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 (as an alternative, you can also use the ElementalAnalysisCalc class directly):

    // 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

Version:

Marvin 5.11, 08/27/2012

Author:

Gyorgy Pirok, Zsolt Mohacsi

Nested Class Summary

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

CalculatorPlugin.HydrogenData

Field Summary

Fields inherited from class chemaxon.marvin.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
ElementalAnalyserPlugin()

Method Summary

Modifier and Type	Method and 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.
java.lang.String	getComposition() Calculates the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
java.lang.String	getDotDisconnectedFormula() Calculates the dot-disconnected molecular formula of a multifragment molecule.
java.lang.String	getDotDisconnectedIsotopeFormula() Calculates the dot-disconnected isotope formula of a multifragment molecule.
java.lang.String	getDotDisconnectedIsotopeFormula(boolean symbolD) Calculates the dot-disconnected isotope formula of a multifragment molecule.
java.lang.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.
java.lang.String	getFormula() Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule.
java.lang.String	getFormula(int digits) Calculates a fixed digit sortable molecular formula.
java.lang.String	getGroupedDotDisconnectedFormula() Calculates the grouped dot-disconnected molecular formula of a multifragment molecule.
java.lang.String	getIsotopeComposition() Returns the molecular composition (w/w%).
java.lang.String	getIsotopeComposition(boolean symbolD) Returns the molecular composition (w/w%).
java.util.List<chemaxon.common.util.Pair<java.math.BigDecimal,java.math.BigDecimal>>	getIsotopeDistribution() Calculates the isotopic distributions for the molecule.
java.lang.String	getIsotopeFormula() Calculates the molecular formula (isotopes are separated).
java.lang.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.
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 atom count of a specific atom.
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.
java.lang.Object[]	getResultTypes() Returns the result types.
java.lang.String	getTypeString(java.lang.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(java.lang.String formula) Specifies a molecule to calculate with.
void	setParameters(java.util.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

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 Detail

ElementalAnalyserPlugin

public ElementalAnalyserPlugin()

Method Detail

setMolecule

public void setMolecule(java.lang.String formula)
                 throws java.lang.IllegalArgumentException

Specifies a molecule to calculate with.

Parameters:

formula - the molecular formula to calculate with

Throws:

java.lang.IllegalArgumentException - if the formula is invalid

Since:

Marvin 5.3.2

getProductName

public java.lang.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(java.util.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 ',', possible values:
  • "mass"
  • "exactmass"
  • "formula"
  • "isotopeformula"
  • "dotdisconnectedformula"
  • "dotdisconnectedisotopeformula"
  • "composition"
  • "isotopecomposition"
  • "atomcount"
  (default: all of these)

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

setFormulaRecognition

public void setFormulaRecognition(boolean recognize)

Recognizes the molecular formulas in pseudo labels.

Parameters:

recognize - true to set recognition

handlesMultiFragmentMolecules

public boolean handlesMultiFragmentMolecules()

Returns true if the plugin handles multifragment molecules, false otherwise. In the latter case the plugin takes the fragment with more atoms if a multifragment molecule is given as input. Returns true if parameter "single" is set to "false", false otherwise (default: false).

Overrides:

handlesMultiFragmentMolecules in class CalculatorPlugin

Returns:

true if the plugin handles multifragment molecules, false otherwise

checkMolecule

public void checkMolecule(Molecule mol)
                   throws PluginException

Checks the input molecule. Throws exception if the molecule is RxnMolecule or if the 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

getMass

public double getMass()

Calculates the molecular weight of the molecule.

Returns:

the molecular weigth of the molecule

Since:

Marvin 3.4.1

getExactMass

public double getExactMass()

Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.

Returns:

the weight of the molecule ion

Since:

Marvin 3.4.1

getNominalMass

public 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.

Returns:

the nominal mass of the molecule

Since:

Marvin 21.14

getFormula

public java.lang.String getFormula()

Calculates the molecular formula which is a string listing all atom types an their occurence in the molecule. For example the formula of benzene is C6H6.

Returns:

the molecular formula

Since:

Marvin 3.4.1

getFormula

public java.lang.String getFormula(int digits)

Calculates a fixed digit sortable molecular formula. If the digits parameter is 4, then the formula of benzene will be "C0006H0006".

Parameters:

digits - number of minimum digits

Returns:

molecular formula

Since:

Marvin 6.0

getIsotopeFormula

public java.lang.String getIsotopeFormula()

Calculates the molecular formula (isotopes are separated). For example, it returns C7D5NaO2 for the deuterated sodium benzoate.

Returns:

isotope formula

Since:

Marvin 3.4.1

getIsotopeFormula

public java.lang.String getIsotopeFormula(boolean symbolD)

Calculates the molecular formula (isotopes are separated). For example, it returns C7[2H]5NaO2 or C7D5NaO2 for the deuterated sodium benzoate depending on symbolD parameter.

Parameters:

symbolD - uses the D symbol for Deuterium and T for Tritium if true, otherwise [2H] and [3H]

Returns:

isotope formula

Since:

Marvin 5.0

getDotDisconnectedFormula

public java.lang.String getDotDisconnectedFormula()

Calculates the dot-disconnected molecular formula of a multifragment molecule. For example, it returns C7H5O2.Na for sodium benzoate.

Returns:

the dot diconnected formula of the molecule

Since:

Marvin 3.4.1

getGroupedDotDisconnectedFormula

public java.lang.String getGroupedDotDisconnectedFormula()

Calculates the grouped dot-disconnected molecular formula of a multifragment molecule.

Returns:

the grouped dot diconnected formula of the molecule

Since:

Marvin 14.8.14

getDotDisconnectedIsotopeFormula

public java.lang.String getDotDisconnectedIsotopeFormula()

Calculates the dot-disconnected isotope formula of a multifragment molecule. For example, it returns C7D5O2.Na for the deuterated sodium benzoate.

Returns:

the dot diconnected isotope formula of the molecule

Since:

Marvin 5.0

getDotDisconnectedIsotopeFormula

public java.lang.String getDotDisconnectedIsotopeFormula(boolean symbolD)

Calculates the dot-disconnected isotope formula of a multifragment molecule. For example, it returns C7[2H]5O2.Na or C7D5O2.Na for the deuterated sodium benzoate depending on symbolD parameter.

Parameters:

symbolD - uses the D symbol for Deuterium and T for Tritium if true, otherwise [2H] and [3H]

Returns:

the dot diconnected isotope formula of the molecule

Since:

Marvin 5.0

getComposition

public java.lang.String getComposition()

Calculates the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).

Returns:

the molecular composition

Since:

Marvin 3.4.1

getIsotopeComposition

public java.lang.String getIsotopeComposition()

Returns the molecular composition (w/w%). Isotopes are separate atom types.

Returns:

the molecular composition

Since:

Marvin 3.4.1

getIsotopeComposition

public java.lang.String getIsotopeComposition(boolean symbolD)

Returns the molecular composition (w/w%). Isotopes are separate atom types.

Parameters:

symbolD - uses the D symbol for Deuterium and T for Tritium if true, otherwise [2H] and [3H]

Returns:

the molecular composition

Since:

Marvin 5.0.3

getIsotopeDistribution

public java.util.List<chemaxon.common.util.Pair<java.math.BigDecimal,java.math.BigDecimal>> getIsotopeDistribution()

Calculates the isotopic distributions for the molecule. The distribution of fragments are merged. Takes charge into account.

Returns:

the list of masses and distributions. the maximum of distribution is normalized to 100.

getAllAtomCount

public int getAllAtomCount()

Returns the atom count (including implicit hydrogens).

Returns:

the atom count

Since:

Marvin 3.4.1

getAtomCount

public int getAtomCount(int z)

Returns the number of atoms with given atomic number (including its isotopes).

Parameters:

z - is the atomic number

Returns:

the number of atoms with given atomic number

Since:

Marvin 3.4.1

getAtomCount

public int getAtomCount(int z,
                        int m)

Returns the number of atoms with given atomic number in the molecule isotope with the specified mass number. If the mass number is 0, then non-isotope atoms with the given atomic number are counted.

Parameters:

z - is the atomic number

m - is the mass number

Returns:

the number of atoms with given atomic number in the molecule isotope with the specified mass number

Since:

Marvin 3.4.1

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:

CalculatorPlugin.getResultTypes()

getResult

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

Returns the atom count of a specific atom.

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type ("atomcount")

arg - is the atomic number or the atomic number and the mass number separated by "." (e.g. "7.14")

Returns:

number of atoms with the specified atomic number and mass number

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

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key.

Overrides:

getResultCount in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the number of result items

See Also:

getResultTypes()

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result key

Returns:

the calculation domain

See Also:

getResultTypes()

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types. Possible result types:

• "mass"
• "exactmass"
• "formula"
• "isotopeformula"
• "dotdisconnectedformula"
• "groupeddotdisconnectedformula"
• "dotdisconnectedisotopeformula"
• "composition"
• "isotopecomposition"
• "atomcount"

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getTypeString

public java.lang.String getTypeString(java.lang.Object type)

Returns a string representation of the given type.

Overrides:

getTypeString in class CalculatorPlugin

Parameters:

type - is the type object

Returns:

the type string

run

public boolean run()
            throws PluginException

Runs the tool.

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()

Description copied from class: CalculatorPlugin

Returns the calculation error information message if CalculatorPlugin.run() returned false (calculation error). The default implementation returns the empty string.

Overrides:

getErrorMessage in class CalculatorPlugin

Returns:

the calculation error information message

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)

Prevents default standardization: does nothing. ElementalAnalyser does not need standardization.

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized