Range

Range

class apav.Range(ion, minmax, vol=1, color=(0, 0, 0))

A single mass spectrum range

Define a singular mass spectrum range composed of a composition, interval, volume, and color. i.e. Created as:

>>> cu = Range("Cu", (62, 66), color=(0.5, 1, 0.25))

Parameters:

• ion (Union[Ion, str]) – the range composition

• minmax (Tuple[Number, Number]) – (min, max) tuple of the mass spectrum range

• vol (Number) – the “volume” of the atom used during reconstruction

• color (Tuple[Number, Number, Number]) – the color as RGB fractions

property color: Tuple[Number, Number, Number]

Get the color of the range as (R, G, B) tuple. Values range from 0-1

contains_mass(mass)

Test if the given mass/charge ratio is contained within range’s bounds :type mass: Number :param mass: mass/charge ratio

Return type:

bool

property formula: str

Get the range composition as a string

property hill_formula: str

Get the range composition as a string

intersects(rng)

Determine if the range intersects a given Range

property interval: Tuple[Number, Number]

Get the (min, max) interval defined the mass spectrum range

property ion: Ion

Get a tuple of the elements that compose this range

property lower: Number

Get the lower (closed) boundary of the range

num_elems()

Get the number of unique elements of the range composition

Return type:

int

property upper: Number

Get the upper (open) boundary of the range

property vol: Number

Get the volume of the range

RangeCollection

class apav.RangeCollection(ranges=())

Operations on multiple ranges

Maintain and operate on a collection of ranges that describe the peaks in a mass spectrum. This is the principle class used for mass spectrum range definitions. A collection may be created by manually supplying the Range objects through the constructor, or 1 by 1 through RangeCollection.add(). A RangeCollection may also be created using the alternate constructors RangeCollection.from_rng() and RangeCollection.from_rrng() to import the ranges from the two common range file types.

A RangeCollection can be created as:

>>> rng_lst = [Range("Cu", (62.5, 63.5)), Range("Cu", (63.5, 66))]
>>> rngs = RangeCollection(rng_list)

Or 1 by 1 as:

>>> rngs = RangeCollection()
>>> rngs.add(Range("Cu", (62.5, 63.5)))
>>> rngs.add(Range("Cu", (63.5, 66)))

Parameters:

ranges (Sequence[Range]) – sequence of Range objects

add(new)

Add a new Range to the RangeCollection :type new: Range :param new: the new Range :return:

check_overlap()

Check if any ranges in the RangeCollection overlap. This returns the first overlap found, not all overlaps. This is provided if Ranges are being directly accessed and modified

Return type:

Union[Tuple, Tuple[float, float]]

clear()

Remove all Ranges from the RangeCollection

elements()

Get a tuple of all elements

Return type:

Tuple[Element]

property filepath: str

Get the file path the RangeCollection was created from, if it was imported from a file

find_by_mass(mass)

Get the range that contains the given m/q

Return type:

Range

classmethod from_rng(filepath)

Build RangeCollection from a .rng file :type filepath: str :param filepath: filepath

classmethod from_rrng(fpath)

Build RangeCollection from *.rrng files :type fpath: str :param fpath: filepath

ions()

Get a tuple of all ions

Return type:

Tuple[Ion, ...]

property ranges: List[Range]

Get a copy of the ranges in the RangeCollection. This returns a copy to prevent accidental modification of the underlying ranges possibly resulting in overlapping ranges.

Instead, remove the old range with RangeCollection.remove_by_mass() and add the new one, or use RangeCollection.replace()

remove_by_mass(mass)

Remove a range overlapping the given mass ratio

replace(old_rng, new_rng)

Replace an existing Range with a new one. Throws an error if the range is not found.

Parameters:

• old_rng (Range) – Range to be replaced

• new_rng (Range) – New range

sorted_ranges()

Get the list of range objects sorted in ascending mass range

Return type:

list