utils package

Submodules

utils.anarcii module

Module containing the Anarcii class and the command line interface.

class utils.anarcii.Anarcii(input_pdb_path: str | Path, output_pdb_path: str | Path, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_haddock Anarcii
Wrapper class for the ANARCII antibody numbering tool.
ANARCII numbers antibody, TCR, and other immune receptor sequences. Given an input PDB structure it renumbers it (IMGT scheme by default) and writes the renumbered PDB structure.
Parameters:

  • input_pdb_path (str) – Path to the input PDB structure file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_pdb_path (str) –

    Path to the output renumbered PDB structure file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • seq_type (str) - (“antibody”) Type of sequence to number. Values: antibody, tcr, vhh, sabdab.

    • mode (str) - (“accuracy”) Numbering mode. Values: accuracy, speed.

    • verbose (bool) - (True) Print verbose output during numbering.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.utils.anarcii import anarcii
prop = { 'seq_type': 'antibody',
         'mode': 'accuracy' }
anarcii(input_pdb_path='/path/to/structure.pdb',
        output_pdb_path='/path/to/renumbered.pdb',
        properties=prop)
Info:
launch() → int[source]

Execute the Anarcii object.

utils.anarcii.anarcii(input_pdb_path: str | Path, output_pdb_path: str | Path, properties: dict | None = None, **kwargs) → int[source]
biobb_haddock Anarcii
Wrapper class for the ANARCII antibody numbering tool.
ANARCII numbers antibody, TCR, and other immune receptor sequences. Given an input PDB structure it renumbers it (IMGT scheme by default) and writes the renumbered PDB structure.
Parameters:

  • input_pdb_path (str) –

    Path to the input PDB structure file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_pdb_path (str) –

    Path to the output renumbered PDB structure file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • seq_type (str) - (“antibody”) Type of sequence to number. Values: antibody, tcr, vhh, sabdab.

    • mode (str) - (“accuracy”) Numbering mode. Values: accuracy, speed.

    • verbose (bool) - (True) Print verbose output during numbering.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

This is a use example of how to use the building block from Python:

from biobb_haddock.utils.anarcii import anarcii
prop = { 'seq_type': 'antibody',
         'mode': 'accuracy' }
anarcii(input_pdb_path='/path/to/structure.pdb',
        output_pdb_path='/path/to/renumbered.pdb',
        properties=prop)
Info: