Using jq to inspect OpenFE JSONs#

Sometimes you may want to get a sense of the contents of JSON files, but the files are too unwieldy to inspect one-by-one in a code editor.

jq is a helpful command-line tool that we recommend for for quickly inspecting JSON files.

Below is a common use-case to get you started, but you can do much more by checking out the jq manual.

To view all the top-level JSON keys, use jq "keys" filename.json, for example with a results JSON from the tutorial:

$ jq "keys" rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json
[
"estimate",
"protocol_result",
"uncertainty",
"unit_results"
]

Note

You can use "keys[]" instead of "keys" for a cleaner output.

Now that you know estimate is at the top-level of the JSON, you can use the following pattern to see the next level of keys:

$ jq ".estimate | keys " rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json
{
"magnitude",
"unit":,
":is_custom:":,
"pint_unit_registry":
}

If you want to show all the keys _and_ their values, simply omit | key from the query:

$ jq ".estimate" rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json
{
"magnitude": 23.347074789078682,
"unit": "kilocalorie / mole",
":is_custom:": true,
"pint_unit_registry": "openff_units"
}

This can be very helpful for quickly checking results for many files, for example:

$ jq ".estimate.magnitude" rbfe*.json
-14.925911852820793
-40.72063957254803
-27.76541486479537
-16.023754604070007
-57.38608716292447
-15.748326155729705
-39.933880531487326
-27.780933075807425
-16.76023951588401
-58.36294851896545
-19.038006312251575
-20.26856586311034
17.338257573349775
15.775784163095102
23.134622420900932
17.071712542470248
15.873122071409249
23.347074789078682

This Page