iphasimulator.pha_melt_builder

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/.

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

PHAMeltBuilder

Build amorphous PHA melt systems.

Module Contents

class iphasimulator.pha_melt_builder.PHAMeltBuilder(root_dir='structure_database')

Build amorphous PHA melt systems.

paths

polymer_builder

run_command(command, workdir=None)

parse_polymer_name(polymer_name)

get_melt_name(polymer_names, number_of_polymers)

validate_melt_inputs(polymer_names, number_of_polymers)

ensure_built_polymer_exists(polymer_name)

ensure_gromacs_polymer_exists(polymer_name)

generate_polymer_melt(polymer_names, number_of_polymers, density=750)

run_acpype(polymer_name)

prepare_polyply_inputs(polymer_names, number_of_polymers, polymer_gromacs_files, melt_dir, melt_name)

run_polyply(polymer_names, number_of_polymers, polymer_gromacs_files, melt_dir, melt_name, density=750)

combine_itps(itp_files, output_file)

edit_acpype_topology_for_polyply(topology_file)

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