pdb4amber package


pdb4amber.pdb4amber_run module

Module containing the Pdb4amber class and the command line interface.

class pdb4amber.pdb4amber_run.Pdb4amberRun(input_pdb_path: str, output_pdb_path: str, properties: dict, **kwargs)[source]

Bases: BiobbObject

biobb_amber.pdb4amber.pdb4amber_run Pdb4amberRun
Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package.
  • input_pdb_path (str) – Input 3D structure PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_pdb_path (str) –

    Output 3D structure PDB 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) –

    • remove_hydrogens (bool) - (False) Remove hydrogen atoms from the PDB file.

    • remove_waters (bool) - (False) Remove water molecules from the PDB file.

    • constant_pH (bool) - (False) Rename ionizable residues e.g. GLU,ASP,HIS for constant pH simulation.

    • binary_path (str) - (“pdb4amber”) Path to the pdb4amber executable binary.

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

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

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.


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

from biobb_amber.pdb4amber.pdb4amber_run import pdb4amber_run
prop = {
    'remove_tmp': True
check_data_params(out_log, err_log)[source]

Checks input/output paths correctness


Launches the execution of the Pdb4amberRun module.

pdb4amber.pdb4amber_run.pdb4amber_run(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) int[source]

Create Pdb4amberRun method