Solution Builder
================

Create Solution Builder project
-------------------------------

To begin, you must first have a :doc:`pdbreader` project. E.g.::

   # alt: pdbreader_project_id = pdbreader.projectId
   pdbreader_project_id = '78080ec8-bfcd-4141-8f22-f0ae805374ff'

   sbuilder = molcube.create_solution_builder_project()
   assert sbuilder.create_project(title="my_solution_project",
      pdbreader_project_id=pdbreader_project_id)

We will combine the individual components to build the system for molecular dynamics (MD) simulation. The following arguments are available for the method:

* boxShape (str): System box shape (default: cubic)
* margin (float): Box margin around the solute, dynamically applied based on solute size (default: 10.0).
* boxSize (float, optional): Fixed box size in Å. When specified, overrides margin-based sizing (default: None).
* ions (str): Type of ions to use (default: "kcl").
* ionConc (float): Ion concentration (default: 0.15).
* neutralize (bool): Whether to neutralize the system (ion-related option) (default: False).
* temperature (float): Temperature for the system in Kelvin (default: 310.0).
* useHmr (bool): Whether to use hydrogen mass repartitioning (default: False).
* mdEngines (list[str]): List of molecular dynamics engines to use (default: ['openmm']).

The available options for ions and mdengine are as follows:

* boxShape: ['cubic', 'truncated_octahedron']
* ions: ['kcl', 'nacl', 'cacl2']
* mdEngines: ['openmm', 'amber', 'gromacs', 'namd', 'genesis', 'desmond']

**Note**: Both ``margin`` and ``boxSize`` are box sizing options, but only one will be applied:

* ``margin``: Creates a box that dynamically fits the solute with the specified margin around it
* ``boxSize``: Sets a fixed box size regardless of solute dimensions
* If ``boxSize`` is provided, it takes precedence and ``margin`` is ignored

::

   mdEngines = ['openmm', 'gromacs']
   assert sbuilder.generate_system(mdEngines=mdEngines)