.. _tautomer_search:

---------------
Tautomer Search
---------------

Tautomer search is a specialized task in computational chemistry that focuses on identifying
the different tautomeric forms of a molecule. Tautomers are isomers that readily interconvert
by the movement of a hydrogen atom and a double bond. This process is crucial in drug discovery
and molecular modeling, as the tautomeric form of a molecule can significantly affect its
biological activity, stability, and interaction with targets.

Our advanced tautomer search engine employs state-of-the-art algorithms 
to efficiently discover stable tautomers while ensuring comprehensive 
coverage of the tautomerism landscape.

Methodology
===========

Tautomer generation happens after consecutive protonation and deprotonation site screening for a molecule. 
Centers for the protonation in the input molecular structure are determined and H\ :sup:`+` ions are added 
to the π and lone pair centers. The geometries are then optimized with the molecular charge increased by 
one. From the initial geometries, protons are removed one-by-one and the resulting input geometries are optimized. 
Through the consecutive protonation and deprotonation steps, an ensemble of tautomers is formed.  

Workflow Architecture
=====================

.. container:: architecture-diagram

    .. code-block:: text

        ┌──────────────────────────────┐
        │       **User Input**         │
        ├──────────────────────────────┤
        │ Atomic coordinates           │
        │ Charge and spin              │
        │ Optional:*xtb* pre-optimized │
        └────────────┬─────────────────┘
                     │
                     ▼
        ┌──────────────────────────────┐
        │ **Workflow Initialization**  │
        ├──────────────────────────────┤
        │ Identification and ranking   │
        │ of protonation sites.        │
        └────────────┬─────────────────┘
                     │
                     ▼
        ┌──────────────────────────────┐
        │ **H⁺ Addition**              │
        ├──────────────────────────────┤
        │ To the π and lone pair       │
        │ centers                      │
        └────────────┬─────────────────┘
                     │
                     ▼
        ┌──────────────────────────────┐
        │ **Deprotonation**            │
        ├──────────────────────────────┤
        │ Removal of protons from the  │
        │ initial structure            │
        └────────────┬─────────────────┘
                     │
                     ▼
        ┌──────────────────────────────┐
        │ **Tautomer Ensemble Out**    │
        ├──────────────────────────────┤
        │                              │
        └──────────────────────────────┘

Input Configuration
===================

The tautomer search requires minimal user input, emphasizing ease of use and automation:

.. grid:: 1 2 2 2
    :gutter: 2

    .. grid-item-card:: **Input Molecule**
        :text-align: left

        Upload your input molecule in a supported format (e.g., XYZ) or 
        you can give a SMILES string.
        The system will automatically generate the initial conformer.
        Check the :ref:`visualiser-input` section for more details.

    .. grid-item-card:: **Model**
        :text-align: left

        Select the computational model for the conformer search. 
        Options include:

        - GFN1
        - GFN2

    .. grid-item-card:: **Solvent**
        :text-align: left

        Choose the solvent model for the conformer search. 
        Options include:

        - Gas phase (Keep it None)
        - Implicit solvent (e.g., water)