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Documentation for ChromAnalyzer

Bases: BaseModel

add_molecule(molecule, init_conc=None, conc_unit=None, retention_tolerance=None)

Adds a molecule to the list of species, allowing to update the initial concentration, concentration unit, and retention time tolerance.

Parameters:

Name	Type	Description	Default
molecule	Molecule	The molecule object to be added.	required
init_conc	float | None	The initial concentration of the molecule. Defaults to None.	None
conc_unit	UnitDefinitionAnnot | None	The unit of the concentration. Defaults to None.	None
retention_tolerance	float | None	Retention time tolerance for peak annotation in minutes. Defaults to None.	None

add_molecule_from_standard(standard, init_conc, conc_unit)

Adds a molecule to the list of species based on a Calibration object.

add_protein(protein, init_conc=None, conc_unit=None)

Adds a protein to the list of proteins or updates an existing protein based on the pubchem_cid of the molecule.

Parameters:

Name	Type	Description	Default
protein	Protein	The protein object to be added.	required

add_standard(molecule, wavelength=None, visualize=True)

Creates a standard curve for a molecule based on the peak areas and concentrations.

Parameters:

Name	Type	Description	Default
molecule	Molecule	The molecule for which the standard curve should be created.	required
wavelength	float | None	The wavelength of the detector. Defaults to None.	None
visualize	bool	If True, the standard curve is visualized. Defaults to True.	True

define_molecule(id, pubchem_cid, retention_time, retention_tolerance=0.1, init_conc=None, conc_unit=None, name=None, wavelength=None, is_internal_standard=False)

Defines and adds a molecule to the list of molecules.

Parameters:

Name	Type	Description	Default
id	str	Internal identifier of the molecule, such as s0 or asd45.	required
pubchem_cid	int	PubChem CID of the molecule, which uniquely identifies the compound.	required
retention_time	Optional[float]	Retention time for peak annotation in minutes. If the molecule is not detected in the chromatograms, this can be set to None.	required
retention_tolerance	float	Tolerance in minutes for retention time used in peak annotation. Defaults to 0.1.	0.1
init_conc	Optional[float]	Initial concentration of the molecule. If not provided, it defaults to None.	None
conc_unit	Optional[str]	Unit of the initial concentration. If not provided, it defaults to None.	None
name	Optional[str]	Name of the molecule. If not provided, the name is fetched from the PubChem database. Defaults to None.	None
wavelength	Optional[float]	Wavelength of the detector where the molecule was detected. If not provided, it defaults to None.	None
is_internal_standard	bool	If True, the molecule is used as internal standard. Defaults to False.	False

Returns:

Name	Type	Description
Molecule	Molecule	The molecule object that was added to the list of species.

define_protein(id, name, init_conc, conc_unit, sequence=None, organism=None, organism_tax_id=None, constant=True)

Adds a protein to the list of proteins or updates an existing protein based on the pubchem_cid of the molecule.

Parameters:

Name	Type	Description	Default
id	str	Internal identifier of the protein such as p0 or asd45.	required
name	str	Name of the protein.	required
init_conc	float	Initial concentration of the protein.	required
conc_unit	str	Unit of the concentration.	required
sequence	str	Amino acid sequence of the protein. Defaults to None.	None
organism	str	Name of the organism. Defaults to None.	None
organism_tax_id	int	NCBI taxonomy ID of the organism. Defaults to None.	None
constant	bool	Boolean indicating whether the protein concentration is constant. Defaults to True.	True

from_json(path) classmethod

Load an instance of the class from a JSON file.

Parameters:

Name	Type	Description	Default
path	str	The file path to the JSON file.	required

Returns:

Type	Description
ChromAnalyzer	An instance of the class populated with data from the JSON file.

Raises:

Type	Description
FileNotFoundError	If the specified file does not exist.
JSONDecodeError	If the file contains invalid JSON.

read_agilent(path, ph, temperature, temperature_unit='C', mode=None, values=None, unit=None, id=None, name='Chromatographic measurement', silent=False) classmethod

Reads Agilent Report.txt or RESULTS.csv files within a *.D directories within the specified path.

Parameters:

Name	Type	Description	Default
path	str	Path to the directory containing the Shimadzu files.	required
ph	float	pH value of the measurement.	required
temperature	float	Temperature of the measurement.	required
temperature_unit	UnitDefinitionAnnot	Unit of the temperature. Defaults to Celsius (C).	'C'
mode	Optional[Literal['timecourse', 'calibration']]	Mode of the data. If "timecourse", values should be a list of reaction times. If "calibration", values should be a list of concentrations. Defaults to None.	None
values	list[float]	A list of reaction times (for "timecourse" mode) or concentrations (for "calibration" mode), corresponding to each measurement in the directory.	None
unit	UnitDefinitionAnnot	Unit of the values provided. It can be the time unit for reaction times or the concentration unit for calibration mode, depending on the mode.	None
id	str	Unique identifier of the ChromAnalyzer object. If not provided, the path is used as ID.	None
name	str	Name of the measurement. Defaults to "Chromatographic measurement".	'Chromatographic measurement'
silent	bool	If True, no success message is printed. Defaults to False.	False

Returns:

Name	Type	Description
ChromAnalyzer	ChromAnalyzer	ChromAnalyzer object containing the measurements.

read_asm(path, ph, temperature, temperature_unit='C', mode=None, values=None, unit=None, id=None, name='Chromatographic measurement', silent=False) classmethod

Reads chromatographic data from a directory containing Allotrope Simple Model (ASM) json files. Measurements are assumed to be named alphabetically, allowing sorting by file name.

