Python API

Profet’s functionality is accessed mainly through the profet.Fetcher class documented below. Lower level functionality for each database in profet can be accessed through the profet.alphafold.Alphafold_DB and profet.pdb.PDB_DB classes.

class profet.Fetcher(main_db: str = 'pdb')

The main class in profet to fetch protein structures from the PDB and alphafold databases.

check_db(uniprot_id: str) → list

Checks which database contains the searched ID.

Parameters:

uniprot_id – ID from Uniprot

Returns:

The list of the databases where the id is available

file_from_db(prot_id: str, filetype: str = 'pdb', filesave: bool = False, db: str = 'pdb') → tuple

Returns the file from the correspondent database.

Parameters:

• uniprot_id – ID from Uniprot.

• filetype – File type to be retrieved: cif, pdb.

• filesave – Option to save into a file.

• db – database from which to retrieve the file.

Returns:

Tuple containing the filename and file from the database

get_default_db() → str

Returns:

The default database.

get_file(uniprot_id: str, filetype: str = 'pdb', filesave: bool = False, db: str = 'pdb') → tuple

Returns the file from an available database, starting with the default that the user provided.

Parameters:

• uniprot_id – ID from Uniprot.

• filetype – File type to be retrieved: cif, pdb.

• filesave – Option to save into a file.

• db – database from which to retrieve the file.

Returns:

1. File name of the saved file

2. File from the database, or None if it is not available in any database.

Return type:

A tuple containing

search_history() → dict

Returns:

The search history of the fetcher.

set_default_db(db: str)

Set the default database.

Parameters:

db – The default db (pdb or alphafold)

set_directory(new_dir: str)

Set the saving directory.

Parameters:

new_dir – The directory to save data

class profet.alphafold.Alphafold_DB

A class to represent the Alphafold database

check_structure(uniprot_id: str) → bool

Check whether a structure is present in the AlphaFold database

Parameters:

uniprot_id – The uniprot id of the protein

Returns:

Is the protein in the Alphafold database (True/False)

get_file_url(uniprot_id: str, filetype: str = 'pdb') → str

Get file url relative to an id from the the Alphafold entry page

Parameters:

• uniprot_id – The uniprot id of the protein

• filetype – The type of file to download (pdb or cif)

Returns:

The URL of the file to download

get_pdb(uniprot_id: str, filetype: str = 'pdb', filesave: bool = False, filedir: str = 'default') → tuple

Returns pdb/cif as strings, saves to file if requested.

Parameters:

• uniprot_id – ID from Uniprot

• filetype – File type to be retrieved: cif, pdb

• filesave – Option to save into a file

• filedir – The directory to save the data

Returns:

Tuple containing the filename and file from the database

make_url(uniprot_id: str, filetype: str = 'pdb') → str

Make the URL for the protein

Parameters:

• uniprot_id – The uniprot id of the protein

• filetype – The type of file to download (pdb or cif)

Returns:

The URL of the file to download

class profet.pdb.PDB_DB

A class to represent the PDB database

check_structure(uniprot_id: str) → bool

Check if a protein is contained within the PDB

Parameters:

uniprot_id – The uniprot id of the protein

Returns:

Is the protein in the PDB (True/False)

get_pdb(uniprot_id: str, filetype: str = 'pdb', filesave: bool = False, filedir: str = 'default') → tuple

Returns pdb/cif as strings, saves to file if requested

Parameters:

• uniprot_id – ID from Uniprot

• filetype – File type to be retrieved: cif, pdb

• filesave – Option to save into a file

• filedir – The directory to save the data

Returns:

Tuple containing the filename and file from the database