.. highlight:: none

.. _ref_cli:

====================================
Command line interface
====================================

PoseBusters provides the command ``bust`` for checking generated molecules
and optionally taking a conditioning protein or ligands into account.

Use ``bust`` to check a series of molecules within one ``.sdf`` file.

.. command-output:: bust generated_molecules.sdf --outfmt long
  :cwd: inputs
  :ellipsis: 21

Check a docked ligand or generated molecule conditioned on a protein.

.. command-output:: bust generated_ligands.sdf -p protein.pdb --outfmt long
  :cwd: inputs
  :ellipsis: 21

Check a series of re-docked ligands against the crystal ligand and protein.

.. command-output:: bust redocked_ligand.sdf -l crystal_ligand.sdf -p protein.pdb --outfmt long
  :cwd: inputs
  :ellipsis: 21

Use the ``-t`` option to bulk check multiple sets of files.

.. command-output:: bust -t molecule_table.csv --outfmt long
  :cwd: inputs
  :ellipsis: 21


Output format options
====================================

The short format is the default output format.

.. command-output:: bust generated_molecules.sdf --outfmt short
  :cwd: inputs

The long format lists each test result for each molecule/conformation.

.. command-output:: bust generated_molecules.sdf --outfmt long
  :cwd: inputs
  :ellipsis: 21

For copying and saving the output use the ``csv`` option.

.. command-output:: bust generated_molecules.sdf --outfmt csv
  :cwd: inputs


For the ``csv`` and ``long`` option, the ``--full-report`` option can
be used to show extra information beyond the pass/fail status of each test.

.. command-output:: bust generated_molecules.sdf --outfmt csv --full-report
  :cwd: inputs
  :ellipsis: 21



Saving the output
====================================

The ``--out`` option can be used to save the output to a file::

  bust generated_molecules.sdf --outfmt csv --out results.csv


Help
====================================

Running with the ``--help`` option prints information about the command line options.

.. command-output:: bust --help

.. command-output:: bust --version


.. Configuration settings
.. ====================================

.. PoseBusters will look for configuration parameters in a yaml file ``posebusters.yml``
.. in standard locations:

.. 1. ``/etc/posebusters.cfg`` or ``c:\posebusters\posebusters.cfg`` (system-wide),
.. 2. ``~/.config/posebusters.cfg`` (``$XDG_CONFIG_HOME``) and ``~/.posebusters.cfg`` (``$HOME``)
..    for global (user-wide) settings, and
.. 3. ``posebusters.cfg`` inside the working directory.
.. 4. File location provided by the ``--config`` command line option.

.. Settings from these files are merged in the listed order of preference:
.. user-defined values have higher priority than system-wide defaults
.. and project-wide settings will override all others, when defined.