iphasimulator.build_single_PHA_systems

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

Attributes

AVOGADRO

Functions

run_tleap(intleap_file, workdir)
write_tleap_file(path, content)
check_required_files(file_dict, keys)
calculate_ion_pairs_from_rst7(rst7_path, ...)
prepare_single_system_inputs(paths, polymer_name, ...)	Copy the already-built polymer PDB and PHA parameter files locally.
build_dry_PHA(polymer_name[, root_dir, forcefield, ...])	Build a dry single-chain PHA system from an already-built polymer.
build_solvated_PHA(polymer_name[, root_dir, ...])	Build a solvated single-chain PHA system from an already-built polymer.
build_solvated_PHA_ions(polymer_name[, root_dir, ...])	Build a solvated single-chain PHA system with ions.

Module Contents

iphasimulator.build_single_PHA_systems.AVOGADRO = 6.02214076e+23

iphasimulator.build_single_PHA_systems.run_tleap(intleap_file, workdir)

iphasimulator.build_single_PHA_systems.write_tleap_file(path, content)

iphasimulator.build_single_PHA_systems.check_required_files(file_dict, keys)

iphasimulator.build_single_PHA_systems.calculate_ion_pairs_from_rst7(rst7_path, concentration_molar)

iphasimulator.build_single_PHA_systems.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

iphasimulator.build_single_PHA_systems.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

iphasimulator.build_single_PHA_systems.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

iphasimulator.build_single_PHA_systems.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}