Package chemaxon.marvin.calculations

Class ElementalAnalyserPlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.ElementalAnalyserPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
public class ElementalAnalyserPlugin
extends CalculatorPlugin

Calculates molecular formula, mass, MS mass and composition.

API usage example:

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

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

    // set plugin parameters
    Properties params = new Properties();
    params.put("precision", "3");
    plugin.setParameters(params);

    // set target molecule
    plugin.setMolecule(mol);

    // run the calculation
    plugin.run();

    // get results
    double exactMass = plugin.getExactMass();
    double mass = plugin.getMass();
    int atomCount1 = plugin.getAtomCount(8); // oxygen atom count
    int atomCount2 = plugin.getAtomCount(8, 0); // non-isotope oxygen count
    int atomCount3 = plugin.getAtomCount(8, 16); // oxygen isotope count with massno=16
    String formula = plugin.getFormula();
    String isotopeFormula = plugin.getIsotopeFormula();
    String composition = plugin.getComposition();
    String isotopeComposition = plugin.getIsotopeComposition();
    // do something with the results ...
 

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

Since:

1.0, 11/03/2002

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ElementalAnalyserPlugin.ResultType	Represents the different result types of the elemental analyser plugin.

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

CalculatorPlugin.HydrogenData

Field Summary

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	Description
ElementalAnalyserPlugin()

Method Summary

Modifier and Type	Method	Description
void	checkMolecule(Molecule mol)	Checks the input molecule.
int	getAllAtomCount()	Returns the atom count (including implicit hydrogens).
int	getAtomCount(int z)	Returns the number of atoms with given atomic number (including its isotopes).
int	getAtomCount(int z, int m)	Returns the number of atoms with given atomic number in the molecule isotope with the specified mass number.
String	getComposition()	Calculates the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
String	getDotDisconnectedFormalChargeFormula()	Calculates the dot-disconnected molecular formula of a multifragment molecule with its formal charge.
String	getDotDisconnectedFormula()	Calculates the dot-disconnected molecular formula of a multifragment molecule.
String	getDotDisconnectedIsotopeFormalChargeFormula()	Calculates the dot-disconnected isotope formula of a multifragment molecule with its formal charge.
String	getDotDisconnectedIsotopeFormalChargeFormula(boolean symbolD)	Calculates the dot-disconnected isotope formula of a multifragment molecule with its formal charge.
String	getDotDisconnectedIsotopeFormula()	Calculates the dot-disconnected isotope formula of a multifragment molecule.
String	getDotDisconnectedIsotopeFormula(boolean symbolD)	Calculates the dot-disconnected isotope formula of a multifragment molecule.
String	getErrorMessage()	Returns the calculation error information message if CalculatorPlugin.run() returned false (calculation error).
double	getExactMass()	Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
String	getFormalChargeFormula()	Calculates the molecular formula with formal charge.
String	getFormalChargeFormula(int digits)	Calculates a fixed digit sortable molecular formula with formal charge.
String	getFormula()	Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule.
String	getFormula(int digits)	Calculates a fixed digit sortable molecular formula.
String	getGroupedDotDisconnectedFormula()	Calculates the grouped dot-disconnected molecular formula of a multifragment molecule.
String	getIsotopeComposition()	Returns the molecular composition (w/w%).
String	getIsotopeComposition(boolean symbolD)	Returns the molecular composition (w/w%).
List<chemaxon.common.util.Pair<BigDecimal,BigDecimal>>	getIsotopeDistribution()	Calculates the isotopic distributions for the molecule.
String	getIsotopeFormalChargeFormula()	Calculates the molecular formula (isotopes are separated).
String	getIsotopeFormalChargeFormula(boolean symbolD)	Calculates the molecular formula with formal charge (isotopes are separated).
String	getIsotopeFormula()	Calculates the molecular formula (isotopes are separated).
String	getIsotopeFormula(boolean symbolD)	Calculates the molecular formula (isotopes are separated).
double	getMass()	Calculates the molecular weight of the molecule.
int	getNominalMass()	Mass of the molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element.
String	getProductName()	Returns the product identifier of the plugin as given by LicenseManager.
Object	getResult(Object type, int index)	Returns the result item for the specified key and index.
Object	getResult(Object type, String arg)	Returns the atom count of a specific atom.
String	getResultAsString(Object type, int index, Object result)	Returns the specified result in String format.
int	getResultCount(Object type)	Returns the number of result items for the given result key.
int	getResultDomain(Object type)	Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
Molecule	getResultMolecule()	Returns the result molecule for display.
List<ElementalAnalyserPlugin.ResultType>	getResultTypeList()	Returns the result types.
Object[]	getResultTypes()	Returns the string IDs of the result types.
String	getTypeString(Object type)	Returns a string representation of the given type.
boolean	handlesMultiFragmentMolecules()	Returns true if the plugin handles multifragment molecules, false otherwise.
boolean	run()	Runs the tool.
void	setFormulaRecognition(boolean recognize)	Recognizes the molecular formulas in pseudo labels.
protected void	setInputMolecule(Molecule mol)	Sets the input molecule.
void	setMolecule(String formula)	Specifies a molecule to calculate with.
void	setParameters(Properties params)	Sets the input parameters for the plugin.
void	standardize(Molecule mol)	Prevents default standardization: does nothing.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

addHeavyAtomLimitChecker, addInputChecker, arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getWarningMessage, isInputMoleculeAromatized, isLicensed, 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 Details

ElementalAnalyserPlugin

public ElementalAnalyserPlugin()

Method Details

setMolecule

public void setMolecule(String formula)
                 throws IllegalArgumentException

Specifies a molecule to calculate with.

Parameters:

formula - the molecular formula to calculate with

Throws:

IllegalArgumentException - if the formula is invalid

Since:

Marvin 5.3.2

getProductName

public String getProductName()

Description copied from class: CalculatorPlugin

Returns the product identifier of the plugin as given by LicenseManager. The name is used by the CalculatorPlugin.isLicensed() method.

Specified by:

getProductName in class CalculatorPlugin

Returns:

product identifier or a default string

setParameters

public void setParameters(Properties params)
                   throws PluginException

Sets the input parameters for the plugin. Parameters:

• single: "true" if single fragment mode (calculation is performed separately for each fragment) (default: "false")
• type: result types, separated by ',' (for possible values, see the string IDs of the constants in the ElementalAnalyserPlugin.ResultType enum) (default: "mass,exactmass,formula,composition")

(default: "mass,exactmass,formula,composition")