diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/404.html b/404.html new file mode 100644 index 0000000..f6e7057 --- /dev/null +++ b/404.html @@ -0,0 +1,500 @@ + + + +
+ + + + + + + + + + + + + + + + +Plate
Graph
+flowchart TB
+ plate(Plate)
+ well(Well)
+ photometricmeasurement(PhotometricMeasurement)
+ initcondition(InitCondition)
+ blankstate(BlankState)
+ unitdefinition(UnitDefinition)
+ baseunit(BaseUnit)
+ unittype(UnitType)
+ plate(Plate) --> well(Well)
+ plate(Plate) --> unitdefinition(UnitDefinition)
+ plate(Plate) --> unitdefinition(UnitDefinition)
+ well(Well) --> initcondition(InitCondition)
+ well(Well) --> photometricmeasurement(PhotometricMeasurement)
+ well(Well) --> unitdefinition(UnitDefinition)
+ photometricmeasurement(PhotometricMeasurement) --> unitdefinition(UnitDefinition)
+ photometricmeasurement(PhotometricMeasurement) --> blankstate(BlankState)
+ initcondition(InitCondition) --> unitdefinition(UnitDefinition)
+ unitdefinition(UnitDefinition) --> baseunit(BaseUnit)
+ baseunit(BaseUnit) --> unittype(UnitType)
+
+ click plate "#plate" "Go to Plate"
+ click well "#well" "Go to Well"
+ click photometricmeasurement "#photometricmeasurement" "Go to PhotometricMeasurement"
+ click initcondition "#initcondition" "Go to InitCondition"
+ click blankstate "#blankstate" "Go to BlankState"
+ click unitdefinition "#unitdefinition" "Go to UnitDefinition"
+ click baseunit "#baseunit" "Go to BaseUnit"
+ click unittype "#unittype" "Go to UnitType"
+Description of a microtiter plate consisting of wells.
+id string
name string
wells list[Well]
date_measured string
temperatures* list[float]
temperature_unit* UnitDefinition
times list[float]
time_unit UnitDefinition
Description of a well on the plate.
+id* string
x_pos* integer
y_pos* integer
ph float
init_conditions list[InitCondition]
measurements list[PhotometricMeasurement]
volume float
volume_unit UnitDefinition
Description of a photometric measurement of a single well and wavelength on the plate.
+wavelength* float
absorption* list[float]
time* list[float]
time_unit* UnitDefinition
blank_states* list[BlankState]
Description of the initial condition of a species in a well.
+species_id* string
init_conc* float
conc_unit* UnitDefinition
Describes if the respective species contributes to the absorption signal.
+species_id* string
contributes_to_signal* boolean
Whether the species' absorption contributes to the absorption signal
+Default
: true
Represents a unit definition that is based on the SI unit system.
+id string
name string
base_units list[BaseUnit]
Represents a base unit in the unit definition.
+kind* UnitType
exponent* integer
multiplier float
scale float
Alias | +Value | +
---|---|
AMPERE |
+ampere | +
AVOGADRO |
+avogadro | +
BECQUEREL |
+becquerel | +
CANDELA |
+candela | +
CELSIUS |
+celsius | +
COULOMB |
+coulomb | +
DIMENSIONLESS |
+dimensionless | +
FARAD |
+farad | +
GRAM |
+gram | +
GRAY |
+gray | +
HENRY |
+henry | +
HERTZ |
+hertz | +
ITEM |
+item | +
JOULE |
+joule | +
KATAL |
+katal | +
KELVIN |
+kelvin | +
KILOGRAM |
+kilogram | +
LITRE |
+litre | +
LUMEN |
+lumen | +
LUX |
+lux | +
METRE |
+metre | +
MOLE |
+mole | +
NEWTON |
+newton | +
OHM |
+ohm | +
PASCAL |
+pascal | +
RADIAN |
+radian | +
SECOND |
+second | +
SIEMENS |
+siemens | +
SIEVERT |
+sievert | +
STERADIAN |
+steradian | +
TESLA |
+tesla | +
VOLT |
+volt | +
WATT |
+watt | +
WEBER |
+weber | +
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 |
+
+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 |
+
+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.
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 |
+
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.
+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:
+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. + |
+
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 |
++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 |
++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
+ |
+
+
+
+description + |
+
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_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 |
+
+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
+ |
+
+
+
+
|
+
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
+ |
+