natorgms.spectra module
- class natorgms.spectra.SpectrumList(spectra: Optional[List[natorgms.spectrum.Spectrum]] = [])[source]
Bases:
collections.UserListClass for work list of Spectrums objects inheritan from list class with some extra features. Store list of Spectrum objects
- __init__(spectra: Optional[List[natorgms.spectrum.Spectrum]] = [])[source]
init SpectrumList Class
- Parameters
spectra (Sequence[Spectrum]) – list of Spectrum objects
- draw_mol_density(mol_density: Optional[pandas.core.frame.DataFrame] = None, ax: Optional[matplotlib.pyplot.axes] = None, **kwargs) None[source]
Draw mol density of spectra in bar diagram
- Parameters
mol_density (pd.DataFrame) – Optional. Table with molecular class density. Default None and cacl by self.
ax (matplotlib axes) – Entarnal axes for plot
**kwargs (dict) – Additional parameters to seaborn heatmap method
- draw_simmilarity(mode: str = 'cosine', values: Optional[numpy.ndarray] = None, ax: Optional[matplotlib.pyplot.axes] = None, annot: bool = True, **kwargs) None[source]
Draw simmilarity matrix by using seaborn
- Parameters
values (np.ndarray) – Optionaly. simmilarity matix. Default None - It is call calculate_simmilarity() method.
mode (str) – Optionaly. If values is none for calculate matrix. Default cosine. one of the simmilarity functions Mode can be: “tanimoto”, “jaccard”, “cosine”
ax (matplotlib axes) – Entarnal axes for plot
annotate (bool) – Draw value of simmilarity onto titles
**kwargs (dict) – Additional parameters to seaborn heatmap method
- get_mol_density() pandas.core.frame.DataFrame[source]
Calculate molecular class density table
- Return type
pandas Dataframe
References
Zherebker, Alexander, et al. “Interlaboratory comparison of humic substances compositional space as measured by Fourier transform ion cyclotron resonance mass spectrometry (IUPAC Technical Report).” Pure and Applied Chemistry 92.9 (2020): 1447-1467.
- get_mol_metrics(metrics: Optional[Sequence[str]] = None, func: Optional[str] = None) pandas.core.frame.DataFrame[source]
Get average molecular metrics
- Parameters
metrics (Sequence[str]) – Optional. Default None. Chose metrics fot watch.
func ({"weight", "mean", "median", "max", "min", "std"}) – How calculate average. My be “weight” (default - weight average on intensity), “mean”, “median”, “max”, “min”, “std” (standard deviation)
- Return type
Pandas Dataframe
- get_names() Sequence[source]
Get names of spectra
- Returns
list with names of spectra in SpectrumList
- Return type
List
- get_simmilarity(mode: str = 'cosine', symmetric=True) numpy.ndarray[source]
Calculate simmilarity matrix for all spectra in SpectrumList
- Parameters
mode ({"tanimoto", "jaccard", "cosine"}) – Optionaly. Default cosine. one of the simmilarity functions Mode can be: “tanimoto”, “jaccard”, “cosine”
symmetric (bool) – Optionaly. Default True. If metric is symmetrical ( a(b)==b(a) ) it is enough to calc just half of table
- Returns
table with simmilirities of spectrum corresponig their index in SpectrumList
- Return type
numpy array
- get_square_vk(how_average: str = 'weight') pandas.core.frame.DataFrame[source]
Calculate Van-Krevelen square density for spectra
- Parameters
how_average ({"count", "weight"}) – How calculate average. My be “count” or “weight” ((default))
- Return type
Pandas Dataframe
References
Zherebker, Alexander, et al. “Interlaboratory comparison of humic substances compositional space as measured by Fourier transform ion cyclotron resonance mass spectrometry (IUPAC Technical Report).” Pure and Applied Chemistry 92.9 (2020): 1447-1467.
- static read_csv(folder: Union[pathlib.Path, str]) natorgms.spectra.SpectrumList[source]
Read csv files from folder to SpectrumList object. Read only ‘csv’ ot ‘txt’ fromat
- Parameters
folder (str) – folder for save spectra in separate files
- Return type
- static read_json(filename: Union[pathlib.Path, str]) natorgms.spectra.SpectrumList[source]
Read SpectrumList from json
- Parameters
filename (str) – path to SpectrumList json file, absoulute or relative
- Return type