HBDAPlugin (Marvin API documentation (c) 1998-2019 ChemAxon Ltd.)

java.lang.Object
- chemaxon.marvin.plugin.CalculatorPlugin
- - chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
  - - chemaxon.marvin.calculations.HBDAPlugin

All Implemented Interfaces:: chemaxon.license.Licensable

@PublicAPI
public class HBDAPlugin
extends MajorMicrospeciesAccessorPlugin

Plugin class for H bond acceptor/donor calculation.

API usage example:

 // create plugin
 HBDAPlugin plugin = new HBDAPlugin();
 
 // set plugin parameters
 plugin.setDoublePrecision(2);
 plugin.setpHLower(2.0);
 plugin.setpHUpper(12.0);
 plugin.setpHStep(2.0);
 
 // optional: take major microspecies at pH=7.4
 // skip this if you want to calculate HBDA for the input molecule as it is
 plugin.setpH(7.4);
 
 // read target molecule
 MolImporter mi = new MolImporter("target.mol");
 Molecule mol = mi.read();
 mi.close();
 
 // set target molecule
 plugin.setMolecule(mol);
 
 // run the calculation
 plugin.run();
 
 // get results
 
 // average acceptor/donor counts by microspecies distributions at given pH-s
 double[] pHs = plugin.getpHs();
 double[] msacc = plugin.getMsAcceptorCounts();
 double[] msdon = plugin.getMsDonorCounts();
 
 System.out.println("pH\tmsacc\tmsdon");
 for (int i = 0; i < pHs.length; ++i) {
     System.out.println("" + plugin.format(pHs[i]) + "\t" + plugin.format(msacc[i]) + "\t"
            + plugin.format(msdon[i]));
 }
 
 // molecular data
 // with multiplicity
 int molecularAcceptorCount = plugin.getAcceptorCount();
 int molecularDonorCount = plugin.getDonorCount();
 // without multiplicity
 int molecularAcceptorAtomCount = plugin.getAcceptorAtomCount();
 int molecularDonorAtomCount = plugin.getDonorAtomCount();
 System.out.println();
 System.out.println("Acceptor count with multiplicity: " + molecularAcceptorCount);
 System.out.println("Donor count with multiplicity: " + molecularDonorCount);
 System.out.println("Acceptor count without multiplicity: " + molecularAcceptorAtomCount);
 System.out.println("Donor count without multiplicity: " + molecularDonorAtomCount);
 
 // atomic data
 System.out.println();
 System.out.println("Atom\tAcceptor count\tDonor count");
 int count = mol.getAtomCount();
 for (int i = 0; i < count; ++i) {
 
     // atomic acceptor/donor count with multiplicity
     int atomicAcceptorCount = plugin.getAcceptorCount(i);
     int atomicDonorCount = plugin.getDonorCount(i);
 
     if (atomicAcceptorCount != -1) { // -1 means H atom
        System.out.println("" + (i + 1) + "\t" + atomicAcceptorCount + "\t" + atomicDonorCount);
     }
 }

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

Version:: 5.3.2 03/16/2010
Author:: Nora Mate, 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 java.lang.String`	`ACCEPTOR_SIGN` Acceptor sign displayed in GUI.
`static java.lang.String`	`DONOR_SIGN` Donor sign displayed in GUI.
`static double`	`EPSILON`

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, 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

HBDAPlugin()
Constructor.

Constructors
Constructor and Description
`HBDAPlugin()` Constructor.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`checkMolecule(Molecule mol)` Checks the input molecule.
`int`	`getAcceptorAtomCount()` Returns the overall acceptor atom count (without multiplicity) in the molecule.
`int`	`getAcceptorCount()` Deprecated. Use `getAcceptorSiteCount()` instead.
`int`	`getAcceptorCount(int index)` Deprecated. Use `getAcceptorSiteCount()` instead!
`int`	`getAcceptorSiteCount()` Returns the overall acceptor count (with multiplicity) in the molecule.
`int`	`getAcceptorSiteCount(int index)` Returns the atomic acceptor count corresponding to the specified atom index.
`int`	`getDonorAtomCount()` Returns the overall donor atom count (without multiplicity) in the molecule.
`int`	`getDonorCount()` Deprecated. Use `getDonorSiteCount()` instead!
`int`	`getDonorCount(int index)` Deprecated. Use `getDonorSiteCount(int)` instead!
`int`	`getDonorSiteCount()` Returns the overall donor count (with multiplicity) in the molecule.
`int`	`getDonorSiteCount(int index)` Returns the atomic donor count corresponding to the specified atom index.
`java.lang.String`	`getErrorMessage()` Returns the calculation error information message if `run()` returned false (calculation error): hydrogen valence error.
`double[]`	`getMsAcceptorCounts()` Returns the average acceptor counts over the microspecies distribution for different pH-s.
`double[]`	`getMsDonorCounts()` Returns the average donor counts over the microspecies distribution for different pH-s.
`double[]`	`getpHs()` Returns the pH array.
`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 type and index.
`int`	`getResultAsRGB(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`	`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 type.
`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 result in GUI-specific String format: `A` for acceptor, `D` for donor.
`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 the calculation warning information message if no H-bond donor/acceptor atoms found, returns the empty string otherwise.
`boolean`	`isLicensed()` Returns `true` if the plugin is licensed.
`protected boolean`	`isMsCalc()` Returns `true` if microspecies calculation.
`boolean`	`isNegligibleResult(java.lang.Object type, int index, java.lang.Object result)` Returns whether the result can be ignored.
`boolean`	`run()` Runs the charge calculation.
`void`	`setExcludeHalogens(boolean e)` Sets if halogens should be excluded from hydrogen bond acceptors.
`void`	`setExcludeSulfur(boolean e)` Sets if sulfur atom should be excluded from hydrogen bond acceptors.
`protected void`	`setGUIMode(boolean guimode)` Deprecated.
`protected void`	`setInputMolecule(Molecule mol)` Sets the input molecule.
`void`	`setMsCalc(boolean mscalc)` Sets microspecies calculation.
`void`	`setParameters(java.util.Properties params)` Sets the input parameters for the plugin.
`void`	`setpHLower(double lower)` Sets pH lower limit for the calculation of microspecies distributions.
`void`	`setpHStep(double step)` Sets pH step for the calculation of microspecies distributions.
`void`	`setpHUpper(double upper)` Sets pH upper limit for the calculation of microspecies distributions.

Methods inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
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, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsString, getResultSource, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isMultiThreadedRunEnabled, 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

- Field Detail
  - EPSILON
```
public static final double EPSILON
```
    See Also:
    
    Constant Field Values
  - ACCEPTOR_SIGN
```
public static final java.lang.String ACCEPTOR_SIGN
```
    Acceptor sign displayed in GUI.
    
    See Also:
    
    Constant Field Values
  - DONOR_SIGN
```
public static final java.lang.String DONOR_SIGN
```
    Donor sign displayed in GUI.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - HBDAPlugin
```
public HBDAPlugin()
```
    Constructor. Creates the 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.HBDA_PLUGIN
  - setParameters
```
public void setParameters(java.util.Properties params)
                   throws PluginException
```
    Sets the input parameters for the plugin. Charge parameters and value ranges:
    - type:
      
      acc: atomic acceptors
      don: atomic donors
      accsitecount: molecular acceptor count with multiplicity
      donsitecount: molecular donor count with multiplicity
      acceptorcount: molecular acceptor atom count without multiplicity
      donorcount: molecular donor atom count without multiplicity
      msacc: average acceptor count over microspecies by pH
      msdon: average donor count over microspecies by pH
      excludesulfur: exclude sulfur atoms from acceptors
    - precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)
    - lower: pH lower limit (default: 0.0)
    - upper: pH upper limit (default: 14.0)
    - count: pH step count between lower and upper limits (default: 0.5)
    Overrides:
    
    setParameters in class MajorMicrospeciesAccessorPlugin
    
    Parameters:
    
    params - is the parameter table
    
    Throws:
    
    PluginException - on error
  - setpHLower
```
public void setpHLower(double lower)
```
    Sets pH lower limit for the calculation of microspecies distributions. Also activates the calculation of microspecies distributions. The default value is 0.0.
    
    Parameters:
    
    lower - is the pH lower limit
    
    Since:
    
    Marvin 3.5.1
  - setpHUpper
```
public void setpHUpper(double upper)
```
    Sets pH upper limit for the calculation of microspecies distributions. Also activates the calculation of microspecies distributions. The default value is 14.0.
    
    Parameters:
    
    upper - is the pH upper limit
    
    Since:
    
    Marvin 3.5.1
  - setpHStep
```
public void setpHStep(double step)
```
    Sets pH step for the calculation of microspecies distributions. Also activates the calculation of microspecies distributions. The default value is 0.5.
    
    Parameters:
    
    step - is the pH step
    
    Since:
    
    Marvin 3.5.1
  - setMsCalc
```
public void setMsCalc(boolean mscalc)
```
    Sets microspecies calculation.
    
    Parameters:
    
    mscalc - is true if microspecies calculation required
    
    Since:
    
    Marvin 3.5.1
    
    See Also:
    
    setpHLower(double lower), setpHUpper(double upper), setpHStep(double step), MajorMicrospeciesAccessorPlugin.setpH(double pH)
  - isMsCalc
```
protected boolean isMsCalc()
```
    Returns true if microspecies calculation.
    
    Overrides:
    
    isMsCalc in class CalculatorPlugin
    
    Returns:
    
    true if microspecies calculation
  - checkMolecule
```
public void checkMolecule(Molecule mol)
                   throws PluginException
```
    Checks the input molecule. Throws exception if the molecule molecule contains R-groups.
    
    Overrides:
    
    checkMolecule in class MajorMicrospeciesAccessorPlugin
    
    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
  - setExcludeSulfur
```
public void setExcludeSulfur(boolean e)
```
    Sets if sulfur atom should be excluded from hydrogen bond acceptors. Default: true
    
    Parameters:
    
    e - if true then sulfur atom is not considered to be hydrogen bond acceptor.
    
    Since:
    
    Marvin 5.3
  - setExcludeHalogens
```
public void setExcludeHalogens(boolean e)
```
    Sets if halogens should be excluded from hydrogen bond acceptors. Default: true
    
    Parameters:
    
    e - if true then halogens are not considered to be hydrogen bond acceptor.
    
    Since:
    
    Marvin 5.3.2
  - run
```
public boolean run()
            throws PluginException
```
    Runs the charge 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 if no H-bond donor/acceptor atoms found, returns the empty string otherwise.
    
    Overrides:
    
    getWarningMessage in class CalculatorPlugin
    
    Returns:
    
    the calculation warning information message
  - getpHs
```
public double[] getpHs()
```
    Returns the pH array.
    
    Returns:
    
    the pH array
  - getMsAcceptorCounts
```
public double[] getMsAcceptorCounts()
```
    Returns the average acceptor counts over the microspecies distribution for different pH-s. The pH array is returned by getpHs() and determined by the "lower", "upper" and "step" plugin parameters.
    
    Returns:
    
    the average acceptor counts over the microspecies distribution for pH-s returned by getpHs()
  - getMsDonorCounts
```
public double[] getMsDonorCounts()
```
    Returns the average donor counts over the microspecies distribution for different pH-s. The pH array is returned by getpHs() and determined by the "lower", "upper" and "step" plugin parameters.
    
    Returns:
    
    the average donor counts over the microspecies distribution for pH-s returned by getpHs()
  - getAcceptorCount
```
@Deprecated
public int getAcceptorCount(int index)
```
    Deprecated. Use getAcceptorSiteCount() instead!
  - getAcceptorSiteCount
```
public int getAcceptorSiteCount(int index)
```
    Returns the atomic acceptor count corresponding to the specified atom index.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    the atomic acceptor count, -1 for H atoms
  - getDonorCount
```
@Deprecated
public int getDonorCount(int index)
```
    Deprecated. Use getDonorSiteCount(int) instead!
  - getDonorSiteCount
```
public int getDonorSiteCount(int index)
```
    Returns the atomic donor count corresponding to the specified atom index.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    the atomic donor count, -1 for H atoms
  - getAcceptorCount
```
@Deprecated
public int getAcceptorCount()
```
    Deprecated. Use getAcceptorSiteCount() instead.
  - getAcceptorSiteCount
```
public int getAcceptorSiteCount()
```
    Returns the overall acceptor count (with multiplicity) in the molecule.
    
    Returns:
    
    the overall acceptor count (with multiplicity) in the molecule
  - getDonorCount
```
@Deprecated
public int getDonorCount()
```
    Deprecated. Use getDonorSiteCount() instead!
  - getDonorSiteCount
```
public int getDonorSiteCount()
```
    Returns the overall donor count (with multiplicity) in the molecule.
    
    Returns:
    
    the overall donor count (with multiplicity) in the molecule
  - getAcceptorAtomCount
```
public int getAcceptorAtomCount()
```
    Returns the overall acceptor atom count (without multiplicity) in the molecule.
    
    Returns:
    
    the overall acceptor atom count (without multiplicity) in the molecule
  - getDonorAtomCount
```
public int getDonorAtomCount()
```
    Returns the overall donor atom count (without multiplicity) in the molecule.
    
    Returns:
    
    the overall donor atom count (without multiplicity) in the molecule
  - getResultTypes
```
public java.lang.Object[] getResultTypes()
```
    Returns the result types. The possible types are described in setParameters(Properties params).
    
    Overrides:
    
    getResultTypes in class CalculatorPlugin
    
    Returns:
    
    the result types
  - setGUIMode
```
@Deprecated
protected void setGUIMode(boolean guimode)
```
    Deprecated.
    
    Sets GUI mode.
    
    Parameters:
    
    guimode - is true if GUI mode
  - getResultDomain
```
public int getResultDomain(java.lang.Object type)
```
    Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE. HBDA returns CalculatorPlugin.ATOM for types "acc" and "don", CalculatorPlugin.MOLECULE for types "accsitecount", "donsitecount", "acceptorcount", "donorcount", and returns CalculatorPlugin.MOLECULE for type "msacc" and "msdon".
    
    Overrides:
    
    getResultDomain in class CalculatorPlugin
    
    Parameters:
    
    type - is the result type
    
    Returns:
    
    the domain as described above
    
    See Also:
    
    getResultTypes()
  - getResultCount
```
public int getResultCount(java.lang.Object type)
```
    Returns the number of result items for the given result type. Returns the atom count for types "acc" and "don", 1 otherwise.
    
    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 type and index. HBDA returns the (pH, acceptor/donor count) arrays for types "msacceptor" and "msdonor" as a double[2][] with the 0-th element being the pH array and the 1-st element being the acceptor/donor count array. For types "acc" and "don" HBDA returns the acceptor/donor count corresponding to the specified atom index. For types "accsitecount" and "donsitecount" HBDA returns the sum of the atomic values. cc * @see #getResultTypes()
    
    Overrides:
    
    getResult in class CalculatorPlugin
    
    Parameters:
    
    type - is the result type ("acc", "don", "msacc", "msdon", "accsitecount", "donsitecount", "acceptorcount", "donorcount")
    
    index - is the atom index for types "acc", "don", N/A for "msacc", "msdon", "accsitecount", "donsitecount", "acceptorcount", "donorcount"
    
    Returns:
    
    the result item for the specified type 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
  - getResultAsRGB
```
public int getResultAsRGB(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). Returns "red" for acceptor "blue" for donor.
    
    Overrides:
    
    getResultAsRGB 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
  - 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). Returns "red" for acceptor "blue" for donor.
    
    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
  - getResultsAsString
```
public java.lang.String getResultsAsString(java.lang.Object type,
                                           int index,
                                           java.lang.Object result)
                                    throws PluginException
```
    Returns the specified result in GUI-specific String format: A for acceptor, D for donor.
    
    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
  - 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
  - isNegligibleResult
```
public boolean isNegligibleResult(java.lang.Object type,
                                  int index,
                                  java.lang.Object result)
                           throws PluginException
```
    Returns whether the result can be ignored. Returns true for microspecies acceptor/donor count below EPSILON. Returns false for all other results.
    
    Overrides:
    
    isNegligibleResult in class CalculatorPlugin
    
    Parameters:
    
    type - is the result type
    
    index - is the result index
    
    result - is the result object
    
    Returns:
    
    true for microspecies acceptor/donor count below EPSILON
    
    Throws:
    
    PluginException
  - 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

Class HBDAPlugin

Nested Class Summary

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

Field Summary

Fields inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Constructor Summary

Method Summary

Methods inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Methods inherited from class java.lang.Object

Field Detail

EPSILON

ACCEPTOR_SIGN

DONOR_SIGN

Constructor Detail

HBDAPlugin

Method Detail

isLicensed

getProductName

setParameters

setpHLower

setpHUpper

setpHStep

setMsCalc

isMsCalc

checkMolecule

setInputMolecule

setExcludeSulfur

setExcludeHalogens

run

getErrorMessage

getWarningMessage

getpHs

getMsAcceptorCounts

getMsDonorCounts

getAcceptorCount

getAcceptorSiteCount

getDonorCount

getDonorSiteCount

getAcceptorCount

getAcceptorSiteCount

getDonorCount

getDonorSiteCount

getAcceptorAtomCount

getDonorAtomCount

getResultTypes

setGUIMode

getResultDomain

getResultCount

getResult

getResultAsString

getResultAsRGB

getResultsAsRGB

getResultsAsString

getTypeString

isNegligibleResult

getResultMolecule