API Reference of PlateManager

Bases: BaseModel

add_molecule(molecule, constant=None)

Adds a molecule to the list of molecules. Allows to update the constant attribute of the molecule.

Parameters:

Name	Type	Description	Default
molecule	Molecule	Molecule object to add to the list of molecules.	required
constant	bool | None	Indicates whether the constant attribute of the molecule should be updated. Defaults to None.	None

add_protein(protein, constant=None)

Adds a protein to the list of proteins. Allows to update the constant attribute of the protein.

Parameters:

Name	Type	Description	Default
protein	Protein	Protein object to add to the list of proteins.	required
constant	bool | None	Indicates whether the constant attribute of the protein should be updated. Defaults to None.	None

assign_init_conditions(species, init_conc, conc_unit, to, ids=None, contributes_to_signal=None, silent=False)

Assigns a Molecule or Protein to specific wells on the plate based on the provided criteria. In this way the initial concentration of the species can be set for the respective wells in a row, column, all wells or all wells except for the specified. During the assignment, either an array of initial concentrations or a single initial concentration can be provided. If a single initial concentration is provided, it is assigned to all wells of e.g., a row or column. If an array of initial concentrations is provided, the length of the array must match the number of wells in the row or column.

Tip

For complex assignment scenarios, consider using the assign_init_conditions_from_spreadsheet function.

Parameters:

Name	Type	Description	Default
species	Molecule | Protein	The species to assign to the wells.	required
init_conc	float | list[float]	The initial concentration(s) of the species.	required
conc_unit	UnitDefinition	The unit of concentration.	required
to	ASSIGN_CASE	The target location(s) for assigning the species. It should be one of the allowed cases.	required
ids	str | int | list[str] | list[int]	The ID(s) of the target wells, rows, or columns. Defaults to None.	None
contributes_to_signal	bool	Indicates if the assigned species contributes to the signal. Defaults to None.	None
silent	bool	If True, no output is printed. Defaults to False.	False

Raises:

Type	Description
AttributeError	If the species does not exist in the list of molecules or proteins.
AttributeError	If the 'to' argument is not a valid ASSIGN_CASE.

Returns:

Type	Description
	None

assign_init_conditions_from_spreadsheet(conc_unit, path, header=0, index=0, silent=False)

Assign initial concentrations from an Excel spreadsheet to the wells on the plate.

Note

This function goes through the sheets in an excel spreadsheet. If the sheet name matches the id of a protein or molecule defined for the plate, the initial concentration form the plate map in the excel spreadsheet is assigned to the respective well.

The excel spreadsheet must have the following structure:

• The first row must contain the column numbers from 1 to 12.
• The first column must contain the row letters from A to H.
• If a cell is left empty for a species, the species is not assigned to the well.
• If the initial concentration is 0, the species is added to the well. This is useful for specifying a product which is not present in the initial reaction mixture, but is formed during the reaction.

Parameters:

Name	Type	Description	Default
conc_unit	UnitDefinition	The unit of concentration.	required
path	str	Path to the Excel spreadsheet.	required
header	int	Row to use as the column names. Defaults to 0.	0
index	int	Column to use as the row labels. Defaults to 0.	0
silent	bool	If True, no output is printed. Defaults to False.	False

blank_species(species, wavelength=None, silent=False)

Blank the signal contribution of a species at a given wavelength. Therefore, control wells of that species must be present on the plate.

Parameters:

Name	Type	Description	Default
species	Molecule | Protein	The species to blank.	required
wavelength	float	The wavelength at which to blank the species.	None
silent	bool	If True, no output is printed. Defaults to False.	False

Raises:

Type	Description
ValueError	If no wells are found to calculate the absorption contribution of the species.

create_assignment_spreadsheet(path='assignment.xlsx', overwrite=False)

Create an Excel spreadsheet for assigning initial concentrations. The spreadsheet contains a separate sheet for each species defined on the plate, with validation to allow only numerical values in the input cells and prevent changes to all other cells.

Parameters:

Name	Type	Description	Default
path	str	Path to save the assignment spreadsheet. Defaults to "assignment.xlsx".	'assignment.xlsx'
overwrite	bool	If True, the file is overwritten if it already exists. Defaults to False.	False

define_molecule(id, pubchem_cid, name=None, constant=False)

Defines a molecule which can be used to assign to wells on the plate. If no name is provided, the molecule name is retrieved from the PubChem database. If the molecule is not known in the PubChem database, please specify pubchem_cid=-1.