Parameters:

Name	Type	Description	Default
path	str	Path to the directory containing the ASM files.	required
ph	float	pH value of the measurement.	required
temperature	float	Temperature of the measurement.	required
temperature_unit	UnitDefinitionAnnot	Unit of the temperature. Defaults to Celsius (C).	'C'
mode	Optional[Literal['timecourse', 'calibration']]	Mode of the data. If "timecourse", values should be a list of reaction times. If "calibration", values should be a list of concentrations. Defaults to None.	None
values	list[float]	A list of reaction times (for "timecourse" mode) or concentrations (for "calibration" mode), corresponding to each measurement in the directory.	None
unit	UnitDefinitionAnnot	Unit of the values provided. It can be the time unit for reaction times or the concentration unit for calibration mode, depending on the mode.	None
id	str	Unique identifier of the ChromAnalyzer object. If not provided, the path is used as ID.	None
name	str	Name of the measurement. Defaults to "Chromatographic measurement".	'Chromatographic measurement'
silent	bool	If True, no success message is printed. Defaults to False.	False

Returns:

Name	Type	Description
ChromAnalyzer	ChromAnalyzer	ChromAnalyzer object containing the measurements.

read_chromeleon(path, ph, temperature, temperature_unit='C', mode=None, values=None, unit=None, id=None, name='Chromatographic measurement', silent=False) classmethod

Reads Chromeleon txt files from a directory. The files in the directory are assumed to be of one calibration or timecourse measurement series.

Parameters:

Name	Type	Description	Default
path	str	Path to the directory containing the Shimadzu files.	required
ph	float	pH value of the measurement.	required
temperature	float	Temperature of the measurement.	required
temperature_unit	UnitDefinitionAnnot	Unit of the temperature. Defaults to Celsius (C).	'C'
mode	Optional[Literal['timecourse', 'calibration']]	Mode of the data. If "timecourse", values should be a list of reaction times. If "calibration", values should be a list of concentrations. Defaults to None.	None
values	list[float]	A list of reaction times (for "timecourse" mode) or concentrations (for "calibration" mode), corresponding to each measurement in the directory.	None
unit	UnitDefinitionAnnot	Unit of the values provided. It can be the time unit for reaction times or the concentration unit for calibration mode, depending on the mode.	None
id	str	Unique identifier of the ChromAnalyzer object. If not provided, the path is used as ID.	None
name	str	Name of the measurement. Defaults to "Chromatographic measurement".	'Chromatographic measurement'
silent	bool	If True, no success message is printed. Defaults to False.	False

Returns:

Name	Type	Description
ChromAnalyzer	ChromAnalyzer	ChromAnalyzer object containing the measurements.

read_csv(path, mode, ph, temperature, temperature_unit, retention_time_col_name, peak_area_col_name, id=None, values=None, unit=None, silent=False) classmethod

Reads chromatographic data from a CSV file.

Parameters:

Name	Type	Description	Default
path	str	Path to the CSV file.	required
mode	Literal['timecourse', 'calibration']	Mode of the data.	required
values	Optional[list[float]]	List of values. Defaults to None.	None
unit	Optional[UnitDefinitionAnnot]	Unit of the values. Defaults to None.	None
ph	float	pH value of the measurement.	required
temperature	float	Temperature of the measurement.	required
temperature_unit	UnitDefinitionAnnot	Unit of the temperature.	required
retention_time_col_name	str	Name of the retention time column.	required
peak_area_col_name	str	Name of the peak area column.	required
id	str	Unique identifier of the ChromAnalyzer object. If not provided, the path is used as ID.	None
silent	bool	If True, no success message is printed. Defaults to False.	False

Returns:

Name	Type	Description
ChromAnalyzer	ChromAnalyzer	ChromAnalyzer object containing the measurements.

read_shimadzu(path, ph, temperature, temperature_unit='C', mode=None, values=None, unit=None, id=None, name='Chromatographic measurement', silent=False) classmethod

Reads chromatographic data from a directory containing Shimadzu files. Measurements are assumed to be named alphabetically, allowing sorting by file name.

Parameters:

Name	Type	Description	Default
path	str	Path to the directory containing the Shimadzu files.	required
ph	float	pH value of the measurement.	required
temperature	float	Temperature of the measurement.	required
temperature_unit	UnitDefinitionAnnot	Unit of the temperature. Defaults to Celsius (C).	'C'
mode	Optional[Literal['timecourse', 'calibration']]	Mode of the data. If "timecourse", values should be a list of reaction times. If "calibration", values should be a list of concentrations. Defaults to None.	None
values	list[float]	A list of reaction times (for "timecourse" mode) or concentrations (for "calibration" mode), corresponding to each measurement in the directory.	None
unit	UnitDefinitionAnnot	Unit of the values provided. It can be the time unit for reaction times or the concentration unit for calibration mode, depending on the mode.	None
id	str	Unique identifier of the ChromAnalyzer object. If not provided, the path is used as ID.	None
name	str	Name of the measurement. Defaults to "Chromatographic measurement".	'Chromatographic measurement'
silent	bool	If True, no success message is printed. Defaults to False.	False

Returns:

Name	Type	Description
ChromAnalyzer	ChromAnalyzer	ChromAnalyzer object containing the measurements.

read_thermo(path, ph, temperature, temperature_unit='C', mode=None, values=None, unit=None, id=None, name='Chromatographic measurement', silent=False) classmethod

Reads chromatographic data from a directory containing Thermo Scientific TX0 files. Measurements are assumed to be named alphabetically, allowing sorting by file name.

Parameters:

Name	Type	Description	Default
path	str	Path to the directory containing the TX0 files.	required
ph	float	pH value of the measurement.	required
temperature	float	Temperature of the measurement.	required
temperature_unit	UnitDefinitionAnnot	Unit of the temperature. Defaults to Celsius (C).	'C'
mode	Optional[Literal['timecourse', 'calibration']]	Mode of the data. If "timecourse", values should be a list of reaction times. If "calibration", values should be a list of concentrations. Defaults to None.	None
values	list[float]	A list of reaction times (for "timecourse" mode) or concentrations (for "calibration" mode), corresponding to each measurement in the directory.	None
unit	UnitDefinitionAnnot	Unit of the values provided. It can be the time unit for reaction times or the concentration unit for calibration mode, depending on the mode.	None
id	str	Unique identifier of the ChromAnalyzer object. If not provided, the path is used as ID.	None
name	str	Name of the measurement. Defaults to "Chromatographic measurement".	'Chromatographic measurement'
silent	bool	If True, no success message is printed. Defaults to False.	False

Returns:

Name	Type	Description
ChromAnalyzer	ChromAnalyzer	ChromAnalyzer object containing the measurements.

set_dilution_factor(dilution_factor)

Sets the dilution factor for all measurements.

to_enzymeml(name, calculate_concentration=True, extrapolate=False)

Creates an EnzymeML document from the data in the ChromAnalyzer.

Parameters:

Name	Type	Description	Default
name	str	Name of the EnzymeML document.	required
calculate_concentration	bool	If True, the concentrations of the species are calculated. Defaults to True.	True
extrapolate	bool	If True, the concentrations are extrapolated to if the measured peak areas are outside the calibration range. Defaults to False.	False

Returns:

Name	Type	Description
EnzymeMLDocument	EnzymeMLDocument	description

to_json(path)

Serialize the instance to a JSON file. Parameters: path (str | Path): The file path where the JSON data will be saved. If the parent directory does not exist, it will be created. Returns: None: This method does not return a value. It writes the instance's attributes to a JSON file at the specified path.

visualize(n_cols=2, figsize=(15, 10), show_peaks=True, show_processed=False, rt_min=None, rt_max=None, save_path=None, assigned_only=False, overlay=False)

Creates a matplotlib figure with subplots for each measurement.

Parameters:

Name	Type	Description	Default
n_cols	int	Number of columns in the subplot grid. Defaults to 2.	2
figsize	tuple[float, float]	Figure size in inches (width, height). Defaults to (15, 10).	(15, 10)
show_peaks	bool	If True, shows detected peaks. Defaults to True.	True
show_processed	bool	If True, shows processed signal. Defaults to False.	False
rt_min	float | None	Minimum retention time to display. If None, shows all data. Defaults to None.	None
rt_max	float | None	Maximum retention time to display. If None, shows all data. Defaults to None.	None
save_path	str | None	Path to save the figure. If None, the figure is not saved. Defaults to None.	None
assigned_only	bool	If True, only shows peaks that are assigned to a molecule. Defaults to False.	False
overlay	bool	If True, plots all chromatograms on a single axis. Defaults to False.	False

visualize_all(assigned_only=False, dark_mode=False, show=False)

Plots the fitted peaks of the chromatograms in an interactive figure.

Parameters:

Name	Type	Description	Default
assigned_only	bool	If True, only the peaks that are assigned to a molecule are plotted. Defaults to False.	False
dark_mode	bool	If True, the figure is displayed in dark mode. Defaults to False.	False

Returns:

Type	Description
Figure	go.Figure: description

visualize_spectra(dark_mode=False)

Plots all chromatograms in the ChromAnalyzer in a single plot.

Parameters:

Name	Type	Description	Default
dark_mode	bool	If True, the figure is displayed in dark mode. Defaults to False.	False

Returns:

Type	Description
Figure	go.Figure: The plotly figure object.