Modifier and Type | Class and Description |
---|---|
class |
Atom
Represents the idea of an chemical atom.
|
class |
AtomType
The base class for atom types.
|
class |
EnzymeResidueLocator
Atom that represents part of an residue in an enzyme, like Arg255.
|
class |
FragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.
|
class |
Isotope
Used to store and retrieve data of a particular isotope.
|
class |
PseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me,
R, X, Phe, His, etc.
|
Modifier and Type | Field and Description |
---|---|
protected Map<String,List<IIsotope>> |
IsotopeFactory.isotopes |
protected Map<String,IIsotope> |
IsotopeFactory.majorIsotopes |
Modifier and Type | Method and Description |
---|---|
IIsotope |
Isotopes.getIsotope(String symbol,
double exactMass,
double tolerance)
Get an isotope based on the element symbol and exact mass.
|
IIsotope |
IsotopeFactory.getIsotope(String symbol,
double exactMass,
double tolerance)
Get an isotope based on the element symbol and exact mass.
|
IIsotope |
Isotopes.getIsotope(String symbol,
int massNumber)
Get isotope based on element symbol and mass number.
|
IIsotope |
IsotopeFactory.getIsotope(String symbol,
int massNumber)
Get isotope based on element symbol and mass number.
|
IIsotope[] |
Isotopes.getIsotopes()
Gets a array of all isotopes known to the IsotopeFactory.
|
IIsotope[] |
IsotopeFactory.getIsotopes()
Gets a array of all isotopes known to the IsotopeFactory.
|
IIsotope[] |
Isotopes.getIsotopes(double exactMass,
double difference)
Gets an array of all isotopes matching the searched exact mass within
a certain difference.
|
IIsotope[] |
IsotopeFactory.getIsotopes(double exactMass,
double difference)
Gets an array of all isotopes matching the searched exact mass within
a certain difference.
|
IIsotope[] |
Isotopes.getIsotopes(String symbol)
Gets an array of all isotopes known to the IsotopeFactory for the given
element symbol.
|
IIsotope[] |
IsotopeFactory.getIsotopes(String symbol)
Gets an array of all isotopes known to the IsotopeFactory for the given
element symbol.
|
IIsotope |
Isotopes.getMajorIsotope(int atomicNumber)
Returns the most abundant (major) isotope with a given atomic number.
|
IIsotope |
IsotopeFactory.getMajorIsotope(int atomicNumber)
Returns the most abundant (major) isotope with a given atomic number.
|
IIsotope |
Isotopes.getMajorIsotope(String symbol)
Returns the most abundant (major) isotope whose symbol equals element.
|
IIsotope |
IsotopeFactory.getMajorIsotope(String symbol)
Returns the most abundant (major) isotope whose symbol equals element.
|
Modifier and Type | Method and Description |
---|---|
protected void |
IsotopeFactory.add(IIsotope isotope)
Protected methods only to be used by classes extending this class to add
an IIsotope.
|
IAtom |
IsotopeFactory.configure(IAtom atom,
IIsotope isotope)
Configures an atom to have all the data of the
given isotope.
|
Modifier and Type | Method and Description |
---|---|
List<IIsotope> |
IsotopeHandler.getIsotopes()
Returns the isotopes read from the XML file.
|
List<IIsotope> |
IsotopeReader.readIsotopes()
Triggers the XML parsing of the data file and returns the read Isotopes.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugAtom
Debugging data class.
|
class |
DebugAtomType
Debugging data class.
|
class |
DebugFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.
|
class |
DebugIsotope
Debugging data class.
|
class |
DebugPDBAtom
Debugging data class.
|
class |
DebugPseudoAtom
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IIsotope> |
DebugMolecularFormula.isotopes()
Returns an Iterator for looping over all isotopes in this IMolecularFormula.
|
Iterable<IIsotope> |
DebugAdductFormula.isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.
|
Modifier and Type | Method and Description |
---|---|
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.
|
boolean |
DebugMolecularFormula.contains(IIsotope isotope)
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
|
boolean |
DebugAdductFormula.contains(IIsotope isotope)
True, if the AdductFormula contains the given IIsotope object and not
the instance.
|
int |
DebugMolecularFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
|
int |
DebugAdductFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
|
void |
DebugMolecularFormula.removeIsotope(IIsotope isotope)
Removes the given isotope from the MolecularFormula.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IIsotope> |
MolecularFormula.isotopes()
Returns an Iterator for looping over all isotopes in this IMolecularFormula.
|
Iterable<IIsotope> |
AdductFormula.isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.
|
Iterable<IIsotope> |
MolecularFormulaRange.isotopes()
Returns an Iterator for looping over all isotopes in this MolecularFormulaExpand.
|
Modifier and Type | Method and Description |
---|---|
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.
|
void |
MolecularFormulaRange.addIsotope(IIsotope isotope,
int countMin,
int countMax)
Adds an Isotope to this MolecularFormulaExpand in a number of
maximum and minimum occurrences allowed.
|
boolean |
MolecularFormula.contains(IIsotope isotope)
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
|
boolean |
AdductFormula.contains(IIsotope isotope)
True, if the AdductFormula contains the given IIsotope object and not
the instance.
|
boolean |
MolecularFormulaRange.contains(IIsotope isotope)
True, if the MolecularFormulaExpand contains the given IIsotope.
|
int |
MolecularFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
|
int |
AdductFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
|
int |
MolecularFormulaRange.getIsotopeCountMax(IIsotope isotope)
Checks a set of Nodes for the maximal occurrence of the isotope in the
MolecularFormulaExpand from a particular isotope.
|
int |
MolecularFormulaRange.getIsotopeCountMin(IIsotope isotope)
Checks a set of Nodes for the minimal occurrence of the isotope in the
MolecularFormulaExpand from a particular isotope.
|
protected boolean |
MolecularFormula.isTheSame(IIsotope isotopeOne,
IIsotope isotopeTwo)
Compare to IIsotope.
|
void |
MolecularFormula.removeIsotope(IIsotope isotope)
Removes the given isotope from the MolecularFormula.
|
void |
MolecularFormulaRange.removeIsotope(IIsotope isotope)
Removes the given isotope from the MolecularFormulaExpand.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IAtom
Represents the idea of an chemical atom.
|
interface |
IAtomType
The base class for atom types.
|
interface |
IFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.
|
interface |
IPDBAtom
A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
|
interface |
IPseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me,
R, X, Phe, His, etc.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IIsotope> |
IMolecularFormula.isotopes()
Returns an
Iterable for looping over all isotopes in this IMolecularFormula. |
Iterable<IIsotope> |
IAdductFormula.isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.
|
Modifier and Type | Method and Description |
---|---|
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.
|
boolean |
IMolecularFormula.contains(IIsotope isotope)
True, if the MolecularFormula contains the given IIsotope object.
|
boolean |
IAdductFormula.contains(IIsotope isotope)
True, if the AdductFormula contains the given IIsotope object.
|
int |
IMolecularFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
|
int |
IAdductFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
|
void |
IMolecularFormula.removeIsotope(IIsotope isotope)
Removes the given isotope from the MolecularFormula.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IQueryAtom
Defines the ability to be matched against
IAtom 's. |
Modifier and Type | Class and Description |
---|---|
class |
InverseSymbolSetQueryAtom
A QueryAtom that matches all symbols but those in this container.
|
class |
QueryAtom |
class |
SymbolAndChargeQueryAtom |
class |
SymbolChargeIDQueryAtom |
class |
SymbolQueryAtom |
class |
SymbolSetQueryAtom
A QueryAtom that matches all symbols in this container.
|
Modifier and Type | Class and Description |
---|---|
class |
AliphaticAtom
This matcher any non-aromatic atom.
|
class |
AliphaticSymbolAtom
This smarts atom matches aliphatic atom with element symbol specified.
|
class |
AnyAtom
This matcher any Atom including explicit hydrogens.
|
class |
AromaticAtom
This matcher any aromatic atom.
|
class |
AromaticSymbolAtom
This class matches aromatic atom with element symbol specified.
|
class |
AtomicNumberAtom
This matches an atom using the atomic number.
|
class |
ChiralityAtom
This matches an atom with chirality property.
|
class |
ExplicitConnectionAtom
Match an atom with the defined degree.
|
class |
FormalChargeAtom
This matcher checks the formal charge of the Atom.
|
class |
HybridizationNumberAtom
This matcher checks the hybridization state of an atom.
|
class |
HydrogenAtom
This matches Hydrogen atoms.
|
class |
ImplicitHCountAtom
This matcher checks the number of implicit hydrogens of the Atom.
|
class |
LogicalOperatorAtom
This class matches a logical operator that connects two query atoms.
|
class |
MassAtom
This class matches an atom based on the atomic mass.
|
class |
NonCHHeavyAtom
This matcher any heavy atom that is not C or H.
|
class |
PeriodicGroupNumberAtom
This matcher checks the periodic group number of an atom.
|
class |
ReactionRoleQueryAtom
Matches atoms with a particular role in a reaction.
|
class |
RecursiveSmartsAtom
This matches recursive smarts atoms.
|
class |
RingIdentifierAtom
This encapsulates an atom with a ring identifier, with an optional ring
bond specified.
|
class |
RingMembershipAtom
This query is found in a specified number of ring.
|
class |
SmallestRingAtom
Match an atom in a specific size ring.
|
class |
SMARTSAtom
Abstract smarts atom.
|
class |
TotalConnectionAtom
This matches an atom using total number of connections - referred to in
SMARTS as the connectivity.
|
class |
TotalHCountAtom
SMARTS query atom for matching the total hydrogen count.
|
class |
TotalRingConnectionAtom
This matcher checks the number of ring connections of the checked Atom with
other Atom's.
|
class |
TotalValencyAtom
This matcher checks the valence of the Atom.
|
Modifier and Type | Class and Description |
---|---|
class |
PharmacophoreAtom
A representation of a pharmacophore group.
|
class |
PharmacophoreQueryAtom
Represents a query pharmacophore group.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBAtom
Represents the idea of an atom as used in PDB files.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IIsotope> |
MolecularFormula.isotopes()
Returns an Iterator for looping over all isotopes in this IMolecularFormula.
|
Iterable<IIsotope> |
AdductFormula.isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.
|
Modifier and Type | Method and Description |
---|---|
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.
|
boolean |
MolecularFormula.contains(IIsotope isotope)
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
|
boolean |
AdductFormula.contains(IIsotope isotope)
True, if the AdductFormula contains the given IIsotope object and not
the instance.
|
int |
MolecularFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
|
int |
AdductFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
|
protected boolean |
MolecularFormula.isTheSame(IIsotope isotopeOne,
IIsotope isotopeTwo)
Compare to IIsotope.
|
void |
MolecularFormula.removeIsotope(IIsotope isotope)
Removes the given isotope from the MolecularFormula.
|
Modifier and Type | Method and Description |
---|---|
static List<IIsotope> |
MolecularFormulaManipulator.getIsotopes(IMolecularFormula formula,
IElement element)
Get a list of IIsotope from a given IElement which is contained
molecular.
|
static List<IIsotope> |
MolecularFormulaManipulator.putInOrder(String[] orderElements,
IMolecularFormula formula) |
Modifier and Type | Method and Description |
---|---|
static int |
MolecularFormulaManipulator.getElementCount(IMolecularFormula formula,
IIsotope isotope)
Occurrences of a given element from an isotope in a molecular formula.
|
Modifier and Type | Method and Description |
---|---|
ValidationReport |
ValidatorEngine.validateIsotope(IIsotope subject) |
ValidationReport |
IValidator.validateIsotope(IIsotope subject) |
ValidationReport |
BasicValidator.validateIsotope(IIsotope subject) |
ValidationReport |
AbstractValidator.validateIsotope(IIsotope subject) |
ValidationReport |
BasicValidator.validateIsotopeExistence(IIsotope isotope) |
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