Parameters:

Name	Type	Description	Default
id	str	Internal identifier of the molecule such as s0 or ABTS.	required
pubchem_cid	int	PubChem CID of the molecule.	required
name	str | None	Name of the molecule. Defaults to None.	None
constant	bool	Indicates whether the molecule concentration is constant throughout the experiment. Defaults to False.	False

Raises:

Type	Description
ValueError	If the PubChem CID is not an integer.
ValueError	If the name is not provided and the PubChem CID is not available.

Returns:

Name	Type	Description
Molecule	Molecule	Molecule object.

define_protein(id, name, uniprot_id=None, sequence=None, constant=True)

Defines a protein which can be used to assign to wells on the plate.

Parameters:

Name	Type	Description	Default
id	str	Internal identifier of the protein such as p0, MAT_K78M or GFP.	required
name	str	Name of the protein.	required
uniprot_id	str | None	UniProt ID of the protein. Defaults to None.	None
sequence	str | None	Amino acid sequence of the protein. Defaults to None.	None
constant	bool	Indicates whether the protein concentration is constant throughout the experiment. Defaults to True.	True

Returns:

Name	Type	Description
Protein	Protein	Protein object.

get_calibrator(molecule, cutoff=None, wavelength=None)

Initialize a CaliPytion Calibrator for a molecule on the plate. The calibrator allows eighter to proceed with predefined suitable calibration models or to define and fit custom models. For more information on the CaliPytion, please refer to the (documentation)[https://fairchemistry.github.io/CaliPytion/usage/]

Parameters:

Name	Type	Description	Default
molecule	Molecule	The molecule for which to initialize the calibrator.	required
cutoff	float | None	The cutoff value for the calibration. Absorption values above the cutoff are not considered for the calibration. Defaults to None.	None
wavelength	float | None	The wavelength at which to initialize the calibrator. If only one wavelength was measured, the wavelength is automatically set. Defaults to None.	None

Returns:

Name	Type	Description
Calibrator	Calibrator	Calibrator object.

get_species(id)

Get a species from the list of molecules and proteins by its id.

Parameters:

Name	Type	Description	Default
id	str	The id of the species.	required

Raises:

Type	Description
ValueError	If the species with the given id is not found.

Returns:

Type	Description
Protein | Molecule	Protein | Molecule: The species object.

get_well(id)

Get a well from the plate by its id.

Parameters:

Name	Type	Description	Default
id	str	The id of the well.	required

Raises:

Type	Description
ValueError	If the well with the given id is not found.

Returns:

Name	Type	Description
Well	Well	The well object.

read_biotek(path, ph=None, name=None) classmethod

Read a *.xlsx file exported from a BioTek Epoch 2 software and create a PlateManager object.

Parameters:

Name	Type	Description	Default
path	str	Path to the BioTek Epoch 2 file.	required
ph	float | None	The pH value of the measurements. Defaults to None.	None
name	str | None	Name of the plate. Defaults to None.	None

Returns:

Name	Type	Description
PlateManager	PlateManager	PlateManager object.

read_multiskan_sky(path, ph=None, name=None) classmethod

Read a *.xlsx file exported from a Multiskan Sky and create a PlateManager object.

Parameters:

Name	Type	Description	Default
path	str	Path to the Multiskan Sky file.	required
ph	float | None	The pH value of the measurements. Defaults to None.	None
name	str | None	Name of the plate. Defaults to None.	None

Returns:

Name	Type	Description
PlateManager	PlateManager	The PlateManager object.

read_multiskan_spectrum_1500(path, time, time_unit, temperature, temperature_unit=C, ph=None, name=None) classmethod

Read a *.txt file exported from a Multiskan Spectrum 1500 and create a PlateManager object.

Parameters:

Name	Type	Description	Default
name	str	Name of the plate.	None
path	str	Path to the Multiskan Spectrum 1500 file.	required
time	list[float]	List of time points.	required
time_unit	UnitDefinition	Unit of time.	required
temperature	float	Temperature of the measurements.	required
temperature_unit	UnitDefinition	Unit of temperature. Defaults to C.	C
ph	float | None	The pH value of the measurements. Defaults to None.	None

Returns:

Name	Type	Description
_type_	PlateManager	description

read_new_device(path, temperature, ph=None, name=None, temperature_unit=C) classmethod

Read a *.xlsx file exported from a new device and create a PlateManager object.

