chemistry_tools.spectrum_similarity
Mass spectrum similarity calculations.
Classes:
|
Calculate the similarity score for two mass spectra. |
Functions:
|
Create a |
|
Returns the normalised intensity for each rows of a |
|
Calculate the similarity score for two mass spectra. |
-
class
SpectrumSimilarity
(spec_top, spec_bottom, b=1, xlim=(50, 1200))[source] Calculate the similarity score for two mass spectra.
- Parameters
spec_top (
ndarray
) – Array containing the experimental spectrum’s peak list with the m/z values in the first column and corresponding intensities in the secondspec_bottom (
ndarray
) – Array containing the reference spectrum’s peak list with the m/z values in the first column and corresponding intensities in the secondb (
float
) – numeric value specifying the baseline threshold for peak identification. Expressed as a percent of the maximum intensity. Default1
.xlim (
Tuple
[int
,int
]) – tuple of length 2, defining the beginning and ending values of the x-axis. Default(50, 1200)
.
New in version 1.0.0.
Methods:
plot
([top_label, bottom_label, filter])Plot the mass spectra head to tail.
Print the dataframe giving aligned peaks in the top and bottom spectra.
score
()Returns the similarity score.
-
create_array
(intensities, mz)[source] Create a
numpy.ndarray
, in a format appropriate forSpectrumSimilarity
, from a list of intensities and a list of m/z values.
-
normalize
(row, max_val)[source] Returns the normalised intensity for each rows of a
pandas.DataFrame
.
-
spectrum_similarity
(spec_top, spec_bottom, t=0.25, b=10, top_label=None, bottom_label=None, xlim=(50, 1200), x_threshold=0, print_alignment=False, print_graphic=True, output_list=False)[source] Calculate the similarity score for two mass spectra.
Attention
The
SpectrumSimilarity
class is recommended over this function.- Parameters
spec_top (
ndarray
) – Array containing the experimental spectrum’s peak list with the m/z values in the first column and corresponding intensities in the secondspec_bottom (
ndarray
) – Array containing the reference spectrum’s peak list with the m/z values in the first column and corresponding intensities in the secondt (
float
) – numeric value specifying the tolerance used to align the m/z values of the two spectra. Default0.25
.b (
float
) – numeric value specifying the baseline threshold for peak identification. Expressed as a percent of the maximum intensity. Default10
.top_label (
Optional
[str
]) – string to label the top spectrum. DefaultNone
.bottom_label (
Optional
[str
]) – string to label the bottom spectrum. DefaultNone
.xlim (
Tuple
[int
,int
]) – tuple of length 2, defining the beginning and ending values of the x-axis. Default(50, 1200)
.x_threshold (
float
) – Default0
.print_alignment (
bool
) – whether the intensities should be printed. DefaultFalse
.output_list (
bool
) – whether the intensities should be returned as a third element of the tuple. DefaultFalse
.
- Return type