iphasimulator.system_builder_packmol
====================================

.. py:module:: iphasimulator.system_builder_packmol

.. autoapi-nested-parse::

   Advanced Packmol-based solvated-system builder.

   This module is intentionally separate from the simple GROMACS solvate/genion
   route. It prepares Packmol inputs for future realistic polymer simulations while
   keeping the quick validation workflow lightweight.



Attributes
----------

.. autoapisummary::

   iphasimulator.system_builder_packmol.AVOGADRO_CONSTANT
   iphasimulator.system_builder_packmol.LITERS_PER_NM3
   iphasimulator.system_builder_packmol.TIP3P_WATER_DENSITY_PER_NM3
   iphasimulator.system_builder_packmol.TIP3P_WATER_PDB
   iphasimulator.system_builder_packmol.SODIUM_PDB
   iphasimulator.system_builder_packmol.CHLORIDE_PDB


Classes
-------

.. autoapisummary::

   iphasimulator.system_builder_packmol.PackmolBuildResult


Functions
---------

.. autoapisummary::

   iphasimulator.system_builder_packmol.estimate_tip3p_water_count
   iphasimulator.system_builder_packmol.estimate_ion_pairs
   iphasimulator.system_builder_packmol.build_packmol_solvated_system


Module Contents
---------------

.. py:data:: AVOGADRO_CONSTANT
   :value: 6.02214076e+23


.. py:data:: LITERS_PER_NM3
   :value: 1e-24


.. py:data:: TIP3P_WATER_DENSITY_PER_NM3
   :value: 33.367


.. py:data:: TIP3P_WATER_PDB
   :value: Multiline-String

   .. raw:: html

      <details><summary>Show Value</summary>

   .. code-block:: python

      """HETATM    1  O   WAT A   1       0.000   0.000   0.000  1.00  0.00           O
      HETATM    2  H1  WAT A   1       0.096   0.000   0.000  1.00  0.00           H
      HETATM    3  H2  WAT A   1      -0.024   0.093   0.000  1.00  0.00           H
      END
      """

   .. raw:: html

      </details>



.. py:data:: SODIUM_PDB
   :value: Multiline-String

   .. raw:: html

      <details><summary>Show Value</summary>

   .. code-block:: python

      """HETATM    1 NA   NA  A   1       0.000   0.000   0.000  1.00  0.00          Na
      END
      """

   .. raw:: html

      </details>



.. py:data:: CHLORIDE_PDB
   :value: Multiline-String

   .. raw:: html

      <details><summary>Show Value</summary>

   .. code-block:: python

      """HETATM    1 CL   CL  A   1       0.000   0.000   0.000  1.00  0.00          Cl
      END
      """

   .. raw:: html

      </details>



.. py:class:: PackmolBuildResult

   Files and counts produced by the Packmol solvated-system builder.


   .. py:attribute:: output_dir
      :type:  pathlib.Path


   .. py:attribute:: solvated_pdb_path
      :type:  pathlib.Path


   .. py:attribute:: packmol_input_path
      :type:  pathlib.Path


   .. py:attribute:: packmol_log_path
      :type:  pathlib.Path


   .. py:attribute:: copied_polymer_paths
      :type:  tuple[pathlib.Path, ...]


   .. py:attribute:: support_structure_paths
      :type:  tuple[pathlib.Path, ...]


   .. py:attribute:: box_size_nm
      :type:  float


   .. py:attribute:: water_count
      :type:  int


   .. py:attribute:: sodium_count
      :type:  int


   .. py:attribute:: chloride_count
      :type:  int


   .. py:attribute:: polymer_counts
      :type:  tuple[int, ...]


.. py:function:: estimate_tip3p_water_count(box_size_nm: float) -> int

   Estimate the number of TIP3P waters for a cubic box at bulk density.


.. py:function:: estimate_ion_pairs(box_size_nm: float, nacl_concentration_molar: float) -> int

   Estimate NaCl ion pairs from molarity and cubic box volume.


.. py:function:: build_packmol_solvated_system(polymer_structures: collections.abc.Sequence[str | pathlib.Path], output_dir: str | pathlib.Path, *, box_size_nm: float, water_model: str = 'tip3p', nacl_concentration_molar: float = 0.15, num_polymers: int | collections.abc.Sequence[int] = 1, polymer_spacing_nm: float = 1.0, packmol_command: str = 'packmol', run_packmol: bool = True, runner=subprocess.run) -> PackmolBuildResult

   Build an advanced solvated PHA/TIP3P/NaCl initial PDB using Packmol.

   This route does not replace the standard GROMACS solvate/genion workflow.
   It is an advanced builder for future realistic polymer simulations and can
   later be extended to enzyme/polymer systems. Membranes are intentionally not
   implemented here yet.