Parameters:

Name	Type	Description	Default
path	str	Path to the file.	required
temperature	float	The temperature of the measurements.	required
ph	float | None	The pH value of the measurements. Defaults to None.	None
name	str | None	Name of the plate. Defaults to None.	None
temperature_unit	UnitDefinition	Unit of temperature. Defaults to C.	C

Returns:

Name	Type	Description
PlateManager	PlateManager	PlateManager object.

read_spectra_max_190(path, ph=None, name=None) classmethod

Read a *.txt file exported from a SpectraMax 190 software and create a PlateManager object.

Parameters:

Name	Type	Description	Default
path	str	Path to the SpectraMax 190 file.	required
ph	float | None	The pH value of the measurements. Defaults to None.	None
name	str | None	Name of the plate. Defaults to None.	None

Returns:

Name	Type	Description
PlateManager	PlateManager	PlateManager object.

read_tecan_spark(path, ph=None, name=None) classmethod

Read a *.xlsx TECAN Spark file and create a PlateManager object.

Parameters:

Name	Type	Description	Default
path	str	Path to the TECAN Spark file.	required
ph	float | None	The pH value of the measurements. Defaults to None.	None
name	str | None	Name of the plate. Defaults to None.	None

Returns:

Name	Type	Description
PlateManager	PlateManager	PlateManager object.

read_tekan_magellan(path, wavelength, ph=None, name=None) classmethod

Read a *.xlsx file exported from a TECAN Magellan software and create a PlateManager object.

Parameters:

Name	Type	Description	Default
path	str	Path to the Magellan file.	required
wavelength	float	The wavelength of the measurements.	required
ph	Optional[float]	The pH value of the measurements. Defaults to None.	None
name	Optional[str]	Name of the plate. Defaults to None.	None

Returns:

Name	Type	Description
PlateManager	PlateManager	PlateManager object.

set_absorption_contribution(species, contributes_to_signal, wavelength=None, silent=False)

Set the contribution of a species to the signal in all wells.

Parameters:

Name	Type	Description	Default
species	Molecule | Protein	The species for which to set the contribution to the signal.	required
contributes_to_signal	bool	If True, the species contributes to the signal. If False, the species does not contribute to the signal.	required
wavelength	float | None	The wavelength at which to set the contribution to the signal. Defaults to None.	None
silent	bool	If True, no output is printed. Defaults to False.	False

slice_data(start, end)

Slices the time and absorption data of all wells in the plate that only contains the data between the start and end time.

Parameters:

Name	Type	Description	Default
start	float	Start time of the slice.	required
end	float	End time of the slice.	required

to_enzymeml(detected_molecule, well_ids=None, catalyzed_only=True, name=None, to_concentration=False, extrapolate=False, wavelength=None, silent=False)

Convert the plate to an EnzymeML document.

Parameters:

Name	Type	Description	Default
name	str | None	Name of the EnzymeML document. Defaults to the name of the plate.	None
detected_molecule	Molecule	The molecule that was detected in the wells.	required
well_ids	list[str] | None	List of well ids to include in the EnzymeML document. If not provided, all wells are included. Defaults to None.	None
to_concentration	bool	If True, the signal is converted to concentration. Therefore, a calibrator must be defined for the respective molecule. Defaults to False.	False
extrapolate	bool	If True, and to_concentration is True, measured absorption values that are outside the range of the calibrator are extrapolated. Defaults to False.	False
catalyzed_only	bool	If True, only wells that contain the detected molecule and a protein are included in the EnzymeML document. Defaults to True.	True
wavelength	float | None	If multiple wavelengths were measured, the wavelength for which to convert the signal to concentration needs to be specified. Defaults to None.	None
silent	bool	If True, no output is printed. Defaults to False.	False

Returns:

Name	Type	Description
EnzymeMLDocument	EnzymeMLDocument	pyenzyme EnzymeMLDocument object.

visualize(zoom=False, wavelengths=[], darkmode=False)

Visualize the plate.

Parameters:

Name	Type	Description	Default
zoom	bool	If False, the scaling of the signal (y-axis) is the same for all wells. If True, the scaling is adjusted for each well. Defaults to False.	False
wavelengths	list[float]	Only visualize the signal at the specified wavelengths. If not specified, all wavelengths are visualized. Defaults to [].	[]
darkmode	bool	If True, the plot is displayed in dark mode. Defaults to False.	False