chemaxon.marvin.calculations

Class HuckelAnalysisPlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

chemaxon.marvin.calculations.HuckelAnalysisPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
public class HuckelAnalysisPlugin
extends MajorMicrospeciesAccessorPlugin

Plugin class for Huckel Analysis calculation.

API usage example:

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

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

    // set plugin parameters
    Properties params = new Properties();
    params.put("type", "hmoorder,hmolocalizationEnergy,hmopiEnergy,hmoelectronDensity,hmochargeDensity");
    plugin.setParameters(params);

    // optional: take major microspecies at pH=7.4
    // skip this if you want to calculate Huckel analysis for the input molecule as it is
    plugin.setpH(7.4);

    // set target molecule
    plugin.setMolecule(mol);
        
    // run the calculation
    plugin.run();

    // get results
    double piEnergy = plugin.getTotalPiEnergy();
    System.out.println("pi energy: "+piEnergy);
    System.out.println();

    // get and print atomic results in a table
    System.out.println("atom\torder E(+)\torder Nu(-)\tenergy E(+)\tenergy Nu(-)\telectron dens.\tcharge dens.");
    int count = mol.getAtomCount();
    for (int i=0; i < count; ++i) {
          int orderE = plugin.getHMOElectrophilicOrder(i);
          int orderN = plugin.getHMONucleophilicOrder(i);           
          double energyE = plugin.getHMOElectrophilicEnergy(i);
          double energyN = plugin.getHMONucleophilicEnergy(i);
          double electronDensity = plugin.getHMOElectronDensity(i);
          double chargeDensity = plugin.getHMOChargeDensity(i);
            
          String str = ""+(i+1);
          str += "\t";
          str += (orderE != -1) ? ""+orderE : "-";
          str += "\t";
          str += (orderN != -1) ? ""+orderN : "-";
          str += "\t";
          str += !Double.isNaN(energyE) ? plugin.format(energyE) : "-";
          str += "\t";
          str += !Double.isNaN(energyN) ? plugin.format(energyN) : "-";
          str += "\t";
          str += !Double.isNaN(electronDensity) ? plugin.format(electronDensity) : "-";
          str += "\t";
          str += !Double.isNaN(chargeDensity) ? plugin.format(chargeDensity) : "-";
          System.out.println(str);
    }
 

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

Since:

Marvin 3.4

Version:

Marvin 5.3, 11/12/2009

Author:

Nora Mate, Zsolt Mohacsi

Nested Class Summary

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

CalculatorPlugin.HydrogenData

Field Summary

Fields inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

ionizer

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
HuckelAnalysisPlugin() Constructor.

Method Summary

Modifier and Type	Method and Description
double	getChargeDensity(int atom) Returns the total charge density of an atom calculated with HMO, Double.NaN for no value.
double[][]	getEigenVector() Deprecated. Use getHMOEigenVector()
double	getElectronDensity(int atom) Returns the electron density of an atom calculated with HMO, Double.NaN for no value.
double	getElectrophilicEnergy(int atom) Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value.
int	getElectrophilicOrder(int atom) Deprecated. Use getHMOElectrophilicOrder(int)
java.lang.String	getErrorMessage() Returns the calculation error information message if run() returned false (calculation error): hydrogen valence error.
double	getHMOChargeDensity(int atom) Returns the total charge density of an atom calculated with HMO, Double.NaN for no value.
double[][]	getHMOEigenVector() Returns the eigenvector.
double	getHMOElectronDensity(int atom) Returns the electron density of an atom calculated with HMO, Double.NaN for no value.
double	getHMOElectrophilicEnergy(int atom) Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value.
int	getHMOElectrophilicOrder(int atom) Returns the electrophilic order of an atom, -1 for no value.
double[][]	getHMOHuckelOrbitalCoefficients() Returns the huckel orbital coefficients.
double	getHMONucleophilicEnergy(int atom) Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value.
int	getHMONucleophilicOrder(int atom) Returns the nucleophilic order of an atom, -1 for no value.
double[]	getHMORealEigenValue() Returns the real part of the eigenvalue.
double	getHMOTotalPiEnergy() Returns the total pi energy of the input molecule.
double[][]	getHuckelOrbitalCoefficients() Deprecated. Use getHMOHuckelOrbitalCoefficients()
double	getNucleophilicEnergy(int atom) Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value.
int	getNucleophilicOrder(int atom) Deprecated. Use getHMONucleophilicOrder(int)
java.lang.String	getProductName() Returns the product identifier of the plugin as given by LicenseManager.
double[]	getRealEigenValue() Deprecated. Use getHMORealEigenValue()
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 CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
Molecule	getResultMolecule() Returns the result molecule for display.
long	getResultsAsRGB(java.lang.Object type, int index, java.lang.Object result) Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
java.lang.String	getResultsAsString(java.lang.Object type, int index, java.lang.Object result) Returns the specified results in String format.
java.lang.Object[]	getResultTypes() Returns the result types.
double	getTotalPiEnergy() Deprecated. Use getHMOTotalPiEnergy()
java.lang.String	getTypeString(java.lang.Object type) Returns a string representation of the given type.
java.lang.String	getWarningMessage() Returns the calculation warning information message.
boolean	isLicensed() Returns true if the plugin is licensed.
boolean	run() Runs the Huckel analysis calculation.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.

