iphasimulator.pha_filepath_manager

PHA structure database management.

This module provides lightweight management classes for a PHA-specific structure database.

Classes

PHAFileManager: Handles directory creation, filepath construction and simple file lookup.
PHAResidueCodeManager: Handles the residue code registry stored in residue_codes.csv.

Notes

This module should not contain chemistry-building logic. Parameterisation, prepin generation and polymer construction should live in the polymer builder layer.

Classes

`PHAFileManager`	Manage paths for a PHA structure database.
`PHAResidueCodeManager`	Manage the PHA residue code registry.

Module Contents

class iphasimulator.pha_filepath_manager.PHAFileManager(root_dir='structure_database')

Manage paths for a PHA structure database.

root_dir

PHA_types_dir

built_PHAs_dir

PHA_melts_dir

dry_PHAs_dir

solvated_PHAs_dir

solvated_ions_PHAs_dir

temp_dir

residue_codes_csv

polymer_smiles_csv

get_root_dir()

get_temp_dir()

get_residue_codes_csv()

get_polymer_smiles_csv()

get_PHA_type_dir(PHA_type)

create_PHA_type_dir(PHA_type)

get_PHA_input_dir(PHA_type)

get_PHA_trimer_dir(PHA_type)

get_PHA_monomer_units_dir(PHA_type)

get_PHA_leap_template_dir(PHA_type)

get_PHA_monomer_unit_files(PHA_type)

get_built_PHA_name(PHA_type, length)

parse_built_PHA_name(polymer_name)

get_built_PHA_dir(PHA_type, length)

create_built_PHA_dir(PHA_type, length)

get_built_PHA_leap_dir(PHA_type, length)

get_built_PHA_amber_dir(PHA_type, length)

get_built_PHA_gromacs_dir(PHA_type, length)

get_built_PHA_amber_files(polymer_name)

get_dry_PHAs_dir()

get_dry_PHA_system_name(polymer_name)

get_dry_PHA_dir(polymer_name)

get_dry_PHA_inputs_dir(polymer_name)

get_dry_PHA_simulations_dir(polymer_name)

create_dry_PHA_dir(polymer_name)

get_solvated_PHAs_dir()

get_solvated_PHA_system_name(polymer_name)

get_solvated_PHA_dir(polymer_name)

get_solvated_PHA_inputs_dir(polymer_name)

get_solvated_PHA_simulations_dir(polymer_name)

create_solvated_PHA_dir(polymer_name)

get_solvated_ions_PHAs_dir()

format_ion_label(ion_names)

format_concentration_label(ion_concentration)

get_solvated_ions_PHA_system_name(polymer_name, ion_names, ion_concentration)

get_solvated_ions_PHA_dir(polymer_name, ion_names, ion_concentration)

get_solvated_ions_PHA_inputs_dir(polymer_name, ion_names, ion_concentration)

get_solvated_ions_PHA_simulations_dir(polymer_name, ion_names, ion_concentration)

create_solvated_ions_PHA_dir(polymer_name, ion_names, ion_concentration)

get_PHA_melt_name(polymer_names, number_of_polymers)

get_PHA_melt_dir(polymer_names, number_of_polymers)

create_PHA_melt_dir(polymer_names, number_of_polymers)

get_PHA_melt_inputs_dir(polymer_names, number_of_polymers)

get_PHA_melt_simulations_dir(polymer_names, number_of_polymers)

create_PHA_melt_simulation_run_dir(polymer_names, number_of_polymers, timestamp=None)

create_named_PHA_melt_simulation_run_dir(polymer_names, number_of_polymers, run_name)

find_file(directory, extension)

find_files(directory, extension)

class iphasimulator.pha_filepath_manager.PHAResidueCodeManager(paths)

Manage the PHA residue code registry.

The residue code CSV links user-facing PHA names to internal Amber-style residue codes.

Expected CSV format:

PHA_type,component,readable_name,residue_code,smiles

3HB,trimer,P3HB_3,AAA,… 3HB,head,hP3HB,AAB,… 3HB,mainchain,mP3HB,AAC,… 3HB,tail,tP3HB,AAD,…

Parameters:: paths (PHAFileManager) – Filepath manager used to locate residue_codes.csv.

forbidden_codes

header = ['PHA_type', 'component', 'readable_name', 'residue_code', 'smiles']

paths

csv_path

load_rows()

Load all rows from residue_codes.csv.

Returns:: List of CSV entries.
Return type:: list[dict]

get_used_codes()

Return all residue codes currently stored in the CSV.

Returns:: Set of used residue codes.
Return type:: set

PHA_type_exists(PHA_type)

Check whether a PHA type has already been registered.

Parameters:: PHA_type (str)
Return type:: bool

get_code(PHA_type, component)

Return the residue code for a given PHA component.

Parameters:

PHA_type (str)
component (str) –
One of:

trimer head mainchain tail

Return type:

str or None

generate_unique_codes(number_of_codes)

Generate multiple unique residue codes.

Examples

Existing CSV:

AAA AAB

generate_unique_codes(4)

Returns:: AAC AAD AAE AAF
Parameters:: number_of_codes (int)
Return type:: list[str]

register_PHA_type(PHA_type, trimer_name, trimer_smiles, monomer_smiles)

Register a new PHA type.

Creates four residue entries:

trimer head mainchain tail

Example

PHA_type = “3HB”

trimer_name = “P3HB_3”

Generates:

AAA trimer AAB head AAC mainchain AAD tail

Parameters:

PHA_type (str)
trimer_name (str)
trimer_smiles (str)
monomer_smiles (str)