Composition¶
Describes an arbitrary elemental composition
- class glypy.composition.composition.CComposition¶
A Composition object stores a chemical composition of a substance. Basically it is a dict object, in which keys are the names of chemical elements and values contain integer numbers of corresponding atoms in a substance.
The main improvement over dict is that Composition objects allow addition and subtraction.
If
formula
is not specified, the constructor will look at the first positional argument and try to build the object from it. Without positional arguments, a Composition will be constructed directly from keyword arguments.- Parameters
- __getitem__()¶
x.__getitem__(y) <==> x[y]
- __setitem__(key, value, /)¶
Set self[key] to value.
- items() a set-like object providing a view on D's items ¶
- keys() a set-like object providing a view on D's keys ¶
- values() an object providing a view on D's values ¶
- glypy.composition.composition.calculate_mass()¶
Calculates the monoisotopic mass of a chemical formula or CComposition object.
- Parameters
composition (CComposition) – A Composition object with the elemental composition of a substance. Exclusive with
formula
formula (str) – A string describing a chemical composition. Exclusive with
composition
average (bool, optional) – If
True
then the average mass is calculated. Note that mass is not averaged for elements with specified isotopes. Default isFalse
.charge (int, optional) – If not 0 then m/z is calculated: the mass is increased by the corresponding number of proton masses and divided by z.
mass_data (dict, optional) – A dict with the masses of the chemical elements (the default value is
nist_mass
).
- Returns
mass
- Return type
- glypy.composition.composition.most_probable_isotopic_composition(*args, **kwargs)[source]¶
Calculate the most probable isotopic composition of a chemical formula or
Composition
object.For each element, only two most abundant isotopes are considered.
- Parameters
formula (str, optional) – A string with a chemical formula.
composition (
Composition
, optional) – AComposition
object with the elemental composition of a substance.elements_with_isotopes (list of str) – A list of elements to be considered in isotopic distribution (by default, every element has a isotopic distribution).
mass_data (dict, optional) – A dict with the masses of chemical elements (.
- Returns
out – A tuple with the most probable isotopic composition and its relative abundance.
- Return type
tuple (
Composition
, float)