Module reference
================

The GoodVibes Python package is organised into the modules listed below.
Most users will only need :py:mod:`goodvibes.api` (the v4.2 façade);
the lower-level modules are documented for advanced/embedded use.

Public API (v4.2)
-----------------

.. automodule:: goodvibes.api
   :members:
   :undoc-members:
   :show-inheritance:

CLI orchestrator
----------------

.. automodule:: goodvibes.GoodVibes
   :members:
   :undoc-members:
   :show-inheritance:

Thermochemistry engine
----------------------

.. automodule:: goodvibes.thermo
   :members:
   :undoc-members:
   :show-inheritance:

Native parsers and ``QCData``
-----------------------------

.. automodule:: goodvibes.io
   :members:
   :undoc-members:
   :show-inheritance:

ASE (extended XYZ) bridge
-------------------------

.. automodule:: goodvibes.ase_helper
   :members:
   :undoc-members:
   :show-inheritance:

Output rendering (Rich tables, JSON)
------------------------------------

.. automodule:: goodvibes.output
   :members:
   :undoc-members:
   :show-inheritance:

Selectivity (v4.1 redesign)
---------------------------

.. automodule:: goodvibes.selectivity
   :members:
   :undoc-members:
   :show-inheritance:

PES — data model (v4.2)
-----------------------

.. automodule:: goodvibes.pes_model
   :members:
   :undoc-members:
   :show-inheritance:

PES — loader and dispatcher (v4.2)
----------------------------------

.. automodule:: goodvibes.pes_loader
   :members:
   :undoc-members:
   :show-inheritance:

PES — legacy line-based parser (deprecated)
-------------------------------------------

.. automodule:: goodvibes.pes_legacy
   :members:
   :undoc-members:
   :show-inheritance:

PES — true-YAML parser (v4.2)
-----------------------------

.. automodule:: goodvibes.pes_yaml
   :members:
   :undoc-members:
   :show-inheritance:

PES — back-compat surface and reaction-profile plot
---------------------------------------------------

.. automodule:: goodvibes.pes
   :members:
   :undoc-members:
   :show-inheritance:

Sorting and duplicate detection
-------------------------------

.. automodule:: goodvibes.sort
   :members:
   :undoc-members:
   :show-inheritance:

File validation
---------------

.. automodule:: goodvibes.validation
   :members:
   :undoc-members:
   :show-inheritance:

Solvent database
----------------

.. automodule:: goodvibes.media
   :members:
   :undoc-members:
   :show-inheritance:

Frequency scaling factors (Truhlar v5)
--------------------------------------

.. automodule:: goodvibes.vib_scale_factors
   :members:
   :undoc-members:
   :show-inheritance:

Constants
---------

.. automodule:: goodvibes.constants
   :members:
   :undoc-members:
   :show-inheritance:

Utilities
---------

.. automodule:: goodvibes.utils
   :members:
   :undoc-members:
   :show-inheritance:

Top-level package
-----------------

.. automodule:: goodvibes
   :members:
   :undoc-members:
   :show-inheritance:
