Command-line tool#

clop#

Group command.

clop [OPTIONS] COMMAND [ARGS]...

Options

--version#

Show the version and exit.

eq1#

pH-deps for Kd.

clop eq1 [OPTIONS] KD1 PKA PH

Arguments

KD1#

Required argument

PKA#

Required argument

PH#

Required argument

fit_titration#

Update old svd or band fit of titration spectra.

clop fit_titration [OPTIONS] CSV_FP NOTE_FP

Options

-d, --out <out>#

destination directory

-t <titration_type>#

titration type (default: pH)

Options:

pH | Cl

-b, --band <band>#

Integration interval from <1> to <2>

-v, --verbose#

increase output verbosity

Arguments

CSV_FP#

Required argument

NOTE_FP#

Required argument

fit_titration_global#

Update old svd or band fit of titration spectra.

clop fit_titration_global [OPTIONS] FILE

Options

-d, --out <out>#

destination directory

-t <titration_type>#

titration type (default: pH)

Options:

pH | Cl

-b, --boot <boot>#

Number of booting iterations

-v, --verbose#

increase output verbosity

Arguments

FILE#

Required argument

pr.enspire#

Save spectra as csv tables from EnSpire xls file.

clop pr.enspire [OPTIONS] CSV [NOTE_FP]

Options

-b, --band-intervals <bands>#

Label and band interval (format: LABEL LOWER UPPER)

-d, --out <out>#

Path to output results.

Default:

Meas-0.8.1

-v, --verbose#

Verbosity of messages.

Arguments

CSV#

Required argument

NOTE_FP#

Optional argument

pr.tecan#

Convert a list of plate reader acquisitions into titrations.

LIST_FILE : List of Tecan files and concentration values.

Save titrations as .dat files.

Fits all wells using 2 labels and produces:

  • K plot

  • ebar and (for selection) ebarZ plot

  • all_wells pdf

  • csv tables for all labelblocks and global fittings.

Notes: Buffer is always subtracted if scheme indicates buffer well positions.

clop pr.tecan [OPTIONS] LIST_FILE

Options

--dil <dil>#

Initial volume and additions

Default:

additions.pH

--norm#

Normalize using metadata (gain, flashes).

--scheme <scheme>#

Positions of buffer and controls wells.

Default:

scheme.txt

--bg#

Subtract buffer (scheme wells==’buffer’).

-k, --kind <kind>#

Kind of titration.

Default:

pH

Options:

pH | Cl

--weight, --no-weight#

Global fitting without relative residues weights.

Default:

False

--fit, --no-fit#

Perform also fit.

Default:

True

--fit-all#

Fit all exported data.

--confint <confint>#

Confidence value for the calculation of parameter errors.

Default:

0.95

--out <out>#

Path to output results.

Default:

out2

--pdf#

Full report in pdf file.

-t, --title <title>#

Title for some plots.

--Klim <klim>#

Range MIN, MAX (xlim) for plot_K.

--sel <sel>#

Errorbar plot for selection with K_min SA_min.

-v, --verbose#

Verbosity of messages.

Arguments

LIST_FILE#

Required argument

note_to_csv#

Convert a tab-separated data file into a CSV file.

note_to_csv [OPTIONS] NOTE

Options

-o, --output <output>#

Output CSV file.

-l, --labels <labels>#

Labels to be appended.

-t, --temp <temp>#

Temperature to be appended.

Arguments

NOTE#

Required argument