CLI¶

Installing the package gives you a plotprofile command. python -m plotprofile works too.

Data comes in as JSON files. Styling lives in a --config JSON file whose keys are exactly the ReactionProfilePlotter keyword arguments. Anything the config cannot express, use the Python API for.

plotprofile INPUT [-o OUT] [-f {png,svg,pdf,eps}] [--dpi N]
                  [--config FILE] [--secondary FILE] [--x FILE]
                  [--annotations FILE] [--point-labels FILE]

Data¶

Flag	Description
`INPUT`	JSON energies: `{"Pathway A": [0.0, 12.5, 2.9]}`, a bare list, or a list of lists. `null` leaves a gap.
`--secondary`	JSON series for the right-hand axis, e.g. bond lengths. See Secondary Axis.
`--x`	JSON list of real x coordinates, for a scan or an IRC. See Data Input.
`--annotations`	JSON object of segment annotations, `{"Step 1": [0, 3]}`. Given in indices.
`--point-labels`	JSON object of per-point labels.

Styling¶

plotprofile examples/input.json --config examples/config.json --annotations examples/annotations.json

examples/config.json:

{
  "curviness": 0.42,
  "point_type": "hollow",
  "linestyle": {"Pathway B": "--"},
  "axes": "box",
  "units": "kcal",
  "energy": "G",
  "legend": {"loc": "upper right", "prop": {"weight": "normal"}}
}

Nested keys work as they do in Python, so legend, y1 and y2 are objects.

Note

An unknown key is an error, not a warning: a typo that is merely logged gives a plot that is silently wrong.

A scan¶

plotprofile scan.json --secondary bonds.json --x coord.json --config scan_style.json -o irc -f svg

svg (or pdf) is what you want for a paper figure: vector, with the text left as real text. --dpi applies to png only.