Methods inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

checkMolecule, createModifiedInputMolecule, getIonizerErrorMessage, getpH, setpH, standardize

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

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

Methods inherited from class java.lang.Object

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

Constructor Detail

HuckelAnalysisPlugin

public HuckelAnalysisPlugin()

Constructor. Creates the Huckel analysis calculator object.

Method Detail

isLicensed

public boolean isLicensed()

Returns true if the plugin is licensed. The license checking is based on the product name, returned by getProductName().

Specified by:

isLicensed in interface chemaxon.license.Licensable

Overrides:

isLicensed in class MajorMicrospeciesAccessorPlugin

Returns:

true if the plugin is licensed

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.HUCKEL_ANALYSIS_PLUGIN

setParameters

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

Sets the input parameters for the plugin. Huckel analysis and value ranges:

• type:
  • hmoorder: Aromatic E(+)/Nu(-) order
  • hmoorder:e: Aromatic E(+) order
  • hmoorder:n: Aromatic Nu(-) order
  • hmolocalizationEnergy: Localization energy L(+)/L(-)
  • hmolocalizationEnergy:e: Localization energy L(+)
  • hmolocalizationEnergy:n: Localization energy L(-)
  • hmopiEnergy: Pi energy
  • hmoeigenValue: eigenvalue
  • hmoeigenVector: eigenvector
  • hmoorbitals: huckel orbital coefficients
  • hmoelectronDensity: electron density
  • hmochargeDensity: charge density
  • order: Aromatic E(+)/Nu(-) order
  • order:e: Aromatic E(+) order
  • order:n: Aromatic Nu(-) order
  • localizationEnergy: Localization energy L(+)/L(-)
  • localizationEnergy:e: Localization energy L(+)
  • localizationEnergy:n: Localization energy L(-)
  • piEnergy: Pi energy
  • eigenValue: eigenvalue
  • eigenVector: eigenvector
  • orbitals: huckel orbital coefficients
  • electronDensity: electron density
  • chargeDensity: charge density
• precision: 0-8 or inf (default: 2) (number of displayed fractional digits, inf for unrounded value)

Types starting with "hmo" are calculated using standard HMO parameters.

Overrides:

setParameters in class MajorMicrospeciesAccessorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

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 Huckel analysis calculation.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false on calculation error

Throws:

PluginException - on error

See Also:

CalculatorPlugin.getErrorMessage()

getErrorMessage

public java.lang.String getErrorMessage()

Returns the calculation error information message if run() returned false (calculation error): hydrogen valence error.

Overrides:

getErrorMessage in class MajorMicrospeciesAccessorPlugin

Returns:

the calculation error information message

getWarningMessage

public java.lang.String getWarningMessage()

Returns the calculation warning information message.

Overrides:

getWarningMessage in class CalculatorPlugin

Returns:

the calculation warning information message

getElectrophilicOrder

@Deprecated
public int getElectrophilicOrder(int atom)

Deprecated. Use getHMOElectrophilicOrder(int)

Returns the electrophilic order of an atom, -1 for no value.

Parameters:

atom - is the atom index

Returns:

the electrophilic order of an atom

getHMOElectrophilicOrder

public int getHMOElectrophilicOrder(int atom)

Returns the electrophilic order of an atom, -1 for no value. Standard HMO parameters are used in calculation.

Parameters:

atom - is the atom index

Returns:

the electrophilic order of an atom

Since:

Marvin 5.3

getNucleophilicOrder

@Deprecated
public int getNucleophilicOrder(int atom)

Deprecated. Use getHMONucleophilicOrder(int)

Returns the nucleophilic order of an atom, -1 for no value.

Parameters:

atom - is the atom index

Returns:

the nucleophilic order of an atom

getHMONucleophilicOrder

public int getHMONucleophilicOrder(int atom)

Returns the nucleophilic order of an atom, -1 for no value. Standard HMO parameters are used in calculation.

Parameters:

atom - is the atom index

Returns:

the nucleophilic order of an atom

Since:

Marvin 5.3

getElectrophilicEnergy

public double getElectrophilicEnergy(int atom)

Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value.

Parameters:

atom - is the atom index

Returns:

the electrophilic energy of an atom

getHMOElectrophilicEnergy

public double getHMOElectrophilicEnergy(int atom)

Returns the electrophilic energy (localization energy L+) of an atom, Double.NaN for no value. Standard HMO parameters are used in calculation.

Parameters:

atom - is the atom index

Returns:

the electrophilic energy of an atom

Since:

Marvin 5.3

getNucleophilicEnergy

public double getNucleophilicEnergy(int atom)

Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value.

Parameters:

atom - is the atom index

Returns:

the nucleophilic energy of an atom

getHMONucleophilicEnergy

public double getHMONucleophilicEnergy(int atom)

Returns the nucleophilic energy (localization energy L-) of an atom, Double.NaN for no value. Standard HMO parameters are used in calculation.

Parameters:

atom - is the atom index

Returns:

the nucleophilic energy of an atom

Since:

Marvin 5.3

getTotalPiEnergy

@Deprecated
public double getTotalPiEnergy()

Deprecated. Use getHMOTotalPiEnergy()

Returns the total pi energy of the input molecule.

Returns:

the total pi energy of the input molecule

getHMOTotalPiEnergy

public double getHMOTotalPiEnergy()

Returns the total pi energy of the input molecule. Standard HMO parameters are used in calculation.

Returns:

the total pi energy of the input molecule

Since:

Marvin 5.3

getRealEigenValue

@Deprecated
public double[] getRealEigenValue()

Deprecated. Use getHMORealEigenValue()

Returns the real part of the eigenvalue.

Returns:

the real part of the eigenvalue

Since:

Marvin 5.1

getHMORealEigenValue

public double[] getHMORealEigenValue()

Returns the real part of the eigenvalue. Standard HMO parameters are used in calculation.

Returns:

the real part of the eigenvalue

Since:

Marvin 5.3

getEigenVector

@Deprecated
public double[][] getEigenVector()

Deprecated. Use getHMOEigenVector()

Returns the eigenvector.

Returns:

the eigenvector

Since:

Marvin 5.1

getHMOEigenVector

public double[][] getHMOEigenVector()

Returns the eigenvector. Standard HMO parameters are used in calculation.

Returns:

the eigenvector

Since:

Marvin 5.3

getHuckelOrbitalCoefficients

@Deprecated
public double[][] getHuckelOrbitalCoefficients()

Deprecated. Use getHMOHuckelOrbitalCoefficients()

Returns the huckel orbital coefficients.

Returns:

the huckel orbital coefficients

Since:

Marvin 5.1.3

getHMOHuckelOrbitalCoefficients

public double[][] getHMOHuckelOrbitalCoefficients()

Returns the huckel orbital coefficients. Standard HMO parameters are used in calculation.

Returns:

the huckel orbital coefficients

Since:

Marvin 5.3

getElectronDensity

public double getElectronDensity(int atom)

Returns the electron density of an atom calculated with HMO, Double.NaN for no value.

Parameters:

atom - is the atom index

Returns:

the electron density of an atom

Since:

Marvin 5.1

getHMOElectronDensity

public double getHMOElectronDensity(int atom)

Returns the electron density of an atom calculated with HMO, Double.NaN for no value. Standard HMO parameters are used in calculation.

Parameters:

atom - is the atom index

Returns:

the electron density of an atom

Since:

Marvin 5.3

getChargeDensity

public double getChargeDensity(int atom)

Returns the total charge density of an atom calculated with HMO, Double.NaN for no value.

Parameters:

atom - is the atom index

Returns:

the total charge density of an atom

Since:

Marvin 5.1

getHMOChargeDensity

public double getHMOChargeDensity(int atom)

Returns the total charge density of an atom calculated with HMO, Double.NaN for no value. Standard HMO parameters are used in calculation.

Parameters:

atom - is the atom index

Returns:

the total charge density of an atom

Since:

Marvin 5.3

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 CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

CalculatorPlugin.ATOM for all types except for "pienergy"

See Also:

getResultTypes()

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key. pKa returns the atom count.

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:

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. This is the rounded charge value in string format: the value is rounded using the 'precision' input parameter that determines the number of fractional digits displayed. If the result is Double.NaN then returns the empty string.

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

getResultsAsString

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

Returns the specified results in String format.

Overrides:

getResultsAsString 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

getResultsAsRGB

public long getResultsAsRGB(java.lang.Object type,
                            int index,
                            java.lang.Object result)
                     throws PluginException

Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).

Overrides:

getResultsAsRGB in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

result - is the result item

Returns:

the specified result in color as int

Throws:

PluginException - if an invalid result item is given

getResultMolecule

public Molecule getResultMolecule()
                           throws PluginException

Returns the result molecule for display. Atomic results are stored in atom extra labels (MolAtom.getExtraLabel()). Molecular results are stored in molecule properties with keys being the result types (Molecule.getProperty(String)).

Overrides:

getResultMolecule in class CalculatorPlugin

Returns:

the result molecule

Throws:

PluginException - on error

Since:

Marvin 4.0