iphasimulator.pha_melt_builder
==============================

.. py:module:: iphasimulator.pha_melt_builder

.. autoapi-nested-parse::

   PHA polymer melt construction tools.

   This module builds amorphous PHA melt systems from previously built
   single-chain PHA polymers.

   Workflow
   --------
   1. Validate polymer names and polymer counts.
   2. Locate or generate required single-chain PHA files.
   3. Convert Amber topologies to GROMACS format using ACPYPE.
   4. Build amorphous polymer melts using Polyply.
   5. Save final melt outputs into structure_database/PHA_melts/.

   .. rubric:: Notes

   This module is deliberately separate from pha_builder.py because melt
   construction is a system-building task rather than a single-polymer
   parameterisation task.



Classes
-------

.. autoapisummary::

   iphasimulator.pha_melt_builder.PHAMeltBuilder


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

.. py:class:: PHAMeltBuilder(root_dir='structure_database')

   Build amorphous PHA melt systems.


   .. py:attribute:: paths


   .. py:attribute:: polymer_builder


   .. py:method:: run_command(command, workdir=None)


   .. py:method:: parse_polymer_name(polymer_name)


   .. py:method:: get_melt_name(polymer_names, number_of_polymers)


   .. py:method:: validate_melt_inputs(polymer_names, number_of_polymers)


   .. py:method:: ensure_built_polymer_exists(polymer_name)


   .. py:method:: ensure_gromacs_polymer_exists(polymer_name)


   .. py:method:: generate_polymer_melt(polymer_names, number_of_polymers, density=750)


   .. py:method:: run_acpype(polymer_name)


   .. py:method:: prepare_polyply_inputs(polymer_names, number_of_polymers, polymer_gromacs_files, melt_dir, melt_name)


   .. py:method:: run_polyply(polymer_names, number_of_polymers, polymer_gromacs_files, melt_dir, melt_name, density=750)


   .. py:method:: combine_itps(itp_files, output_file)


   .. py:method:: edit_acpype_topology_for_polyply(topology_file)


   .. py:method:: test_polymer_melt_simulation(melt_name, topology_file, coordinate_file, run_name='Test', test_steps=1000, temperature=300, timestep=1.0)