Other utilites

careless includes a number of command-line utilities for performing common analyses and of careless outputs. These utilities and their command-line usage are documented below.

careless.cchalf

Compute CChalf from careless output.

usage: careless.cchalf [-h] [-s] [-i IMAGE] [-o OUTPUT]
                       [-m {spearman,pearson}] [-b BINS] [--overall]
                       mtz [mtz ...]

mtz: MTZs containing crossvalidation data from careless

-h, --help: show this help message and exit

-s, --show: Make a plot of the results and display it using matplotlib.

-i <image>, --image <image>: Make a plot of the results and save it to this filename. The filetype will be determined from the filename. Any filetype supported by your matplotlib version will be available.

-o <output>, --output <output>: Optionally save results to this file in csv format instead of printing them to the terminal.

-m {spearman,pearson}, --method {spearman,pearson}: Method for computing correlation coefficient (spearman or pearson). The Pearson CC uses maximum-likelihood weights. Pearson is the default.

-b <bins>, --bins <bins>: Number of resolution bins to use, the default is 10.

--overall: Pool all prediction mtz files into a single calculation rather than treating each file individually.

careless.ccanom

Compute CCanom from careless output.

usage: careless.ccanom [-h] [-s] [-i IMAGE] [-o OUTPUT]
                       [-m {pearson,spearman}] [-b BINS] [--overall]
                       mtz [mtz ...]

mtz: MTZs containing crossvalidation data from careless

-h, --help: show this help message and exit

-s, --show: Make a plot of the results and display it using matplotlib.

-i <image>, --image <image>: Make a plot of the results and save it to this filename. The filetype will be determined from the filename. Any filetype supported by your matplotlib version will be available.

-o <output>, --output <output>: Optionally save results to this file in csv format instead of printing them to the terminal.

-m {pearson,spearman}, --method {pearson,spearman}: Method for computing correlation coefficient (spearman or pearson). The Pearson CC uses maximum-likelihood weights. Pearson is the default.

-b <bins>, --bins <bins>: Number of resolution bins to use, the default is 10.

--overall: Pool all prediction mtz files into a single calculation rather than treating each file individually.

careless.ccpred

Compute CCpred from careless output.

usage: careless.ccpred [-h] [-s] [-i IMAGE] [-o OUTPUT]
                       [-m {pearson,spearman}] [-b BINS] [--overall]
                       mtz [mtz ...]

mtz: MTZ(s) containing prediction data from careless

-h, --help: show this help message and exit

-s, --show: Make a plot of the results and display it using matplotlib.

-i <image>, --image <image>: Make a plot of the results and save it to this filename. The filetype will be determined from the filename. Any filetype supported by your matplotlib version will be available.

-o <output>, --output <output>: Optionally save results to this file in csv format instead of printing them to the terminal.

-m {pearson,spearman}, --method {pearson,spearman}: Method for computing correlation coefficient (spearman or pearson). The Pearson CC uses maximum-likelihood weights. Pearson is the default.

-b <bins>, --bins <bins>: Number of resolution bins to use, the default is 10.

--overall: Pool all prediction mtz files into a single calculation rather than treating each file individually.

careless.completeness

Compute completeness from careless output.

usage: careless.completeness [-h] [-s] [-i IMAGE] [-o OUTPUT] [-b BINS] mtz

mtz: MTZ containing merged data from careless

-h, --help: show this help message and exit

-s, --show: Make a plot of the results and display it using matplotlib.

-i <image>, --image <image>: Make a plot of the results and save it to this filename. The filetype will be determined from the filename. Any filetype supported by your matplotlib version will be available.

-o <output>, --output <output>: Optionally save results to this file in csv format instead of printing them to the terminal.

-b <bins>, --bins <bins>: Number of resolution bins to use, the default is 10.

careless.history

Plot training history from careless output.

usage: careless.history [-h] [-o O] [-s] history_csv

history_csv: A _history.csv file generated by careless

-h, --help: show this help message and exit

-o <o>: Output image file name

-s, --show

careless.prior_b

Estimate the Wilson b-factor from unmerged data.

usage: careless.prior_b [-h] [-i INTENSITY_KEY] [-s SIGMA_KEY] [-b BINS]
                        [-c ISIGI_CUTOFF | -d DMIN] [-x DMAX] [--plot]
                        input [input ...]

input: MTZs or stream files containing unmerged data

-h, --help: show this help message and exit

-i <intensity_key>, --intensity-key <intensity_key>: Intensity column to use. The first one will be used by default.

-s <sigma_key>, --sigma-key <sigma_key>: Sigma intensity column to use. The first one will be used by default.

-b <bins>, --bins <bins>: Number of bins into which to divide the data.

-c <isigi_cutoff>, --isigi-cutoff <isigi_cutoff>: If this option is supplied, the script tries to estimate an appropriate resolutioncutoff from the signal to noise in resolution bins. The default value is 1.5 (I/SigI).

-d <dmin>, --dmin <dmin>: Minimum resolution cutoff in (Å) which overrides the more automated –isigi-cutoff.

-x <dmax>, --dmax <dmax>: Maximum resolution cutoff in (Å) which defaults to infinity.

--plot: Make a plot of the results and display it using matplotlib.

careless.rescale

Rescale careless output to match a given Wilson b-factor.

usage: careless.rescale [-h] -b WILSON_B mtz_in mtz_out

mtz_in: MTZs file containing unmerged data

mtz_out: Output mtz file name.

-h, --help: show this help message and exit

-b <wilson_b>, --wilson-b <wilson_b>: Target wilson b-factor.

careless.rsplit

Compute CChalf from careless output.

usage: careless.rsplit [-h] [-s] [-i IMAGE] [-o OUTPUT] [-b BINS] [--overall]
                       mtz [mtz ...]

mtz: MTZs containing crossvalidation data from careless

-h, --help: show this help message and exit

-s, --show: Make a plot of the results and display it using matplotlib.

-i <image>, --image <image>: Make a plot of the results and save it to this filename. The filetype will be determined from the filename. Any filetype supported by your matplotlib version will be available.

-o <output>, --output <output>: Optionally save results to this file in csv format instead of printing them to the terminal.

-b <bins>, --bins <bins>: Number of resolution bins to use, the default is 10.

--overall: Pool all prediction mtz files into a single calculation rather than treating each file individually.