iphasimulator.build_single_PHA_systems
======================================

.. py:module:: iphasimulator.build_single_PHA_systems

.. autoapi-nested-parse::

   Build dry, solvated, and ionised single-chain PHA systems from already-built
   PHA polymers.



Attributes
----------

.. autoapisummary::

   iphasimulator.build_single_PHA_systems.AVOGADRO


Functions
---------

.. autoapisummary::

   iphasimulator.build_single_PHA_systems.run_tleap
   iphasimulator.build_single_PHA_systems.write_tleap_file
   iphasimulator.build_single_PHA_systems.check_required_files
   iphasimulator.build_single_PHA_systems.calculate_ion_pairs_from_rst7
   iphasimulator.build_single_PHA_systems.prepare_single_system_inputs
   iphasimulator.build_single_PHA_systems.build_dry_PHA
   iphasimulator.build_single_PHA_systems.build_solvated_PHA
   iphasimulator.build_single_PHA_systems.build_solvated_PHA_ions


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

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


.. py:function:: run_tleap(intleap_file, workdir)

.. py:function:: write_tleap_file(path, content)

.. py:function:: check_required_files(file_dict, keys)

.. py:function:: calculate_ion_pairs_from_rst7(rst7_path, concentration_molar)

.. py:function:: prepare_single_system_inputs(paths, polymer_name, output_dir)

   Copy the already-built polymer PDB and PHA parameter files locally.

   Expected monomer-unit parameter filenames now follow:

       hP3HB.prepin
       mP3HB.prepin
       tP3HB.prepin

   The filepath manager should return these as:

       head_prepin
       mainchain_prepin
       tail_prepin
       frcmod


.. py:function:: build_dry_PHA(polymer_name, root_dir='structure_database', forcefield='gaff2', box_radius=20.0)

   Build a dry single-chain PHA system from an already-built polymer.

   Output name:
       {polymer_name}_dry


.. py:function:: build_solvated_PHA(polymer_name, root_dir='structure_database', forcefield='gaff2', water_leaprc='water.tip3p', water_box='TIP3PBOX', box_radius=20.0)

   Build a solvated single-chain PHA system from an already-built polymer.

   Output name:
       {polymer_name}_solvated


.. py:function:: build_solvated_PHA_ions(polymer_name, root_dir='structure_database', forcefield='gaff2', water_leaprc='water.tip3p', water_box='TIP3PBOX', box_radius=20.0, salt='KCl', pos_ion='K+', neg_ion='Cl-', ion_conc=0.15)

   Build a solvated single-chain PHA system with ions.

   Output name:
       {polymer_name}_solvated_{ion_names}_{ion_concentration}