How to use Pandora?¶

Quickstart is a single walkthrough of one typical workflow. This section is the per-component reference underneath it — one page per component, covering every function's signature, edge cases, and (where one exists) the equivalent pandora CLI subcommand.

Most pages open with a short setup block (parse a fixture, canonicalise it) that the rest of the page's examples build on — skim that first if you're jumping straight to a page rather than reading in order.

Library vs. CLI¶

Every operation that a pandora subcommand wraps is shown twice:

Call the Python function directly — for scripting the pipeline in
one process, or when you need something a subcommand doesn't
expose (a keyword argument, an in-memory object).

The equivalent pandora <subcommand> invocation — for running a
stage from the shell over a directory of files, chaining it with
the next stage's --input-dir.

Both call the same underlying function; the CLI just reads/writes files where the library form passes objects in memory. A handful of steps (loading a policy, filtering ligands standalone, reshaping records) have no CLI equivalent — those pages say so inline instead of showing an empty tab.

Pages¶

See Policies for every canonicalisation/curation policy field, and Functions / Schemas for generated API reference.