.. Qpi-Pharma documentation master file, created by
   sphinx-quickstart on Mon May 19 10:37:03 2025.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

QpiAI-Pharma documentation
==========================



Welcome to **QpiAI-Pharma**, the next-generation computational chemistry platform specifically 
designed for *computational chemists* and *drug discovery scientists*. 
Our platform combines the power of quantum mechanics, machine learning, 
and high-performance computing to accelerate molecular research and drug development.

Getting Started
---------------

QpiAI-Pharma provides powerful computational tools for molecular analysis and drug discovery.
Whether you're calculating molecular properties, optimizing geometries, or running 
molecular dynamics simulations, our platform offers the performance and accuracy you need.


.. toctree::
   :maxdepth: 2
   :caption: Visualiser:

   user_guide/visualiser_input

Available Tasks
---------------

.. toctree::
   :maxdepth: 2
   :caption: Computational Chemistry Tasks:

   tasks/single_point_energy
   tasks/geometry_optimization
   tasks/freq_ir
   tasks/orient_reactants
   tasks/reaction_path_search
   tasks/tsopt
   tasks/pes_scan
   tasks/irc_user_guide

.. toctree::
   :maxdepth: 2
   :caption: Drug Discovery Tasks:

   tasks/conformer_search
   tasks/tautomer_search
   tasks/ligand_preparation
   tasks/protein_preparation
   tasks/molecular_docking
   tasks/adme_guide

Workflows
---------
Workflows in QpiAI-Pharma provide a robust and flexible framework for automating complex computational chemistry processes. 
These predefined sequences of tasks enable users to efficiently execute multi-step analyses, 
ensuring both reproducibility and ease of use.

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

   .. grid-item::
      :class: card-highlight

      **🔬 Workflow Example**

      **⚙️ Geometry Optimization:**  
      Initiated at a lower level of theory to efficiently determine molecular structures with minimal computational cost.

      **📈 Energy Calculation:**  
      Performed at a higher level of theory to obtain accurate energy values using the optimized geometry.

      **🧠 QpiAI-Pharma:**  
      Automates and streamlines multi-stage molecular optimizations, including transition state searches and advanced quantum chemistry tasks.



Beyond the comprehensive suite of predefined workflows, 
QpiAI-Pharma empowers users to construct custom workflows by chaining together individual tasks. 
This flexibility extends to:

**Parameter Customization:** Users can fine-tune the parameters of each task within a workflow.

**Execution Order Definition:** The sequence of task execution can be precisely defined to meet specific analytical requirements.

**Level of Theory Specification:** The computational level of theory can be specified independently for different stages of a workflow.

**Conditional Logic Integration:** Advanced users can incorporate conditional logic to manage diverse scenarios and optimize workflow 
execution based on intermediate results.
This powerful workflow capability in QpiAI-Pharma 
facilitates sophisticated computational chemistry studies, 
accelerating research and development efforts. 


.. toctree::
   :maxdepth: 2
   :caption: Workflows:

   workflows/multistage_optimization
   workflows/transition_state_search


Support
-------

.. toctree::
   :maxdepth: 2
   :caption: Help & Support:

   support/contact


.. Indices and tables
.. ==================

.. * :ref:`genindex`
.. * :ref:`modindex`
.. * :ref:`search`