poli.core.util.proteins.foldx.FoldxInterface

class poli.core.util.proteins.foldx.FoldxInterface(working_dir: Union[Path, str], verbose: bool = False)

A class for interacting with FoldX, a protein engineering software.

Parameters

working_dir (Union[Path, str]) – The working directory where FoldX files and output will be stored.

repair(pdb_file, remove_and_rename=False, pH=7.0, remove_heteroatoms=True)

Repairs a PDB file with FoldX, overwriting the original file if remove_and_rename is True.

_repair_if_necessary_and_provide_path(pdb_file)

Repairs a PDB file if necessary and returns the path of the repaired PDB.

_simulate_mutations(pdb_file, mutations=None)

Simulates mutations on a PDB file with FoldX.

_read_energy(pdb_file)

Reads the energy from a FoldX results file.

_compute_sasa(pdb_file)

Computes the SASA (solvent-accessible surface area) from a FoldX results file.

compute_stability(pdb_file, mutations=None)

Computes the stability of a protein structure using FoldX.

compute_sasa(pdb_file, mutations=None)

Computes the SASA (solvent-accessible surface area) of a protein structure using FoldX.

compute_stability_and_sasa(pdb_file, mutations=None)

Computes the stability and SASA (solvent-accessible surface area) of a protein structure using FoldX in a single run.

copy_foldx_files(pdb_file)

Copies the necessary FoldX files to the working directory.

write_mutations_to_file(wildtype_resiudes, mutations, output_dir)

Writes the list of mutations to a file in the given directory.

working_dir

The working directory for FoldX.

Type

Union[Path, str]

verbose

If True, the FoldX output will be printed to stdout.

Type

bool

Notes

This class expects you to use the binary for FoldX v.5. Previous versions relied on a “rotabase.txt” file, which is no longer used.

__init__(working_dir: Union[Path, str], verbose: bool = False)

Initialize the FoldX object.

Parameters

• working_dir (Union[Path, str]) – The working directory for FoldX.

• verbose (bool, optional) – If True, the FoldX output will be printed to stdout. Default is False.

Methods

__init__(working_dir[, verbose])	Initialize the FoldX object.
compute_sasa(pdb_file[, mutations])	Compute the solvent-accessible surface area (SASA) score for a given protein structure.
compute_stability(pdb_file[, mutations])	Compute the stability of a protein structure using FoldX.
compute_stability_and_sasa(pdb_file[, mutations])	Computes stability and sasa with a single foldx run, instead of two separate runs.
copy_foldx_files(pdb_file)	Copies the pdb file to the working directory.
repair(pdb_file[, remove_and_rename, pH, ...])	Repairs a PDB file with FoldX, overwriting the original file if remove_and_rename is True (default: False).
write_mutations_to_file(wildtype_resiudes, ...)	Writes the list of mutations to a file in the given directory.