pKaPlugin (Marvin API documentation (c) 1998-2012 ChemAxon Ltd.)

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chemaxon.marvin.calculations
Class pKaPlugin

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

All Implemented Interfaces:: chemaxon.license.Licensable

public class pKaPlugin
extends CalculatorPlugin
extends CalculatorPlugin

Plugin class for macro/micro pKa calculation.

API usage example:

        // instantiate plugin
        pKaPlugin plugin = new pKaPlugin();

        // set parameters
        plugin.setMaxIons(6);
      plugin.setBasicpKaLowerLimit(-5.0);
      plugin.setAcidicpKaUpperLimit(25.0);
      plugin.setpHLower(3.0); // for ms distr
      plugin.setpHUpper(6.0); // for ms distr
      plugin.setpHStep(1.0);  // for ms distr

        MolImporter importer = new MolImporter("mols.sdf");
        Molecule mol = null;
        while ((mol = importer.read()) != null) {
            // set molecule and run calculation
            plugin.setMolecule(mol);
            plugin.run();
            
            // get the 3 strongest ACIDIC pKa values
            double[] acidicpKa = new double[3];
            int[] acidicIndexes = new int[3];
            plugin.getMacropKaValues(pKaPlugin.ACIDIC, acidicpKa, acidicIndexes);

            // get the 3 strongest BASIC pKa values
            double[] basicpKa = new double[3];
            int[] basicIndexes = new int[3];
            plugin.getMacropKaValues(pKaPlugin.BASIC, basicpKa, basicIndexes);

            // get pKa values for each atom
            int count = mol.getAtomCount();
            for (int i=0; i < count; ++i) {

                // get ACIDIC and BASIC pKa values
                double apka = plugin.getpKa(i, pKaPlugin.ACIDIC);
                double bpka = plugin.getpKa(i, pKaPlugin.BASIC);
          }

          // get microspecies distributions
            double[] pHs = plugin.getpHs(); // pH values
            int mscount = plugin.getMsCount();
            for (int i=0; i < mscount; ++i) {
                Molecule ms = plugin.getMsMolecule(i);
                double[] distr = plugin.getMsDistribution(i); // distr values for pHs
            }
      }
      importer.close();

Another example showing microspecies distributions at a single pH value:

        // instantiate plugin
        pKaPlugin plugin = new pKaPlugin();

        // set pH
        plugin.setpH(3.0);

        MolImporter importer = new MolImporter("mols.sdf");
        Molecule mol = null;
        while ((mol = importer.read()) != null) {
            // set molecule and run calculation
            plugin.setMolecule(mol);
            plugin.run();

          // get microspecies data (molecule and distribution)
            int count = plugin.getMsCount();
            for (int i=0; i < count; ++i) {
                Molecule ms = plugin.getMsMolecule(i);
                double distr = plugin.getSingleMsDistribution(i);
            }
      }
      importer.close();

Another example showing macro pKa calculation:

        // instantiate plugin
        pKaPlugin plugin = new pKaPlugin();

        MolImporter importer = new MolImporter("mols.sdf");
        Molecule mol = null;
        while ((mol = importer.read()) != null) {
            // set molecule and run calculation
            plugin.setMolecule(mol);
            plugin.run();

          // get the acidic and basic macro pKa values
          double[] acidicpKaValues = plugin.getMacropKaValues(pKaPlugin.ACIDIC); 
          double[] basicpKaValues = plugin.getMacropKaValues(pKaPlugin.BASIC); 
      }
      importer.close();

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

Since:: Marvin 3.0
Version:: 5.2 02/03/2009
Author:: Nora Mate, Zsolt Mohacsi

Nested Class Summary

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

Field Summary
`static int`	`ACIDIC` Constant denoting acidic pKa.
`static int`	`BASIC` Constant denoting basic pKa.
`static int`	`DEF_MAXIONS` The default value of the number of ionizable atoms to consider.
`static double`	`DEF_TEMPERATURE` The default temperature in Kelvins.
`static int`	`DYNAMICpKaPREFIX` pKa's prefix (acidic/basic) does depend on the submitted micro state
`static int`	`MODEL_LARGE` Calculation model: large (always precise, can take more time).
`static int`	`MODEL_SMALL` Calculation model: small (precise up to the specified number of ionizable atoms).
`static int`	`STATICpKaPREFIX` pKa's prefix (acidic/basic) does not depend on the submitted micro state (default)
`static java.lang.String`	`TYPE_DISTR` Type constant for microspecies distribution.

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
`pKaPlugin()` Constructor.

Method Summary
`void`	`checkMolecule(Molecule mol)` Checks the input molecule.
`protected Molecule`	`createModifiedInputMolecule(Molecule mol)` Returns the canonical tautomeric form of the molecule.
`static java.lang.String[]`	`getCorrectionLibraryIds()` Returns the id's of available pKa correction libraries.
`java.lang.String`	`getErrorMessage()` Returns the calculation error information message if `run()` returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.
`double[]`	`getMacropKaValues(int pkatype)` Calculates the acidic pKa values in ascending order or the basic pKa values in descending order.
`void`	`getMacropKaValues(int pkatype, double[] values, int[] indexes)` Calculates the least acidic pKa values in ascending order or the biggest basic pKa values in descending order.
`int`	`getMacroSpeciesCharge(int msIndex)` Returns the formal charges of a given macrospecies.
`int`	`getMsCount()` Returns the number of microspecies.
`double[]`	`getMsDistribution(int msIndex)` Returns the microspecies distribution array.
`double[][]`	`getMsDistributions()` Returns the microspecies distribution arrays for all microspecies: the i-th element is the disrtibution array of the i-th microspecies.
`Molecule`	`getMsMolecule(int msIndex)` Returns the microspecies molecule.
`double[]`	`getpHs()` Returns the pH array.
`double`	`getpKa(int index)` Returns the most significant pKa value for the given atom index.
`double`	`getpKa(int index, int type)` Deprecated. Use `getpKaValues(int, int)`
`int`	`getpKaPrefixType()` Returns the pKa prefix type.
`int`	`getpKaType(int index)` Returns the pKa type: `ACIDIC`, `BASIC` or `0` if there is no pKa value for the given atom.
`double[]`	`getpKaValues(int index, int type)` Returns the pKa values for the given atom index and pKa type.
`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.Object`	`getResult(java.lang.Object type, java.lang.String arg)` Returns the result item for the specified type ("acidic" or "basic") and the specified strength index ("1" means the strongest value, "2" means the second strongest value, etc.) given in the argument string.
`int`	`getResultAsRGB(java.lang.Object type, int index, java.lang.Object result)` Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue): RED for acidic pKa, BLUE for basic pKa.
`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 result with possible subresults (both pKa values instead of the most significant pKa) in String format.
`java.lang.Object[]`	`getResultTypes()` Returns the result types (possible types: pKa, acidic, basic, msdistr).
`double`	`getSingleMsDistribution(int msIndex)` Returns the microspecies distribution at the specified pH value set in `setpH(double)`.
`void`	`getSortedValues(int pkatype, double[] values, int[] indexes)` Deprecated. Use `getMacropKaValues(int,double[],int[])` instead
`java.lang.String`	`getWarningMessage()` Returns the calculation warning information message.
`protected boolean`	`isMsCalc()` Returns `true` if microspecies calculation.
`protected boolean`	`isNegligible(double[] distr)`
`boolean`	`isNegligibleResult(java.lang.Object type, int index, java.lang.Object result)` Returns whether the result can be ignored.
`boolean`	`isOverflowCalculation()` Returns `true` if overflow calculation: maximum number of ionizable atoms exceeded and protein ionization invoked.
`boolean`	`run()` Runs the macro pKa calculation.
`void`	`setAcidicpKaUpperLimit(double maxA)` Sets the maximum acidic pKa (default: `20`).
`void`	`setBasicpKaLowerLimit(double minB)` Sets the minimum basic pKa (default: `-10`).
`void`	`setCalcAlways(boolean calcAlways)` Deprecated. replaced by `setModel(int)`
`void`	`setConsiderTautomerization(boolean considerTautomerization)` Sets to consider tautomerization.
`void`	`setCorrectionLibrary(java.lang.String correctionLibraryId)` Sets the correction library.
`protected void`	`setInputMolecule(Molecule mol)` Sets the input molecule.
`void`	`setKeepExplicitHydrogens(boolean keepExplicitHydrogens)` Sets if result molecule keeps explicit hydrogens or not
`void`	`setMaxIons(int n)` In case of `MODEL_SMALL` model, it sets the maximum number of ionizable atoms to be considered and uses simple calculation method to compute pKa values.
`void`	`setMicropKaCalc(boolean micro)` Sets micro pKa calculation.
`void`	`setModel(int model)` Sets the calculation model.
`void`	`setMsCalc(boolean mscalc)` Sets calculation of microspecies distributions.
`void`	`setParameters(java.util.Properties params)` Sets the input parameters for the plugin.
`void`	`setpH(double pH)` Sets the pH value for the calculation of microspecies distributions.
`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.
`void`	`setpKaPrefixType(int pKaPtype)` Sets pKa prefix type (default: `STATICpKaPREFIX`) STATIC pKa prefix: pKa's prefix does not depend on the submitted micro state DYNAMIC pKa prefix: pKa's prefix does depend on the submitted micro state
`void`	`setProgressMonitor(chemaxon.common.util.MProgressMonitor pmon)` Sets a progress observer to be used in `run()` to display progress status.
`void`	`setTakeMajorTatomericForm(boolean takeMajorTautomericForm)` Deprecated. Use `setConsiderTautomerization(boolean)`
`void`	`setTemperature(double temperature)` Sets the temperature (default: `298` Kelvin).
`void`	`standardize(Molecule mol)` Standardizes the molecule.
`void`	`useCorrectionLibrary(boolean use)` Deprecated. Use `setCorrectionLibrary(String)`

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, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsString, getResultSource, getTypeString, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isLicensed, isMultiThreadedRunEnabled, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, standardizeIonicGroups, standardizeNeutralGroups

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, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsString, getResultSource, getTypeString, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isLicensed, isMultiThreadedRunEnabled, 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

ACIDIC

public static final int ACIDIC

Constant denoting acidic pKa.

See Also:: Constant Field Values

BASIC

public static final int BASIC

Constant denoting basic pKa.

See Also:: Constant Field Values

TYPE_DISTR

public static final java.lang.String TYPE_DISTR

Type constant for microspecies distribution.

See Also:: Constant Field Values

STATICpKaPREFIX

public static final int STATICpKaPREFIX

pKa's prefix (acidic/basic) does not depend on the submitted micro state (default)

See Also:: Constant Field Values

DYNAMICpKaPREFIX

public static final int DYNAMICpKaPREFIX

pKa's prefix (acidic/basic) does depend on the submitted micro state

See Also:: Constant Field Values

DEF_MAXIONS

public static final int DEF_MAXIONS

The default value of the number of ionizable atoms to consider.

See Also:: Constant Field Values

DEF_TEMPERATURE

public static final double DEF_TEMPERATURE

The default temperature in Kelvins.

See Also:: Constant Field Values

MODEL_SMALL

public static final int MODEL_SMALL

Calculation model: small (precise up to the specified number of ionizable atoms).

See Also:: Constant Field Values

MODEL_LARGE

public static final int MODEL_LARGE

Calculation model: large (always precise, can take more time).

See Also:: Constant Field Values

Constructor Detail

pKaPlugin

public pKaPlugin()

Constructor. Creates the macro pKa calculator object.

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.PROTONATION_PLUGIN_GROUP

setProgressMonitor

public void setProgressMonitor(chemaxon.common.util.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 monitor, may be null

setParameters

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

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

type: pKa,acidic,basic (pKa is either the basic or the acidic pKa)
precision: 0-8 or inf (default: 2) (number of displayed fractional digits, inf for unrounded value)
mode: macro or micro (default: macro)
prefix: static or dynamic acid/base prefix (default: static)
min: minimal basic pKa
max: maximal acidic pKa
temperature: temperature (in Kelvin, default: 298)
ions: maximum number of ionizable atoms (default: 8)
calcAlways: true if calculation to be performed even if the maximum number of ionizable atoms is exceeded (deprecated, see 'model' below)
model: "small" or "large" (replaces 'calcAlways')
- small: precise up to the number of ionizable atoms given in 'ions' (8 by default), equivalent to calcAlways=false (cxcalc and API default)
- large: always precise but can take more time, equivalent to calcAlways=true (GUI default)

If mode is "macro" then we have additional parameters for microspecies distribution:

mscalc: true if microspecies distribution to be shown, false otherwise (default: false)
lower: pH lower limit (default: 0.0)
upper: pH upper limit (default: 14.0)
step: pH step to be taken between lower and upper limits (default: 0.2)
majortautomer: true or false (take major tautomeric form)

Overrides:: setParameters in class CalculatorPlugin

Parameters:: params - is the parameter table
Throws:: PluginException - on error

useCorrectionLibrary

public void useCorrectionLibrary(boolean use)

Deprecated. Use setCorrectionLibrary(String)

Sets the usage of the correction library. (default: false)

Parameters:: use - if true, then the calculation will use the correction library
Since:: Marvin 5.2

setCorrectionLibrary

public void setCorrectionLibrary(java.lang.String correctionLibraryId)

Sets the correction library.

Parameters:: correctionLibraryId - is the correction library identifier
Since:: Marvin 5.4

getCorrectionLibraryIds

public static java.lang.String[] getCorrectionLibraryIds()

Returns the id's of available pKa correction libraries.

Returns:: the id's of available pKa correction libraries
Since:: Marvin 5.4

setMicropKaCalc

public void setMicropKaCalc(boolean micro)

Sets micro pKa calculation. Default: false (macro pKa calculation).

Parameters:: micro - is true if micro pKa calculation is required.
Since:: Marvin 4.1

setCalcAlways

public void setCalcAlways(boolean calcAlways)

Deprecated. replaced by setModel(int)

Sets whether to perform calculation if the maximum number of ionizable atoms is exceeded. If set to true, pK_a values are calculated with a different, more time-consuming method in this case. Note, that microspecies are not determined in this case. Default: false.

Parameters:: calcAlways - is true if calculation should be performed if the maximum number of ionizable atoms is exceeded
See Also:: setMaxIons(int), setModel(int)

setModel

public void setModel(int model)

Sets the calculation model.

Parameters:

model - is the calculation model:

MODEL_SMALL: optimized for a small number of ionizable atoms (default)
MODEL_LARGE: optimized for a large number of ionizable atoms

Since:

Marvin 4.0

See Also:

setMaxIons(int)

setMaxIons

public void setMaxIons(int n)

In case of MODEL_SMALL model, it sets the maximum number of ionizable atoms to be considered and uses simple calculation method to compute pKa values. In case of MODEL_LARGE model, it switches the simple calculation method to a more complicated one when the number of ionizable atoms exceeds this limit. The default value is 8.

Parameters:: n - is the maximum number of ionizable atoms to be considered
See Also:: setModel(int)

setBasicpKaLowerLimit

public void setBasicpKaLowerLimit(double minB)

Sets the minimum basic pKa (default: -10).

Parameters:: minB - is the minimum basic pKa

setAcidicpKaUpperLimit

public void setAcidicpKaUpperLimit(double maxA)

Sets the maximum acidic pKa (default: 20).

Parameters:: maxA - is the maximum acidic pKa

setTemperature

public void setTemperature(double temperature)

Sets the temperature (default: 298 Kelvin).

Parameters:: temperature - is the temperature (Kelvin)
Since:: Marvin 3.5.1

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

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

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 1.0.

Parameters:: step - is the pH step

setpH

public void setpH(double pH)

Sets the pH value for the calculation of microspecies distributions. This method activates the calculation of microspecies distributions at a single pH value.

Parameters:: pH - is the pH value

setMsCalc

public void setMsCalc(boolean mscalc)

Sets calculation of microspecies distributions. By default, microsepcies distributions are computed in the [0.0, 14.0] pH interval with pH step size 1.0.

Parameters:: mscalc - is true if calculation of microspecies distributions is required
See Also:: setpHLower(double lower), setpHUpper(double upper), setpHStep(double step), setpH(double pH)

isMsCalc

protected boolean isMsCalc()

Returns true if microspecies calculation.

Overrides:: isMsCalc in class CalculatorPlugin

Returns:: true if microspecies calculation

setpKaPrefixType

public void setpKaPrefixType(int pKaPtype)

Sets pKa prefix type (default: STATICpKaPREFIX)

STATIC pKa prefix: pKa's prefix does not depend on the submitted micro state
DYNAMIC pKa prefix: pKa's prefix does depend on the submitted micro state

Parameters:: pKaPtype - may have two values: STATICpKaPREFIX or DYNAMICpKaPREFIX
Since:: Marvin 4.1.3

getpKaPrefixType

public int getpKaPrefixType()

Returns the pKa prefix type.

STATICpKaPREFIX: pKa's prefix does not depend on the submitted micro state
DYNAMICpKaPREFIX: pKa's prefix does depend on the submitted micro state

Returns:: the pKa prefix type
Since:: Marvin 4.1.3

setConsiderTautomerization

public void setConsiderTautomerization(boolean considerTautomerization)

Sets to consider tautomerization. Default: false.

Parameters:: considerTautomerization - the calculation will consider tautomerization and resonance if set (true)
Since:: Marvin 5.4

setTakeMajorTatomericForm

public void setTakeMajorTatomericForm(boolean takeMajorTautomericForm)

Deprecated. Use setConsiderTautomerization(boolean)

Sets to use major tautomeric form in calculation. Default: false.

Parameters:: takeMajorTautomericForm - the calculation will be performed on the major tutomeric form of the input molecule if set (true)
Since:: Marvin 5.0

createModifiedInputMolecule

protected final Molecule createModifiedInputMolecule(Molecule mol)
                                              throws PluginException

Returns the canonical tautomeric form of the molecule.

Overrides:: createModifiedInputMolecule in class CalculatorPlugin

Parameters:: mol - is the input molecule
Returns:: the canonical tautomeric form of the molecule
Throws:: PluginException - on error
Since:: Marvin 5.0

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 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 macro pKa calculation.

Specified by:: run in class CalculatorPlugin

Returns:: true if the calculation was successful, false if the number of ionizable atoms exceeds the specified limit
Throws:: PluginException - on error
See Also:: CalculatorPlugin.getErrorMessage()

getMsCount

public int getMsCount()

Returns the number of microspecies. Calculated only if macro pKa is computed and the "mscalc" parameter is set to "true".

Returns:: the number of microspecies

getMsMolecule

public Molecule getMsMolecule(int msIndex)

Returns the microspecies molecule. Calculated only if macro pKa is computed and the "mscalc" parameter is set to "true".

Parameters:: msIndex - is the microspecies index
Returns:: the microspecies molecule

getSingleMsDistribution

public double getSingleMsDistribution(int msIndex)

Returns the microspecies distribution at the specified pH value set in setpH(double).

Parameters:: msIndex - is the microspecies index
Returns:: the microspecies distribution at the previously given pH

getpHs

public double[] getpHs()

Returns the pH array.

Returns:: the pH array

getMsDistribution

public double[] getMsDistribution(int msIndex)

Returns the microspecies distribution array.

Parameters:: msIndex - is the microspecies index
Returns:: the microspecies distribution array

getMsDistributions

public double[][] getMsDistributions()

Returns the microspecies distribution arrays for all microspecies: the i-th element is the disrtibution array of the i-th microspecies.

Returns:: the microspecies distribution arrays

getpKa

public double getpKa(int index)

Returns the most significant pKa value for the given atom index. Use this to get the pKa if STATICpKaPREFIX prefix type is set. The pKa calculation has to be run beforehand by calling run().

Parameters:: index - is the atom index
Returns:: the pKa value, or Double.NaN if there is no pKa value for the given atom index and pKa type
Since:: Marvin 3.6
See Also:: setpKaPrefixType(int), getpKaValues(int, int)

getpKa

public double getpKa(int index,
                     int type)

Deprecated. Use getpKaValues(int, int)

Returns the pKa value for the given atom index and pKa type. The pKa calculation has to be run beforehand by calling run().

Parameters:: index - is the atom index; type - is the pka type: ACIDIC or BASIC
Returns:: the pKa value, or Double.NaN if there is no pKa value for the given atom index and pKa type
See Also:: setpKaPrefixType(int), getpKaValues(int, int)

getpKaValues

public double[] getpKaValues(int index,
                             int type)

Returns the pKa values for the given atom index and pKa type. The pKa calculation has to be run beforehand by calling run().

Parameters:: index - is the atom index; type - is the pka type: ACIDIC or BASIC
Returns:: the pKa values, or null if there is no pKa value for the given atom index and pKa type
Since:: Marvin 4.1.3
See Also:: setpKaPrefixType(int)

getpKaType

public int getpKaType(int index)

Returns the pKa type: ACIDIC, BASIC or 0 if there is no pKa value for the given atom.

Parameters:: index - is the atom index
Returns:: the pKa type: ACIDIC, BASIC or 0.
Since:: Marvin 3.6

getMacroSpeciesCharge

public int getMacroSpeciesCharge(int msIndex)

Returns the formal charges of a given macrospecies. Valid only in case of overflow calculation.

Parameters:: msIndex - is the macrospecies index
Returns:: the formal charges of a given macrospecies
See Also:: isOverflowCalculation()

isOverflowCalculation

public boolean isOverflowCalculation()

Returns true if overflow calculation: maximum number of ionizable atoms exceeded and protein ionization invoked.

Returns:: true if overflow calculation

getErrorMessage

public java.lang.String getErrorMessage()

Returns the calculation error information message if run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.

Overrides:: getErrorMessage in class CalculatorPlugin

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

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types (possible types: pKa, acidic, basic, msdistr).

Overrides:: getResultTypes in class CalculatorPlugin

Returns:: the result types

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE. pKa always returns CalculatorPlugin.ATOM.

Overrides:: getResultDomain in class CalculatorPlugin

Parameters:: type - is the result type
Returns:: CalculatorPlugin.ATOM
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. If the type is "msdistr" then returns the pH - distribution table as a double[][] with the 0-th element the pH array and the 1-st element the distribution array corresponding to the microspecies with the specified index (result index). Otherwise pKa returns the required pKa value as a Double object for the given atom index (result index). Returns Double.NaN if the atom with the given index does not have a valid macro pKa value for the specified result type.

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()

getResult

public java.lang.Object getResult(java.lang.Object type,
                                  java.lang.String arg)
                           throws PluginException

Returns the result item for the specified type ("acidic" or "basic") and the specified strength index ("1" means the strongest value, "2" means the second strongest value, etc.) given in the argument string. Returns Double.NaN for non-existent values (e.g. when the type is "acidic" and the arg string is "2" but there is only one acidic pKa value for the input molecule).

Overrides:: getResult in class CalculatorPlugin

Parameters:: type - is the result type ("acidic" or "basic"); arg - is the strength order index
Returns:: the result item for the specified type and strength index
Throws:: PluginException - if the result cannot be returned
See Also:: CalculatorPlugin.getResultTypes()

getSortedValues

public void getSortedValues(int pkatype,
                            double[] values,
                            int[] indexes)
                     throws PluginException

Deprecated. Use getMacropKaValues(int,double[],int[]) instead

Calculates the least acidic pKa values in ascending order or the biggest basic pKa values in descending order. The pKa calculation has to be run beforehand by calling run(). The length of the result value array determines the number of pKa values to be computed. If the index array is non-null then it is assumed to have the same length as the value array and will be filled with the corresponding atom indices (0-based).

Parameters:: pkatype - is the pKa type (ACIDIC or BASIC); values - is the pKa value array to be filled with pKa values in descending strength order (increasing for acidic pKa, descending for basic pKa values), the last entries are set to Double.NaN if there are less pKa values than the array length; indexes - is the corresponding atom index array to be filled (may be null), the index is set to -1 for non-existent values (Double.NaN)
Throws:: PluginException - if an error occurs during the calculation

getMacropKaValues

public void getMacropKaValues(int pkatype,
                              double[] values,
                              int[] indexes)
                       throws PluginException

Parameters:: pkatype - is the pKa type (ACIDIC or BASIC); values - is the pKa value array to be filled with pKa values in descending strength order (increasing for acidic pKa, descending for basic pKa values), the last entries are set to Double.NaN if there are less pKa values than the array length; indexes - is the corresponding atom index array to be filled (may be null), the index is set to -1 for non-existent values (Double.NaN)
Throws:: PluginException - if an error occurs during the calculation
Since:: Marvin 5.0.7

getMacropKaValues

public double[] getMacropKaValues(int pkatype)
                           throws PluginException

Calculates the acidic pKa values in ascending order or the basic pKa values in descending order. The pKa calculation has to be run beforehand by calling run().

Parameters:: pkatype - is the pKa type (ACIDIC or BASIC)
Returns:: the pKa value array with pKa values in descending strength order (increasing for acidic pKa, descending for basic pKa values) or null if there are no ionizable atoms in the molecule
Throws:: PluginException - if an error occurs during the calculation
Since:: Marvin 5.0.7

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. If the type is "msdistr" then returns the pH - distribution table as a 2-column tab-separated table with the 0-th element the pH array and the 1-st element the distribution array corresponding to the microspecies with the specified index (result index). Otherwise pKa returns the rounded pKa 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 result with possible subresults (both pKa values instead of the most significant pKa) 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

getResultAsRGB

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

Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue): RED for acidic pKa, BLUE for basic pKa.

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 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). (e.g. both pKa colors instead of the most significant pKa color) as long (lower and upper bits).

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

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 distributions below CalculatorPlugin.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 distributions below CalculatorPlugin.EPSILON
Throws:: PluginException

isNegligible

protected boolean isNegligible(double[] distr)

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

standardize

public void standardize(Molecule mol)

Standardizes the molecule. This is done by performing the transformations necessary to run the plugin (e.g. aromatize, dehydrogenize, bring nitro groups to common form). Apart from the default standardization (aromatize and nitro) removes explicit hydrogens and stores the index-map between atom indices in the original and the new molecule. This map is used when the macropKa values and types are queried and the new atom indices should be mapped to the original ones. TODO: replace by call to chemaxon.reaction.Standardizer

Overrides:: standardize in class CalculatorPlugin

Parameters:: mol - is the molecule to be standardized

setKeepExplicitHydrogens

public void setKeepExplicitHydrogens(boolean keepExplicitHydrogens)

Sets if result molecule keeps explicit hydrogens or not

Parameters:: keepExplicitHydrogens - if the result should keep explicit hydrogens or not

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chemaxon.marvin.calculations Class pKaPlugin

ACIDIC

BASIC

TYPE_DISTR

STATICpKaPREFIX

DYNAMICpKaPREFIX

DEF_MAXIONS

DEF_TEMPERATURE

MODEL_SMALL

MODEL_LARGE

pKaPlugin

getProductName

setProgressMonitor

setParameters

useCorrectionLibrary

setCorrectionLibrary

getCorrectionLibraryIds

setMicropKaCalc

setCalcAlways

setModel

setMaxIons

setBasicpKaLowerLimit

setAcidicpKaUpperLimit

setTemperature

setpHLower

setpHUpper

setpHStep

setpH

setMsCalc

isMsCalc

setpKaPrefixType

getpKaPrefixType

setConsiderTautomerization

setTakeMajorTatomericForm

createModifiedInputMolecule

checkMolecule

setInputMolecule

run

getMsCount

getMsMolecule

getSingleMsDistribution

getpHs

getMsDistribution

getMsDistributions

getpKa

getpKa

getpKaValues

getpKaType

getMacroSpeciesCharge

isOverflowCalculation

getErrorMessage

getWarningMessage

getResultTypes

getResultDomain

getResultCount

getResult

getResult

getSortedValues

getMacropKaValues

getMacropKaValues

getResultAsString

getResultsAsString

getResultAsRGB

getResultsAsRGB

isNegligibleResult

isNegligible

getResultMolecule

standardize

setKeepExplicitHydrogens

chemaxon.marvin.calculations
Class pKaPlugin