pygecko.gc_tools.injection package

Submodules

pygecko.gc_tools.injection.fid_injection module

class pygecko.gc_tools.injection.fid_injection.FID_Injection(metadata: dict, chromatogram: ndarray, solvent_delay: float | None = None, pos: bool = False)

Bases: Injection

Class to represent FID injections.

injector_pos

Position of the injector used for the injection.

Type:

int

sample_number

Number of the sample in the sequence.

Type:

int

acq_time

Acquisition time of the injection.

Type:

str

data_method

Data method used for the injection.

Type:

Analysis_Settings

solvent_delay

Solvent delay applied to the injection.

Type:

float

chromatogram

Chromatogram of the injection.

Type:

np.ndarray

processed_chromatogram

Processed chromatogram of the injection.

Type:

np.ndarray|None

peaks

Peaks of the injection.

Type:

dict[float, FID_Peak]

detector

Detector used for the injection.

Type:

str

acq_time: str

analysis_settings: Analysis_Settings

baseline_correction(**kwargs: dict) → None

Applies a baseline correction to the injection’s chromatogram and sets the corrected chromatogram as the injection’s processed chromatogram.

Parameters:

**kwargs – Keyword arguments for the baseline correction.

chromatogram: ndarray

detector: str

injector_pos: int

integrate() → None

Integrates the area under the curve of the injection’s peaks and sets the area as the peak’s area attribute.

peaks: None | list[FID_Peak]

pick_peaks(inplace: bool = True, **kwargs: dict) → None | dict[float, FID_Peak]

Picks peaks from the injection’s chromatogram.

Parameters:

• inplace (bool) – If True, the peaks are assigned to the injection’s peaks attribute. Default is True.

• **kwargs – Keyword arguments for the peak picking.

Returns:

The peaks of the injection if the inplace argument is False, None otherwise.

Return type:

None|dict[float, FID_Peak]

processed_chromatogram: ndarray | None

quantify(rt: float, method: str = 'polyarc', **kwargs) → int

Returns the yield of the analyte with the given retention time calculated using the internal standard of the injection.

Parameters:

• rt (float) – Retention time of the analyte.

• method (str) – Method to use for the quantification. Default is ‘polyarc’.

Returns:

Yield of the analyte.

Return type:

int

report(path: str) → None

Writes a csv report for the injection to the given path.

Parameters:

path (str) – Path to write the report to.

sample_number: int

solvent_delay: float

pygecko.gc_tools.injection.injection module

class pygecko.gc_tools.injection.injection.Injection(metadata: dict, peaks: dict[float, Peak] | None = None, pos: bool = False)

Bases: object

Base class for all injections.

acq_method

Name of the acquisition method.

Type:

str

instrument_name

Name of the instrument.

Type:

str

sample_description

Description of the sample.

Type:

str

sample_name

Name of the sample.

Type:

str

sample_type

Type of the sample.

Type:

str

vial_pos

Position of the sample’s vial in the autosampler.

Type:

int

internal_standard

Internal standard of the sample.

Type:

Analyte

peaks

Peaks of the sample.

Type:

dict[float, Peak]

acq_method: str

analysis_settings: None

chromatogram: None

detector: None | str

flag_peak(rt: float, flag: str | None = None, tolerance: float = 0.05, analyte: Analyte | None = None) → None | Peak

Assigns a flag to the peak with the closest retention time to the given retention time within the tolerance.

Parameters:

• rt (float) – Retention time of the peak.

• flag (str|None) – Flag to be assigned to the peak. Default is None.

• tolerance (float) – Tolerance for the retention time matching. Default is 0.05.

• analyte (Analyte|None) – Analyte object to be assigned to the peak. Default is None.

Returns:

The peak with the closest retention time to the given retention time or None if no peak was found within the tolerance.

Return type:

None|Peak

get_plate_position()

Returns the plate position of the sample as string.

instrument_name: str

internal_standard: Analyte | None

match_ri(ri: float, tolerance: int = 20, analyte: str | None = None, return_candidates: bool = False) → Peak | None

Returns the peak with the closest retention index to the given retention index within the tolerance. Returns None if no peak was found within the tolerance.

Parameters:

• ri (float) – Retention index to match.

• tolerance (int) – Tolerance for the retention index matching. Default is 20.

• analyte (str|None) – Analyte object to be assigned to the peak. Default is None.

Returns:

The peak with the closest retention index to the given retention index or None if

no peak was found within the tolerance.

Return type:

Peak|None

peaks: dict[float, Peak] | None

plate_pos: str | None

sample_description: str

sample_name: str

sample_type: str

save(filename: str) → None

Saves an Injection to a .pkl file.

Parameters:

filename (str) – Name of the file to save the injection to.

set_internal_standard(rt: float | int, tolerance: float = 0.05, name: str | None = None, smiles: str | None = None) → None

Assigns the internal standard of the injection to the corresponding peak by creating an Analyte object for the internal standard and setting it as the peak’s analyte.

Parameters:

• rt (float|int) – Retention time of the internal standard.

• tolerance (float) – Tolerance for the retention time matching. Default is 0.05.

• name (str) – Name of the internal standard. Default is None.

• smiles (str) – SMILES string of the internal standard. Default is None.

set_plate_position(pos: str)

Takes in a plate position and sets it as the sample’s position.

vial_pos: int

view_chromatogram(path: str | None = None, **kwargs) → None

Plots the chromatogram of the injection.

Parameters:

**kwargs – Keyword arguments for the visualization.

pygecko.gc_tools.injection.injection.load_injection(filename) → Injection

Loads an Injection from a .pkl file.

Parameters:

filename (str) – Name of the file to load the ínjection from.

Returns:

Injection object loaded from the file.

Return type:

Injection

pygecko.gc_tools.injection.ms_injection module

class pygecko.gc_tools.injection.ms_injection.MS_Injection(metadata: dict | None, chromatogram: ndarray, peaks: dict | None, scans: DataFrame, pos: bool = False)

Bases: Injection

Class to represent MS injections.

chromatogram

Chromatogram of the injection.

Type:

np.ndarray

peaks

Peaks of the injection.

Type:

dict[float, MS_Peak]

scans

Scans of the injection.

Type:

pd.DataFrame

detector

Detector used for the injection.

Type:

str

analysis_settings

Data method used for the injection.

Type:

Analysis_Settings

solvent_delay

Solvent delay applied to the injection.

Type:

float

analysis_settings: Analysis_Settings

chromatogram: ndarray

detector: str

match_mol(smiles: str, return_canidates=False, check_iso=True, **kwargs) → MS_Peak'>, None)] | None

Returns the peak with the lowest isotope error for the m/z corresponding to the given molecule’s parent peak. Returns None if no peak was found matching the criteria.

Parameters:

smiles (str) – SMILES string of the analyte.

Returns:

The peak with the lowest isotope error for the given molecule or None if no peak was found matching the criteria.

Return type:

MS_Peak|None

match_mz(mz: float, **kwargs) → MS_Peak | list[MS_Peak] | None

Returns the peak or a list of peaks whose mass spectra contain the given m/z. Returns None if no peak was found matching the criteria.

Parameters:

mz (float) – m/z to match.

Returns:

The peak or a list of peaks whose mass spectra contain the given m/z or None if no peak was found matching the criteria.

Return type:

MS_Peak|list[MS_Peak]|None

peaks: dict[float, MS_Peak] | None

pick_peaks(inplace: bool = True, **kwargs: dict) → None | dict[float, MS_Peak]

Picks peaks from the injection’s chromatogram.

Parameters:

• inplace (bool) – If True, the peaks are assigned to the injection’s peaks attribute. Default is True.

• **kwargs – Keyword arguments for the peak picking.

Returns:

The peaks of the injection if the inplace argument is False, None otherwise.

Return type:

None|dict[float, MS_Peak]

save_peaks_mass_spectrum(rt: float, path: str) → None

Saves the mass spectrum of all peaks in the injection to a CSV file. :param path: Path to the file where the mass spectra will be saved. :type path: str

scans: DataFrame

solvent_delay: float

Module contents