Command-line tools¶

ProteinDF_pytools installs a set of pdf-* command-line scripts on top of the proteindf_tools library. Each one is a thin wrapper that reads ProteinDF’s binary parameter files (pdfparam.mpac / HDF5) and other result files, and produces a report, plot, or converted file. Run any of them with -h / --help for the full list of options.

Command dispatcher¶

Script	Description
`pdf` (`pdfcmd.py`)	dispatch a `pdf-*` subcommand by name, e.g. `pdf report` runs `pdf-report.py`

Archiving, reporting & testing¶

Script	Description
`pdf-archive.py`	archive ProteinDF results
`pdf-archive-h5.py`	archive ProteinDF results (HDF5)
`pdf-report.py`	make a ProteinDF report
`pdf-report-h5.py`	make a ProteinDF report (HDF5)
`pdf-test.py`	compare ProteinDF results
`pdf-test-h5.py`	compare ProteinDF results (HDF5)
`pdf-test-eri.py`	test ERI (electron repulsion integral) values

Inspecting results¶

Script	Description
`pdf-env.py`	report the ProteinDF runtime environment
`pdf-atom-index.py`	output the atom index
`pdf-info-geom.py`	output the molecular geometry in XYZ format
`pdf-info-iteration.py`	output per-iteration geometry in XYZ format
`pdf-info-orb.py`	output orbital information
`pdf-info-xyz.py`	output the geometry as an XYZ file
`pdf-mat-info.py`	show matrix metadata (size, type, …)
`pdf-mat-show.py`	show matrix contents
`pdf-estimate-ao.py`	estimate the AO cell size
`pdf-show-profile.py`	[expert] show a profile from a `cProfile` stats file

Plotting¶

Script	Description
`pdf-plot-basisset.py`	plot a basis set
`pdf-plot-elevel.py`	plot energy levels (single, vertical)
`pdf-plot-mo-tracer.py`	plot energy levels across iterations
`pdf-plot-mat.py`	plot a matrix
`pdf-plot-decaymat.py`	plot a matrix (decay/thinning view)
`pdf-plot-dos.py`	plot the density of states
`pdf-plot-gvalues.py`	plot G-values
`pdf-plot-pop.py`	plot population analysis results
`pdf-plot-vector.py`	plot a vector

Population analysis & charges¶

Script	Description
`pdf-pop-resp.py`	calculate RESP charges
`pdf-pop-classo.py`	fit charges via constrained LASSO regression
`pdf-pop-ridge.py`	fit charges via ridge regression
`pdf-pop-rrms.py`	calculate the relative RMS (rrms) of a charge fit
`pdf-set-charges.py`	write fitted charges into a `pdfparam` file
`pdf-reg-harris.py`	register results in the Harris DB

Format conversion & input generation¶

Script	Description
`pdf-make-basis2.py`	build a `basis2` basis-set database file
`xyz2pdf.py`	make a ProteinDF input from an XYZ file
`xyz2gau.py`	make a Gaussian input from an XYZ file
`g0xeri2mpac.py`	convert Gaussian output to MessagePack