, standardizeIonicGroups, standardizeNeutralGroups

Methods inherited from class java.lang.Object

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

Field Detail

TETRAHEDRAL

public static final int TETRAHEDRAL

See Also:

Constant Field Values

DOUBLE_BOND

public static final int DOUBLE_BOND

See Also:

Constant Field Values

BOTH

public static final int BOTH

See Also:

Constant Field Values

Constructor Detail

StereoisomerPlugin

public StereoisomerPlugin()

Method Detail

getProductName

public java.lang.String getProductName()

Returns the product identifier of the plugin as given by LicenseManager.

Specified by:

getProductName in class CalculatorPlugin

Returns:

The identifier LicenseManager.ISOMERS_PLUGIN_GROUP

handlesMultiFragmentMolecules

public boolean handlesMultiFragmentMolecules()

Returns true if the plugin handles multifragment molecules, false otherwise. In the latter case the plugin takes the fragment with more atoms if a multifragment molecule is given as input.

Overrides:

handlesMultiFragmentMolecules in class CalculatorPlugin

Returns:

true if the plugin handles multifragment molecules, false otherwise

setProgressMonitor

public void setProgressMonitor(chemaxon.common.util.MProgressMonitor pmon)

Sets a progress monitor to be used in run() to display progress status. Short calculations may ignore the observer object. The default implementation does nothing.

Overrides:

setProgressMonitor in class CalculatorPlugin

Parameters:

pmon - is the progress observer object, may be null

setParameters

public void setParameters(java.util.Properties params)
                   throws PluginException

Sets the input parameters for the plugin. Parameters and value ranges:

• type: structure,structures,count
• generateall: if true all stereoisomers are generated (default: true)
• maxstereoisomers: maximum number of stereoisomers to generate, if generateall option is set to false (default: 2048)
• verify3D: if true generated stereoisomers are checked for a valid 3D conformation (default: false)
• in3D: if true stereoisomers are checked for a valid 3D conformation and stored in 3D (default: false)

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

isIn3D

public boolean isIn3D()

Returns true if structures are returned in 3D.

Returns:

true if structures are returned in 3D

Since:

Marvin 5.0

setProtectTetrahedralStereo

public void setProtectTetrahedralStereo(boolean protect)

Sets the protection of tetrahedral stereo centers: if true then stereo configuration of tetrahedral stereo centers with preset stereo information will not be changed. Default: false.

Parameters:

protect - is true if preset tetrahedral stereo centers should be protected

Since:

Marvin 5.2.3

setProtectDoubleBondStereo

public void setProtectDoubleBondStereo(boolean protect)

Sets double bond stereo protection: if true then the stereo configuration of double bonds with preset stereo information will not be changed. Default: false.

Parameters:

protect - is true if preset double bond stereo information should be protected

Since:

Marvin 5.2.3

checkMolecule

public void checkMolecule(Molecule mol)
                   throws PluginException

Checks the input molecule. Throws exception if the molecule is RxnMolecule or if the molecule contains R-groups.

Overrides:

checkMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Throws:

PluginException - with error message for the user if the molecule is refused

setInputMolecule

protected void setInputMolecule(Molecule mol)
                         throws PluginException

Sets the input molecule.

Specified by:

setInputMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Throws:

PluginException - on error

isChiralCenter

public boolean isChiralCenter(int a)

Determines if an atom can be a tetrahedral stereogenic center.

Parameters:

a - index of the atom

Returns:

true if the atom is stereogenic.

chiralCenterCount

public int chiralCenterCount()

Calculates the number of tetrahedral stereogenic centers. This function identifies two chiral centers in 1,4-dimethylcyclohexane, which does not contain asymmetric atoms.

Returns:

number of tetrahedral stereogenic center atoms

setMaxNumberOfStereoisomers

public void setMaxNumberOfStereoisomers(int n)

Sets the maxinum number of stereoisomers to be generated. If not set the plugin generates all stereoisomers of the molecule. It is recommended to use when there are too much stereoisomers to fit to the memory.

Parameters:

n - is the number of stereoisomers to be generated

setStereoisomerismType

public void setStereoisomerismType(int itype)

Sets which type of stereoiseomers should be generated. Available values:

• TETRAHEDRAL : tetrahedral stereoisomers are generated
• DOUBLE_BOND : double bond stereoisomers are generated
• BOTH : tetrahedral and double bond stereoisomers are generated (in fact tetrahedral stereoisomers of double bond stereoisomers are generated)

Parameters:

itype - is the stereoisomerism type (represented by an integer constant)

setCheck3DStereo

public void setCheck3DStereo(boolean c)

Sets the 3D stereo conformation checking of the structure.

Parameters:

c - if true structure is checked for a valid stereo conformation.

setIn3D

public void setIn3D(boolean b)

Sets to display the molecule in 3D.

Parameters:

b - if true structure is displayed in 3D

getResultSource

public chemaxon.marvin.plugin.PluginMDocSource getResultSource()
                                                        throws PluginException

Returns the result as a document source object. This is useful for displaying the molecules in a viewer dynamically as they become available instead of collecting all results before display.

Overrides:

getResultSource in class CalculatorPlugin

Returns:

the document source interface

Throws:

PluginException - on error

Since:

Marvin 5.0

getStereoisomerCount

public int getStereoisomerCount()

Returns the number of different stereoisomers.

Returns:

the number of different stereoisomers

getStereoisomer

public Molecule getStereoisomer(int index)

Returns a stereoisomer.

Parameters:

index - is the index of the stereoisomer

Returns:

a stereoisomer

getStereoisomers

public Molecule[] getStereoisomers()

Returns the stereoisomers in a Molecule[] array.

Returns:

stereoisomers

run

public boolean run()
            throws PluginException

Runs the plugin.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false if unsuccesful

Throws:

PluginException - on error

See Also:

CalculatorPlugin.getErrorMessage()

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types.

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getTypeString

public java.lang.String getTypeString(java.lang.Object type)

Returns a string representation of the given type.

Overrides:

getTypeString in class CalculatorPlugin

Parameters:

type - is the type object

Returns:

the type string

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain.

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the calculation domain

See Also:

getResultTypes()

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key.

Overrides:

getResultCount in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the number of result items

See Also:

getResultTypes()

getResult

public java.lang.Object getResult(java.lang.Object type,
                                  int index)
                           throws PluginException

Returns the result item for the specified key and index.

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

Returns:

the result item for the specified key and index

Throws:

PluginException - if the result cannot be returned

See Also:

CalculatorPlugin.getResultTypes()

getResultAsString

public java.lang.String getResultAsString(java.lang.Object type,
                                          int index,
                                          java.lang.Object result)
                                   throws PluginException

Returns the specified result in String format.

Overrides:

getResultAsString in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

result - is the result item

Returns:

the specified result in String format

Throws:

PluginException - if an invalid result item is given

getWarningMessage

public java.lang.String getWarningMessage()

Returns a warning message if there are no stereoisomers, null otherwise.

Overrides:

getWarningMessage in class CalculatorPlugin

Returns:

a warning message if stereoisomer calculation aborted

standardize

public void standardize(Molecule mol)

Clears enhanced stereo information.

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized