chemaxon.marvin.calculations

Class MSAPlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

chemaxon.marvin.calculations.MSAPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
public class MSAPlugin
extends MajorMicrospeciesAccessorPlugin

Plugin class for molecular surface area calculation. Both the incremental values for atoms and the overal surface area for the molecule can be calculated by this plugin.

Reference:

1. Ferrara, P,. Apostolakis J., Caflisch A., Proteins 2002, 46, 24-33

API usage example:

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

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

    // optional: take major microspecies at pH=7.4
    plugin.setpH(7.4);

    // set surface area type (default: VAN_DER_WAALS)
    plugin.setSurfaceAreaType(SOLVENT);

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

    // get result
    double area = plugin.getSurfaceArea();

    // print result
    System.out.println("Solvent accessible surface area (pH=7.4): "+area);
 

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

Since:

Marvin 4.1

Version:

Marvin 5.0, 12/11/2007

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	SOLVENT Surface area type: 3D solvent accessible surface area.
static int	VAN_DER_WAALS Surface area type: 3D van der Waals surface area.

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
MSAPlugin() Constructor.

Method Summary

Modifier and Type	Method and Description
void	checkMolecule(Molecule mol) Checks the input molecule.
Molecule	get3DMolecule() Returns the 3D molecule used in 3D surface area calculation.
double	getASA() Returns water accessible surface area calculated using a radius of 1.4 A for the water molecule.
double	getASAHydrophobic() Returns water accessible surface area of all hydrophobic (|qi|<0.125) atoms.
double	getASANegative() Returns water accessible surface area of all atoms with negative partial charge (strictly less than 0).
double	getASAPlus() Returns water accessible surface area of all atoms with positive partial charge (strictly greater than 0).
double	getASAPolar() Returns water accessible surface area of all polar (|qi|>=0.125) atoms.
double	getAtomicSurfaceAreaIncrement(int index) Returns the 3D surface area increments.
protected Molecule	getDisplayMolecule() Returns the molecule object to be used for GUI display.
java.lang.String	getErrorMessage() Returns the calculation error information message if run() returned false (calculation error).
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 CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULE in case of increments .
Molecule	getResultMolecule() Returns the result molecule for display.
java.lang.Object[]	getResultTypes() Returns the result types.
double	getSurfaceArea() Returns the surface area, calculation type is previously set in setSurfaceAreaType(int).
java.lang.String	getTypeString(java.lang.Object type) Returns a string representation of the given type.
double	getVDWSA() Returns van der Waals surface area.
boolean	isLicensed() Returns true if the plugin is licensed.
boolean	isMultiThreadedRunEnabled() For internal use only.
boolean	run() Runs the surface area calculation.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	setSolventRadius(double r) Sets solvent radius.
void	setSurfaceAreaType(int saType) Sets surface area calculation type: VAN_DER_WAALS or SOLVENT.

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, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getWarningMessage, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isMsCalc, 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

Field Detail

VAN_DER_WAALS

public static final int VAN_DER_WAALS

Surface area type: 3D van der Waals surface area.

See Also:

Constant Field Values

SOLVENT

public static final int SOLVENT

Surface area type: 3D solvent accessible surface area.

See Also:

Constant Field Values

Constructor Detail

MSAPlugin

public MSAPlugin()

Constructor. Creates the MSA 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.GEOMETRY_PLUGIN_GROUP

setParameters

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

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

• precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)
• type: "vanderwaals", "solvent" (default: "vanderwaals")
• increments: "true" if surface increments should be returned (for 3D surface ("vanderwaals", "solvent") only)
• pH: major microspecies on given pH is taken as input molecule if omitted then the input molecule is taken as it is

Overrides:

setParameters in class MajorMicrospeciesAccessorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

setSurfaceAreaType

public void setSurfaceAreaType(int saType)

Sets surface area calculation type: VAN_DER_WAALS or SOLVENT. The surface area is returned by getSurfaceArea(). The atomic increments and the 3D molecule can also be enquired by getAtomicSurfaceAreaIncrement(int) and get3DMolecule(). Default: VAN_DER_WAALS.

Parameters:

saType - is VAN_DER_WAALS or SOLVENT

checkMolecule

public void checkMolecule(Molecule mol)
                   throws PluginException

Checks the input molecule. Throws exception if the molecule is RxnMolecule, if the molecule contains R-groups or if the molecule consists of more than one fragments.

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 (standardized) input molecule

Throws:

PluginException - on error

run

public boolean run()
            throws PluginException

Runs the surface area calculation.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false on calculation problems

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). This implementation returns the empty string.

Overrides:

getErrorMessage in class MajorMicrospeciesAccessorPlugin

Returns:

the calculation error information message

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types. Possible result types: "vanderwaals", "solvent", "increments".

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULE in case of increments .

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

CalculatorPlugin.MOLECULE

See Also:

getResultTypes()

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key. TPSA returns 1 for surface area, the atom count for increments.

Overrides:

getResultCount in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the number of result items

See Also:

getResultTypes()

setSolventRadius

public void setSolventRadius(double r)

Sets solvent radius. Default: 1.4 Angstrom.

getSurfaceArea

public double getSurfaceArea()

Returns the surface area, calculation type is previously set in setSurfaceAreaType(int). Default: VAN_DER_WAALS.

Returns:

the surface area

getVDWSA

public double getVDWSA()

Returns van der Waals surface area. Calculation type must be set to VAN_DER_WAALS using setSurfaceAreaType(int), and the alculation should be run beforehand by run()

Returns:

van der Waals surface area

Since:

Marvin 5.0

getASA

public double getASA()

Returns water accessible surface area calculated using a radius of 1.4 A for the water molecule. Calculation type must be set to SOLVENT using setSurfaceAreaType(int), and the calculation should be run beforehand by run()

Returns:

water accessible surface area

Since:

Marvin 5.0

getASAPlus

public double getASAPlus()

Returns water accessible surface area of all atoms with positive partial charge (strictly greater than 0). Calculation type must be set to SOLVENT using setSurfaceAreaType(int), and the calculation should be run beforehand by run()

Returns:

water accessible surface area of all atoms with positive partial charge

Since:

Marvin 5.0

getASANegative

public double getASANegative()

Returns water accessible surface area of all atoms with negative partial charge (strictly less than 0). Calculation type must be set to SOLVENT using setSurfaceAreaType(int), and the calculation should be run beforehand by run()

Returns:

water accessible surface area of all atoms with negative partial charge

Since:

Marvin 5.0

getASAHydrophobic

public double getASAHydrophobic()

Returns water accessible surface area of all hydrophobic (|qi|<0.125) atoms. Calculation type must be set to SOLVENT using setSurfaceAreaType(int), and the calculation should be run beforehand by run()

Returns:

water accessible surface area of all hydrophobic atoms

Since:

Marvin 5.0

getASAPolar

public double getASAPolar()

Returns water accessible surface area of all polar (|qi|>=0.125) atoms. Calculation type must be set to SOLVENT using setSurfaceAreaType(int), and the calculation should be run beforehand by run()

Returns:

water accessible surface area of all polar atoms

Since:

Marvin 5.0

getAtomicSurfaceAreaIncrement

public double getAtomicSurfaceAreaIncrement(int index)

Returns the 3D surface area increments. Calculated only if surface area type is set to SOLVENT or VAN_DER_WAALS in setSurfaceAreaType(int).

Parameters:

index - is the atom index

Returns:

the surface area increment for the specified atom index

get3DMolecule

public Molecule get3DMolecule()

Returns the 3D molecule used in 3D surface area calculation. Can be called only if surface area type is set to SOLVENT or VAN_DER_WAALS in setSurfaceAreaType(int).

Returns:

the 3D molecule used in 3D surface area calculation

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.

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

getDisplayMolecule

protected Molecule getDisplayMolecule()

Returns the molecule object to be used for GUI display. This is the 3D molecule returned by get3DMolecule().

Overrides:

getDisplayMolecule in class CalculatorPlugin

Returns:

the molecule object to be used for GUI display

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

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

isMultiThreadedRunEnabled

public boolean isMultiThreadedRunEnabled()

For internal use only.

Overrides:

isMultiThreadedRunEnabled in class CalculatorPlugin

Returns:

true if multi-threaded run is enabled