chemaxon.marvin.calculations

Class ConformerPlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.ConformerPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
public class ConformerPlugin
extends CalculatorPlugin

Plugin class for conformer calculation. Data types:

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

API usage example:

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

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

    // set target molecule
    plugin.setMolecule(mol);
    
    // set parameters for calculation
    plugin.setMaxNumberOfConformers(400);
    plugin.setTimelimit(900);

    // run the calculation
    plugin.run();

    // get results
    Molecule[] conformers = plugin.getConformers();
    int conformerCount = plugin.getConformerCount();
    Molecule m;
    for (int i = 0; i < conformerCount; ++i) {
        m = conformers[i];   // same as m = plugin.getConformer(i);
        // do something with molecule ...
    }

    // do something with the results ...
 

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

Since:

Marvin 4.1, 02/07/2006

Version:

5.3.3, 03/23/2010

Author:

Zsolt Mohacsi

Nested Class Summary

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

CalculatorPlugin.HydrogenData

Field Summary

Fields

Modifier and Type	Field and Description
static int	OPTIMIZATION_NORMAL
static int	OPTIMIZATION_STRICT
static int	OPTIMIZATION_VERY_LOOSE
static int	OPTIMIZATION_VERY_STRICT

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

Constructors

Constructor and Description
ConformerPlugin() Constructor.

Method Summary

Modifier and Type	Method and Description
void	checkMolecule(Molecule mol) Checks the input molecule.
Molecule	getConformer(int index) Returns a conformer.
int	getConformerCount() Returns the number of different conformers.
Molecule[]	getConformers() Returns all conformers in a Molecule[] array.
double	getEnergy() Returns the energy of the lowest energy conformer in kcal/mol.
double	getEnergy(int i) Returns the energy of the i-th conformer in kcal/mol.
Molecule	getLowestEnergyConformer() Returns the calculated lowest energy conformer.
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.
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 conformers, null otherwise.
boolean	handlesMultiFragmentMolecules() Returns true if the plugin handles multifragment molecules, false otherwise.
boolean	hasValidConformer() Returns true if the input molecule has a valid conformer (has a valid structure in 3D space).
boolean	run() Runs the conformer calculation.
void	setDiversity(double limit) Sets the diversity limit for the calculation.
void	setHyperfine(boolean hyp) Sets the hyperfine option for calculation.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setLowestEnergyConformerCalculation(boolean le) Switchs the lowest energy conformer calculation on/off.
void	setMaxNumberOfConformers(int n) Sets the maximum number of conformers to be calculated.
void	setMMFF94(boolean mmff) Sets the forcefield to MMFF94.
void	setOptimization(int optimization) Sets the optimization criteria for the calculation.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	setPrehydrogenize(boolean preH) Turns the prehydrogenization on/off.
void	setProgressMonitor(MProgressMonitor pmon) Sets a progress observer to be used in run() to display progress status.
void	setTimelimit(int sec) Sets the timelimit for the calculation.
void	standardize(Molecule mol) Expands sgroups.

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, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, 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, setAtomIndexMap, 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

OPTIMIZATION_VERY_LOOSE

public static final int OPTIMIZATION_VERY_LOOSE

See Also:

Constant Field Values

OPTIMIZATION_NORMAL

public static final int OPTIMIZATION_NORMAL

See Also:

Constant Field Values

OPTIMIZATION_STRICT

public static final int OPTIMIZATION_STRICT

See Also:

Constant Field Values

OPTIMIZATION_VERY_STRICT

public static final int OPTIMIZATION_VERY_STRICT

See Also:

Constant Field Values

Constructor Detail

ConformerPlugin

public ConformerPlugin()

Constructor.

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.CONFORMATION_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(MProgressMonitor pmon)

Sets a progress observer 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, hasvalidconformer
• optimization: optimization criteria for the calculation (default: 1 (=Normal))
• maxconformers: maximum naumber of conformers to be calculated (default: 100)
• timelimit: timelimit in sec for the calculation (default: 900)
• prehydrogenize: true if prehydrogenize is needed before calculation (default: false)

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

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

run

public boolean run()
            throws PluginException

Runs the conformer calculation.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false if unsuccessful

Throws:

PluginException - on error

See Also:

CalculatorPlugin.getErrorMessage()

setMMFF94

public void setMMFF94(boolean mmff)

Sets the forcefield to MMFF94.

Parameters:

mmff - if true, sets MMFF94

setLowestEnergyConformerCalculation

public void setLowestEnergyConformerCalculation(boolean le)

Switchs the lowest energy conformer calculation on/off. If true lowest energy conformer calculation is done, if false conformers of the molecule are calculated.

Parameters:

le - switchs the lowest energy conformer calculation on/off

setMaxNumberOfConformers

public void setMaxNumberOfConformers(int n)

Sets the maximum number of conformers to be calculated. The number of calculated conformers is equal or lower then this number, and can be readed with method getConformerCount().

Parameters:

n - is the max number of conformers to be calculated

See Also:

getConformerCount()

setTimelimit

public void setTimelimit(int sec)

Sets the timelimit for the calculation.

Parameters:

sec - is the timelimit for the calculation

setDiversity

public void setDiversity(double limit)

Sets the diversity limit for the calculation. Diversity limit should be at least 0.1 (no upper limit).

Parameters:

limit - is the diversity limit for the calculation

Since:

Marvin 4.1.3

setOptimization

public void setOptimization(int optimization)
                     throws PluginException

Sets the optimization criteria for the calculation. Possible optimization values are:

• OPTIMIZATION_VERY_LOOSE
• OPTIMIZATION_NORMAL
• OPTIMIZATION_STRICT
• OPTIMIZATION_VERY_STRICT

Parameters:

optimization - is the optimization method for the calculation

Throws:

PluginException

setPrehydrogenize

public void setPrehydrogenize(boolean preH)

Turns the prehydrogenization on/off. If true prehydrogenization is done before calculation, if false no prehydrogenization is done before calculation.

Parameters:

preH - turns the prehydrogenization on/off

setHyperfine

public void setHyperfine(boolean hyp)

Sets the hyperfine option for calculation.

Parameters:

hyp - sets/unsets the hyperfine option for calculation

hasValidConformer

public boolean hasValidConformer()
                          throws PluginException

Returns true if the input molecule has a valid conformer (has a valid structure in 3D space). Otherwise returns false.

Returns:

true if the input molecule has a valid conformer

Throws:

PluginException

getLowestEnergyConformer

public Molecule getLowestEnergyConformer()

Returns the calculated lowest energy conformer.

Returns:

the lowest energy conformer

getEnergy

public double getEnergy()

Returns the energy of the lowest energy conformer in kcal/mol.

Returns:

the energy of the lowest energy conformer

Since:

Marvin 4.1.4 12/04/2006

See Also:

setLowestEnergyConformerCalculation(boolean)

getEnergy

public double getEnergy(int i)

Returns the energy of the i-th conformer in kcal/mol.

Returns:

the energy of the i-th conformer

Since:

Marvin 4.1.4 12/04/2006

See Also:

getConformerCount()

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

getConformerCount

public int getConformerCount()

Returns the number of different conformers.

Returns:

the number of different conformers

getConformer

public Molecule getConformer(int index)

Returns a conformer.

Parameters:

index - is the conformer index

Returns:

the conformer

getConformers

public Molecule[] getConformers()

Returns all conformers in a Molecule[] array.

Returns:

all conformers

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 conformers, null otherwise.

Overrides:

getWarningMessage in class CalculatorPlugin

Returns:

a warning message if conformercalculation aborted

standardize

public void standardize(Molecule mol)

Expands sgroups.

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized