Modifier and Type | Method and Description |
---|---|
static void |
Isotopes.clearMajorIsotopes(IMolecularFormula formula)
Clear the isotope information from istopes that are major (e.g.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugMolecularFormula
Debugging implementation of
IMolecularFormula . |
Modifier and Type | Method and Description |
---|---|
IMolecularFormula |
DebugMolecularFormula.add(IMolecularFormula formula)
Adds an molecularFormula to this MolecularFormula.
|
IMolecularFormula |
DebugMolecularFormula.addIsotope(IIsotope isotope)
Adds an Isotope to this MolecularFormula one time.
|
IMolecularFormula |
DebugMolecularFormula.addIsotope(IIsotope isotope,
int count)
Adds an Isotope to this MolecularFormula in a number of occurrences.
|
IMolecularFormula |
DebugMolecularFormulaSet.getMolecularFormula(int position)
Returns the MolecularFormula at position
number in the
chemObject. |
IMolecularFormula |
DebugAdductFormula.getMolecularFormula(int position)
Returns the MolecularFormula at position
number in the
chemObject. |
Modifier and Type | Method and Description |
---|---|
Iterator<IMolecularFormula> |
DebugMolecularFormulaSet.iterator()
Returns an Iterator for looping over all IMolecularFormula
in this MolecularFormulaSet.
|
Iterator<IMolecularFormula> |
DebugAdductFormula.iterator()
Returns an Iterator for looping over all IMolecularFormula
in this adduct formula.
|
Iterable<IMolecularFormula> |
DebugMolecularFormulaSet.molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula
in this MolecularFormulaSet.
|
Iterable<IMolecularFormula> |
DebugAdductFormula.molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula
in this adduct formula.
|
Modifier and Type | Method and Description |
---|---|
IMolecularFormula |
DebugMolecularFormula.add(IMolecularFormula formula)
Adds an molecularFormula to this MolecularFormula.
|
void |
DebugMolecularFormulaSet.addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.
|
void |
DebugAdductFormula.addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.
|
boolean |
DebugMolecularFormulaSet.contains(IMolecularFormula formula)
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
|
boolean |
DebugAdductFormula.contains(IMolecularFormula formula)
True, if the AdductFormula contains the given IMolecularFormula object.
|
void |
DebugMolecularFormulaSet.removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.
|
void |
DebugAdductFormula.removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.
|
Constructor and Description |
---|
DebugAdductFormula(IMolecularFormula formula) |
DebugMolecularFormulaSet(IMolecularFormula formula) |
Modifier and Type | Class and Description |
---|---|
class |
MolecularFormula
Class defining a molecular formula object.
|
Modifier and Type | Method and Description |
---|---|
IMolecularFormula |
MolecularFormula.add(IMolecularFormula formula)
Adds an molecularFormula to this MolecularFormula.
|
IMolecularFormula |
MolecularFormula.addIsotope(IIsotope isotope)
Adds an Isotope to this MolecularFormula one time.
|
IMolecularFormula |
MolecularFormula.addIsotope(IIsotope isotope,
int count)
Adds an Isotope to this MolecularFormula in a number of occurrences.
|
IMolecularFormula |
IsotopeContainer.getFormula()
Get the IMolecularFormula object of this container.
|
IMolecularFormula |
MolecularFormulaSet.getMolecularFormula(int position)
Returns the MolecularFormula at position
number in the
chemObject. |
IMolecularFormula |
AdductFormula.getMolecularFormula(int position)
Returns the MolecularFormula at position
number in the
chemObject. |
IMolecularFormula |
MolecularFormulaGenerator.getNextFormula()
Returns next generated formula or null in case no new formula was found
(search is finished).
|
IMolecularFormula |
MolecularFormulaChecker.isValid(IMolecularFormula formula)
Validate if a IMolecularFormula is valid.
|
Modifier and Type | Method and Description |
---|---|
List<IMolecularFormula> |
IsotopeContainer.getFormulas()
Access the formulas of this isotope container.
|
Iterator<IMolecularFormula> |
MolecularFormulaSet.iterator()
Returns an Iterator for looping over all IMolecularFormula
in this MolecularFormulaSet.
|
Iterator<IMolecularFormula> |
AdductFormula.iterator()
Returns an Iterator for looping over all IMolecularFormula
in this adduct formula.
|
Iterable<IMolecularFormula> |
MolecularFormulaSet.molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula
in this MolecularFormulaSet.
|
Iterable<IMolecularFormula> |
AdductFormula.molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula
in this adduct formula.
|
Modifier and Type | Method and Description |
---|---|
IMolecularFormula |
MolecularFormula.add(IMolecularFormula formula)
Adds an molecularFormula to this MolecularFormula.
|
void |
IsotopeContainer.addFormula(IMolecularFormula formula)
Add a formula to this isotope container.
|
void |
MolecularFormulaSet.addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.
|
void |
AdductFormula.addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.
|
boolean |
MolecularFormulaSet.contains(IMolecularFormula formula)
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
|
boolean |
AdductFormula.contains(IMolecularFormula formula)
True, if the AdductFormula contains the given IMolecularFormula object.
|
IsotopePattern |
IsotopePatternGenerator.getIsotopes(IMolecularFormula molFor)
Get all combinatorial chemical isotopes given a structure.
|
IMolecularFormula |
MolecularFormulaChecker.isValid(IMolecularFormula formula)
Validate if a IMolecularFormula is valid.
|
Double |
MolecularFormulaChecker.isValidSum(IMolecularFormula formula)
Validate if a IMolecularFormula is valid.
|
void |
MolecularFormulaSet.removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.
|
void |
AdductFormula.removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.
|
void |
IsotopeContainer.setFormula(IMolecularFormula formula)
Set IMolecularFormula object of this container.
|
Constructor and Description |
---|
AdductFormula(IMolecularFormula formula)
Constructs an AdductFormula with a copy AdductFormula of another
AdductFormula (A shallow copy, i.e., with the same objects as in
the original AdductFormula).
|
IsotopeContainer(IMolecularFormula formula,
double intensity)
Constructor of the IsotopeContainer object setting a IMolecularFormula
object and intensity value.
|
MolecularFormulaSet(IMolecularFormula formula)
Constructs a MolecularFormulaSet with a copy MolecularFormulaSet of another
MolecularFormulaSet (A shallow copy, i.e., with the same objects as in
the original MolecularFormulaSet).
|
Modifier and Type | Method and Description |
---|---|
List<Double> |
RDBERule.getRDBEValue(IMolecularFormula formula)
Method to extract the Ring Double Bond Equivalents (RDB) value.
|
double |
ChargeRule.validate(IMolecularFormula formula)
Validate the charge of this IMolecularFormula.
|
double |
ElementRule.validate(IMolecularFormula formula)
Validate the occurrence of this IMolecularFormula.
|
double |
NitrogenRule.validate(IMolecularFormula formula)
Validate the nitrogen rule of this IMolecularFormula.
|
double |
MMElementRule.validate(IMolecularFormula formula)
Validate the occurrence of this IMolecularFormula.
|
double |
IRule.validate(IMolecularFormula formula)
Analyze the validity for the given IMolecularFormula.
|
double |
RDBERule.validate(IMolecularFormula formula)
Validate the RDBRule of this IMolecularFormula.
|
double |
IsotopePatternRule.validate(IMolecularFormula formula)
Validate the isotope pattern of this IMolecularFormula.
|
double |
ToleranceRangeRule.validate(IMolecularFormula formula)
Validate the Tolerance Range of this IMolecularFormula.
|
boolean |
RDBERule.validate(IMolecularFormula formula,
double value)
Validate the ion state.
|
Modifier and Type | Method and Description |
---|---|
IMolecularFormula |
IMolecularFormula.add(IMolecularFormula formula)
Adds an molecularFormula to this MolecularFormula.
|
IMolecularFormula |
IMolecularFormula.addIsotope(IIsotope isotope)
Adds an Isotope to this MolecularFormula one time.
|
IMolecularFormula |
IMolecularFormula.addIsotope(IIsotope isotope,
int count)
Adds an Isotope to this MolecularFormula in a number of occurrences.
|
IMolecularFormula |
IMolecularFormulaSet.getMolecularFormula(int position)
Returns the IMolecularFormula at position
number in the
chemObject. |
Modifier and Type | Method and Description |
---|---|
Iterable<IMolecularFormula> |
IMolecularFormulaSet.molecularFormulas()
Returns the array of IMolecularFormula of this chemObject.
|
Modifier and Type | Method and Description |
---|---|
IMolecularFormula |
IMolecularFormula.add(IMolecularFormula formula)
Adds an molecularFormula to this MolecularFormula.
|
void |
IMolecularFormulaSet.addMolecularFormula(IMolecularFormula formula)
Adds an IMolecularFormula to this chemObject.
|
boolean |
IMolecularFormulaSet.contains(IMolecularFormula formula)
True, if the IMolecularFormulaSet contains the given IMolecularFormula object.
|
void |
IMolecularFormulaSet.removeMolecularFormula(IMolecularFormula formula)
Removes the given IMolecularFormula from the IMolecularFormulaSet.
|
Modifier and Type | Method and Description |
---|---|
IMolecularFormula |
MolecularFormula.add(IMolecularFormula formula)
Adds an molecularFormula to this MolecularFormula.
|
IMolecularFormula |
MolecularFormula.addIsotope(IIsotope isotope)
Adds an Isotope to this MolecularFormula one time.
|
IMolecularFormula |
MolecularFormula.addIsotope(IIsotope isotope,
int count)
Adds an Isotope to this MolecularFormula in a number of occurrences.
|
IMolecularFormula |
MolecularFormulaSet.getMolecularFormula(int position)
Returns the MolecularFormula at position
number in the
chemObject. |
IMolecularFormula |
AdductFormula.getMolecularFormula(int position)
Returns the MolecularFormula at position
number in the
chemObject. |
Modifier and Type | Method and Description |
---|---|
Iterator<IMolecularFormula> |
MolecularFormulaSet.iterator()
Returns an Iterator for looping over all IMolecularFormula
in this MolecularFormulaSet.
|
Iterator<IMolecularFormula> |
AdductFormula.iterator()
Returns an Iterator for looping over all IMolecularFormula
in this adduct formula.
|
Iterable<IMolecularFormula> |
MolecularFormulaSet.molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula
in this MolecularFormulaSet.
|
Iterable<IMolecularFormula> |
AdductFormula.molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula
in this adduct formula.
|
Modifier and Type | Method and Description |
---|---|
IMolecularFormula |
MolecularFormula.add(IMolecularFormula formula)
Adds an molecularFormula to this MolecularFormula.
|
void |
MolecularFormulaSet.addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.
|
void |
AdductFormula.addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.
|
boolean |
MolecularFormulaSet.contains(IMolecularFormula formula)
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
|
boolean |
AdductFormula.contains(IMolecularFormula formula)
True, if the AdductFormula contains the given IMolecularFormula object.
|
void |
MolecularFormulaSet.removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.
|
void |
AdductFormula.removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.
|
Constructor and Description |
---|
AdductFormula(IMolecularFormula formula)
Constructs an AdductFormula with a copy AdductFormula of another
AdductFormula (A shallow copy, i.e., with the same objects as in
the original AdductFormula).
|
MolecularFormulaSet(IMolecularFormula formula)
Constructs a MolecularFormulaSet with a copy MolecularFormulaSet of another
MolecularFormulaSet (A shallow copy, i.e., with the same objects as in
the original MolecularFormulaSet).
|
Modifier and Type | Method and Description |
---|---|
static IMolecularFormula |
MolecularFormulaManipulator.getMajorIsotopeMolecularFormula(String stringMF,
IChemObjectBuilder builder)
Construct an instance of IMolecularFormula, initialized with a molecular
formula string.
|
static IMolecularFormula |
MolecularFormulaRangeManipulator.getMaximalFormula(MolecularFormulaRange mfRange,
IChemObjectBuilder builder)
Returns the maximal occurrence of the IIsotope into IMolecularFormula
from this MolelecularFormulaRange.
|
static IMolecularFormula |
MolecularFormulaSetManipulator.getMaxOccurrenceElements(IMolecularFormulaSet mfSet)
Extract from a set of MolecularFormula the maximum occurrence of each element found and
put the element and occurrence in a new IMolecularFormula.
|
static IMolecularFormula |
MolecularFormulaRangeManipulator.getMinimalFormula(MolecularFormulaRange mfRange,
IChemObjectBuilder builder)
Returns the minimal occurrence of the IIsotope into IMolecularFormula
from this MolelecularFormulaRange.
|
static IMolecularFormula |
MolecularFormulaSetManipulator.getMinOccurrenceElements(IMolecularFormulaSet mfSet)
Extract from a set of MolecularFormula the minimal occurrence of each element found and
put the element and occurrence in a new IMolecularFormula.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer)
Method that actually does the work of convert the atomContainer
to IMolecularFormula.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer,
IMolecularFormula formula)
Method that actually does the work of convert the atomContainer
to IMolecularFormula given a IMolecularFormula.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(String stringMF,
IChemObjectBuilder builder)
Construct an instance of IMolecularFormula, initialized with a molecular
formula string.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(String stringMF,
IMolecularFormula formula)
add in a instance of IMolecularFormula the elements extracts form
molecular formula string.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMostAbundant(IAtomContainer mol)
Compute the most abundant MF.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMostAbundant(IMolecularFormula mf)
Compute the most abundant MF.
|
static IMolecularFormula |
MolecularFormulaManipulator.removeElement(IMolecularFormula formula,
IElement element)
Removes all isotopes from a given element in the MolecularFormula.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
MolecularFormulaManipulator.adjustProtonation(IMolecularFormula mf,
int hcnt)
Adjust the protonation of a molecular formula.
|
static boolean |
MolecularFormulaManipulator.compare(IMolecularFormula formula1,
IMolecularFormula formula2)
Compare two IMolecularFormula looking at type and number of IIsotope and
charge of the formula.
|
static boolean |
MolecularFormulaSetManipulator.contains(IMolecularFormulaSet formulaSet,
IMolecularFormula formula)
True, if the IMolecularFormulaSet contains the given IMolecularFormula but not
as object.
|
static boolean |
MolecularFormulaManipulator.containsElement(IMolecularFormula formula,
IElement element)
True, if the MolecularFormula contains the given element as IIsotope object.
|
static List<IElement> |
MolecularFormulaManipulator.elements(IMolecularFormula formula)
Get a list of all Elements which are contained
molecular.
|
static IAtomContainer |
MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula)
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer.
|
static IAtomContainer |
MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula,
IAtomContainer atomContainer)
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer given a IAtomContainer.
|
static int |
MolecularFormulaManipulator.getAtomCount(IMolecularFormula formula)
Checks a set of Nodes for the occurrence of each isotopes
instance in the molecular formula.
|
static double |
MolecularFormulaManipulator.getDBE(IMolecularFormula formula)
Returns the number of double bond equivalents in this molecule.
|
static int |
MolecularFormulaManipulator.getElementCount(IMolecularFormula formula,
IElement element)
Checks a set of Nodes for the occurrence of the isotopes in the
molecular formula from a particular IElement.
|
static int |
MolecularFormulaManipulator.getElementCount(IMolecularFormula formula,
IIsotope isotope)
Occurrences of a given element from an isotope in a molecular formula.
|
static int |
MolecularFormulaManipulator.getElementCount(IMolecularFormula formula,
String symbol)
Occurrences of a given element in a molecular formula.
|
static List<IElement> |
MolecularFormulaManipulator.getHeavyElements(IMolecularFormula formula)
Returns a set of nodes excluding all the hydrogens.
|
static String |
MolecularFormulaManipulator.getHillString(IMolecularFormula formula)
|
static String |
MolecularFormulaManipulator.getHTML(IMolecularFormula formula)
Returns the string representation of the molecular formula based on Hill
System with numbers wrapped in <sub></sub> tags.
|
static String |
MolecularFormulaManipulator.getHTML(IMolecularFormula formula,
boolean chargeB,
boolean isotopeB)
Returns the string representation of the molecular formula based on Hill
System with numbers wrapped in <sub></sub> tags and the
isotope of each Element in <sup></sup> tags and the total
charge of IMolecularFormula in <sup></sup> tags.
|
static String |
MolecularFormulaManipulator.getHTML(IMolecularFormula formula,
String[] orderElements,
boolean showCharge,
boolean showIsotopes)
Returns the string representation of the molecular formula with numbers
wrapped in <sub></sub> tags and the isotope of each Element
in <sup></sup> tags and the total showCharge of IMolecularFormula
in <sup></sup> tags.
|
static List<IIsotope> |
MolecularFormulaManipulator.getIsotopes(IMolecularFormula formula,
IElement element)
Get a list of IIsotope from a given IElement which is contained
molecular.
|
static double |
MolecularFormulaManipulator.getMajorIsotopeMass(IMolecularFormula formula)
Deprecated.
|
static double |
MolecularFormulaManipulator.getMass(IMolecularFormula mf)
Calculate the mass of a formula, this function takes an optional
'mass flavour' that switches the computation type.
|
static double |
MolecularFormulaManipulator.getMass(IMolecularFormula mf,
int flav)
Calculate the mass of a formula, this function takes an optional
'mass flavour' that switches the computation type.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer,
IMolecularFormula formula)
Method that actually does the work of convert the atomContainer
to IMolecularFormula given a IMolecularFormula.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(String stringMF,
IMolecularFormula formula)
add in a instance of IMolecularFormula the elements extracts form
molecular formula string.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMostAbundant(IMolecularFormula mf)
Compute the most abundant MF.
|
static double |
MolecularFormulaManipulator.getNaturalExactMass(IMolecularFormula formula)
Deprecated.
|
static String |
MolecularFormulaManipulator.getString(IMolecularFormula formula)
Returns the string representation of the molecular formula.
|
static String |
MolecularFormulaManipulator.getString(IMolecularFormula formula,
boolean setOne)
Returns the string representation of the molecular formula.
|
static String |
MolecularFormulaManipulator.getString(IMolecularFormula formula,
boolean setOne,
boolean setMassNumber)
Returns the string representation of the molecular formula.
|
static String |
MolecularFormulaManipulator.getString(IMolecularFormula formula,
String[] orderElements,
boolean setOne)
Returns the string representation of the molecular formula.
|
static String |
MolecularFormulaManipulator.getString(IMolecularFormula formula,
String[] orderElements,
boolean setOne,
boolean setMassNumber)
Returns the string representation of the molecular formula.
|
static double |
MolecularFormulaManipulator.getTotalExactMass(IMolecularFormula formula)
Deprecated.
calls
MolecularFormulaManipulator.getMass(IMolecularFormula, int) with option
MolecularFormulaManipulator.MonoIsotopic and adjusts for charge with
MolecularFormulaManipulator.correctMass(double, Integer) . These functions should be used
directly. |
static double |
MolecularFormulaManipulator.getTotalMassNumber(IMolecularFormula formula)
Get the summed mass number of all isotopes from an MolecularFormula.
|
static double |
MolecularFormulaManipulator.getTotalNaturalAbundance(IMolecularFormula formula)
Get the summed natural abundance of all isotopes from an MolecularFormula.
|
static List<IIsotope> |
MolecularFormulaManipulator.putInOrder(String[] orderElements,
IMolecularFormula formula) |
static IMolecularFormulaSet |
MolecularFormulaSetManipulator.remove(IMolecularFormulaSet formulaSet,
IMolecularFormula formulaMin,
IMolecularFormula formulaMax)
Remove all those IMolecularFormula which are not fit theirs IElement
occurrence into a limits.
|
static IMolecularFormula |
MolecularFormulaManipulator.removeElement(IMolecularFormula formula,
IElement element)
Removes all isotopes from a given element in the MolecularFormula.
|
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