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 Reaction Analysis (PyMOL)
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This page covers reaction pathway visualization using PyMOL, including IRC trajectories and molecular dynamics during
chemical reactions.

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 IRC Jobs
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Generate IRC movies and trajectory visualizations.

.. code:: bash

   chemsmart run [OPTIONS] mol [MOL_OPTIONS] irc [SUBCMD_OPTIONS]

IRC Options
===========

.. list-table::
   :header-rows: 1
   :widths: 30 15 55

   -  -  Option
      -  Type
      -  Description

   -  -  ``-r, --reactant``
      -  string
      -  IRC file for reactant side

   -  -  ``-p, --product``
      -  string
      -  IRC file for product side

   -  -  ``-a, --all``
      -  string
      -  File containing complete IRC trajectory

.. note::

   IRC jobs inherit all visualization options.

Basic Usage
===========

Standard IRC visualization:

.. code:: bash

   chemsmart run mol -f irc_output.log irc

With separate reactant/product files:

.. code:: bash

   chemsmart run mol -f ts_structure.xyz irc -r reactant.log

From complete trajectory:

.. code:: bash

   chemsmart run mol -f ts.xyz irc -a full_irc_trajectory.log